microbiologytoday

today vol36|may09 quarterly magazine of the society for general

microbiology vol 36 | may 09

darwin 200 darwin and the origin of infection the phylogenomic species concept retire the prokaryote a microbial cockatrice a glimpse of micro-evolution evolution contents

vol36(2) regular features 66 News 102 Schoolzone 110 Going Public 74 Microshorts 106 Gradline 114 Hot off the Press 100 Conferences 109 Addresses 117 Reviews other items 91 Letters

articles 76 Darwin: from the origin 92 A glimpse of of species to the origin of microevolution in infection nature: bacterial Mark Pallen adaptation and Charles Darwin was born 200 years ago. What did he know speciation in about micro-organisms? ‘Evolution Canyon’, 80 The phylogenomic Israel species concept Johannes Sikorski The natural environment could have an Jim Staley important impact on microbial evolution. 16S rRNA gene sequences are no use for classifying at species level, but alternative approaches are possible. 96 Virus evolution 84 It’s time to retire the Peter Simmonds The latest discoveries of new are providing clues prokaryote to viral evolution. Norman R. Pace Is the term prokaryote an anachronism in modern biology?. 120 Comment: 88 Archaea: a microbial cockatrice An April diary Edward L. Bolt & Stephane Delmas Robin Weiss The genomes of these ancient organisms contain elements The SGM President reflects on a busy month in from both bacteria and eukaryotes. microbiology.

Cover image A ‘tree of life’ sketch from one of Darwin’s notebooks. Mario Tama / Getty Images The views expressed

Editor Dr Matt Hutchings––Editorial Board Dr Sue Assinder, Dr Paul Hoskisson, Professor Mark Harris Managing Editor Janet Hurst by contributors are not Editorial Assistant Yvonne Taylor––Design & Production Ian Atherton––Contributions are always welcome and should be addressed to the Editor c/o SGM HQ, Marlborough House, necessarily those of the Basingstoke Road, Spencers Wood, Reading RG7 1AG–Tel. 0118 988 1809–Fax 0118 988 5656–email [email protected]–web www.sgm.ac.uk Society; nor can the Advertising David Lancaster, Ten Alps Publishing, London Office, 10 Savoy Street, London WC2E 7HR–t 0207 878 2316–f 0207 379 7118–e [email protected] Regular feature images pp. 67 SGM; 79 Digital Vision / Getty; 91, Punchstock; 101, 103, 117 Comstock / Jupiter Images; 107, 115 Stockbyte; 111, AbleStock claims of advertisers © 2009 The Society for General Microbiology––ISSN 1464-0570––Printed by Latimer Trend & Company Ltd, Plymouth, UK be guaranteed. news

Journals First SGM Prize Medallist receives award Journal back archive project completed! Open access – a serial killer? Dr Stanley Prusiner, the first winner of the Society’s new Prize Medal, is seen below being presented with his medal by SGM President Robin Weiss. He also April saw two significant milestones in the project to put addenda and corrigenda had to be linked to the corrected Most learned societies depend on received a certificate and £1,000. the entire back content of the Society’s journals online. articles. I’m grateful to Robin Dunford and his colleagues in income from publishing journals to The entire archive of Microbiology/Journal of General the editorial offices for their skill, patience and industry, and carry out their charitable aims. In Dr Prusiner’s lecture – Prion biology and disease – was delivered to a packed Microbiology, back to volume 1 issue 1 in January 1947, and for detecting and solving a number of problems. recent years the issue of free open lecture theatre at the Harrogate meeting, where it was greeted with much Journal of Medical Microbiology, back to volume 1 issue 1 in access to research papers has become acclaim. The back archives of Journal of General and August 1968, went live on the journals’ HighWire sites at a threat to the current business model International Journal of Systematic and Evolutionary The medal was specially struck for the event and was based on a design by http://mic.sgmjournals.org/ and http://jmm.sgmjournals. on which such publishing operations Microbiology had already been placed online, so this SGM Design Manager Ian Atherton. The prize is to be awarded annually to a org/, respectively. Around 125,000 pages of back content are based. The Biosciences Federation, completes the project. All the archive material is freely microbiologist of international standing whose work has had a far-reaching had to be scanned and assembled for Microbiology/JGM, which represents 35 organizations, set accessible, without access controls, as part of SGM’s impact beyond microbiology. and a further 25,000 pages for JMM. Each article is present up a subcommittee to investigate the charitable remit to support microbial science. Thanks are as a full-text PDF, and research articles have HTML headers impact of open access, amongst other also due to the many individuals and libraries who donated (titles, authors, abstracts, etc.), which had to be re-keyed, pertinent topics. They carried out a back runs of all four journals for scanning. allowing compilation of an HTML table of contents for survey of member societies and the each issue. The archives also contain PDF ‘front’ and ‘back’ Ron Fraser, Chief Executive researchers who belong to them to matter: covers, advertising, editorial boards, instructions to find out their policies on open access authors, original tables of contents, indexes and conference and self-archiving by authors, and to proceedings. Over the next few weeks, full text searching of The ‘Nature’ of IJSEM back issues gather information on the financial the article PDFs will be installed. contribution made by the societies to The launch of online access to the entire back content their disciplines. In addition, society These retrospective conversion projects are not just a of International Journal of Systematic and Evolutionary members were invited to complete matter of packing up the volumes and sending them off Microbiology last November was marked by a one-page an online questionnaire on their for scanning, but involve an immense amount of work in feature in Nature Reviews Microbiology. It noted that the experience and views on open access checking for accuracy and sorting out a variety of questions availability of the archive would be a ‘boon for scientists, publishing and self-archiving. SGM about what goes where, and some amazing historical historians, and the public’ and made a good job of raising Chief Executive Dr Ron Fraser has idiosyncrasies of journal makeup. Not least, all errata, the profile of SGM and its publishing activities. been helping to lead this initiative.

The survey is now complete and the results have been published in Serials, SGM introduces new pricing model for institutional journal a journal read by librarians and people subscriptions from 2010 working in the publishing industry. In 2010, SGM is changing the way it Under the new tiered pricing model, now, ahead of many other smaller The article was written by Sue Thorn, charges for its journals to make pricing the price customers pay will depend publishers, to stay at its forefront Sally Morris and Ron Fraser. The Antibiotics in history fairer and to offer greater flexibility of on the type and size of organization and to protect its journals’ futures. findings show that member societies The Harrogate meeting was themed around the Legacy of Fleming, to mark access to readers and libraries. and how many sites they want to be contributed twice as much financially ‘As a not-for-profit publisher we’ve the anniversary of the discovery of the publication of penicillin. Kevin Brown, able to access journals from. Librarians in the form of grants and awards to Like many publishers, SGM has always worked hard to minimize the curator of the Fleming Museum, kindly supplied some posters telling the will be able to purchase subscriptions UK higher education institutions than historically operated a ‘one price for costs of our journals, which are among story. with online access in up to two cities they received in publication sales from all’ model for its journal subscriptions the most inexpensive and yet highly as standard, rather than having to this source. None of the societies The scientific session entitled Production, formulation and delivery of to institutions. But, as journal readers cited in microbiology, and our prices enter into negotiation for access currently offers full open access, but biotherapeutics, organized by Frances Burke, Chris Hewitt and Stuart Stocks, increasingly access articles online, remain lower than many competing for additional sites. This new model all provide delayed free access, mostly with welcome support from commercial colleagues, covered the theme from an the traditional licensing agreements titles produced by commercial also ends the inequality that saw a after 12 months. Researchers appear industrial perspective. As well as looking back, speakers considered the latest that accompany such a model are publishers’ commented Dr Ron small college paying the same to be very confused about open access developments in the field. becoming out-dated. Students and Fraser, Chief Executive of SGM. amount for an online journal journals altogether. The full article is researchers want to be able to access ‘Our model seeks to deliver a fair The accompanying poster session included some displays on the history of the subscription as, for example, a large available at: journals from multiple campuses price based on the value of our development of various antibiotics, mainly penicillin. Two offprints were available corporation. including, for example, the university journals to any one institution, with http://serials.uksg.org/openurl.asp? to delegates: People, Penicillin and Pursuit of Excellence: Eli Lilly and Co Ltd Speke medical school, which might be Publishing is an industry that is the flexible licensing terms that libraries genre=article&issn=0953-0460& Operations and The Life and Work of Guy Newton (1919–1969). Spare copies are located in a completely different changing rapidly. SGM is making the need in order to maximize the value volume=22&issue=1&spage=39 still available for members unable to attend the Harrogate meeting. Contact Janet city from the central library. move to a tiered pricing structure of their purchase.’ (doi:10.1629/2239) Hurst ([email protected]) if you would like one.

66 microbiology today may 09 microbiology today may 09 67 SGM Council People February meeting highlights Scientific meetings American Academy of Microbiology Professor Hilary Lappin-Scott, the Scientific Meetings The following SGM members have been elected Fellows of the American Academy of Election of new SGM Council Officers from September 2009 Officer, reported on a meeting of the SGM Divisions in Microbiology: London. Topics discussed included meeting the needs of Mark J. Buttner, John Innes Centre, Norwich The President reported on the deliberations of the academic clinical virologists at Society conferences and how , The Wellcome Trust Sanger Institute, Cambridge subcommittee he had chaired to discuss nominations for to improve cross-theme working within the organizational David W. Holden, the Council Officer posts that fall vacant in September. After planning matrix. Good progress was made on both fronts. considering their recommendations, Council agreed Congratulations to … to approach the following members. Finances Microbiology Today Editor Matt Hutchings (left) and his wife Cerian on the birth of President: Professor Hilary Lappin-Scott Council was pleased to accept the Treasurer’s Financial baby Noah Benjamin on 29 January 2009. Noah weighed in at 7lb 4oz and is doing very Bangor University Report for the year ended 31 December 2008. They also well. heard about the presentation given on the previous evening General Secretary: Dr David Blackbourn Professor Roger Pickup, on appointment to a chair in the Biomedical and Life Sciences at Treasurer’s Committee by Mr Willie Hartley Russell, Division, Lancaster University. the SGM’s Investment Manager. SGM’s portfolio has lost Publications Officer: Professor Howard Jenkinson value, in line with the poor global economic circumstances. Professor Tracy Palmer, University of Dundee on her election to Fellowship of the Royal University of Bristol Council discussed the situation and will continue to Society of Edinburgh. Education and Public Affairs Officer: Professor Joanna Verran monitor it closely. Professor David Baulcombe, Department of Plant Sciences, University of Cambridge, on his Manchester Metropolitan University. The income from commercial journal subscriptions, appointment to the Council of the Biotechnology and Biological Research Council. Professor Hilary Lappin-Scott, the outgoing SGM Scientific which enables SGM to fund many of its charitable activities, Professor Maria Zambon who has been appointed Director of the Health Protection Meetings Officer, was present at the Council meeting and AGM 2009 was reviewed and in general considered to be satisfactory. Agency’s Centre for Infections at Colindale, London. was delighted to accept the Presidency to much acclaim. Council was interested to learn about the new tiered The Society AGM will Subsequent to the Council meeting, all of the other newly pricing system for journal sales, which had been extensively be held on Tuesday, 8 Deaths elected officers were contacted by the President and discussed at Treasurer’s Committee. After discussion, they September 2009 at the The Society notes with regret the deaths of Miss Mairin Clarke, County Louth, Ireland accepted their roles. From September 2009, Council will accepted the recommendation to implement the new Society Meeting at Heriot- (member since 1975) and Dr Ronald M. Keddie, formerly of the University of Reading be working in the transitional stage to its new structure, system. Watt University, Edinburgh. (member since 1949). We are also sad to note that Professor Rob Goldbach, a former which has 6 officers and reducing to 6 elected members by Agenda papers, including Editor of Journal of General Virology and Head of the Laboratory of Virology, University September 2011. European Society for Virology reports from Officers and of Wageningen, has died in a tragic accident whilst on holiday. The Inaugural Meeting of the European Society for Dr Evelyn Doyle, University College, Dublin, was appointed Division Chairs and the Virology (ESV) took place in Rome on 24 April 2009. as Deputy Scientific Meetings Officer from September 2009 Accounts of the Society SGM staff Our President Professor Robin Weiss FRS was a keynote and she will attend Council meetings by invitation. for 2008 will be circulated We bid farewell to Staff Editor Nicolas Fanget, who is taking up a new post as a speaker. After some discussion, Council decided to support with the August issue of copy-editor on Nature. Nico has worked mainly on JGV where his input has been much Honorary Membership ESV in general and become a corporate member but they Microbiology Today. appreciated. Council decided unanimously to offer Honorary Membership hoped that future eurovirology congresses would to Dr Rita R. Colwell, Chairman, Canon US Life Sciences, be scheduled to avoid clashes with the SGM’s spring and Distinguished Professor, University of Maryland meetings. New Outreach Award College Park and Johns Hopkins University Bloomberg Biosciences Federation (BSF) and Institute of School of Public Health, for her significant contribution to Biology (IoB) merger The new Education Division has instituted an annual microbiology worldwide and her support of SGM. prize to be awarded for excellence in outreach work in Council noted the provisional business plan for the microbiology. Yakult Ltd have kindly agreed to sponsor proposed merger of the BSF (of which SGM is a Member SGM Prizes this prize for the first 3 years, which consists of £250, a Organization) and the IoB. It is hoped that the new Society A draft document outlining revised procedures for certificate and free attendance at an SGM meeting. nominating and awarding SGM Prizes, prepared by Ulrich of Biology will provide UK bioscientists with a single Jo Heaton of University of Lancashire was given the award Desselberger and Janet Hurst, was discussed and accepted and authoritative voice on issues relating to scientific, for 2009 in recognition of her enthusiastic promotion of with minor amendments. From 2009 onwards the timing of educational, economic and social aspects of biology. In microbiology to school children. She is pictured here being nominations and Council decisions will be moved forward principle Council supported the initiative, but felt that more presented with her cheque by Linda Thomas, Science to enable the President to approach the prize-winners at detailed information should be made available to member Director of Yakult Ltd, at the Gala Dinner in Harrogate. an earlier stage and to give SGM meetings organizers more organizations of the BSF about their liabilities if the time to make appropriate arrangements for the delivery of merger took place. the prize lectures. Details of Prizes to be awarded in 2010 are on p. 70. Ulrich Desselberger, General Secretary

68 microbiology today may 09 microbiology today may 09 69 20437_Chloramphenicol Ad_Micro Today_AW:layout 1 17/3/09 11:36 Page 1 CHLORAMPHENICOL For treating life threatening infections when other antibiotics will not suffice New SGM Prize Lectures Cronobacter A range of prestigious awards is made by the Society in recognition of distinguished international contributions to microbiology. Nominations are now sought for the 2010 prize lectures. The award panel will consider the submissions in the autumn and take their recommendations collaboration to November Council for approval. The outcome will be announced in the February 2010 In 2008, biogroups of issue of Microbiology Today. Prize lecture rules and a nomination form are on the SGM Enterobacter sakazakii were website: www.sgm.ac.uk/about/prize_lectures.cfm placed in the new genus Fleming Award – This is awarded annually for outstanding research in any branch of Cronobacter. These bacteria, microbiology by a young microbiologist in the early stages of his/her career. The winner which are widespread in receives £1,000 and gives a lecture based on his/her work to a Society meeting. The text is the environment, have been usually published in a Society journal. linked to the incidence of infant meningitis and Prize Lecture – The Society’s principal prize, awarded biennially necrotizing enterocolitis, for an outstanding contribution of current importance in microbiology. The winner receives probably caused by post- £1,000 and gives a lecture on his/her work at a Society meeting. The lecture is usually process contamination of published in a Society journal. milk-based infant formula Peter Wildy Prize for Microbiology Education – This is awarded annually for an or feed. This important outstanding contribution to any area of microbiology education. The winner receives £1,000 threat to the health of and gives a lecture on a topic of his/her choice at a Society meeting. neonates was the theme of the 1st International Completed nomination forms, together with supporting documents, should be sent to Conference on Cronobacter Ulrich Desselberger, c/o SGM HQ. Closing date for all nominations is 30 September 2009. held at University College Dublin in January. SGM was Undergraduate Microbiology Prizes pleased to provide support for speakers via the Joint The prizes aim to encourage excellence in the study of microbiology by undergraduate Abbreviated Prescribing Information Chloramphenicol Capsules BP 250mg Meetings Scheme. SGM’s students and to promote scholarship in, and awareness of, microbiology in universities. The prizes are awarded annually to the undergraduate student in each qualifying institution who Presentation: Capsules containing 250mg chloramphenicol BP. antipsychotics, procainamide, nucleoside reverse transcriptase Irish Division members Indications: Typhoid fever and life-threatening infections, particularly inhibitors, propylthiouracil. provided significant input. performs best in microbiology in their penultimate year of study for a Bachelor’s degree. those caused by Haemophilus Influenzae, where other antibiotics will Pregnancy and Lactation: The use of chloramphenicol is contra- not suffice. indicated as the drug crosses the placenta and is excreted in breast milk. The event attracted 200 Each winning student will be awarded £150, a certificate and a free year’s undergraduate Posology: For oral administration. Effects on ability to drive and use machines: No significant effect membership of the SGM. One prize is available to each university in the UK and Republic Adults and elderly: 50mg/kg body weight daily in 4 divided doses. For on driving ability. delegates from around the severe infections (meningitis, septicaemia), this dose may be doubled Undesirable Effects: Reversible dose related bone marrow depression, of Ireland offering a degree course with a significant content of microbiology. The university initially, but must be reduced as soon as clinically possible. irreversible aplastic anaemia, increased bleeding time, hypersensitivity world and was opened Children: Not recommended. reactions including allergic skin reactions, optic neuritis leading to by Mr Brendan Smith, TD, chooses the assessed microbiological work for which the prize is awarded. The submission Contra-indications: Known hypersensitivity or toxic reaction to blindness, ototoxicity, acidotic cardiovascular collapse, nausea, chloramphenicol or to any of the excipients. Should not be used for vomiting, glossitis, stomatitis, diarrhoea, enterocolitis, Gray Baby Ireland’s Minister for should be supported by formal marks, not an informal assessment. Winning students the prophylaxis or treatment of minor infections; during active Syndrome particularly in the newborn, which consists of abdominal should have attained at least 2(I) overall in their degree examinations at the stage at which immunisation; in porphyria patients; in patients taking drugs liable to distension, pallid cyanosis, vomiting, progressing to vasomotor collapse, Agriculture and Food. At depress bone marrow function; during pregnancy, labour or by breast- irregular respiration and death within a few hours of the onset of the close of the conference, the award is made. Universities are now invited to nominate a student for a 2009 SGM feeding mothers. symptoms. Special warnings and precautions for use: Use only if other Overdose: Stop chloramphenicol immediately if signs of adverse Peter Ben Embarek of the Undergraduate Microbiology Prize. Submissions can only be accepted on the form which treatments are ineffective. Use should be carefully monitored. Reduce events develop. Treatment is mainly supportive. If an allergy develops, has been sent to all institutions. The full rules and further copies of the form may be dose and monitor plasma levels in hepatic or renal impairment in the oral antihistamines may be used. In severe overdosage e.g. Gray Baby WHO announced that the elderly and in patients concurrently treated with interacting drugs. Syndrome, reduce plasma levels of chloramphenicol rapidly. Resin downloaded from the SGM website or obtained from the Grants Office at Marlborough Interactions: Chloramphenicol prolongs the elimination, increasing the haemoperfusion (XAD-4) has been reported to substantially increase UCD Centre for Food blood levels of drugs including warfarin, phenytoin, sulphonylureas, chloramphenicol clearance. Safety had been designated House. The closing date for nominations is 28 August 2009. tolbutamide. Doses of anticonvulsants and anticoagulants may need to Pack size and Price: 60 capsules £377.00 be adjusted if given concurrently. Complex effects (increased/decreased Legal Category: POM the first laboratory to be . Two recipients of 2009 UG prizes receiving their certificates – Graham Hood, University of Reading (left), plasma levels) requiring monitoring of chloramphenicol plasma levels Market Authorisation Number: PL17736/0075 and Marta Kaleta, London Metropolitan University (right). have been reported with co-administration of penicillins and rifampicin. Market Authorisation Holder: Chemidex Pharma Limited, a WHO Collaborating Paracetamol prolongs chloramphenicol half-life. Chloramphenicol may Chemidex House, 7 Egham Business Village, Crabtree Road, Egham, Centre for Cronobacter. increase the plasma levels of calcineurin inhibitors e.g. ciclosporin Surrey TW20 8RB, UK. and tacrolimus. Barbiturates such as phenobarbitone increase the Date of preparation: January 2009. Ad Chloramphenical - GENERICS ESSENTIAL See www.ucd.ie/crono09 metabolism of chloramphenicol, resulting in reduced plasma See Chloramphenicol Summary of Product Characteristics for full chloramphenicol concentrations. In addition, there may be a decrease prescribing information. for details. in the metabolism of phenobarbitone with concomitant chloramphenicol use. There is a small risk that chloramphenicol may reduce the Information on the contraceptive effect of oestrogens. Chloramphenicol reduces the Adverse events should be reported. response to hydroxocobalamin. Chloramphenicol is contra-indicated Reporting forms and information can be found at SGM’s Joint Meeting in patients taking drugs liable to suppress bone marrow function e.g. www.yellowcard.gov.uk. Adverse events should also be

CAPSULES mm Supply as hi-res PDF Job no: 20437 Scheme is available at carbamazepine, sulphonamides, phenylbutazone, penicillamine, cytotoxic reported to Chemidex Pharma Limited on 01784 477167. EG/CH/FEB/2009/02a agents, some antipsychotics including clozapine and particularly depot 210 www.sgm.ac.uk/meetings/ PIP: 106-5796 x

JointMeetingsForm.doc 297 LINK: CHL600B Type Area: Type PROSPER: O65995 Journal: Microbiology Today 70 microbiology today may 09 microbiologyFor further information, today may please 09 contact: Essential Generics, 7 Egham Business Village, Crabtree Road, Egham, Surrey TW20 8RB, UK 71 20434_Ampicillin Ad_Micro Today_AW:layout 1 11/3/09 10:46 Page 1 AMPICILLIN For the treatment of bacterial infections caused by ampicillin sensitive organisms Grants SGM has a wide range of grant schemes to support UK Society of microbiology. See www.sgm.ac.uk/grants for details Biology to go Scientific Meetings and closing dates. Travel Grants ahead Enquiries should be made to the: Grants Office, SGM, This scheme offers Marlborough House, Basingstoke Road, Spencers Wood, Members of the UK’s members who are early- Reading RG7 1AG (t 0118 988 1821; f 0118 988 5656; two leading biology career scientists limited e [email protected]). organizations, the Institute grants to present their of Biology (IoB) and the Check out the current schemes, to ensure that you work at scientific meetings. Biosciences Federation don’t miss any deadlines. Applicants in the following (BSF), have voted categories are eligible overwhelmingly in favour of to apply: postgraduate The Watanabe Medical Book Fund unification to form a single students, resident and Microbiology organization, the Society Members who are registered for a higher Support Grants of Biology. This positive permanently resident in degree in a country in the development takes the IoB a developing country Elective grants EU; postdoctoral scientists and BSF a step closer to the may apply for funding to Funding for UK/Ireland within 3 years of their first creation of an organization acquire microbiology medical/dental/veterinary appointment in a country in that combines the expertise books for their libraries. students to work on the EU, graduate scientists of the learned societies and These annual awards are microbiological research within 3 years of their other biology organizations available as a result of a projects in their elective first appointment to a with the professional skills generous donation from periods. microbiological post in the of the IoB and its individual Professor T. Watanabe UK or Republic of Ireland; Trainee support grants members. Professor Dame of Japan. university lecturers (LA or Funding for SGM members Nancy Rothwell, Chair of equivalent) within 3 years The closing date for these carrying out small lab-based the Interim Council said, Abbreviated Prescribing Information of appointment to their first Ampicillin 500mg Vials for Injection international schemes is microbiology projects ‘The Society of Biology post in the UK or Republic 25 September 2009. will have a sufficient critical Presentation: Vial containing 500mg Ampicillin as Ampicillin Sodium EP. methods of investigation are used. Enzymatic glucose oxidase methods during either foundation Indications: Treatment of bacterial infections caused by ampicillin- should be used. of Ireland. or specialty postgraduate mass to enable it to speak sensitive organisms such as ear, nose and throat infections, bronchitis, Pregnancy and Lactation: Animal studies have shown no teratogenic with authority over the pneumonia, urinary tract infections, gonorrhoea, gynaecological effects. Use in human pregnancy is well documented in clinical studies. Student schemes medical training. Up to infections, septicaemia, peritonitis, endocarditis, meningitis, enteric Ampicillin may be considered appropriate in pregnancy. Trace quantities £3,000 is available towards breadth of topics covered by fever, gastro-intestinal infections. Prevention of infection following of penicillins can be detected in breast milk. Adequate human and animal International abdominal surgery when applied extraperitoneally to wounds. data on use of ampicillin during lactation are not available. schemes Postgraduate Student the consumables costs of a modern biology’. SGM, as a Posology: For intramuscular, intravenous, intraperitoneal, intrapleural, Effects on ability to drive and use machines: No effects observed. Meeting Grants project. member of the BSF, voted intrarticular or extraperitoneal administration. Undesirable Effects: Hypersensitivity reactions, skin rash, pruritis, International Adults and elderly: Septicaemia, endocarditis, osteomyelitis: 500mg four urticaria, purpura, nausea, vomiting, diarrhoea, transient rise in Grants cover travel and in favour of the merger. to six times a day IM or IV for 1-6 weeks. Peritonitis and intra-abdominal transaminases. Rarely: erythema multiforme, Steven’s Johnson Development Fund The closing date for these accommodation expenses sepsis: 500mg four times a day IM or IV. Meningitis requires 2g six syndrome, toxic epidermal necrolysis, anaphylaxis, interstitial nephritis, The fund exists to schemes is 25 September For more information, see hourly IV. Children: Meningitis: 150mg/kg daily IV in divided doses. pseudomembranous colitis, haemorrhagic colitis, hepatitis, cholestatic for attendance at ONE Usual dosage in children under 10 years old is half the adult routine dosage. jaundice, transient leucopenia, transient thrombocytopenia, haemolytic provide training courses, 2009. www.newbio.info Renal Impairment: Reduce or extend dose interval – See SPC. anaemia, prolonged bleeding time and prothrombin. SGM meeting each year. For administration information, see SPC. Overdose: Nausea, vomiting and diarrhoea may be evident and should publications and other Applications for a grant Contra-indications: Hypersensitivity to beta-lactam antibiotics be treated symptomatically. Ampicillin may be removed from circulation assistance to microbiologists or excipients. by haemodialysis. to attend the Heriot-Watt Special warnings and precautions for use: Enquire if any history of Pack size and price: Pack of 10 vials £78.30 in developing countries. Public Inquiry into South previous hypersensitivity reactions to beta-lactam antibiotics. Serious Legal Category: POM meeting (7–10 September) and occasionally fatal hypersensitivity reactions have been reported. Market Authorisation Number: PL 17736/0070 President’s Fund for must be submitted by Wales E. coli O157 outbreak Avoid ampicillin if infectious mononucleosis and/or acute or chronic Market Authorisation Holder: Chemidex Pharma Limited, Research Visits leukaemia of lymphoid origin are suspected. Skin rash is associated with Chemidex House, 7 Egham Business Village, Crabtree Road, 4 September 2009. Former SGM President Hugh Pennington has completed these conditions following administration of ampicillin. Prolonged use Egham, Surrey, TW20 8RB, UK. may result in overgrowth of non-susceptible organisms. Date of preparation: January 2009. ESSENTIAL GENERICS - Ampicillin Vials The fund enables early his inquiry into the outbreak of Escherichia coli O157 Each vial contains 33.7mg of sodium. See Ampicillin Vials Summary of Product Characteristics for full career scientists, as defined GRADschool Grants Interactions: If ampicillin is prescribed concurrently with an prescribing information. which affected at least 157 people in South Wales in 2005. aminoglycoside, the antibiotics should not be mixed in the syringe, in the scheme rules, to Awards to contribute the Tragically, one 5-year-old child died. intravenous fluid container or giving set as this may cause loss of visit any other country full course fees of a UK activity of the aminoglycoside. Bacteriostatic drugs may interfere The work took 2 years to complete and the report with the bactericidal action of ampicillin. Concomitant use with oral Adverse events should be reported. for 1–3 months to carry GRAD national (personal contraceptives may lead to a reduction in efficacy of the oral contraceptive. Reporting forms and information can be found at concluded that cooked meats that had become Concurrent use with Probenecid may increase blood levels of ampicillin. www.yellowcard.gov.uk. Adverse events should also be out a defined piece of or career development) Increased likelihood of allergic skin reactions with concomitant allopurinol VIALS contaminated with the pathogen due to severe breakdowns reported to Chemidex Pharma Limited on 01784 477167. microbiological research. residential course.

EG/AM/MAR/2009/03 use. False positive urinary glucose readings are common if chemical Grants contribute towards Applicants must be resident in good food hygiene practice at a catering butcher business PIP: 112-2183 travel, subsistence and and registered for a PhD in were the cause of the outbreak. some consumables. the UK. The full report is available at www.ecoliinquirywales.org Size: 297 x 210 mm Bleed: 3 mm Supply as hi-res PDF Job no: 20434 LINK: AMP304P Journal: Microbiology Today PROSPER: 145847 For further information, please contact: Essential Generics, 7 Egham Business Village, Crabtree Road, Egham, Surrey TW20 8RB, UK microbiology today may 09 73 microshorts

Jane Westwell takes a look at some recent Fighting Hand washing, not isolation, controls MRSA A recent study, by UK researchers, has shown that careful hand hygiene among staff on hospital microbiological stories counterfeit intensive care units (ICUs) could be the best way to halt the spread of MRSA among patients. ICU fungi wards tend to have higher levels of MRSA than general wards and patients with the infection are As Microbiology Today went to press, a new influenza A H1N1 virus Mexican nationals. Guests in a hotel where one case of H1N1 was often isolated in separate wards to minimize the risk of cross-infecting other patients. However, some from Mexico hit the headlines. Jane Westwell tracks some of the identified have been confined to the hotel irrespective of whether Italian and French researchers experts argue that moving infected patients carries a risk. The study took place over a year; for 6 reactions to this new ‘swine ’flu’ as it began to spread around the they display symptoms of the infection. In Vietnam, visitors from are unravelling the secrets months patients with MRSA were moved to isolation wards and for the remainder of the year they world. affected countries are to be isolated on arrival. Other approaches to of truffles. The black truffle were not moved. Throughout the study, staff were encouraged to wash their hands and frequency preventing outbreaks include a cull of all pigs (in Egypt) and bans (Tuber melanosporum) genome of hand-washing was monitored. The findings show that rates of cross-infection with MRSA were Swine ’flu – the story so far on pork imports from affected countries despite no evidence to has been sequenced and is similar during both periods. At the end of the study there were no differences in cross-infection suggest that H1N1 can be transmitted by eating pig-meat. expected to be followed by the rates, suggesting that isolating patients does not substantially reduce the risk of infection. Ten days after the first case of swine ’flu was announced in Mexico white truffle Tuber( magnatum) www.telegraph.co.uk/health/healthnews/5077135/Handwashing-more-effective-at-controlling- on 24 April, over 1,000 cases had been reported worldwide. In later this year. For decades Economic impact MRSA-than-isolating-patients.html Mexico, over 700 cases were recorded; 26 resulting in death and scientists have assumed that in the USA almost 300 cases of the virus had been reported across One thing is certain, the outbreak of H1N1 is already having there is very little genetic 36 states, whilst in Canada about 100 cases were confirmed. In 16 economic consequences. Airline share prices fell sharply after the variation between truffles other countries, the virus was infecting far fewer people (between news broke. Holiday companies temporarily withdrew planned growing in different regions. 1 and 3) with highest number of occurrences in Spain (54) and UK trips to Mexico where concern is growing over the potential loss The black truffle genome has Old (32). in income from the tourist trade. The pig-farming industry in ’flu- areas with variable amounts In Alberta, Canada, the first case was recorded of the H1N1 affected countries is also facing economic losses due to trade bans of repetitive DNA which microbes of virus passing from human to another species when a farm worker imposed by several countries. On the other hand, opportunists have been used as markers infected over 200 pigs after returning from a holiday in Mexico. started to cash in on the outbreak by selling ‘miracle cures’ and in genetically fingerprinting the sea The WHO called for increased surveillance of pig-farms in products claimed to prevent transmission of the virus. 200 truffles from 13 different Scientists have discovered countries with H1N1 infections in humans due to concern that regions of southern Europe. evidence of an ancient repeated transmission of the virus between humans and pigs may Media coverage This has revealed regional microbial community that increase the chances of it mutating into a form that could lead to Coverage of H1N1 in the UK media has been extensive and fairly varieties of genetically has survived for more than a higher mortality rate in humans. balanced. Newspaper and TV website users can download maps distinct truffles rather than 1.5 million years under the Antarctic ice. Analysis of brine The WHO increased the state of alert to level 5 and was illustrating outbreaks and read regular news updates, commentary the monoculture that was (four times more salty than monitoring a surge of reported cases in Spain just as measures to and background information from scientific experts (including previously assumed to exist. ordinary seawater), flowing counteract spread of the virus were being relaxed in Mexico. several SGM members). Interactivity of websites has encouraged Preliminary data on 300 white people to express their fears and opinions. Those airing eccentric truffles, from 26 different areas, through a crack in the wall of the Taylor Glacier, indicated a Just how ready were we? views or attitudes to the situation have received vigorous responses indicate that they also form from other members of the public. Twitter has recorded over distinct regional variations. complete absence of oxygen, Across the globe, levels of individual countries’ preparedness varied 10,000 tweets per hour on the subject – some might say a case of but did reveal presence of enormously. Some had significant stocks of antiviral drugs laid-by Such a rare and high-value information overload. As time has progressed, the media coverage microbial life beneath the and had clear plans to deal with outbreaks. product attracts counterfeiters m Coloured freeze-fractured TEM of a section through a red blood cell is lessening and on day 11 website updates were far less frequent ice. Scientists believe that the A few countries were less well-prepared and who mix a small amount infected with a malaria parasite (Plasmodium sp.). Dr Tony Brain / SPL than in earlier days of the story. This is probably a reflection that microbes have evolved from are only now forming task-forces to plan of ‘true’ black truffle with swine ’flu has not yet reached pandemic proportions and the marine organisms that became responses to disease outbreaks. more plentiful (and cheaper) symptoms are far less severe than first feared. trapped in a landlocked briny Combating malaria with Actions to control spread of the disease varieties. Whilst DNA analysis pond that was subsequently has been used to identify a lab-on-a-chip were also diverse. The UK government What next? covered by the glacier. The put in place a communications campaign ‘imposter’ species, researchers pond currently lies 1,300 feet Scientists at University of Glasgow have developed an electronic Experts predict that a new wave of cases could appear in the advising people to ‘catch it, bin it, kill it’ – good are planning to refine the below the ice. In darkness and chip which identifies individual species of malaria. In April, the autumn, if the present outbreak dies down as expected over advice for preventing spread of any cold or fingerprinting to establish without oxygen, the microbes team tested their malaria chip and it correctly identified a test the summer months. Will there be a pandemic or not? Will ’flu infection. They also, along with other whether it is possible to have survived by using sample of human blood infected with P. malariae provided by microbiologists win the race to produce an effective vaccine countries, adopted a ‘containment’ approach distinguish between truffles of minerals and decayed organic the Scottish Parasite Diagnostic Laboratory. The researchers were quickly? Watch this space… to dealing with outbreaks: isolate the infected the same species from different matter as nutrient sources and greatly encouraged by this initial result and are working on further regions. This technique will be person and those they have been in contact www.independent.co.uk/life-style/health-and-wellbeing/health-news/network-of- respired anaerobically with tests that aim to produce a chip to test for the presence of malaria with then administer anti-viral drugs to the flu-friends-could-help-says-health-ministry-1679713.html vital if governments adopt a iron as the terminal electron and indicate drug resistance in less than 60 minutes. At present, controlled geographical origin the most accurate way to diagnose malaria is by examination of a patient and contacts. There is not very much www.independent.co.uk/news/world/americas/swine-flu-snake-oil-web-sites-get- acceptor. The microbes found system, similar to the wine blood smear by skilled personnel – a time-consuming process – evidence that this approach works but it does roasted-by-fda-1679187.html in the brine are genetically have the advantage of reducing severity of industry, which would require closely related to modern and there is no rapid test for drug resistance in use. A 2008 study www.newscientist.com/article/dn17049-expert-analysis-mexican-swine-flu--the- symptoms and shortening the illness if ’flu authentication of where a marine micro-organisms. by the UK Health Protection Agency showed that in recent years story-so-far.html truffle was harvested. does develop. Authorities in China have taken www.independent.co.uk/news/science/ there has been an increase in cases of the most dangerous forms of http://news.bbc.co.uk/1/hi/world/americas/8022516.stm the containment approach to a much further www.sciencemag.org/cgi/content/ microbes-that-breathe-iron-are-found- malaria being brought back by travellers from overseas. extreme – enforcing quarantine conditions on http://news.bbc.co.uk/1/hi/world/americas/8034284.stm fllsci;323/5917/1006 in-antarctic-1669966.html news.bbc.co.uk/1/hi/scotland/glasgow_and_west/8015241.stm

74 microbiology today may 09 microbiology today may 09 75 Darwin: from the origin of species to the origin of infection

009 marks the bicentenary of the birth of his thoughts on evolution shortly after his return from the In this special issue of Microbiology Today to mark the two Charles Charles Darwin and the 150th anniversary of the Beagle voyage, recording a riot of ideas, sometimes earthy or publication of On the Origin of Species by Means of even vulgar, in a series of notebooks. For inspiration on his Darwin anniversaries in 2009, Mark Pallen, a Darwin enthusiast, Natural Selection. The impact of Darwin’s theory ideas of the struggle for existence and natural selection, he of evolution by natural selection is felt throughout drew on the work of Robert Malthus, who had suggested that biology and even beyond it — in disciplines as human populations always eventually out-run the means to explores the links between the great man and microbiology. 2diverse as computer science and cosmology. Darwin’s theory sustain them. Darwin outlined his theory in a ‘pencil sketch’ is widely touted as ‘the best idea anyone ever had’ and arguably of 1842 and an essay of 1844, but, preoccupied with other ranks as the most influential change in human thought in work, delayed publication until the late 1850s, when he In the decades after his death, while that variation precedes selection, rather m Title page from an early edition of On The modern times (although as microbiologists, we may wish to was spurred into action by the rival work of Alfred Russel Darwin’s ideas of evolutionary change than arising in response to it, and thrust Origin of Species, first published in 1859. GustoImages / Science Photo Library claim that the germ theory of infection is of more practical Wallace. and common ancestry were widely bacteria centre stage as biological significance). In On the Origin of Species by Means of Natural Selection, first accepted, his principal mechanism entities with fully-fledged genetics. the on-going controversy. In 1860, in What about Darwin and microbiology? Antibiotic resis- published in 1859, Darwin eloquently (and presciently, given for change, natural selection, was A few years later, in 1945, Milislav a letter to his friend Lyell, he refers to tance is widely cited as a tangible example of Darwinian its subsequent influence on antibiotic resistance) emphasizes not. However, in the mid-20th Demerec repeated the fluctuation test the work of Pasteur’s rival Pouchet: evolution. But Darwin himself lived through the birth of our the remarkable power of natural selection: century, Darwin’s intellectual legacy on penicillin resistance in Staphylo- ‘I have seen something about the discipline, so it is not surprising to learn that there are links ‘We have seen that man by selection can certainly produce was reconciled with Mendelian coccus aureus, showing for the first infusorial experiments in Paris: between Darwin and the founding fathers of microbiology. great results, and can adapt organic beings to his own uses, genetics in what is often called ‘The time the awesome power of natural Quatrefage objected to their accuracy. through the accumulation of slight but useful variations, Modern Synthesis’. As part of this selection to curtail our biochemical Some old experiments were several Darwin and natural selection given to him by the hand of Nature. But Natural Selection, as reconciliation, bacteria were brought victories over micro-organisms. years ago tried in Germany with Charles Darwin was born and schooled in Shrewsbury, an we shall hereafter see, is a power incessantly ready for action, into the broader evolutionary genetic astonishing precautions (air all English market town close to the Welsh border. He tried, and is as immeasurably superior to man’s feeble efforts, as framework, principally through the Darwin and Pasteur passed through sulphuric acid & and ducked out of, a medical education in Edinburgh, then the works of Nature are to those of Art.’ experiments on the genetics of phage Shortly after Darwin published The caustic potash) and infusoria never studied at Cambridge with a view to joining the clergy. But Later, in The Descent of Man, despite his ignorance of the susceptibility published by Salvador Origin, in Paris, Louis Pasteur per- appeared.’ his reputation as a naturalist earned him a place on a round- nature of inheritance, Darwin points out that the variation Luria and Max Delbrück in 1941. In formed a series of experiments that A few years later in 1863, he wrote the-world trip on HMS Beagle, which primed him for his that is a prerequisite of natural selection originates inde- their famous fluctuation test, Luria and demolished the theory of spontaneous to the English botanist George revolutionary ideas on evolution. He started to formulate pendently of the selection itself. Delbrück confirmed Darwin’s hunch generation. Darwin was well aware of Bentham:

76 microbiology today may 09 microbiology today may 09 77 Quarter Page Advert:Layout 1 10/09/2008 16:04 Page 1KC_3717 AD:Layout 1 9/5/08 10:46 Page 1

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been present. But if (and oh! what a big if!) we could conceive Lab M online eNews in some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, etc., present, that a THE GATEWAY TO MICROBIOLOGY TM proteine [sic] compound was chemically formed ready to undergo still more complex changes, at the present day such matter would be instantly devoured or absorbed, which would not have been the case before living creatures were formed.’ As far as I am aware, Pasteur never made any direct reference www.labm.com to Darwin, although he opened his 1864 address to the Sorbonne on spontaneous generation with these expressive m Charles Darwin in old age. Popperfoto / Getty Images lines: ‘ Great problems are in question today, keeping every thinking Darwin’s response is a triumphant celebration of the birth of UNIVERSITY COLLEGE LONDON man in suspense: the unity or multiplicity of human races, medical microbiology: AND THE the creation of man 1,000 years or 1,000 centuries ago; the ‘I thank you sincerely for your most kind letter and I return BRITISH SOCIETY FOR fixity of species, or the slow and progressive transformation your wishes for the New Year with all my heart. Your letter MEDICAL MYCOLOGY of one species into another…’ has interested me greatly. Dr Sanderson showed me some www.sgmjournals.org Half a century later, an essay in Science magazine concluded: admirable photographs on glass by Dr Koch of the Organisms MSc/Diploma in Medical Mycology ‘Darwin, master of the organic world sleeps near Newton, which cause Splenic Fever. But your letter and the valuable

master of the inorganic, in the great [Westminster] Abbey, work which you have given me make the case much clearer Volume 155 , Part 3 , pp. 665–996 Volume 90 , Part 5 , pp. 1055–1301 Volume 59 , Part5 , pp. 923–1258 Volume 58 , Part5 , pp. 535–695 March 2009 May 2009 May 2009 May 2009 This unique course provides postgraduate training in all aspects of Volume 155, part 3 Volume 90, part 5 Volume 59, part 5 Volume 58, part 5 among the most famous of his race. Pasteur rests alone in to me. I well remember saying to myself between 20 and 30 Pages 665–996 Pages 1055–1301 Pages 923–1258 Pages 535–695 Medical Mycology and is aimed at those with a keen interest in International International Journal of Systematic and Evolutionary Microbiology Journal of General Virology Journal of Medical Microbiology the chapel of his laboratory … Both rest forever among the years ago, that if ever the origin of any infectious disease Microbiology Journal of laboratory or clinical mycology. JGV JGV Journal Systematic and Journal

of General EvolutionaryJMM JMM of Medical IJSEM IJSEM

ISSN 1350-0872 http://mic.sgmjournals.org Microbiology ISSN 0022-1317 http://vir.sgmjournals.org Virology ISSN 1466-5026 http://ijs.sgmjournals.org Microbiology ISSN 0022-2615 http://jmm.sgmjournals.org Microbiology immortals. the last half of the nineteenth century may well could be proved, it would be the greatest triumph to Science; MIC 155-3.EPS VIR 90-5.EPS IJS 59-5.EPS JMM 58-5.EPS be called their age “the Age of Darwin and Pasteur”.’ and now I rejoice to have seen the triumph.’ Open to laboratory scientists, registered medical practitioners and

Published by the Society Published by the Society Published by the Society Published by the Society for General Microbiology for General Microbiology for General Microbiology for General Microbiology other health care professionals holding relevant qualifications, www.sgm.ac.ukthe www.sgm.ac.uk www.sgm.ac.uk www.sgm.ac.uk Typeset and printed Typeset and printed Typeset and printed Typeset and printed in Great Britain by in Great Britain by in Great Britain by in Great Britain by The Charlesworth Group The Charlesworth Group The Charlesworth Group The Charlesworth Group ISSN 1350-0872 ISSN 0022-1317 ISSN 1466-5026 ISSN 0022-2615 March 2009 course is delivered by UCL through distance learning and is taught May 2009 May 2009 May 2009 Published by the Society for General Microbiology Mark Pallen 0022-1317(200905)90:5;1-OPublished by the Society for General Microbiology Published by the Society for General Microbiology on behalf of BAM, IUMS and ICSP Published by the Society for General Microbiology Darwin, Cohn and the origin of infection jointly with the British Society of Medical Mycology giving Darwin maintained an extensive network of correspondents. Professor of Microbial Genomics, Centre for Systems students access to national and international expertise. Among them was the German Jewish botanist and Biology, University of Birmingham, Birmingham B15 2TT bacteriologist, Ferdinand Cohn (1828–1898), who is widely (t 0121 414 7163; e [email protected]) This modular course allows a flexible approach to learning, enabling students to complete in two to five years. Course material recognized as the father of bacterial taxonomy. Cohn was is delivered via DVD and supported by a web based teaching Online submission the first to classify bacteria according to their microscopic Further reading Darwin, C. (1859). On The Origin of Species By Means of Natural environment. Practical training is provided by BSMM courses in appearance and the first to describe sporulation inBacillus . Leeds and Bristol and completion of a project. No page charges Selection. London: John Murray. He was instrumental in publishing Robert Koch’s work on Publication ahead of print Bacillus anthracis. Pallen, M. (2009). The Rough Guide to Evolution. London: Rough For further information please contact: Guides. Free colour reproduction From 1874 until 1882, Darwin and Cohn maintained Anne Dickens, Programme Administrator Creager, A.N.H. (2007). Adaptation or selection? Old issues and a lively correspondence, principally on botany. On 26 Centre for Medical Microbiology Open access option September 1876 Darwin writes to invite Cohn and his wife new stakes in the postwar debates over bacterial drug resistance. Department of Infection to visit him at Down House. And then, the very next day, Stud Hist Phil Biol Biomed Sci 38, 159–190. Royal Free & UCL Medical School Darwin writes to his son Frank, saying that he hopes they Sedgwick, W.T. (1923). Darwin and Pasteur: an essay in Rowland Hill Street will not come! Apparently the subsequent visit was a success. comparative biography. Science 52, 286. London NW3 2PF Tel 0207 794 0500 ex 33546 society for g e n e r a l However, for microbiologists, one particular exchange of http://darwin-online.org.uk/ – The complete works of Charles letters stands out. In January 1878, Cohn writes to Darwin, Darwin online. Email: [email protected] Microbiology discussing Koch’s recent discovery of the anthrax bacillus. www.darwinproject.ac.uk/ – Darwin Correspondence Project

78 microbiology today may 09 The tree of life is based on phylogeny which infers the evolution of lineages of organisms by the analysis of the sequences of their macromolecules, in particular genes and proteins. The 16S rRNA gene sequences used in the hierarchical classification of Bacteria and Archaea from domain to genus are too highly conserved to be of taxonomic use at the species level and Jim Staley proposes an alternative approach. The phylogenomic species concept

peciation is the process whereby organisms evolve as temperature and pH range for growth, carbon sources to form new strains and species. Like speciation utilized, habitat, Gram stain, size and shape, etc. in plants and animals, bacterial speciation is In the 1960s molecular characterizations were introduced. driven by ecological and geographical factors. These included DNA base composition (mol% G+C content) For example, consider the bacteria that have and DNA–DNA hybridization. The combination of DNA evolved to become pathogens of specific plant hybridization with phenotypic features has culminated in andS animal species. These pathogenic bacterial species are the currently accepted polyphasic species definition used illustrative products of ecological speciation. for bacteria and archaea. Two strains that have distinctive Geographic separation in which divergence to form phenotypes and show greater than 70% DNA hybridization new species is caused by mutation, selection and genetic between them are considered to be members of the same drift, is common in animals and plants. Evidence for the species, whereas those that exhibit less than 70% are effect of geographic factors on bacterial speciation has considered to be different species. The introduction of been more difficult to establish. Recently, however, Rachel DNA hybridization and the polyphasic species definition Whitaker and colleagues showed that Sulfolobus islandicus, a brought uniformity to the species definition and has served thermoacidophilic archaeon isolated from globally separated bacteriologists very well since its adoption in the 1980s. hot springs, forms different clades depending on the their However, the current definition is not conceptual and DNA location. Strains isolated from hot springs in Iceland differ hybridization has two major drawbacks: from those from Yellowstone (Fig. 1) and Lassen National 1 the difficulty of conducting the DNA hybridization assay, Parks of North America, and these groups differ from strains and isolated from Kamchatka, Russia. This finding indicates that 2 its inability to assess speciation, the evolutionary process geography also plays a role in bacterial speciation and quite whereby organisms form species. probably a major one, although more research is needed to The 1980s brought protein and RNA sequencing as well better understand the importance and commonality of it as phylogeny into taxonomy. Most importantly, phylogenetic among bacteria and archaea. analyses of the 16S rRNA genes of bacteria and archaea, and

Taxonomy of bacteria and archaea Early classifications of bacteria depended entirely on the c Fig. 1. A view of Norris Geyser Basin, Yellowstone National Park, which was the source of several strains used in the biogeographic expressed or phenotypic properties of the organism. Each study of the thermoacidophile, Sulfolobus islandicus. US National species has its characteristic phenotypic attributes, such Park Service.

80 microbiology today may 09 microbiology today may 09 81 S. pseudopneumoniae highly conserved genes for the identification of species as now, literally hundreds of strains of HGT is too extensive, it can lead James T. Staley well as genomic approaches. some pathogenic bacterial species are to ambiguous classifications and Former Chairman of Bergey’s NT26 being sequenced. potentially an erasure of the evolu- Manual Trust, Professor Emeritus The phylogenomic species concept (PSC) tionary pathway. This phenomenon of Microbiology, Department of The time has arrived for bacteriologists to adopt a concept The issue of horizontal might in part help explain the fuzzy Microbiology, University of for species. The PSC relies on phylogenetic and genomic gene transfer species that are sometimes encountered Washington, Seattle, WA 98195, information to identify species. Genes that are less highly One of the most perplexing issues when MLSA is used. HGT affects not USA (e [email protected]) conserved than 16S rRNA are selected for phylogenetic confronting bacterial taxonomists is only phylogenetic classifications but analysis to determine the relatedness among a group of that of horizontal gene transfer (HGT). those based on phenotypic properties S. mitis Further reading S. pneumoniae strains. In addition, genomic information, which includes Evidence for HGT is found at all as well. Bishop, C.J. & other authors (2009). all gene sequences, information on synteny (the arrangement levels of classification from domain However, as thorny an issue as Assigning strains to bacterial species of genes), and the use of DNA hybridization and expression to species. For example, at the inter- HGT is, it does not appear to be an via the internet. BMC Biol 7, 3 approaches, supplement the phylogenetic analyses. domain level, homologues for genes overwhelming problem for phylogeny. (doi:10.1186/1741-7007-7-3). The advantages of the PSC are: such as those for eukaryotic a- and It seems probable that genomic studies Feil, E J. & Spratt, B.G. (2001). d it is based on phylogenetic theory which infers the evolution b-tubulins that are responsible for will help lead to a clarification of the Recombination and the population of an organism from the sequence of its macromolecules; forming microtubules, have been likely potential source and nature of structures of bacterial pathogens. Annu d it is pragmatic in that it relies on phylogenetic analyses reported in Prosthecobacter, a bacterial genes that have been transferred from Rev Microbiol 55, 561–590. that have been developed to assess the relatedness among genus in the phylum Verrucomicrobia other organisms. Hanage, W.P., Fraser, C. & Spratt, 0.5 macromolecules of different strains; (Fig. 3). Since these genes have been B.G. (2005). Fuzzy species among d PSC information is archival; found only in this single genus of Universal PSC recombinogenic bacteria. BMC Biology d PSC information is portable and can be transferred the Verrucomicrobia, the most likely The PSC is applicable to all living 3, 6–13. anywhere electronically; explanation is that they were transferred organisms, so its espousal by biologists Jenkins, C. & other authors (2002). d it has the potential to be universally applied to all to this group from a eukaryote millions could lead to the establishment of a Genes for the cytoskeletal protein tubulin organisms. of years ago. complete hierarchical taxonomy of all in the bacterial genus Prosthecobacter. There is even greater evidence for life on Earth. If the PSC were adopted, Proc Natl Acad Sci U S A 99, 17049– The PSC in practice HGT at the species level than there is it could, like the tree of life, serve as a 17054. Actually, the PSC is already being used to identify bacterial at higher taxonomic levels. Clearly, if unifying step for all biology. König, H. & Stetter, K.O. (1989). species. Brian Spratt’s laboratory has pioneered the use Section 25 – Archaeobacteria. In Bergey’s S. oralis of multiple locus sequence analysis (MLSA) as a phylo- . Fig. 3. An electron micrograph showing numerous cells of Prosthecobacter debontii. The bacteria Manual of Systematic Bacteriology, vol. 3, genetic method to identify strains of many pathogenic in this genus contain BtubA and BtubB, which are homologues for eukaryotic a- and b-tubulin. pp. 2171–2173. Edited by J.T. Staley & Although it is a hallmark feature of all members of the Eukarya, this is the only known example bacteria including the genera Streptococcus, Neisseria and of tubulin-containing bacteria. J.T. Staley others. Baltimore: Williams & Wilkins. m Fig. 2. An MLSA phylogenetic tree showing the positions of Burkholderia. Konstantinidis, K.T. & Tiedje, J.M. numerous strains of Streptococcus pneumoniae, S. pseudopneumoniae, S. mitis and S. oralis. Note that one strain, NT 26, lies between The MLSA approach relies on assessing the sequences of (2005). Genomic insights that advance Streptococcus pneumoniae, S. pseudopneumoniae, and therefore typically five to eight genes from each strain. The sequences the species definition for prokaryotes. cannot be identified. The bar indicates 0.5 substitutions per 100 of each gene are concatenated (linked together end to end) Proc Natl Acad Sci U S A 102, 2567–2572. nucleotides. Reproduced with permission from Hanage et al. (2006), prior to phylogenetic analyses. The result is a phylogenetic Phil Trans R Soc B 361, 1917–1926 Konstantinidis, K.T., Ramette, A. & tree of the strains of a species (Fig. 2). Tiedje, J.M. (2006). The bacterial species the 18S rRNA genes of eukaryotic organisms revealed that The work on Sulfolobus islandicus discussed previously definition in the genomic era.Phil Trans there were three primary lines of descent in the tree of life. also used the MLSA approach. The 16S rRNA gene was R Soc B 361, 1929–1940. These major phylogenetic divisions, now called domains, included in that study, but it was too highly conserved to be Staley, J.T. (1989). On using the are Bacteria, Archaea and Eukarya. This led to changes in useful. However, eight genes selected for analysis by MLSA Manual. In Bergey’s Manual of Systematic bacterial taxonomy. In Volume 3 (1989) of the first edition of indicated that the strains from each geographic location Bacteriology, vol. 3, pp. xix–xxi. Edited Bergey’s Manual of Systematic Bacteriology (www.bergeys.org), formed separate clades. by J.T. Staley & others. Baltimore: the Archaea (Archaeobacteria) were the first to be classified Genomic approaches are now becoming important in the Williams & Wilkins. taxonomically on the basis of 16S rRNA gene sequence study of speciation. Kostas Kontaninidis and James Tiedje Staley, J.T. (2006). The bacterial species analyses. In the second edition of the Manual, 16S rRNA have led this effort. Not only do genomes provide all of dilemma and the genomic–phylogenetic is being used as the basis for the entire classification of the the organism’s genes, but they provide the arrangement of species concept. Phil Trans R Soc B 361, Bacteria and Archaea from domain to genus. the genes, or synteny, and hybridization and expression 1899–1909. There was initially great anticipation that the 16S rRNA microarrays can be applied to compare strains. Whitaker, R.J., Grogan, D.W. & gene could be used for identifying species as well. But, alas, Genomic approaches require that complete sequences are Taylor, J.W. (2003). Geographic this was not to be. Unfortunately, it is too highly conserved available of several strains of a species and its close relatives. barriers isolate endemic populations of to identify species. For this reason this article proposes a Although this might appear to pose a major problem, it may hyperthermophilic archaea. Science 301, phylogenomic species concept that entails the use of less not be such a significant issue in the future, because even 976–978.

82 microbiology today may 09 microbiology today may 09 83 xperimental results rarely upset the common wisdom of a scientific discipline, but that Norman R. Pace happened to biology late in the 20th century. The common wisdom in deep evolution and believes that the term how we classify organisms was rendered sorely It’s time in need of modernization. And that modern- Eization is happening too slowly. ‘prokaryote’ is an The anachronism here is the notion of ‘prokaryote’ and the model of biological organization and evolution that it elicits. anachronism in modern This model, which I term the ‘prokaryote–eukaryote’ model, to retire posits that fundamentally there are two kinds of organisms, prokaryotes and eukaryotes, defined by the presence or biology. Here he explains absence of a nucleus (more properly nuclear membrane). Additionally, the model proposes that prokaryotes gave rise to eukaryotes, as shown in the figure overleaf. the why and seeks the The problem, however, is that the prokaryote concept has been undermined critically by sequence-based phylogenetic help of microbiologists results. Indeed, the notion of prokaryote was scientifically illogical from the beginning because the definition, an ‘organism without a nucleus’, is a negative definition. No prokaryote in stopping its use. one can tell you what a prokaryote is, interchangeable in the textbooks with they can only tell you what it is not. ‘prokaryote’. It is curious that the Yet, institutional biology embraced nomenclature of ‘monera’ never caught- the notion of prokaryote and it came on among earlier microbiologists, to dominate textbooks, journals and whereas ‘prokaryote’ was immediately discourse in matters of deep evolution. incorporated into the lexicon. But in But the hypothesis of the prokaryote fact, prokaryote was never much more was never tested. than a name-change from monera, a 19th century notion based on far Where it came from – more limited knowledge than is now the very short history of available. prokaryote It is important to understand that The disproof of prokaryote the concept of prokaryote is not The idea of prokaryote was disproved based on scientific results. Rather, it in 1977, with Carl Woese’s discovery is based on historical conjecture. To of archaea and the first articulation of simplify the history considerably, I a rudimentary molecular phylogenetic think that prokaryote had its origins tree that related the most diverse in evolutionary models of the late forms of life. Woese saw through 1800s, with ‘monera’ at the origin of comparisons of ribosomal RNA a tree of complex eukaryotes. Monera (rRNA) sequences that life’s diversity persists today at the base of the five- is composed not of two deeply related kingdom classification scheme, which groups, prokaryote and eukaryote, but was introduced in the 1960s and is rather three such groups. These three popular in current textbooks. Also in phylogenetic ‘domains’ came to be the 1960s, the name ‘monera’ became called Bacteria, Eukarya (eukaryotes, which indeed proved monophyletic) and Archaea. Woese originally named the latter group Archaebacteria, but b ‘Prokaryotes’ heading into the sunset. this was changed to Archaea when it Medical R.F.Com / Science Photo Library (bacteria); Photos.com/Jupiter Images became clear they are fundamentally (sunset) distinct from Bacteria.

84 microbiology today may 09 microbiology today may 09 85 (a) Prokaryote–eukaryote model (b) Three-domain model

Bacteria

Origin Origin

Prokaryotes Eukaryotes Eukarya

m Prokaryote–eukaryote (a) versus three-domain (b) models for biological organization and the course of deep evolution. The wedges indicate radiations within the respective groups.

Archaea

The three-domain model of relationships and evolution the nuclear membrane. At the last resort, the proponents What to do about it and how modernization. This is because their to be sure, but it also provides a stands in stark contrast to the prokaryote–eukaryote model, of prokaryote insist, ‘You have to call them something!’ But microbiologists are critical organisms span the three domains, solid foundation for progress toward as shown in the figure above. The three-domain pattern that’s the problem: there isn’t any ‘them’. The molecular Institutional biology is now heavily and the phylogenetic perspective is answering those questions. shows that eukaryotes constitute a phylogenetically coherent phylogenetic results, bolstered by decades of biochemical invested in the prokaryote concept. referentially necessary and an obvious group, but there is no specific group to label ‘prokaryote’. corroboration, show that there is no natural grouping that The language permeates our literature utility. Modern treatment of issues Norman R. Pace Both archaea and bacteria would qualify through their would correspond to prokaryote. and thereby distorts understanding of in classification and evolution by Department of MCD Biology, lack of a nuclear membrane, but these two groups are Proponents of the concept of the prokaryote sometimes foundational issues. One hurdle that microbiological journals and textbooks University of Colorado, Boulder, not specific relatives. Indeed, archaea are more closely argue that the prokaryote terminology is a convenient faces efforts to modernize this matter eventually will lead to upgraded CO 80309-0347 (e nrpace@ related to eukaryotes than archaea are to bacteria. This classification and that historical usage justifies contin- is that most students, biologists and general texts. One catalytic step that colorado.edu) relationship is supported not only by molecular phylogeny, ued usage. But these rationalizations are scientifically authors of general textbooks don’t any microbiologist can contribute, but also by many properties of archaeal and eukaryotic inappropriate. A critical point here, one usually missed think very much about microbes. however, is simply to stop using the cells compared to bacterial cells. by proponents of the prokaryote concept, is that scientific Their world is generally that of large term ‘prokaryote’. This may be hard to Further reading Additionally, the phylogenetic model shows no specific classification is not a convenience. As scientists we must organisms of limited diversity. They, do because of long conditioning, but Pace, N.R. (1997). A molecular view group of organisms that preceded the eukaryotes. The observe nature and classify accordingly, so as to promote unlike microbiologists, are not faced it is an important step for educators of microbial diversity and the biosphere. textbook and common wisdom that eukaryotic cells arose scientific understanding. As Darwin insisted, Our‘ classifi- with trying to make sense of a vast particularly. Science 276, 734–740. late in the history of Earth by fusion of two prokaryotes is cations will come to be, as far as they can be so made, genealogies’. diversity of life with comparatively How can teachers broach this issue Sapp, J. (2005). The prokaryote– incorrect. Mitochondria and chloroplasts were derived from ‘Prokaryote’ doesn’t fit the observed genealogy. It needs to little observable variation without in the face of the currently pervasive eukaryote dichotomy: meanings and symbiotic bacteria, but the nucleus is far more ancient. The be retired from the language of biology. It has become a resort to biochemistry and gene reference to prokaryotes in journals mythology. Microbiol Mol Biol Rev 69, history of the nucleus is seen in the molecular phylogenetic distraction. sequences. The three-domain phylo- and textbooks? One way to do so is to 292–305. tree as the eukaryal line of descent. The tree shows that the genetic model is beginning to appear use the discordance between recently Woese, C.R. (1994). There must be a nuclear line is as old as the archaeal line and was derived Why it matters in textbooks, but usually as just emerging data and the textbooks as a prokaryote somewhere: microbiology’s from neither archaea nor bacteria. The molecular results The legitimacy of prokaryote is more than an issue in another method of classification, prime example of how science, biology search for itself. Microbiol Mol Biol Rev say nothing at all about whether or not the earliest terminology. It is also a matter of proper understanding alongside the five-kingdom scheme. in this case, is an ongoing, living 58, 1–9. eukaryotes possessed nuclear membranes. In the light of of important biological concepts. Any scientific field rests The evolutionary implications of the process, evolving in response to new Woese, C.R. & Goldenfeld, N. the sequence comparisons, the presence or absence of the essentially on two conceptual foundations. One foundation three-domain pattern of evolution are experimental data. Dealing with the (2009). How the microbial world nuclear membrane or other morphological trait is irrelevant requires understanding of the order, the organization of seldom broached, and the language prokaryote issue is an opportunity saved evolution from the Scylla of for classification or for deduction of the paths of deep the subjects of study. The other conceptual foundation is of prokaryote perseveres. What to do to demonstrate the testing of specific molecular biology and the Charybdis evolution. how the subjects of study change. Foundational issues for about it? hypotheses with experimental data, of the Modern Synthesis. Microbiol progress in biology, therefore, are proper perceptions of The retirement of prokaryote from with results important for biology. Mol Biol Rev 73, 14–21. Some would argue phylogenetic groups and relationships and, consequently, the lexicon of biology will be slow Phylogenetic trees, maps of evo- Some authors defend prokaryote as a useful classification. the path of evolution. because it is now so deeply entrenched. lutionary relationships, are straight- They argue, for instance, that bacteria and archaea are united The prokaryote–eukaryote notion fails in both these Consequently, that retirement process forward metaphors for the course of by their very small size or their use of coupled transcription regards. In contrast, the three-domain pattern of life’s organi- needs to be catalysed. Microbiologists evolution and are not hard for students and translation. These arguments are not meaningful; rather, zation and large-scale path of evolution is solidly grounded are in the best position to understand to understand in essence. The three- they are just other twists on the presence or absence of on scientific observations. the issues and to participate in domain concept poses many questions,

86 microbiology today may 09 microbiology today may 09 87 A cockatrice was a flamboyant sight at medieval banquets, featuring a roasted chimaera of winged rooster fused to a suckling pig. Edward L. Bolt and Stephane Delmas take a look at archaea, ancient micro-organisms whose genomes look like chimaeras of apparent bacteria-like and eukaryote-like features and metabolic systems.

rchaea and bacteria are micro-organisms that are similar, yet different. Archaea are evolutionarily ancient organisms that have soaked up diverse ecosystems for at least 2.5 billion years. They are, like bacteria, Archaea: unencumbered by various complex sub- Acellular structures (e.g. mitochondria, a membrane-bound nucleus) and as such have been for most of their long exist- ence, or at least from when microbiologists started looking at them, considered to be bacteria that had evolved to thrive in a microbial extreme environments (e.g. at high temperature or salinity). For this reason they were often called archeabacteria. However, DNA sequencing experiments in the 1970s drove a wedge through the bacteria, splitting it into two cockatrice separate domains of cellular life: the Bacteria and the Archaea. The genetic distinction between bacteria and archaea is now generally accepted since its original proposal in 1977, but has its evolutionary root much earlier, probably pre-dating and it is possible to compare the genetic contains approximately 7,500 COGs. the emergence of oxygen 2.5 billion years ago. Therefore, relatedness of any metabolic pathway About 45–55% of these, depending the classification of cellular organisms is now usually that takes your fancy. on how strict are the rules of inclusion, represented in a tree of life consisting of three domains, are also bacterial. The similarities Bacteria, Archaea and Eukarya. This notion, and the Comparing archaea to other between some fundamental metabolic difficulties arising from it, especially with regard to micro- organisms can make puzzling pathways in bacteria and archaea organisms, can be pursued in other articles in this issue of patterns are striking and it is apparent from Microbiology Today. The diversity of available DNA sequence genome sequencing that bacteria and Nevertheless, since 1977, detailed whole-genome sequence information highlights how the same archaea are promiscuous, as they information has been obtained from many nooks and genes are often conserved throughout have swapped genetic material with crannies of bacterial and archaeal life: at the time of writing, the three domains of cellular life. These one another in ‘lateral gene transfers’. according to the NCBI database, there are 1,456 genomes genes, referred to as COGs (conserved These observations illustrate that available for bacteria and 69 for archaea. Add to this the orthologous genes), may indicate com- although archaea and bacteria are substantial number of genomes sequenced from eukaryotes mon descent as some metabolic path- presented as distinct cellular domains ways are conserved in organisms as they retain the capacity for genetic flux c Scanning electron micrograph of the thermophilic archaeon they diverge through modification dur- between domains, and the potential for Pyrococcus furiosus. Eye of Science / Science Photo Library ing evolutionary time. The Archaea diversity.

88 microbiology today may 09 microbiology today may 09 89 letters

Comparative genetics and biochemistry have also shuffling genes around inside a cell and allowing integration illustrated how very different archaea are from bacteria. of foreign DNA into the chromosome. A topical example of this is how some types of bacteria All these recombination processes need a protein called and archaea derive motility from functionally similar a recombinase. The recombinase in archaea is similar to structures called flagella. However, the protein structures eukaryote recombinase, although they have different names of the flagellum in archaea are quite different from those in (RadA and Rad51), but differs from bacterial recombinase bacteria. The shape and effect of this cell structure are the (RecA). same in bacteria and archaea, but are fine-tuned differently. In the cell, the recombinase protein does much to set up Structural differences between archaea and bacteria are also recombination events, but other proteins finish them off. seen in their genomes, despite the fact that in shape these One of the finishing events is the forming of an elaborate micro-organisms appear alike because they lack a membrane- DNA structure called a Holliday Junction, named after covered nucleus. Bacterial cells clone themselves by copying the molecular biologist Robin Holliday. This is a physical their genetic material (DNA replication) from a single point manifestation of a recombination event in which two on the genome (an origin), but archaeal cells are known to different DNA molecules are co-joined. Another protein, copy their DNA from several points (origins) on the genome. called a resolvase, may be needed to disentangle the co-joined This is intriguing because features like having several DNA molecules set up by the recombinase. The identities of origins rather than a single origin are commonly ascribed resolvase proteins are now known in bacteria (e.g. RuvC), to eukaryotes only. On the other hand, the arrangement archaea (Hjc) and eukaryotes (GEN1/Yen1) and they are all of many archaeal genes into operational units where different: there is little similarity between them in sequence several genes are transcribed together (operons) is a bacterial or structure, but they do the same job in cells, finishing off trait. homologous recombination. This lack of similarity between Stockxpert / Jupiter Images resolvase from archaea and eukaryotes indicates that the Antibiotics Archaea are chimaeras in DNA processing DNA processing pathway in archaea is not just a mirror of Returning to the distribution of COGs in cellular life, and the eukaryotic one. Dear Editor Sir having pointed out that about 50% of genes in the archaea The machinery that controls the fidelity of homologous are also common to bacteria, we see that the other 50% are recombination, (mismatch repair proteins) also highlights The latest issue was once again very interesting. What I do enjoy most about The increasing resistance of bacteria confined to archaea or conserved with the domainEukarya this because it is conserved in bacteria and eukaryotes, but Microbiology Today is that it publishes articles concerning real issues and challenges to antibiotics is of grave concern, (which contains fungi and metazoans). A notable example is largely absent from archaea. Perhaps archaea evolved that we bioscientists have to confront in our daily lives, one of them being the but reversing this trend seems very of this dichotomy is in the arena of genetic information their own protein tools for resolving and monitoring demand for new antibiotics to counteract re-emerging and resistant infections difficult. The following approach may processing and genome dynamics (DNA replication, gene recombination, but have shared tools with eukaryotes for such as XDR tuberculosis and MRSA. be of interest. transcription, recombination and DNA repair). With some triggering it. The explosion in the number of archaeal genome I really enjoyed Flavia Marinelli’s article ‘Antibiotics and Streptomyces: the future Consider, as a hypothetical example, exceptions, proteins in archaea that drive DNA processing are sequences available and laboratory analyses give a blurred of antibiotic discovery’. I agree that the search for new antibiotics is declining and a molecule with two antibacterial not conserved in bacteria, but about 150 COGs in archaeal vision of archaea as a kind of cockatrice between bacteria and that microbial product screening particularly for effective Streptomyces spp. would activities, a penicillin activity and DNA processing are conserved in eukaryotes. For example, eukaryotic cells. However, this mixture obviously works very be a good start. I believe that research institutes and biopharmaceutical companies tetracycline activity, but in which the complex gene transcription machine (RNA polymerase) well, to have been around for so long. should carry out mass isolation and screening of soil microbes as they did in the tetracycline is not active until of archaea is very similar to the eukaryotic one. However, the ‘golden age’. I also believe that isolating microbes from other environments the b-lactam ring of the penicillin is might be interesting in discovering a new class of antibiotics as pointed out in opened. Then the bacterial cell would it was then unearthed that the proteins regulating the Edward L. Bolt & Stephane Delmas Flavia’s article. be killed by tetracycline. running of this machine in archaea are conserved in bac- The School of Biomedical Sciences & Institute of Articles such as Flavia’s help to raise awareness amongst microbiologists about This would in theory select for teria, not eukaryotes, highlighting the mixed-up nature Genetics, University of Nottingham NG7 2UH of this aspect of gene processing in archaea. How this has important issues such as these, but I believe we need to convey or channel strains possessing a b-lactamase, and (t 0115 8230194; e [email protected]) arisen during evolution has been tackled in one way by these strong messages to government and other relevant parties more effectively in thus for penicillin sensitivity. The invoking the action of ancient viruses. We now turn to a order for realistic progress to made. For instance if this Society can put pressure approach might be possible with many specific example of DNA processing in archaea that Further reading on the government and research councils that more money is needed to invest different pairs of activity, and it may illustrates recently discovered protein functions: homolo- Howland, J.L. (2000). The Surprising Archaea. Oxford: Oxford in research projects such as antibiotic discovery and mass isolation and screenings be that fairly small differences in the University Press. gous recombination. of potentially useful microbes, then the sooner these problems and demands activities would be sufficient to permit Blum, P. (editor) (2007). Archaea: New Models for Prokaryotic can be dealt with more practically. We would find a new class of antibiotics such selection. Biology. Norwich: Caister Academic Press. Two faces of homologous recombination sooner and they would be manufactured by interested biopharmaceutical Yours sincerely Homologous recombination is a cellular process used in all Doolittle, W.F. & Bapteste, E. (2007). Pattern pluralism and the companies. P.H.A. Sneath organisms and it serves two purposes. In one, homologous tree of life hypothesis. Proc Natl Acad Sci U S A 104, 2043–2049. Regards recombination promotes genetic stability by repairing Forterre, P. (2006). Three RNA cells for ribosomal lineages Department of Infection, Immunity broken chromosomes and rescuing DNA replication when it and three DNA viruses to replicate their genomes: a hypothesis Imran Hayat BSc AMIBiol and Inflammation, University of gets blocked as it moves away from origins. On the flip side, for the origin of cellular domain. Proc Natl Acad Sci U S A 103, 5/3 Northfield Drive, Edinburgh EH8 7RR Leicester, University Road, homologous recombination facilitates genetic diversity by 3669–3674. (e [email protected]) Leicester LE1 9HN

90 microbiology today may 09 microbiology today may 09 91 acteria and archaea are and speciate. Shouldn’t we look at a geologically uplifting canyon, not genetically, phylogenet- how evolution happens in nature, an erosion canyon, and until now ically and physiologically even though as passive observers, relatively undisturbed by humans. very diverse. But how we researchers cannot control this Despite having the same macroclimate does such diversity start process? What are the decisive factors? (overall seasonal temperature, rain- to evolve? How do the Is it possible to catch a glimpse of such fall, etc.), the south- and north- firstB subtle and tender lineages begin to a natural evolutionary experiment? facing slopes have substantially accrue? Oh, you might say, that’s trivial. different microclimatic temperatures Have a look at the textbooks and you ‘Evolution Canyon’, a natural and drought stress, which allow us will find everything there about the evolutionary laboratory to identify natural selective abiotic evolutionary interplay of mutation, The ‘Evolution Canyon’ system in Israel pressures and to study their effect in recombination, natural selection has turned out to be a suitable site nature. For over 20 years, the adapta- and genetic drift. The theoretical for such microevolutionary studies. tion and speciation of macro-organisms A glimpse of framework of population genetics is Eviatar Nevo, the former director of has been explored in ‘Evolution Canyon’ extremely well-developed. Even more, the Institute of Evolution in Haifa, using Drosophila and wild barley as you insist, microbial microevolution Israel, first realized the beauty and the main model organisms. Model has and still is being analysed in very scientific potential of this natural micro-organisms studied include the elegant laboratory experiments, where evolutionary laboratory. ‘Evolution cyanobacterium Nostoc linckia and microevolution in microbes are allowed to mutate, adapt Canyon’ 1 (Fig. 2) at Nahal Oren the fungi Sordaria fimicola, Penicillium and evolve in test tubes under very in the Carmel Mountains close to lanosum and Aspergillus niger. stringent and therefore reproducible Haifa is an east–west orientated can- and adjustable conditions (see the yon. The ‘African’ south-facing slope Bacillus simplex from nature: articles in the November 2004 issue of is constantly irradiated by sun, which ‘Evolution Canyon’ Microbiology Today). But may I remind makes it hotter and drier – savannah- In 2003, during my postdoc, I isolated you that the majority of bacteria are like – whereas the shady ‘European’ a population of about 1,000 strains of neither evolving in a computer, nor north-facing slope is a mesic, lush Bacillus simplex bacteria from soils from bacterial adaptation are they living in the pencils of mathe- forest. The scientific attraction of maticians and theoretical population ‘Evolution Canyon’ is obvious. The b Fig. 1. ‘Evolution Canyon’ 2 at Nahal Keziv, geneticists, nor in laboratory test tubes, slopes are separated by just 50–400 western Upper Galilee, Israel. Courtesy Michael Margulis although all these approaches yield metres. Thus, geographical separation and speciation in tremendous results. Most bacteria live cannot account for any slope-specific . Fig. 2. Cross-section of ‘Evolution outside in the environment, in water, differences in organisms belonging to Canyon’ 1 at Nahal Oren, Mount Carmel, soil, rocks, plants, etc. Here, where the same species. Haifa, Israel, showing the south-facing ‘African’ slope on the right and the north- they face a great plethora of biotic The canyon system is approximately facing ‘European’ slope on the left. ‘Evolution Canyon’, Israel and abiotic challenges, they evolve 3 million–5 million years old. It is Courtesy Michael Margulis

North-facing 'European' slope South-facing 'African' slope Many of the factors responsible for microbial evolution are becoming well understood, but Johannes Sikorski believes that not enough attention is being paid to the effects of the natural environment of organisms.

92 microbiology today may 09 microbiology today may 09 93 ‘Evolution Canyons’ 1 and 2 (Fig. 1), the latter being located But, are these putative ecotypes really ecologically distinct, the fluidity of the membrane, bacilli is classified as ‘Terra rossa’, small precisely in those sites from where in the western Upper Galilee Mountains and separated form as one would assume from their preference for slope type? incorporate predominantly anteiso- but significant differences exist, for the B. simplex bacteria were isolated, ‘Evolution Canyon’ 1 by about 40 km (Fig. 3). It turned out Indeed, at the upper temperature limit of growth, the branched fatty acids. In contrast, iso- example in the organic carbon content. taking into account that there are that strains from the same slope type were very similar, des- ‘African’ strains generally grow faster than the ‘European’ branched fatty acids are favoured at This prompted us to test for quanti- probably thousands of such east– pite the geographical distance, whereas strains from differ- strains. Apparently, ‘African’ strains are still metabolically higher temperatures. Interestingly, tative differences in the utilization of west-directed canyons on the globe ent slope types but in the same canyon were substantially active at the very high temperatures at which ‘European’ the ‘African’ strains generally produce a variety of different carbon sources. and that sporulating bacteria like distinct, despite their geographical proximity. This sug- strains start to capitulate. This was a first indication of the more iso-branched fatty acids than Interestingly, the observed differences bacilli easily migrate with the wind gested that a distance of 40 km has no effect on genetic high-temperature adaptation of the ‘African’ strains. Further the ‘European’ strains, irrespective were not associated with the dif- from continent to continent. But differentiation, but that the differential abiotic conditions support came from fatty acid analysis of the cell membranes. of the lab temperature at which the ferent habitats, but rather with the most probably, such marked micro- between the two slope types are probably driving the Compared with proteins and genomes, the cell membrane strains are grown. This strongly sug- phylogenetic split into GL1 and GL2. climatic contrasts in close proximity diversification. Further analysis of genetic diversity, on a is hardly a focus of mainstream research. Yet a functioning gests a genetically fixed difference reinforce within-species evolutionary reduced set of approximately 130 strains, revealed two major cell membrane is crucial for microbial life. Just imagine between ‘African’ and ‘European’ strains, Future research splits, and thereby ‘Evolution Canyon’ phylogenetic genomic lineages, termed GL1 and GL2. Using a bottle of your favourite wine. Obviously, you are only with respect to fatty acid branching, Many questions remain. For example, represents a beautiful site in which Ecotype Simulation, a program developed by Frederick interested in the wine, not in the bottle itself, but once the most probably as a result of long-term do ‘African’ and ‘European’ strains differ to study microevolution in natural Cohan (Wesleyan University, Connecticut, USA) that models disregarded bottle gets damaged, all the precious wine spills exposure to different environmental in their drought resistance, since the habitats. the sequence diversity within a bacterial clade, we identified out. This illustrates the substantial importance of an intact temperatures. south-facing slope soil is significantly putative ecotypes within GL1 and GL2 that Ecotype cell membrane. The cell membrane reacts very flexibly However, not all traits follow the drier? Do the spores of ‘African’ and Johannes Sikorski Simulation predicts to be ecologically and evolutionary to changing environments, for example by changing its south-/north-facing slope dichotomy. ‘European’ strains differ in their heat Deutsche Sammlung von distinct (see phylogenetic tree in Fig. 4). fatty acid composition. Under cold conditions, to ensure Although the soil on both slopes resistance? Do the strains contain Mikroorganismen und Zellkulturen plasmids, and if so, does the abun- GmbH (DSMZ), Inhoffenstrasse 7b, dance or diversity of plasmids corre- D-38124 Braunschweig, Germany LEBANON SYRIA b Fig. 3. Geographical locations of ‘Evolution late with either the phylogenetic Canyons’ 1 and 2 in Israel. Satellite image (t +49 531 2616 132; e johannes. – Earth Satellite Corporation / Science Photo structure or the ecological origin of ‘Evolution PE5 [email protected]) Library the host strains? The possibilities Canyon’ 2 Haifa are endless. Finally, how do c Fig. 4. Phylogenetic tree demonstrating Further reading the genetic similarity of 131 Bacillus these diverse traits relate to each Koeppel, A., Perry, E.B., Sikorski, J. & simplex strains isolated from ‘Evolution other among the wealth of the other authors (2008). Identifying the Canyons’ 1 and 2. The orange clades are PE3 131 B. simplex strains analysed fundamental units of bacterial diversity: Jerusalem from the 'African' south-facing slope, in this study? We are currently addres- a paradigm shift to incorporate ecology whereas the blue clades are from the 'European' north-facing slope. Each clade sing some of these issues. Once we into bacterial systematics. Proc Natl Acad consists of strains from ‘Evolution Canyons’ have enough phenotypic characteri- Sci U S A 105, 2504–2509. 1 and 2. J. Sikorski zations, genome sequence compari- PE4 Sikorski, J., Brambilla, E., Kroppenstedt, GL1 sons will help us to understand R.M. & Tindall, B.J. (2008). The ISRAEL how these evolutionary changes are temperature adaptive fatty acid content PE6 implemented at the molecular level. in Bacillus simplex strains from ‘Evolution JORDAN Despite the paucity of information, Canyon’, Israel. Microbiology 154, we do already understand that the 2416–2426. PE7 observed evolutionary lineages (puta- EGYPT Sikorski, J., Pukall, R. & Stackebrandt, tive ecotypes) represent speciation E. (2008). Carbon source utilization events. These putative ecotypes are PE8 patterns of Bacillus simplex ecotypes genetically different, reside prefer- do not reflect their adaptation to entially in different habitats and show ecologically divergent slopes in PE9 characteristic physiological traits ‘Evolution Canyon’, Israel. FEMS related to the habitats in which they Microbiol Ecol 66, 38–44. live. In fact, from a biological and evolutionary perspective, they probably PE1 already represent different species, though this proposal is currently not GL2 supported by the current pragmatic ‘Evolution but rather artificial taxonomic rules of Canyon’ 1 PE2 microbial species delineation. It is perhaps too naïve to expect that the traits observed have evolved

94 microbiology today may 09 microbiology today may 09 95 n the spirit of Darwin 200, which marks the bicentenary were found to harbour a number of intracellular Legionella- of these three, mimiviruses are actually (a) U. urealyticum Mimivirus of Charles Darwin’s birth, I will describe a little of like organisms. There the issue might have been forgotten most similar to those of eukaryotes what we know about the evolution of viruses and their were it not for a attempt several years later by La Scola and (Fig. 1c). Remarkably though, they ultimate origins. One of the immediate problems facing colleagues in Marseilles to catalogue the bacteria in these adopt a phylogenetic position ances- such studies is the evident fact that viruses are hugely and other environmental samples collected worldwide by tral to the split of the animal, plant diverse in size, appearance, even the nature of their ribosomal RNA (rRNA) sequencing. Puzzlingly, one of the and other component kingdoms of geneticI material (DNA or RNA). From this, it is reasonably Gram-positive amoeba-infecting bacteria with a diameter of eukaryotes, implying an extraordinarily clear that they are a not a single evolutionary group, and around 500–700 nm (Fig. 1a) proved resistant to attempts long evolutionary existence, possibly cannot be easily added as a single unit to the tree of life with to amplify the rRNA genes. Fortunately for future studies, reaching back as far as the origin of its three main divisions (Bacteria, Archaea and Eukarya). the decision to sequence its genome revealed the presence life. Mimiviruses additionally lack By the same token, it seems likely that different virus of an entirely novel, large virus-like genome, 1.2 Mb in ribosomal genes, an absence universal (b) groups (e.g. animal RNA viruses, retroviruses, large DNA size and containing over 900 genes, far larger than many to viruses and which confine them to viruses, bacteriophages) may indeed have entirely separate parasitic bacteria such as Rickettsia, Ureaplasma and some their obligate parasitic life cycle. Their evolutionary origins. Legionella species with which it was first confused (Fig. 1a). genomes are linear with covalently In this short article I will describe two areas where recent Remarkably, the genome of what is now called mimivirus closed ends, comparable to other large discoveries have produced tantalizing new insights into the (‘microbe-mimicking’ virus) contained many genes involved DNA viruses, such as asfarviruses (e.g. origin and ubiquity of some of these groups. Through the in translation, such as amino acyl-tRNA synthetases, African swine fever virus) and poxviruses application of new, mass-sequencing techniques and scope translation initiation, elongation and peptide release factors (e.g. smallpox virus), and distinct from for large-scale environmental sampling for virus genomic not found in other viruses, as well as a huge complement the circular genomes of most bacteria sequences, we may finally be able to understand the extent of genes (76%) encoding proteins with no identifiable and archaea. Finally, they replicate in and complexity of the ‘virosphere’ in which we live, and the homology and unknown function. the infected cell through construction extraordinary diversity of viruses that infect us. What are mimiviruses? While they breach the size and of multiple virus assembly structures complexity barrier that traditionally separates viruses and rather than by binary fission. This latter The tale of a ‘Gram-positive’ virus bacteria (Fig. 1a, b), they clearly aren’t bacteria. Mimiviruses feature seems to preclude the existence Amoebae growing in a water-cooling tower during the contain only seven genes homologous to a set of 61 core of free-living mimiviruses in nature (c) investigation of an outbreak of pneumonia in Bradford, UK, genes shared among bacteria, archaea and eukaryotes, and that might retain a greater proportion Mimivirus of ribosomal and other core genes required for autonomous replication. Eukaryotes A final emarkabler feature of mimi- Archaea viruses is their pervasive presence in Human the environment. Large-scale meta- Aeropyrum pernix genomic sampling has revealed a Yeast plethora of viruses related to mimi- viruses in seawater at frequencies 91 Pyrococcus abyssi that rival bacteriophages in detection Arabidopsis thaliana 100 frequency. What these viruses infect 100 98 and whether there are indeed free- 100 Archaeoglobus Virus evolution fulgidus c Fig. 1. (a) Left: mimiviruses (arrows) infecting the amoeba Acanthamoeba polyphaga, resembling Gram-positive particles. Right: comparison of the size of mimivirus with the intracellular bacteria 100 Ureaplasma urealyticum. Reproduced from Suzan-Monti et al. (2006) (see ‘Further reading’ for details) with permission from 0.2 substitutions per site As new mass sequencing techniques reveal that the Elsevier. (b) Left: appearance of mimiviruses in the cytoplasm of infected amoebae cells (bar, 2 μm. Right: electron micrograph of diversity of viruses is much greater than ever imagined, the non-enveloped icosahedral mimivirus virion surrounded by fibrils (bar, 100 nm). 100 (c) Phylogenetic relationship of core genes Bacteria Peter Simmonds shows that the latest discoveries of of representative eukaryotes, bacteria and archaea with homologues in mimiviruses, Escherichia coli showing their ancestral position relative Bacillus subtilis new viruses are providing some clues to how viruses to eukaryotes. (b, c) Reproduced with permission from La Scola et al. (2003) (see ‘Further reading’ for details) with evolved. permission from AAAS Mycobacterium tuberculosis

96 microbiology today may 09 microbiology today may 09 97 TTV Group 3 the unsuspected existence of a range of newly discovered directly study evolution in action as they colonize diverse parvoviruses (human bocavirus, PARV4), picornaviruses, environments and adapt to new hosts. TTV Group 4 paramyxoviruses, coronaviruses (including SARS virus), three new polyomaviruses and several new anelloviruses Peter Simmonds again highlights our current ignorance of the true size of the Centre for Infectious Diseases, University of Edinburgh, ‘virosphere’ infecting humans and animals. Summerhall, Edinburgh, EH9 1QH One of the remarkable characteristics of these newly (t 0131 650 7927; e [email protected]) discovered viruses is their frequent wide distribution in human and animal populations. In the picornavirus family, Further reading TTMV past or current infection with Saffold virus (SAFV), a newly Claverie, J.M., Ogata, H., Audic, S., Abergel, C., Suhre, K. discovered member of the genus Cardiovirus, was detected & Fournier, P.E. (2006). Mimivirus and the emerging concept in >95% of children by the age of two, even though the of ‘giant’ virus. Virus Res 117, 133–144. virus itself has remained undetectable by conventional virus isolation methods applied over the last 50 years and Ghedin, E. & Claverie, J.M. (2005). Mimivirus relatives in the Sargasso sea. Virol J 2, 62. whose actual existence was entirely unsuspected until 2 TTV Group 5 years ago. Cosavirus, a newly discovered genus of human Jones, M.S., Lukashov, V.V., Ganac, R.D. & Schnurr, D.P. picornaviruses, with dozens of serotypes and several species, (2007). Discovery of a novel human picornavirus in a stool which is likely to be as diverse genetically and clinically as sample from a pediatric patient presenting with fever of human enteroviruses, has been detected in 50% or more unknown origin. J Clin Microbiol 45, 2144–2150. of faecal samples from young children in locations all over Kapoor, A., Victoria, J., Simmonds, P., Slikas, E., the world (Pakistan, Nigeria, Egypt). Similarly, infections Chieochansin, T., Naeem, A., Shaukat, S., Sharif, S., Alam, TTV Group 2 with TTV and related small DNA viruses, collectively M.M., Angez, M., Wang, C., Zaidi, S., Shafer, R.W., Zaidi, termed anelloviruses, are ubiquitous in human, primate and S. & Delwart, E. (2008). A highly prevalent and genetically probably all mammalian species, a finding more surprising diversifiedPicornaviridae genus in South Asian children. Proc for their persistence and ongoing lifelong replication in Natl Acad Sci U S A 105, 20482–20487. the lymphoreticular system (including bone marrow), La Scola, B., Audic, S., Robert, C., Jungang, L., De Lamballerie, and multiple infection in each person with a plethora of X., Drancourt, M., Birtles, R., Claverie, J. M. & Raoult, D. TTMDV different types and species (Fig. 2). A wealth of further small, (2003). A giant virus in amoebae. Science 299, 2033. persistent and ubiquitous DNA viruses undoubtedly await to Ninomiya, M., Takahashi, M., Hoshino, Y., Ichiyama, K., TTV Group 1 be discovered in the coming years. Simmonds, P. & Okamoto, H. (2009). Analysis of the entire The frequent ubiquity and non-pathogenicity of many genomes of torque teno midi virus variants in chimpanzees: of the recently discovered viruses may indeed be a parti- infrequent cross-species infection between humans and 0.1 cular attribute that has hindered their identification in chimpanzees. J Gen Virol 90, 347–358. d r j Human the past. Most virus isolation and detection attempts have Raoult, D., Audic, S., Robert, C., Abergel, C., Renesto, P., d r Chimpanzee been necessarily clinically driven, aimed at identifying m Other primates (e.g. macaque, tupaia) Ogata, H., La Scola, B., Suzan, M. & Claverie, J.M. (2004). causes of various diseases with a suspected or demon- The 1.2-megabase genome sequence of mimivirus. Science m Other mammals (cats, dogs, pigs) strated infectious aetiology, SARS and AIDS being two 306, 1344–1350. recent examples. Secondly, and particularly for DNA viruses, tight control of replication is a commonly used Simmonds, P. (2002). TT virus infection: a novel virus–host strategy to avoid immune recognition and elimination, but relationship. J Med Microbiol 51, 455–458. m Fig. 2. Diversity of human and other mammalian TTV-like viruses (family Anelloviridae). The phylogenetic tree of ORF1 sequences reveals a large number of divergent types and groups (e.g. TTV, TTMDV, TTMV) as well as more divergent viruses infecting other primates and mammalian also one that hinders their detection and diagnosis. In the Suzan-Monti, M., La Scola, B. & Raoult, D. (2006). Genomic species. The greater number and diversity of TTV-like viruses found in humans (yellow circles) compared to other primates (blue) and other future, virus discovery programmes, such as those based on and evolutionary aspects of Mimivirus. Virus Res 117, 145–155. mammals (red) is undoubtedly the simple outcome of the greater attention being paid to human samples. Similar or probably greater diversity massively parallel sequencing of RNA and DNA in samples Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., of TTV-like viruses certainly exists in these other species. Adapted from Ninomiya et al. (2009) in J Gen Virol (see ‘Further reading’ for full details) and tissues will reveal much more about the viruses that Rusch, D., Eisen, J.A., Wu, D., Paulsen, I., Nelson, K.E., infect humans, their ecology and host adaptation, and, Nelson, W., Fouts, D.E., Levy, S., Knap, A.H., Lomas, M.W., living relatives built on the same metagenomic analyses doesn’t produce Unsuspected human viruses for some, their role in currently unexplained human and Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., structural plan are vital research only bacterial sequences. The development and recent spectac- veterinary diseases. Baden-Tillson, H., Pfannkoch, C., Rogers, Y.H. & Smith, H.O. questions for the future, as is the The transition of the mimivirus from ular success of and These examples of the very large and the very small viruses (2004). Environmental genome shotgun sequencing of nature of the huge complement of its humble, unsuspected origin in a methodologically related molecular- give a flavour of their unexpected pervasiveness in the the Sargasso Sea. Science 304, 66–74. unidentifiable gene sequences in the water tank in the Midlands to one of based virus discovery methods has also environment and their diversity. Viruses are numerically the Zoll, J., Erkens Hulshof, S., Lanke, K., Verdyn Lunel, F., sea that probably belong to further the most abundant life-forms on the greatly expanded the number and pace most abundant and the most genetically diverse organisms Melchers, W.J.G., Schoondermark-van de Ven, E., Roivainen, M., uncharacterised virus groups and planet in the space of 4 years is a stark of discovery of human and veterinary on earth. With their short generation times, often huge Galama, J.M. & Kuppeveld, F.J.M. (2009). Saffold virus, a human families. Because of their large size, demonstration of how little we really viruses. The wealth of data emerging population sizes and rapid sequence change over time, Theiler’s-like cardiovirus, is ubiquitous and causes infection early filtering seawater for bacteria in know of viral diversity and evolution. about the diversity of viruses and viruses additionally provide us with the opportunity to in life. PLoS Pathog 5, doi:10.1371/journal.ppat.1000416.

98 microbiology today may 09 microbiology today may 09 99 conferences

Autumn09 Heriot-Watt University Spring10 Edinburgh International Meetings Committee Scientific Meetings Officer Edinburgh Conference Centre Professor Hilary Lappin-Scott (e [email protected]) 7–10 September 2009 www.sgmheriot-watt2009.org.uk 29 March–1 April 2010 Deputy Scientific Meetings Officer www.sgmeicc2010.org.uk Professor Chris J. Hewitt Putting microbes to work – (e [email protected]) Education Division the latest in translational and applied microbial science Systems microbiology Professor Joanna Verran (e [email protected]) Top international speakers will consider current Putting microbes to work Eukaryotic Microbiology Division challenges and developments in translational Microbial polysaccharides Professor Geoff Gadd microbiology. Sessions will cover wide-ranging OtherEvents IrishDivision (e [email protected]) Microbial factories applications of micro-organisms in food and drug Irish Division production, disease diagnosis and prevention, Alternative models to study mammalian pathogens FEMS 2009 – 3rd Spring 2010 Dr Evelyn Doyle environmental clean-up, as microbial factories Cultivating and sensing microbes in micro-scale devices Congress of European University of Cork, (e [email protected]) and as model organisms. (industry session) Microbiologists Ireland Prokaryotic Microbiology Division Glycoengineering Gothenburg, Sweden Recombinant protein synthesis Professor Petra Oyston Who should attend? (e [email protected]) Conjugate vaccines 28 June –2 July 2009 Organizer Gerard Wall Anyone who wants to keep up to date with Virology Division Microbial stress and food production: coping with the work Microbes and man – interdependence modern microbial science, no matter what their Professor Stuart Siddell environment and future challenges field or stage of their career. The conference will Autumn 2010 (e [email protected]) also provide a great opportunity for networking. Bioenergy fuel sources www.kenes.com/fems-microbiology University of Maynooth, Suggestions for topics for future Bacterial cell walls Ireland Where is it? ASM/SGM Joint Meetings symposia are always welcome. Contribution of the global N cycle to global processes Cambridge MA, USA, 1–4 July 2009 Joint meeting with Irish Society for Meetings Administrator Located on a pleasant rural campus on the Meningitis (clinical microbiology) Prokaryotic Development Clinical Microbiology Mrs Josiane Dunn outskirts of Scotland’s capital city, Edinburgh Organizer Kevin Kavanagh (t 0118 988 1805; f 0118 988 Conference Centre has excellent facilities, including Polar microbiology Aix-en-Provence, France 5656; e [email protected]). the purpose-designed James Watt Centre. High 5–9 October 2009 quality en-suite overnight accommodation is Darwin’s tree of life 3rd International Conference on For details of all Irish Division Abstracts available on-site. Situated next to the city bypass A symposium on microbial evolution to mark the 200th anniversary Salmonella activities, contact Evelyn Doyle Titles and abstracts for all and central to Scotland’s motorway network, of the birth of Charles Darwin www.asm.org/meetings (e [email protected]). presentations must be submitted the Centre is only ten minutes from Edinburgh’s through the SGM website by International Airport and has good public Fred Griffith Prize Lecture the advertised deadlines. For transport links. From spores to antibiotics via the cell cycle – Jeff Errington FRS further information contact the Harrogate Meeting Abstract Book Administrator. Grants Other highlights The legacy of Fleming: diagnosing, preventing, controlling and www.sgm.ac.uk/meetings Conference grants are available to SGM Young Microbiologist of the Year treating infectious diseases in the modern world Postgraduate Student Associate Members. Microbial genomics (hands-on workshop) The full text of the abstracts book is available online at: Deadlines CV skills (workshop for early career microbiologists) www.sgm.ac.uk/meetings/pdfabstracts/harrogate2009abs.pdf Abstract submission 29 May 2009 Trade exhibition/Poster sessions Gala dinner and ceilidh Earlybird registration 7 August 2009

100 microbiology today may 09 microbiology today may 09 101 schoolzone

Schools Membership costs only £10 a year. Benefits include Microbiology Today, advance copies of new teaching resources Teachers! Students! and discounted fees on SGM INSET courses. To join see The Big Bang Have your say www.sgm.ac.uk/membership. Enquiries: [email protected] Makeover for www.microbiologyonline.org.uk or go to www.microbiologyonline.org.uk for full details of 4–6 March, 2009 The SGM microbiology education website is going to resources and activities. QE2 Centre, London be completely redesigned. The new version of www. microbiologyonline.org.uk will be launched late in 2009 and will reflect the needs of both teachers and students. We want to know who uses the site and what they hope to gain from it both now and in the future. The SGM is looking for a group of 10 teachers and students either working or studying in institutions across the secondary education sector to comment on the content and design of the new website. We hope that the first focus group meeting will take place on Friday 26 June Refreshments and lunch will be provided. The SGM will reimburse reasonable travel costs. If you would like to join our focus group and be involved in this exciting new project please contact Dariel Burdass ([email protected]) New SGM resources The Good, The Bad and The Ugly: Microbes is aimed at the 11–16 age group and comprises a well-illustrated book and CD- ROM covering all aspects of microbiology in The Big Bang was an exciting event that brought together exhibited in the Health zone with a display that focused on ‘Starglow’ was enough to make a student’s finger turn green the UK school specifications. Copies have the science and engineering communities to celebrate and ‘Microbes and Us’. under UV! already been sent to all School Corporate Members of the Society, but single copies are promote the very best of UK science and engineering to Dariel Burdass, Janet Hurst, Yvonne Taylor and Jane At the end of the activity the students were given some also free to UK-based SGM Ordinary and school students of all ages. Nearly 5,000 young people and Westwell demonstrated to over 600 students how SGM goodies to remind them of the importance of ‘when Associate members who engage in outreach more than 1,500 teachers, politicians, exhibitors, sponsors, hand washing is one of the easiest ways to prevent the and how to wash their hands’. work in schools. Otherwise the cost is £10 scientists and engineers were there. transmission of infection. With a kit that makes use of The feedback from both the teachers and the students including postage and packaging. Special Sir Anthony Cleaver, Chair of the Engineering Training Starglow UV germ technology, we were able to reveal was very positive as all enjoyed the ‘yuk’ factor of the prices apply for bulk purchases by schools. Board (ETB), Co-patron of The Big Bang, said: through a simulation how, for example, cold and ’flu viruses activity. However, there was a serious point to get across Contact [email protected] for ‘The Big Bang lived up to its name. To have been able to are spread and how correct hand washing can reduce the and the comment below, made by one of the participant’s details. give nearly 5,000 young people the opportunity to look at risk of becoming infected. A harmless cream that shows up reflects the overall feedback that we received during the science and engineering with fresh eyes and explore the under UV light is used to mimic the virus. 3 days. Microbiologists Make a Difference is exciting opportunities on offer in the sector, is a tremendous a colourful 12-page booklet for 16- to The students, who ranged in age from 5 to 18 and came ‘I hadn’t realized the huge difference that washing my hands 18-year-olds, packed with information on achievement. I thank the nearly 50 organizations from the from schools in both the public and private sector, were all could make to the spread of colds. Next time I sneeze I won’t public and private sectors for coming together to give so careers in microbiology. It includes details amazed at how far the ‘germs’, a tiny blob of the cream on be wiping my hands down my jumper!’ of how to train and profiles of nine young many young people a boost towards something that might their hands, could spread. After hand washing, finger nails just change their lives.’ In 2010 the Big Bang will be in Manchester and the microbiologists. Copies are free from and the cracks between fingers often gave off an unearthly organizers anticipate that over 10,000 young people [email protected] Hand hygiene can be fun! green glow under UV light, highlighting the fact that during will witness the UK’s biggest celebration of science and The Science Council co-ordinated a cross-disciplinary cleaning, some areas are frequently missed. engineering. The SGM hopes to be there to raise the profile New editions of existing resources themed exhibition area under the banner ‘Fusion’. Three We also showed how pathogens can be spread in the of microbiology in an engaging and informative manner. Cold Wars, Hand Hygiene, TB and MRSA areas relevant to students’ lives were addressed: ‘Your home – on remote controls, door handles and mobile have all been revised and redesigned. For Health’, ‘Your Planet’ and ‘Your Environment’. The SGM phones. Just touching a light switch sprayed with invisible Dariel Burdass, SGM copies, contact [email protected]

102 microbiology today may 09 microbiology today may 09 103 Darwin-related free resources for secondary schools The Wellcome Trust has sponsored Nuffield Science Darwin and Survival Rivals, a set of Darwin- inspired experiments. The kits are available free to all state secondary Bursaries antimicrobial schools across the UK. Survival Rivals aims to provide The Nuffield Science Bursary scheme offers first-year post-16 science students opportunities for young people to throughout the UK a chance to work alongside practising scientists in science-, undertake practical science. The series technology-, engineering- and maths-based projects. Unlike work experience resistance comprises three kits: I’m a Worm, Get schemes, students carry out a project of their own that will make a contribution Me Out of Here (11–14); Brine Date to the work of the host organization. Projects last between 4 and 6 weeks, and (14–16); and The X-Bacteria (post-16), students complete them during their summer holiday. which is about antibiotic resistance. 2009 is Darwin Year and Dariel Burdass The SGM has provided bursaries for microbiology projects for several years. In In The X-bacteria students learn 2008 we funded 10 bursaries, which took place in a range of institutions and on how antibiotic resistance spreads a broad variety of topics, some of which are shown in the table below. explains how antimicrobial resistance between bacteria by ‘mating’ two strains of E. coli that are resistant to demonstrates some of Darwin’s ideas in different antibiotics and testing to Project provider Project title Supervisor see if resistance has been transferred Food Microbiology, Evaluation of the efficiency of probiotic Michael Rowe from one to the other by conjugation. Agriculture & Food bacteria to inhibit the growth of Science Photo Library practice. Students will learn practical Science Dept, Queen’s Mycobacterium smegmatis used as a skills required for culturing micro- University Belfast surrogate for M. paratuberculosis implicated as nutrients by preventing the growth was discovered in 1946 by Joshua Darwin – the father of organisms, practice aseptic techniques as a cause of Crohn’s disease in humans of other micro-organisms around evolution Lederberg and Edward Tatum and is a and consider experimental design. them. Antibiotic-producing microbes Marine Biological Growth of microalgae, relating algal Dr Richard Pipe Charles Darwin was born 200 years mechanism of horizontal gene transfer. are resistant to their own antibiotic, so Each experiment will illustrate Association pigments to wavelength of light ago on 12 February 1809, and 2009 is It mainly occurs in Gram-negative there has probably always been a gene the link between Darwin’s ideas, University College The effect of Epstein–Barr virus on Professor also the 150th anniversary of the bacteria. in nature for resistance to antibiotics. modern evolutionary principles and London membrane trafficking in B lymphocytes, Theresa Ward publication of On the Origin of Species. Conjugation involves a donor cell (F+) contemporary biomedicine and will Doctors prescribe antibiotics to which contains a conjugative plasmid using microscopy and some biochemical In this book, Darwin introduced the help teachers to deliver the relevant techniques. treat bacterial infections. Giving a (F plasmid) and a recipient cell (F–) term ‘natural selection’ – the process parts of the UK curricula. The that forms the basis of evolution: patient antibiotics causes the harmful which does not (F = fertility). Royal Free Hospital The molecular epidemiology of the Dr X-Bacteria in particular may be used to penicillin-binding (pbp) genes of B. Charalambos microbes to adapt or die; this is Conjugation is initiated when a pilus ‘As many more individuals of each introduce discussions around topical Streptococcus pneumoniae (affect sensitivity known as ‘selective pressure’. (encoded by the F plasmid) grows species are born than can possibly issues such as MRSA. to penicillin-like antibiotics). If a strain of a bacterial species from the F+ donor cell, attaches to a survive; and as, consequently, there The kits provide everything required acquires resistance to an antibiotic, specific receptor on the F– recipient National Institute of Characterization of promoters of genes Yvonne Braun is a frequently recurring struggle for to carry out the experiments in it will survive the treatment. As the cell and draws the two cells together. Medical Research that play a part in the pathogenicity of Roger Buxton existence, it follows that any being, if it school, including notes for teachers, bacterial cell with acquired resistance One strand of the F plasmid DNA is Mycobacterium tuberculosis vary however slightly in any manner technicians and students, and online multiplies, this resistance is passed nicked, by an enzyme, and a single Health Protection Microbiology of air Katy-Anne profitable to itself, under the complex videos will demonstrate how to to its offspring. In ideal conditions strand of DNA is transferred to the Agency Thompson and sometimes varying conditions of life, successfully deliver these practicals. will have a better chance of surviving, some bacterial cells can divide every recipient cell. A strand complementary University of Glasgow Studies on cell division in the trypanosome Tansy Clare Matterson, Director of Medicine, and thus be naturally selected.’ 20 minutes; this means that after to the single-stranded plasmid in the parasitic protozoan Hammarton Society and History at The Wellcome only 8 hours in excess of 16 million F+ cell is synthesized. Then synthesis Royal Holloway, How endophytic fungi, Cladosporium and Professor Evolution of antibiotic Trust, said: “2009 is going to be a bacterial cells carrying resistance to of a complementary strand begins in University of London Trichoderma affect the creeping thistle Alan Gange resistance that antibiotic could exist. the F– recipient cell, forming a new fantastic year celebrating the life and science of Charles Darwin, one of the Antibiotics are chemical compounds One of the main ways that resistance plasmid. The recipient cell is now an world’s most famous and influential This year the Nuffield Foundation is offering up to 1,000 bursaries for produced by soil fungi and bacteria. genes can be spread is through F+ donor cell. The cells then separate. scientists. The Wellcome Trust is funding enthusiastic students. As the scheme is expanding, they are looking for more Antibiotics kill or inhibit the growth bacterial conjugation. Antibiotic resistance is transferred a range of national projects throughout project providers for this summer and are always keen to hear from anyone who of other micro-organisms in the on conjugative resistance (R) plasmids the year to engage people of all ages with is interested in hosting a student. If you would like further information, please natural environment where they Bacterial conjugation that carry genes for resistance to the scientific legacy of Darwin’s ideas.” contact Sarah Saunders at The Nuffield Foundation on 020 7681 9626 who live. Microbes that secrete antibiotics Bacterial conjugation is the transfer antibiotics and other drugs. are more successful as they reduce of genetic material between bacteria Survival Rivals kits are available to pre- will put you in touch with your local Co-ordinator. competition for limited resources such through direct cell-to-cell contact. It Dariel Burdass, SGM order now, see www.survivalrivals.org For more information, see the Bursary website: www.nuffieldfoundation.org/scb

104 microbiology today may 09 microbiology today may 09 105 gradline

Gradline aims to inform and entertain early-career Table 1. Planned happenstance vs the traditional approach to career planning microbiologists. If you have any news or stories, or would Traditional approach Planned happenstance like to see any topics featured, contact Jane Westwell Makes clear decisions Embraces indecision (e [email protected]). Process is logical and systematic Recognizes that the future is unpredictable and uncertain Identifies an ideal job Unexpected events offer opportunities

Matches skills and interests to job Curiosity-driven

Narrows down choices Adopts a flexible attitude to changes in Planned happenstance: circumstances Planned happenstance means ‘planned’ part. Whilst working in the views of how things should happen an alternative approach following your curiosity or ‘tuning department I had the opportunity to – there is often not a right way (or a into’ those activities that you feel get involved with outreach activities. direct route) into a job naturally drawn to. The happenstance I discovered that I really enjoyed d Follow up on your curiosity. Don’t part is all about noticing situations communicating science and organizing worry about whether you will be to career development that you could not have anticipated events, and gave up quite a lot of successful or where it will lead – if and recognizing the potential my free time to help run open days you don’t try new ideas you’ll never opportunities they might offer. The and hands-on exhibitions. It was know where they might have led. A common approach to career planning is to identify your planned part is about being prepared this experience combined with the ‘ideal job’ and work out a route to get there. However, to take advantage of the situations – administrative work that gave me the Which approach is best? knowing what your interests are, being for many of us, life can get in the way of the grand plan. skills needed to obtain an interesting On the face of it, the traditional receptive to unfolding events and Maybe you are forced to move by a partner’s career change post in the External Relations Office approach to career planning and being ready to act on them. or perhaps you have family commitments that restrict at SGM. planned happenstance seem poles your job mobility. Sometimes, people are indecisive about apart. The former is fairly structured Equip yourself to their careers and don’t really have any long-term aims. A Planned happenstance and systematic, and works well if you embrace change traditional, fairly rigid approach to career-planning can in action know what you want to do. Planned make it difficult to respond to imposed changes. Also, There are things you can do to At a recent workshop I attended, happenstance allows for indecision people who are racked by indecision can feel overwhelmed take advantage of the opportunities almost every participant was in their and unpredictability (Table 1). when faced with the task of identifying their perfect job. brought by chance events: current job due to chance events. Most people are likely to use a mixture As a researcher, there are likely to be several factors Take my own career for instance. As a d Become more self-aware – think of both approaches in their working (professional and personal) influencing your career PhD student I was ambivalent about about what interests you and follow lifetime. Whatever approach you decision-making: research. At the end of my studentship up on it adopt in your next career step, to d Difficulties in finding a suitable postdoc or academic I was looking for postdoc positions d Don’t dismiss apparently off-the- ensure success there are several key position and administrative posts with an equal wall jobs – are they really that crazy? features common to both: learning and d Dilemma over leaving academic research – is it the right lack of success (probably due to a Consider how you might be able to developing new skills, networking, time? Would it be judged a sign of failure? What job can I very unfocused CV). However, fate develop them being proactive. Not to mention an actually do outside the lab? took me to Reading where my partner d Be positive and don’t dismiss an idea excellent CV! had recently been appointed to a before you have had a chance to d Family commitments lectureship. I was resigned to doing think about it Further information d Financial concerns. temporary shop-work until a second d If things don’t go to plan, look for career.berkeley.edu/Article/ 040910 Planned happenstance – an approach to career development chance event led to a part-time junior new opportunities as they crop up a-dm.stm based on chaos theory – has gained popularity in recent technician post at the university. It Career development via planned d Make good contacts and network as years. It recognizes that people can be indecisive or that was not the most exciting job, but happenstance widely as possible outside factors influence our work and it offers a different it was a 1 year contract so I took it. www.careers.salford.ac.uk/students/ perspective to the more traditional approach. It abandons The job put me in the right position d Don’t be afraid to approach people phd/blog/?p=105 the idea of mapping-out a perfect career and instead to apply successfully for a research for advice Why you should leave your career plans views a career as something that will gradually unfold and administration position (again part- d Look for opportunities to learn and to luck? by Fiona Christie encourages you to make the most of opportunities as they time) at the end of the year. So much develop new skills career.berkeley.edu/Article/020809a.stm Thinkstock / Jupiter Images arise. for the ‘happenstance’, now for the d Don’t be held back by stereotypical Serendipity and the job search

106 microbiology today may 09 microbiology today may 09 107 addresses

Myers–Briggs Type Indicator: council08–09 Officers Members personality at work President – Prof. Robin Weiss Prof. Mike R. Barer Division of Infection and Immunity, University College London, Infection, Immunity and Inflammation, University of Leicester, 46 Cleveland Street, London W1T 4JF Medical Sciences Building, PO Box 138, University Road, It is not the purpose of a psychological Combining all these preferences leads t–0207 679 9554;–f–0207 679 9555;–e–[email protected] Leicester LE1 9HN typology to classify human beings into to 16 personality types made up of a t–0116 252 2933;–f–0116 252 5030;–e–[email protected] Treasurer – Prof. Colin R. Harwood categories – this in itself would be pretty combination of 4 binary dimensions: Dr David J. Blackbourn pointless – Carl Jung School of Cell and Molecular Biosciences, University d Extroversion (E) or Introversion (I) – d Thinking (T) or Feeling (F) – of Newcastle Medical School, Framlington Place, University of Birmingham, Cancer Research UK Institute for At the recent SGM Harrogate Meeting, where you derive your energy how you make decisions Newcastle upon Tyne NE2 4HH Cancer Studies, Edgbaston, Birmingham B15 2TT a group of early-career microbiologists t–0191 222 7708;–f–0191 222 7736 t–0121 415 8804;–f–0121 414 4486 d Sensing (S) or Intuition (N) – d Judging (J) or Perceiving (P) – enjoyed a fascinating and interactive e–[email protected] e–[email protected] workshop led by Sarah Blackford, how you take in information how you organize your life an experienced careers advisor and General Secretary – Dr Ulrich Desselberger Prof. Neil A. R. Gow Dept of Medicine, University of Cambridge, Level 5, School of Medical Sciences, Institute of Medical Sciences, qualified MBTI practitioner. ISTJ ISFJ INFJ INTJ Addenbrooke’s Hospital, Cambridge CB2 2QQ University of Aberdeen, Aberdeen AB25 2ZD Sarah outlined how the MBTI (Myers– Systematic Sympathetic Insightful Visionary t–01223 763403;–e–[email protected] or t–01224 555879;–f–01224 555844;–e–[email protected] Briggs Type Indicator) classifies ISTP ISFP INFP INTP [email protected] Dr Richard M. Hall personality in terms of an individual’s Pragmatic Considerate Idealistic Logical preferred way of gathering information Scientific Meetings Officer – Prof. Hilary M. Lappin-Scott GlaxoSmithKline Biopharm R&D, Gunnels Wood Road, and making decisions. The scheme ESTP ESFP ENFP ENTP Room 11, Main Arts Building, Bangor University, College Road, Stevenage SG1 2NY measures only preferences, not Action-oriented Friendly Enthusiastic Innovative Bangor, Gwynedd LL57 2DG t–01438 762735; e–[email protected] abilities, values or skills. She stressed e–[email protected] ESTJ ESFJ ENFJ ENTJ Dr Kim R. Hardie that there is no right or wrong way Decisive Helpful Appreciative Enterprising International Secretary – Prof. George P. C. Salmond University of Nottingham, Centre for Biomolecular Sciences, to be and made comparison to left Dept of Biochemistry, University of Cambridge, Tennis Court University Park, Nottingham NG7 2RD or right handedness – you have a By the end of the session most give a taste of MBTI (an accurate Road, Building O, Downing Site, Cambridge CB2 1QW t–0115 846 7958;–f–0115 586 7950 preferred hand, but with a lot of effort delegates had a feel for what their profile requires completion of a t–01223 333650;–f–01223 766108 e–[email protected] you can write with the other. However preferences were and could probably questionnaire and a discussion with a e–[email protected] by recognizing your MBTI personality Prof. Mark Harris recognize features of friends, qualified practitioner), delegates had type you gain self-awareness and Education Officer – Dr Susan J. Assinder Institute of Molecular & Cellular Microbiology, Faculty colleagues and family members. an understanding of how personality understanding of others. Director of Education, Liverpool School of Tropical Medicine, of Biological Sciences, University of Leeds, Leeds Although the workshop could only can play a part in making career Pembroke Place, Liverpool L3 5QA LS2 9JT In an entertaining presentation, Sarah choices and in their interactions with t–0151 705 2515;–e–[email protected] t–0113 343 5632;–e–[email protected] encouraged delegates to consider other people at work and at home. how they derive their energy (e.g. Editor, Microbiology Today – Dr Matt Hutchings Dr Paul A. Hoskisson by thinking things through or Further information School of Biological Sciences, University of East Anglia, Strathclyde Institute of Pharmacy & Biomedical Sciences, talking it over with others); Norwich Research Park, Norwich NR4 7TJ University of Strathclyde, 204 George Street, Glasgow www.myersbriggs.org take in information (e.g. t–01603 592257;–e–[email protected] G1 1XW The Myers & Briggs Foundation concentrating on the t–0141 548 2819;–e–[email protected] Editor-in-Chief, Microbiology – Prof. Charles J. Dorman factual or seeing www.personalitypathways. Dept of Microbiology, Moyne Institute, Trinity College, Dr Catherine O’Reilly concepts), how they com/type_inventory.html Dublin 2, Ireland Dept of Chemical and Life Sciences, Waterford Institute make decisions (e.g. Quick informal MBTI t–+353 1 608 2013;–f–+353 1 679 9294;–e–[email protected] of Technology, Cork Road, Waterford, Ireland thinking with the quiz t–+353 51 302858;–f–+353 51 378292;–e–[email protected] head or feeling Editor-in-Chief, JGV – Prof. Richard M. Elliott en.wikipedia.org/wiki/ with the heart), Centre for Biomolecular Sciences, School of Biology, University Prof. Petra C. F. Oyston how they organize Myers-Briggs_Type_ Indicator of St Andrews, North Haugh, St Andrews, Fife KY16 9ST TL Molecular Bacteriology, Dstl, B07A Microbiology, their lifestyles (e.g. t–01334 463396;–e–[email protected] Porton Down, Salisbury SP4 0JQ using lists and www.bbc.co.uk/science/ t–01980 613641;–f–01980 614307;–e–[email protected] Editor-in-Chief, JMM – Prof. Charles W. Penn filing systems or humanbody/mind/ Dr Gary Rowley taking a less surveys/whatamilike/ School of Biosciences, University of Birmingham, Edgbaston, structured index.shtml Birmingham B15 2TT School of Biological Sciences, University of East Anglia, t–0121 414 6562;–f–0121 414 5925 Norwich NR4 7TJ approach). Stockxpert / Jupiter Images Quick informal quiz e–[email protected] t–01603 592889;–e–[email protected]

108 microbiology today may 09 microbiology today may 09 109 goingpublic

SGM aims to promote microbiology to a whole range of audiences. Through CELS, academic staff bacteria’ and ‘Dead long ago…diseases within the university’s microbiology undertake sabbatical projects in from history’ (a look at infectious teaching labs to carry out their In this issue we feature an initiative by academics to promote teaching, learning and outreach. diseases at different times in the practical investigations. Sabbatical cover is provided by our past, including the Egyptians and the microbiology to schools, the inside story behind The Wellcome The most popular of these sessions novel CELS Lectureship scheme, and black death), through to the more is ‘Forensic microbiology’ in which Window and a way to use a departmental website to disseminate free projects are supported by the CELS topical ‘Bird ‘flu’, as well as careers- the students investigate an outbreak team with its teacher fellow. (For more related seminars such as the general of dysentery on a housing estate, educational resources. information see www.ntu.ac.uk/cels) ‘w.w.w.bioscience – a why, what & suspected of being associated with a As a result of her CELS sabbatical, SGM where guide to the biosciences’, which local school with poor toilet facilities. member Gina Manning developed can cover any discipline within the The students are told that various her role as Bioscience Outreach biosciences, or the more focused samples have been taken from patients Coordinator. She identified a number ‘A cultured career – a career in and sent to the lab for analysis. The of key staff who could give relevant microbiology’. students try to work out the source and interesting talks to school Getting careers information into the of the outbreak using bacteriological Getting students, and equally importantly, right hands is always a challenge. and DNA fingerprinting techniques. help to develop and enhance practical We’ve been developing some new The session can also be expanded bioscience activities for schools. approaches, e.g. web pages on to include a consideration of what the As Gina is a microbiologist, she and ‘50 reasons to study science’, Science happens in the patient’s blood in microbiology colleagues have come up graduate profiles and links to careers response to an infection. Students get with a number of specific microbiology sites, as well as posters for classrooms an insight into a biomedical science talks and taster sessions for schools to (‘Where can I go with biology?’) and environment and how specimens are bug in try to encourage students to become pocket-sized ‘biology careers’ leaflets. handled, e.g. streaking out from a interested in microbiology as a subject mock sample and examining pre- in its own right, as well as in its At the bench inoculated selective media and pre- potential as a future career path. prepared Gram films of these bacteria. schools Building upon the evidence that They use these to try to identify the ‘It is encouraging that these pupils practical work is very effective at source of the outbreak. The DNA Rising to the challenge of getting are interested in science which goes engaging young people with science, fingerprinting is used to introduce against the prevalent view from the we have developed some laboratory- the students to molecular analysis, school students enthused about media.’ (Michael Loughlin). based sessions to demonstrate and they get the chance to perform ‘It is rewarding to think we might our point about the relevance of restriction enzyme digests and gel microbiology can be done, as Karen have triggered a few people’s microbiology to everyday life. These interest to become a biologist.’ sessions are inquiry-based and allow . Students preparing to load DNA digests on Moss and Gina Manning describe. (Alan McNally) students the opportunity to work an agarose gel. CELS

Since 2003, there has been a 28% drop in the number of m Plates prepared to welcome students to the lab session. CELS Activities students in the UK applying for degrees with microbiology Our seminars are designed to fit any somewhere in their award title, according to the recent encourage innovation. Sharing of resources and improved age group from 11 to 18, and can be Higher Education Academy Centre for Bioscience report. outreach work by universities would help many educational tailor-made to fit with the delivery This is an alarming statistic given that microbiology impacts establishments further develop their work (Biosciences of a school’s timetable. Teachers on human lives in so many ways, both positive and negative. Federation, 2008). tell us time is their most precious One major factor is ignorance – students do not know what With this in mind, staff from the School of Science and commodity. Given practical or sort of careers they can go into with a microbiology degree, Technology at Nottingham Trent University (NTU) have economic restrictions on taking a class and the study of microbiology in schools is often theoretical tackled the problem head-on, specifically developing a out of school, having talks and events rather than hands-on. programme of science outreach activities in microbiology for that can be taken into the schools is a Recently, the university sector has been charged with re- schools and colleges. big advantage. It also allows maximum engaging the next generation in the thrill and challenge of This is part of a wider programme of science outreach work exposure to students of all abilities, scientific discovery. here at NTU where CELS – the Centre for Effective Learning some of whom may have never What more can the education community do to develop in Science – is based. CELS aims to teach science more considered microbiology as a subject scientific literacy in young people? More hands-on science effectively and inspire the next generation of scientists. worth studying further. and good teaching of practical skills by enthusiastic, In our strategy to attract more young people into science The focus of our talks is carefully specialist teachers are needed … Creativity in science careers, we offer a wide portfolio of practical sessions with chosen to catch the attention of the needs to be encouraged along with more cross-curricular a strong emphasis on practical scientific enquiry, for ages teen audience with titles such as links to help enthuse pupils, make science relevant and 5–18, covering a range of science curriculum areas. ‘Flesh-eating bugs and other friendly

110 microbiology today may 09 microbiology today may 09 111 electrophoresis with data analysis to to a twilight information session, confirm their suspicions. A general were able to discuss areas in which discussion as to how easy infection is they need help, e.g. with aspects of spread and good hygiene concludes the curriculum, whilst at the same the session. time allowing us opportunities to When Mike Wilson and Another popular activity is the bird update them on recent developments ‘flu taster session. This is a dry-lab in university research, teaching and Derren Ready were invited activity which can be run in a seminar outreach activities. Co-existence – room. The students are guided through If you’d like to discuss any of these to work with an artist to the biology of the avian ‘flu virus and activities further please contact us. the latest molecular techniques used produce a window display in tracking infections. The students Karen Moss & Gina Manning The Wellcome window then take part in a detective activity Nottingham Trent University on bacteria, much ingenuity where, through the analysis of clues (e [email protected] or and deduction, they track the likely [email protected]) was required. path of an international outbreak, display suggesting how it could have been Acknowledgements In September 2008 we were invited found ‘internally’, i.e. in the respiratory, with a digital camera attached. The contained. The activities mentioned were developed Microbes and Me to collaborate with the artist Julia gastrointestinal and genital tracts. magnification of the objective needed by Alan McNally, Gina Manning, Phil Related to this window display is Lohmann to produce a display that to be altered from isolate to isolate Outcomes Cheetham, Michael Loughlin and Steve Culturing and photographing images another project we are currently would show the distribution of of the colonies of members of our as some colonies were very small Feedback from the students attending Forsythe. Special thanks go to Mike engaged in – Microbes and Me. This Brice, Pam Horne and the rest of the bacteria on and in a healthy human. indigenous microbiota was a great (mollicutes), whereas other were much these sessions has been very positive is a travelling exhibition, financed by Microbiology Technical Support Team. Julia already had the idea of using opportunity that we’re sure any larger (clostridia), and we had been with comments such as: a People Award from The Wellcome CELS is funded by HEFCE as a Centre for Petri dishes with backlighting as a microbiologist would enjoy. We used asked to collect images of discrete Trust, which aims to inform the general ‘The hands-on approach! It was one Excellence in Teaching and Learning. framework for the display and she a number of different selective and colonies and also groups of colonies. public about the microbial communities amazing experience.’ wanted to place in these microscopic elective culture media and needed The lighting made a tremendous that inhabit healthy humans. As well ‘The practical experience was quite Further reading images of the various members of the to use several different atmospheric difference to the final image and as describing the composition of the fascinating.’ indigenous microbiota. However, we for the majority of the images we Biosciences Federation (2008). conditions to allow us to grow a microbial communities inhabiting the ‘Learned something new.’ Independent Review of ‘A Vision for explained to her that these images diverse group of micro-organisms. illuminated the colonies from above. various body sites, it will emphasize ‘The practical side. Getting hands- Science and Society’. A response to the would not be particularly exciting Fortunately, we already work with However, if there were interesting the many benefits that we derive from on experience really helped me to Department for Innovation, Universities as bacteria came in only three basic a large number of different genera internal structures, such as the star- our indigenous microbiota. It will also understand the subject.’ and Skills, available at www.bsf.ac.uk/ shapes and that there was much more and species, so we were able to like structures seen in Aggregatibacter describe important concepts. such Obviously, you can’t always win – in responses/ScienceAndSocietyOct08.pdf variation in the size, shape and colour readily obtain images of streptococci, actinomycetemcomitans colonies then as symbiosis, antibiotic resistance, response to ‘what did you like the www.ntu.ac.uk/cels of colonies – especially when selective staphylococci, micrococci, clostridia, we also needed to illuminate from superbugs, biofilms, probiotics, least about the session’, one student The CELS website and elective media were used. After Prevotella spp., Campylobacter and, of below the colony. We finally obtained competitive exclusion, disease showing her some of the beautiful in excess of 750 digital images from wrote ‘The germs’, and another ‘The The Higher Education Academy course, working in a dental institute transmission, etc. One of the main colony shapes and colours she became 32 different genera. More than microscopes made my eyes go funny’! Centre for Bioscience (2008). culturing members of the oral objectives of the exhibition is to We are constantly seeking to improve National Subject Profile for Higher convinced that this was the way to go. microbiota wasn’t a challenge for us. 9,000 glass Petri dishes were used to rehabilitate microbes to the general our communication with schools Education Programmes in Microbiology As a guide to which bacteria were However, we were less experienced construct the two figures. public by making them aware that, as through active consultation with available at www.bioscience. to be found at which body site we with a few of the organisms, making One of the problems that Julia faced well as causing disease, microbes are teachers. For example, teachers invited heacademy.ac.uk used a book recently published by it necessary not only to buy in several was conveying a three-dimensional essential to human well-being. The first one of us: Bacteriology of humans: an strains such as Helicobacter and effect using only the petri dishes and exhibition venue will be the Cheltenham ecological perspective (Michael Wilson, mollicutes, but also to get out the text colonial images. Shading of some kind Science Festival, 3–7 June and the In the Loop – www.sci-eng.mmu.ac.uk/intheloop Blackwell Publishing, 2008). Because books for recipes of culture media. was essential for this purpose so Julia website (currently under construction) Chair of the SGM Education Division, Jo Verran, has recently launched her of the enormous complexity of the We also tried to collect images of the decided to superimpose on the images is www.ucl.ac.uk/microbesandme/ website In the Loop. Whilst this aims to promote microbiology services at microbiota at certain body sites, we same bacterial species on a selection some black line drawings depicting Michael Wilson MMU, it also provides a valuable resource of information for teachers, both obviously had to compromise with of different culture media, to allow the what she had imagined bacteria to look UCL Eastman Dental Institute, in schools and of undergraduates, and outreach activities for the general regard to the number of different artist to have a range of images and like before learning more about their University College London public. Going to the section ‘Education and Communication’ leads to a microbes that could be included at a colours to choose from. true nature from us. The two images (e [email protected]) whole range of activities, services and links. You can also download free particular one. Also, we used one body In many ways collecting the images went on display in January 2009 and chapters from an audio-visual aid, an Introduction to Practical Microbiology, image to display the composition of was more challenging than the Julia and one of us (MW) gave talks at Derren Ready which was filmed with undergraduate students and shows all the basic the various bacterial communities that microbiological aspects of the work. the Wellcome Collection explaining Eastman Dental Hospital, University techniques necessary to carry out microbiology investigations. reside on the skin and the other image We decided to photograph the the artistic and scientific background to College London Hospitals (UCLH) to represent the communities to be colonies using a light microscope the project. (e [email protected])

112 microbiology today may 09 microbiology today may 09 113 hotoffthepress

Science writer Meriel Jones takes a look at some recent Routine arbovirus surveillance reveals a novel animal virus papers in SGM journals which highlight new and exciting Cowled, C., Palacios, G., Melville, L., Weir, R., Walsh, S., Researchers in Australia and the USA have been working on Davis, S., Gubala, A., Lipkin, W.I., Briese, T. & Boyle, D. this problem. The results of tests suggested that most of the developments in microbiological research. (2009). Genetic and epidemiological characterization of unidentified virus collection was from the familyReoviridae , Stretch Lagoon orbivirus, a novel orbivirus isolated from and more specifically the genusOrbivirus . They focused Culex and Aedes mosquitoes in northern Australia. J Gen their attention on the only virus isolated in 2002 from a b Coloured SEM of Pseudomonas aeruginosa bacteria on ciliated Virol 90, 1433–1439. homogenized pool of 25 Culex mosquitoes collected at Stretch human nasal epithelium. Juergen Berger / Science Photo Library Lagoon in the Kimberly region of Western Australia. The tests Animals are important to the Australian economy. Export of showed that it was not among the 11 orbivirus species that live cattle, sheep and goats as breeding stock and for their the same in plants and animals, so plant leaves provide a had previously been recognized in Australia. more humane test. Bacterial strains lacking PhoQ consistently meat provides a significant income for the country. For this caused a less-severe soft rot. Taken together with other global trade, it is important that disease-causing viruses are not The criteria for defining orbivirus species relate to the genes for laboratory tests showing impaired characteristics that usually exported along with the animals. Unfortunately, viruses do not several of the viral proteins. When the researchers worked out correlate with bacterial pathogenicity, the researchers felt respect national boundaries, especially the arboviruses which the sequences from the Stretch Lagoon isolate, they confirmed confident that PhoQ was important in infections. are transmitted to animals by insects. These can cause serious that it was definitely an orbivirus, but only distantly related to animal diseases such as bluetongue. Australia therefore has all known species. The obvious name for it was Stretch Lagoon Further tests, using cultures of human cells from the surface of a national arbovirus-monitoring programme. the lung, showed that P. aeruginosa cells containing the PhoQ orbivirus (SLOV). They developed and used a rapid diagnostic protein were at least twice as effective at damaging these cells Northern Australia is an important location for arbovirus test to identify six further isolates among the collection of than bacteria without PhoQ. To discover whether these surveillance. Its geographical location means that cyclones unidentified isolates. When the researchers tested stored blood pathogenic effects were mediated by PhoQ within a living make landfall in the region and these strong winds can bring for a reaction to SLOV, the results indicated that some horses, lung, and following recommendations from the ethics committee new insects from the tropics. As well as insect traps, herds donkeys and goats had potentially been infected with SLOV as for animal treatment at their university, the researchers infected of young cattle that have not previously been exposed to far back as 1984. Animal samples from before 2000 need to be rats with mutant and normal P. aeruginosa cells. Although these arboviruses are used as sentinel animals to see if the new tested to confirm this hypothesis. However, several important colleagues had studied lung infections for many years, they insects carry any new viruses. Many well-known, insect-borne questions remain unanswered. These include whether SLOV had never seen such a dramatic difference between two strains viruses are regularly identified, but a key problem is to detect causes a disease, and whether it is really transmitted by of P. aeruginosa before. In a group of seven rats, four managed previously unknown viruses that could be the cause of new mosquitoes. Horses, donkeys and goats are not routinely tested to remove all the mutant bacteria from their lungs within 4 diseases. Hundreds of unidentified viruses have been collected for arboviruses in Australia so the researchers do not yet know Sense and respond days, and the overall level of the infection was reduced by since the start of the monitoring programme, waiting for the real distribution of SLOV within Australia. Putting a name more than 10,000-fold. PhoQ therefore appears to be essential attention. to the unknown isolate is clearly only the beginning. Gooderham, W.J., Gellatly, S.L., Sanschagrin, F., McPhee, for P. aeruginosa to set up a lung infection. J.B., Bains, M., Cosseau, C., Levesque, R. & Hancock, R.E.W. (2009). The sensor kinase PhoQ mediates virulence To find out what PhoQ was doing to make the bacteria virulent, A novel bacterium from deep glacial ice in Pseudomonas aeruginosa. Microbiology 155, 699–711. the researchers turned to transcriptomics. These are methods Loveland-Curtze, J., Miteva, V.I. & Brenchley, Until the drill brought it to the surface, this ice had Pseudomonas aeruginosa is an intriguing bacterium. It is a to determine which genes are in use. Over 5,500 genes have J.E. (2009). Herminiimonas glaciei sp. nov., a lain undisturbed for over 120,000 years. It was normal inhabitant of soil, but is also a pathogen of plants, been identified inP. aeruginosa and the Institute for Genomic novel ultramicrobacterium from 3042 m deep discovered that there are many living bacteria in insects and animals. It rarely infects healthy people, but Research Pathogenic Functional Genomics Resource Center Greenland glacial ice. Int J Syst Evol Microbiol 59, this ice, although patience is required to coax them exploits opportunities offered by other illnesses – it is the most in the USA supplies microscope slides containing DNA from 1272–1277. back to activity. The authors’ strategy is to incubate common cause of acute hospital-acquired pneumonia and each of them for scientific research. The researchers used these water from the ice core in anaerobic conditions at causes chronic lung infections in patients with cystic fibrosis. slides to test which genes were in use when P. aeruginosa was Is there life on other planets? The answer requires 2°C and, after several months, spread it over special How does P. aeruginosa, amongst all the bacteria in the air, grown under different circumstances, both with and without a us to be able to recognize living creatures when we oxygen-free culture medium to see what grows. manage this when, despite inhaling over 10,000 litres of air a functional version of PhoQ. Lack of PhoQ affected the use of see them. This is not always easy to do, especially day, healthy people have few bacteria in their lower lungs? 474 genes. Many of these were already known to be regulated for bacterial life. Bacteria may be recognized by The authors’ most recent discovery is a novel by PhoQ, but others were new. These included genes for the consequences of their activities, which range Bacteria have to sense and respond to their environment, and species with very small cells that they have called proteins involved in transporting materials into or out of the from soured milk, corroded metal and concrete to one way is via two-component regulatory systems that consist Herminiimonas glaciei. Its small, initially brown– cell, and some for scavenging iron, which is well known to be glowing water, but these can also have chemical, of two proteins. One is a sensor protein embedded in the purple colonies of thin, mobile cells could actually an important activity for pathogens. Others that were used less rather than biological causes. Most life on our cell membrane. Once this picks up a signal from outside the grow in air, although seemed to enjoy oxygen in the mutant were involved in providing energy for the cell, planet has always consisted of bacteria, so it is cell, it can interact with a second, response regulator protein levels below that of the current atmosphere. The and in controlling the function of other genes. certainly reasonable to consider that this might be in the cytoplasm which will alter the cell’s metabolism to fit researchers carried out a battery of tests, leading true on other planets as well. With this in mind, the new circumstances. The PhoQ sensor with its associated The outcome of this study is new confidence that PhoQ to identification of the novel species. They were the NASA Astrobiology Institute in the USA has PhoP response regulator is important for virulence of several is essential for success of P. aeruginosa as an opportunist intrigued to discover that it was resistant to three- funded several projects to study bacteria that live bacterial species, but its role in P. aeruginosa was unknown extracellular pathogen. Researchers already knew about some quarters of the antibiotics used in the tests, even

in extreme conditions on Earth. Stockxpert / Jupiter Images until researchers in Canada took a closer look. of the virulence-related processes in P. aeruginosa. However, though it came from long before the era of modern For initial tests, lettuce leaves were used to test whether this new, complex control-system for around 12% of the genes The authors have cultivated very small bacteria medicine. Projects like this extend our knowledge mutant bacterial strains without the PhoQ protein could still in P. aeruginosa provides more targets for researchers working from 3,042 m below the Greenland ice cap, of life on Earth as well as providing ideas about

cause infections. Several P. aeruginosa infection processes are towards treatments for these infections. collected during the Greenland Ice Sheet Project life on other planets. Greenland.

114 microbiology today may 09 microbiology today may 09 115 reviews

Management of antibiotic side-effects using probiotics If you would like your name to be added to our database of Engelbrektson, A., Korzenik, J.R., Pittler, A., Sanders, M.E., Klaenhammer, T.R., book reviewers, please complete the book reviewer interests Leyer, G. & Kitts, C.L. (2009). Probiotics to minimize the disruption of faecal microbiota in healthy subjects undergoing antibiotic therapy. J Med Microbiol 58, form at www.sgm.ac.uk. A classified compendium of reviews 663–670. from 1996 to the present is also available on the website. Probiotics are marketed as food healthy volunteers in their 30s after supplements that can confer health they were giving a 7-day course of benefits. They come in the forms antibiotics. The antibiotic used was of capsules, powders, yoghurt or Augmentin because it is in common Charles Darwin: On in other publications – or look at the Cellular Signaling other fermented foods that contain medical use and has a reputation for the Origin of Species – insets and bypass Origin. Though it and Innate Immune live bacteria similar to some of those causing diarrhoea. The volunteers took is pretty, this book doesn’t really offer known to reside in the gut. Knowledge capsules that contained a carbohydrate The Illustrated Edition anything new in a very crowded market. Responses to RNA of benefits conferred by probiotics either with or without probiotics Edited and with an introduction by Surely there’s a little evolutionary tale Virus Infections is of both medical and commercial along with the antibiotics. As well as here? David Quammen Edited by A.R. Brasier, importance. One situation where keeping a diary of their eating and Published by Sterling Publishing (2008) Hilary Fraser, Berkshire A. Garcia-Sastre & S.M. Lemon researchers think probiotics could be toilet experiences over this time, the £20.00 pp. 560 Published by American Society for of real value is for patients undergoing volunteers delivered faeces to the study ISBN 1-40275-639-9 Microbiology (2008) antibiotic treatment. co-ordinator on several days before On the Origin of Species would be my Horizontal Gene Transfer US$139.95 pp. 454 and after taking the antibiotics. These desert island book – and with luck, in the Evolution of ISBN 1-55581-436-6 Antibiotics are life savers from bacterial were analysed for both their diversity the island would be as fascinating as diseases, but they can also cause of bacterial DNA and contents of living Pathogenesis This is an excellent and authoritative problems. One of these is disruption the Galapagos. But would I take this bacteria. Edited by M. Hensel & H. Schmidt collection of detailed chapters from to the normal, beneficial bacterial edition? Probably not. I would prefer Published by Cambridge University some of the worlds leading scientists inhabitants of the gastrointestinal tract a first edition, plain and unadorned. There were some very clear results from Press (2008) working on the nature of RNA virus through the killing of some of them This one is a coffee table book, the study. The level of diarrhoea and £75.00 pp. 355 interactions with the host innate as well as the bacteria causing the lavishly illustrated, and interspersed vaginal yeast infections in the ISBN 0-52186-297-4 immune system. Usefully, the book with extracts from the ‘Beagle’ letters infection. The consequences can range volunteers, whether they were taking is organized both by topic area and and other documents. This seems to from mild discomfort to diarrhoea the probiotic or the placebo, was similar This is a very interesting book which then separately by RNA virus family, to inflammation and serious illness. suggest that the Origin text might need to that reported in other clinical trials presents an up-to-date overview of providing a systematic and cross- Managing antibiotic therapy to have sweetening for a new, and perhaps involving Augmentin. It was also very the current understanding of this field referenced approach invaluable to those fewer of these unwanted impacts is reluctant, reader. But if that is the case, obvious that the antibiotic altered the of research. The book includes lively who are interested in specific viruses as obviously desirable, but not easy to do. the insertions break up the text of Origin gut bacterial flora. The researchers discussions of both philosophical well as those interested in the detailed in a way that actually makes reading it monitored the molecular signals of and theoretical aspects of evolution biochemistry of host response to virus Studying bacteria from the human more difficult. You either have to read over 200 types of bacteria as well as due to HGT in addition to chapters infection. Each chapter provides a gut means analysing faeces. Although the Origin text and try to ignore the on ‘paradigms of bacterial evolution’ stand-alone review; inevitably, this clinicians have grown bacteria from the diversity of species that grew on other material – all of which is available which explore both human and plant approach does lead to some repetition, this source for over a century, real five distinct culture media. Comparing the bacterial profiles of each individual pathogens. The inclusion of eukaryotic but this is a minor criticism for what

appreciation of their numbers and Stockxpert / Jupiter Images before and after taking Augmentin examples of HGT provides a well- is overall a very timely state-of-the-art diversity is only now starting to become rounded account of the subject. It showed that the probiotic minimized samples from volunteers during the 2 specialist review text book suited to a apparent. Estimates of the total number would have been more comprehensive any disturbance, which was presumably weeks before they took the antibiotics. postgraduate and professional virology in each person’s gut range up to 100 to include one or more examples of 14 beneficial. Although the researchers Surprisingly, the volunteers differed in and cell biology audience. trillion (10 ) and the vast majority of HGT-mediated evolution in animal did not specifically test a mechanism how similar the results were for these these bacteria have never been grown in pathogens as these are often adapted The cost of the book indicates that it for this effect, they speculated that three samples. They were similar from a laboratory culture. To identify these to conditions in a host-specific niche; is unlikely to be a personal purchase, the additional Bifidobacterium and some people, but distinctly different uncultured bacteria, researchers use however, this could be included in any but is highly recommended for Lactobacillus bacteria from the probiotic from others. Since this is the first the latest DNA technologies so that the future edition. The chapters are well- laboratories and institutes working on could act on the contents of the gut detailed and repeated analysis of healthy diversity of bacterial genes is a measure edited, extremely well-referenced and viral pathogenesis, and innate immune to make it a more suitable habitat for people supplied with probiotics, it is of the diversity of the bacteria. mostly up to date. The book is aimed responses. It should also have a place in bacteria, so providing extra stability to not clear whether this diversity is a real at graduate students and researchers university biological science libraries for A collaboration between microbiologists the normal population. picture of the variety of human gut in the field and is a must for relevant reference purposes during those in the USA working in medical flora, or whether it is an artefact caused institutional libraries and laboratories final year essay crises. Highly gastroenterology, genome sequencing Two other interesting features came out by the way the samples were processed, alike. recommended. and the dairy technology and food of this study because it was based on despite efforts to use a standardized industries has studied the effects of quite a large group of healthy people. procedure. This is obviously an Adam P. Roberts, UCL Eastman Dental Maria Zambon, Health Protection probiotics on the intestinal flora of 40 The researchers analysed three faecal important subject for future studies. Institute Agency

116 microbiology today may 09 microbiology today may 09 117 were instrumental to increase clarity, intrinsic, innate and adaptive immune control, and the pharmaceutical Homeopathy is given a lot of attention, Filoviruses: A Compendium of and many internationally recognized responses. Factors determining the industry in the UK covering the because it ‘has an elaborate and sciencey- 40 years of Epidemiological, Clinical virologists with special expertise outcome of persistent or latent viral era from the late 1950s until today. sounding framework for how it works, and Laboratory Studies have reviewed different parts of the infection are described. A separate Amongst other topics, the history and without scientific evidence to demonstrate Emerging Infections 8 books. The outcome is splendid: basic chapter is dedicated to the pathogenesis discovery of MRSA, its epidemiology its veracity’. (pp. 28–29) Gene Therapy Protocols Vol. 2: information is presented in a succinct of HIV infections. Mechanisms of viral and spread, resistance mechanisms, As any reader of his column in The and refreshing manner, interspersed by transformation and oncogenesis are changing attitudes to infection and Design and Characterization of Gene Guardian might expect, an entire Transfer Vectors, 3rd edn original and unexpected observations described in their full diversity. The infection control, pharmaceutical chapter is devoted to the life and work and short reports on research highlights. chapter on vaccines touches many responses and new drugs are discussed. of Dr Gillian McKeith PhD. Fascinating, Stem Cell and Gene-based Therapy Compared to the second edition, many important issues, e.g. the controversy Most compellingly it is revealed that shocking and written fairly, this is Clostridia Molecular Biology in the Post- very recent research data are reported, over the MMR vaccine as a possible similar epidemics of (then) multidrug- my favourite bit. genomic Era allowing witness to the excitement of cause of autism (now solidly refuted) resistant Staphylococcus aureus had good contemporary science. Original and the difficulties encountered in occurred in the 50s and early 60s, We hear numerous reports about Mycobacterium: Genomics and photographs, illustrations and diagrams developing an AIDS vaccine. The generating an understanding of the magic pills that can cure behavioural Molecular Biology are of excellent quality. The text is development of antivirals is described mechanisms of spread and transmission problems, or even improve intelligence Dictionary of the Fungi, 10th edn further complemented by information as being guided by rational design of epidemic S. aureus and measures in children. Goldacre refers to this as ‘medicalization’ and, in some depth, Wound Care: A Collaborative Practice boxes on background, terminology, according to viral targets and molecular to curtail its spread, which has been Manual for Health Professionals, 3rd edn methods, particular experiments mechanisms of action. A final forgotten or overshadowed by other discusses its problems. From pills to and items for discussion, and the chapter introduces the various factors priorities in dealing with the current pharmaceuticals, where companies Handbook of Plant-based Biofuels perspectives of relevant research are influencing viral evolution. MRSA problem. There are also concise crunch numbers to make their products The Septins outlined at the end of each chapter. biographical sketches of key figures of look good. Detailed replication strategies for Medical Product Regulatory Affairs: The content of different chapters has the field and instructive illustrations. Despite all the pitfalls of some of the particular virus families, diagrams of Pharmaceuticals, Diagnostics, Medical been carefully cross-referenced. The research he cites, we still read incorrect the pathogenesis and epidemiology This is a must read for every Devices references are very up-to-date, reaching interpretations in the papers. Why? ‘My of selected animal viruses and an microbiologist, which is also fascinating Mycoplasma Diseases of Ruminants Principles of Virology, from ‘classics’ in the 1930’s to journal basic hypothesis is this: the people who run introduction to unusual infectious and accessible to the layman. publications in early 2009, with the media are humanities graduates with Real-time PCR Current Technology and 3rd edn: Vols I and II agents (viroids, satellites, prions) are particular emphasis on publications Dietrick Mack, University of Swansea little understanding of science, who wear Applications By S.J. Flint, L.W. Enquist, found in appendices to both volumes. of 2005–2008. their ignorance as a badge of honour … Microbial Ecology of the Oceans, 2nd edn V.R. Racaniello & A.M. Skalka The collated information in the two in their choice of stories, and the way they The basics of the viral infectious Geomicrobiology, 5th edn Published by American Society volumes represents the state-of-the- cover them, the media create a parody of cycle are described in a very short Bad Science for Microbiology (2009) art of many topics and is of interest science.’ (pp. 207–208) Practical Handbook of Microbiology, US$169.95 pp. 1,032 chapter, followed by hundreds of pages for students and teachers of virology By B. Goldacre 2nd edn ISBN 1-55581-443-4 reviewing details of the underlying Published by Fourth Estate Ltd (2008) Statistics, he says, are often misreported, alike. In addition, the books are Changing Trends in Managing Aquatic molecular biology. Viral genomes £12.99 pp. 338 or interpreted in an irresponsible way. Over a period of only 9 years this strongly recommended to an interested And then there’s the health scares, like Animal Disease Emergencies, Vol. 27 (1) and the various viral structures are readership of molecular biologists, cell ISBN 0-00724-019-7 book has now reached its third edition. introduced in close correlation with the ‘MRSA hoax’ and the ‘MMR hoax’, Biotechnology, 5th edn biologists and general microbiologists, It is difficult to explain just how Declared to be a textbook for students, their functions. Transcriptional which dominated the headlines for a and their wide distribution is highly engaging and entertaining this book is. Insect Symbiosis, Volume 3 it aims for the highest standards. strategies of viral DNA are extensively decade. Compared to the second edition desirable. Much of the content is aimed at doctors OIE Quality Standard and Guidelines discussed. Good coverage is given to This book is intelligent, well-researched (2004), a number of changes have taken and people who want to defend good for Veterinary Laboratories: Infectious various techniques of manipulating Ulrich Desselberger, Cambridge and funny. Goldacre has a talent for place. One novelty is that the book is science, but I would go as far as to Diseases viral RNA genomes and to the potential explaining complex ideas without being now published in two volumes, with say this is essential reading for anyone for reversion analysis ‘to order’. The patronizing, so, in my opinion, Bad An Introduction to Genetic Engineering, principles of the molecular biology of who has ever read a scare story in the possibilities for gene therapy using Science will be a great read for anyone. 3rd edn animal viruses being presented in Vol. I, Superbugs and tabloids, picked up a book by Gillian mutated DNA and RNA viruses as He has a tendency to slip off into a rant and aspects of pathogenesis, treatment Superdrugs: A History of McKeith or bought a homeopathic Mushrooms as Functional Foods vectors are outlined. Various aspects occasionally, but he pulls himself back and prevention, and evolution reviewed MRSA remedy. Bluetongue in Northern Europe of viral messenger RNA synthesis and to the point. (To be honest, I agreed in Vol. II. Whilst Field’s Virology, fifth mechanisms of translation control are Edited by L.A. Reynolds & E.M. Tansey Ben Goldacre starts with ear candles, with almost every word, so even the Biotechnological Approaches for edition (2007), is recommended as all- discussed in detail. The relatively novel Published by The Wellcome Trust detox patches and the Brain Gym, long tangents were appreciated.) Pest Management and Ecological inclusive and for detailed information but very active research area of cellular Centre for the History of Medicine at which is ‘riddled with transparent, Sustainability on specific virus families, it is evident Lucy Goodchild, Imperial College and viral small interfering RNAs is UCL (2008) shameful and embarrassing nonsense’. that plenty of special and novel London Handbook of Nucleic Acid Purification introduced. Mechanisms of intracellular £6.00 pp. 144 (p. 13) information is contained in these two HIV Protocols, 2nd edn trafficking of viral components are ISBN 0-85484-114-1 volumes too. The books gain strength Cosmetics are up next, and ingredients recognized as critical for proper virus Reviews on the web Handbook of Probiotics and Prebiotics, from explaining the basic molecular particle assembly. This is a transcript of a Witness like Regenium XY Technology, 2nd edn principles of animal virology with Seminar held in 2006 involving many Nutrileum Complex and Covabeads Reviews of the following books are examples from different virus families, The chapters on viral pathogenesis eminent researchers, past and present, are all tools of an ‘utterly defensible available on the website at www.sgm. MicrobeLibrary Atlas CD-ROM, 2nd edn constantly comparing them. Students deal with the molecular mechanisms of concerned with staphylococci, infection pseudoscience’. (p. 21) ac.uk/pubs/micro_today/reviews.cfm Clinical and Diagnostic Virology

118 microbiology today may 09 microbiology today may 09 119 The SGM President, Robin

Weiss, reflects on a busy

month, not only for himself,

but for microbiologists comment worldwide. an april diary I have never quite fathomed why cells are more likely to become to gain her doctorate before the birth T.S. Eliot began The Waste Land with infected by HIV. As 90% of sub- of her baby, a mission satisfactorily ‘April is the cruellest month’ although Saharan Africans are DARC-negative accomplished. April 2009 has certainly ended cruelly (it confers resistance to vivax malaria) 24 April. In Rome for the formal with the unseasonable emergence of we attributed 11% of the African inauguration of the European Society Mexican ’flu. AIDS burden (some 2.6 million HIV- for Virology. Ron Desrosiers (Harvard), 1 April. In Harrogate for the infected Africans) to this genetic risk. Ab Osterhaus (Rotterdam) and I were Spring Meeting of the SGM. It was my In other words, prehistoric selection for the speakers in the scientific session. privilege to introduce the first recipient resistance to malaria appeared to make Shortly after Ab’s talk, his mobile phone of the SGM Prize Medal Lecture, Africans more susceptible to HIV today. rang. It was the WHO calling about the Stanley Prusiner from the University My problem was that other groups outbreak of H1N1 influenza in Mexico. of California, San Francisco. In 1982, cannot confirm our results. I presented Thus I gained inside knowledge 3 hours Stan isolated prion proteins that induce our data but announced that the before the public announcement, and spongiform encephalopathy and was findings had become controversial. Ab had to leave hurriedly. awarded the Nobel Prize in 1997 (see 19 April. Lago d’Iseo, Italy, for a 27 April. My phone rings frequently Microbiology Today, February 2009). small workshop on HIV infection of with journalists asking for comments Stan’s fascinating story ended with his macrophages. It is the best kind of on the new ’flu outbreak. Not being a current research on inhibitors of the specialist meeting, intense yet friendly, genuine expert, I give the media the protein conversion process. The day lubricated with excellent Francia names of four SGM members who really included a mini-symposium on prion Corte wine. It is 101 years since Ilya are, and who can explain the situation diseases with British contributors. The Mechnikov was awarded the Nobel authoritatively and clearly. UK is at the forefront of research in Prize for discovering phagocytosis, and 30 April. I’m clearing out old this field, as well we should be, having we now know that macrophages are files and piles. Can I dump 3 years of generated mad cow disease and its antigen-presenting cells in addition to SGM Council papers straight into the human form, variant Creutzfeldt–Jakob mopping up opsonized microbes. HIV recycling box or should I shred them disease. The notion that ‘infectious’ is not cytopathic in macrophages, but first? The first Londoner is confirmed proteins lacking nucleic acids cause it does adversely affect their various to have Mexican ’flu. Was it just scrapie seemed preposterous when functions. Amongst all the elegant imagination, or were more people Tikvah Alper et al. first postulated it microarray data and cytokine signalling than usual coughing and sneezing on in 1967 and had it been published in presented by others, I suggested that the Northern Line Underground this Nature on April 1st rather than May the wasting syndrome in AIDS is due morning? I rationalize the situation by 20th it might well have been regarded to infection of macrophages, not CD4+ telling myself that it might be smart to as an April Fool prank. lymphocytes, by invoking Maedi–Visna catch the ’flu early, before it becomes 3 April. In Liverpool to give the disease in sheep. more virulent, and gains resistance to Keynote Talk at the Annual Meeting of 22 April. Istituto San Raffaello, Tamiflu. But then again, I’m not an the British HIV Association. The reason Milano. I joined two avuncular Italian expert. why I had been invited to speak to 500 scientists to conduct a viva voce AIDS physicians was that my laboratory examination of a student who had Robin Weiss had collaborated with Sunil Ahuja’s written a thesis (in English) on a novel University College London, 46 in Texas on Duffy antigen receptor for method for isolating immortalized Cleveland Street, London W1T 4JF chemokines (DARC) as a risk factor for B-memory cells secreting monoclonal (e [email protected])

HIV. Our paper last year claimed that antibodies that neutralize H3N2 Please note that views expressed in Comment do not people who lack DARC on red blood influenza virus. The student wished necessarily reflect official policy of the SGM Council.

120 microbiology today may 09