microbiologytoday

vol35|feb08 quarterly magazine of the society for general microbiology

life on us skin microbes

s. aureus: ‘superbug’

life in your mouth

bacteria in the bowel

human endogenous retroviruses contents

vol35(1) regular features 02 News 34 Meetings 44 Hot off the press 08 Microshorts 36 Schoolzone 48 Going public 10 Addresses 40 Gradline 50 Reviews other items 08–Microshorts articles 12 Life on us 26 A lifelong commitment to Robin Weiss bowel bacteria Humans are mobile ecosystems that harbour a wide range of Gerald Tannock micro-organisms. Commensal bacteria in the bowel of young humans play a vital role in determining their future health. 14 Skin microbes Mark Farrar & Richard Bojar 30 Human endogenous Despite the harsh environment in which retroviruses: from they live, microbes on the skin are amazingly diverse. ancestral pathogens to bona fide genes 18 S. aureus: a ‘superbug’ David Griffiths & Simon Foster Cécile Voisset Although S. aureus can be a killer, it is not always harmful Human retroviruses have invaded our germ-line for centuries and it has a tough fight to survive on our bodies. and now make up ~8% of our genomes.

22 Microbial life in the 52 Comment: Microbes as mouth climate engineers Dave Spratt Dave Reay The surfaces of the oral cavity offer a home to a Policy-makers around the world can no longer ignore the variety of microbial communities. role played by micro-organisms in climate change.

Cover image Image taken in ultraviolet light of a woman’s hands covered in bacteria. Coneyl Jay / Science Photo Library The views expressed

Editor Dr Matt Hutchings––Editorial Board Dr Sue Assinder, Professor Iain Hagan, Professor Bert Rima––Managing Editor Janet Hurst––Assistant Editor Lucy Goodchild by contributors are not Design & Production Ian Atherton––Contributions are always welcome and should be addressed to the Editor c/o SGM Headquarters, 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. 3 SGM; 10 Digital Vision / Getty; 35, 37, 51 Comstock / Jupiter Images; 41, 45 Stockbyte; 49 Ablestock / Jupiter Images claims of advertisers © 2008 The Society for General Microbiology––ISSN 1464-0570––Printed by Latimer Trend & Company Ltd, Plymouth, UK be guaranteed. news

New Editor-in-Chief for JGV at the Institute of Virology SGM Council November meeting highlights in Glasgow with a remit to Professor Richard Elliott establish recombinant DNA technologies with negative SGM Prizes 2008 Joint ASM/SGM Burnet/Hayes Postgraduate Professor Elliott began his 5-year term of office on strand RNA viruses, and Council approved the following awards: Travel Awards 1 January. from here my interest The Australian Society for Microbiology (ASM) and the I undertook my graduate studies in Oxford, under the in bunyaviruses grew. I Fleming Prize SGM have agreed to establish ASM/SGM Burnet/Hayes supervision of the late Dr David Kelly, investigating protein was awarded an MRC Dr Cameron Paul Simmons, Oxford University Clinical Postgraduate Travel Awards. This scheme is designed to synthesis by a large DNA virus, frog virus 3. In 1979 I Senior Fellowship in 1986 Research Unit, Hospital for Tropical Diseases, Ho Chi Minh benefit PhD students in both countries by giving them the moved to the laboratory of Dr Peter Palese in New York for and then appointed to a City, Vietnam, for his achievements in exploiting cutting- opportunity of travelling overseas to present their work and postdoctoral training, taking a conscious decision to study Personal Chair by Glasgow edge molecular and immunological techniques in the study experience the best of microbiology in the partner country. an RNA virus (influenza virus) and to learn more about viral University in 1995. I of human tropical and emerging infections. Two awards will be made per annum, one in each country. nucleic acids. At that time cDNA cloning and nucleic acid served as Joint Head of the Excellent PhD students will be able to apply to attend the Marjory Stephenson Prize sequence determination were technologies still in their Division of Virology in Glasgow from 1998 until September annual meeting of either the ASM or the SGM where they Professor Alan B. Rickinson FRS, University of Birmingham, infancy, and I was involved in cloning influenza genome 2005 when I moved to the University of St Andrews to take are expected to make a presentation. They will then be able for outstanding achievements in research relating to the segments, including the first influenza B virus hemagglutinin up the Chair of Virology. I was elected a Fellow of the Royal to visit laboratories which carry out research relating to their molecular biology and immunology of Epstein–Barr Virus gene. In 1981 the opportunity to return to the UK arose Society of Edinburgh in 1999. interests. The society of the country of origin will cover and the immune surveillance and evasion of Burkitt’s the costs of international air fare and national travel (as lymphoma. appropriate), accommodation and subsistence; the society European Society for Clinical Virology SGM of the host country will provide the conference registration Peter Wildy Prize SGM has been delighted to accept the invitation of the ESCV Council to provide fee. Details will be announced on the SGM website. Council Dr Christopher Smith, University of Cambridge, for administrative and financial services with effect from 2008. The Society will be processing developing innovative ways of publicising and explaining SGM Finances all membership subscription applications and renewals and provide banking and accounting Nominations achievements and problems in science, especially At the end of the third quarter of 2007 SGM’s finances services for ESCV. The membership database will be hosted on the secure SGM server 2008 microbiology, to the public, such as radio broadcasts, the were in a healthy state. Council decided to choose the and online credit card payments will be available, a new facility for ESCV members. Most Nature podcasts and The Naked Scientists website. tobacco-restricted option of Charishare for the UK equity communications will be carried out by email. ESCV officers will continue to organize the Professors Iain Hagan component of the Society’s investments portfolio. Society’s very successful scientific meetings and manage their website (www.escv.org). and Bert Rima, retire A more detailed appreciaton of the prizewinners’ work will from Council in September appear elsewhere in Microbiology Today. The lectures will be Review of Council composition and functions ESCV President, Bruno Lina, commented, ‘Through this agreement, ESCV’s management can 2008. Nominations delivered at SGM meetings in 2008. A short oral report was received from Petra Oyston who is become more professional than in the past, and Executive Officers of ESCV will be able to focus are invited to fill three chairing the working group looking at the responsibilities of on scientific matters rather than having to worry about administrative problems. Also, regular vacancies on Council. All The SGM Medal members of Council, the roles of SGM officers and Elected replacements of Officers, as required by the Society’s Constitution, can take place without nominations must include Council agreed to create a new prize, called the SGM Members, and the functioning of Council. A written report creating breaks in continuity of administration.’ the written consent of the Medal. This will be bestowed annually (starting in 2009) will be presented at the next Council meeting in February The ESCV arose from the merger of two European virology organizations in 1997. It aims nominee and the names of on an individual from anywhere in the world whose 2008 for detailed consideration. to bring together scientists and clinicians throughout Europe and to promote public health the proposer and seconder, research is of internationally high reputation and has been Journal of General Virology and advance education, particularly medical education, in Clinical and Basic Virology. ESCV both of whom must be of significance in reaching beyond microbiology. The Professor Richard M. Elliott, University of St Andrews, will became a charity registered in England and Wales in 2003 and its registered office is already Ordinary Members. Prize comprises a Medal and a cheque for £1,000. The start as Editor-in-Chief of the Journal of General Virology, in at Marlborough House, SGM’s headquarters. winner will deliver a lecture at an SGM meeting. A search January 2008 for a period of 5 years (for profile see p. 2). Members submitting committee will accept nominations until 31 August 2008 The President Robin Weiss thanked the retiring Editor- nominations should ([email protected]) and make a People in-chief, Professor Geoffrey L. Smith, for all his efforts in indicate the main area of recommendation to Council in November 2008. Congratulations to… microbiological interest of maintaining and increasing the quality of the journal, and for his contributions to Council. Professor Clive Ronson (Otago University, of the General Advisory Committee on their nominee, who must Associate Membership have been an ordinary Safety of computer-stored information New Zealand) who has been elected as a Science by the Food Standards Agency. It was reported to Council that the new Associate member of the Society Fellow of the Royal Society of New Zealand. This body will offer independent advice on Membership category, to include recent graduate and Council learned that the Society was in the process of for at least two years. upgrading its email and internet connections and had taken Brian G. Spratt (Professor of Molecular how the FSA collects and uses scientific postgraduate students, early career postdoctoral fellows, Nominations should be further measures to increase the security of its computer- Microbiology at Imperial College London) evidence. clinical trainees, technicians and retired members, had sent to the SGM General stored information. on the award of a CBE for services to been approved at the Society’s Annual General Meeting in Deaths Secretary, Dr Ulrich science in the New Years Honours 2008. September 2007 and was now part of the bye-laws. Ulrich Desselberger, General Secretary The Society notes with regret the death of Desselberger, c/o SGM Professor Duncan Maskell (University of Dr K.R. Cameron, Cockermouth, Cumbria Headquarters to arrive no Cambridge) has been appointed a member (member since 1965). later than 30 April 2008.

2 microbiology today feb 08 microbiology today feb 08 3 Prize Lectureships Fleming Lecturer Marjory Stephenson Prize Dr Cameron Simmons will deliver his prize lecture, Lecturer entitled Understanding emerging pathogens: H5N1 influenza Professor Alan B. Rickinson, FRS and Dengue in Vietnam, on Wednesday 2 April 2008 will deliver his prize lecture, entitled at the Society’s meeting at the Edinburgh International Studies with an oncogenic virus: how Conference Centre. The Fleming Lecture is awarded for to survive a lifetime with EBV, on outstanding research by a microbiologist in the early stages Tuesday 1 April 2008 at the Society’s of their career. meeting at the Edinburgh International Cameron Simmons is a Reader in Tropical Medicine at Conference Centre. The Marjory Oxford University and based at the Hospital for Tropical Stephenson Prize Lecture is awarded Diseases in Ho Chi Minh City, Vietnam. Cameron completed for an outstanding contribution of his PhD at the University of Melbourne (Australia) and current importance in microbiology. postdoctoral studies at Imperial College (UK). Since arriving Alan Rickinson did his PhD in Radiotherapeutics in in Vietnam in 2001, Cameron’s research focus has been in Cambridge and, after spending 3 years as a postdoctoral understanding the pathogenesis of important diseases in the fellow in Sydney, moved to Bristol in 1972 to join Tony region, beginning with tuberculous meningitis and, more Epstein’s group working on Epstein–Barr virus. There he recently, H5N1 influenza and dengue. These studies have began to study EBV’s interaction with the B lymphoid been deliberately holistic and encompass investigations of the system, the role of the virus in B cell lymphomagenesis, pathogen, immune response and host genetics. It is hoped and later (in collaboration with Denis Moss in Brisbane) the these investigations will provide the foundation for improved host’s cellular immune response to virus infection. Since patient management and new clinical interventions in these moving to become Head of the CRUK Institute for Cancer diseases. Cameron’s contributions to dengue research have Studies in Birmingham in 1983, he has continued these seen him appointed to various WHO advisory committees. themes, working in the area where virology, immunology Cameron has three small children and loves tennis, football and oncology meet, and is currently developing and testing (Fulham), travel and (rarely) sleeping in on a Sunday therapeutic vaccines against EBV-positive malignancies. He morning! was elected a Fellow of the Royal Society in 1997. SGM/RMS meeting – microscopy and microbes Getting inside cells: the pathogens progress

This one-day meeting is a new bacteria invade cells and then Prof. Held alongside the prestigious collaboration between the Royal Urs Greber (University of Zürich) will Microscience 2008 exhibition and Microscopical Society (RMS) and SGM. describe interactions of viruses with conference, at the Excel conference The synergy is an obvious one – there the cell cytoskeleton. Dr Michelle S. centre, delegates to the SGM-RMS are not a lot of microbes that can be Swanson (University of Michigan) will meeting will have access to the seen with the naked eye – but up introduce the role of autophagy (a exhibition where over 100 exhibitors until now there have been no formal normal cellular process that helps cells will cover almost all aspects of light joint ventures. last through times of nutrient stress), and electron microscopy. If it is new in bacterial and viral infection. There and exciting in microscopy – it will be The event takes place on Tuesday is some uncertainty as to whether there. SGM members will be able to 24 June 2008 in London and will pathogens induce autophagy as an aid register at RMS member rate (£45). concentrate on the cellular aspects of to replication or the process is used by infection and will consider both cell For further information email paul. the cell as a defence mechanism. invasion processes and the ‘tussle’ [email protected] or clare@ that takes place once a pathogen has There will be ample opportunity for rms.org.uk. For full details of the started to replicate within the host delegates to present their own work Microscience 2008 programme see cell and the cell tries to fight back. either by poster or oral contribution. www.microscience.org.uk Dr Mark Jepson (University of Bristol) Oral contributions will be selected Organizers: Dr Paul Monaghan (RMS) will be looking at the way in which from the submitted abstracts. and Professor Joanna Verran (SGM)

4 microbiology today feb 08 Grants SGM has a wide range of schemes to support microbiology. See Travel & meetings www.sgm.ac.uk/grants Postgraduate Student Enquiries should be made to the SGM Grants Office, Marlborough House, Conference Grants Basingstoke Road, Spencers Wood, Reading RG7 1AG (t 0118 988 1821; All postgraduate student associate f 0118 988 5656; e [email protected]). members are eligible to apply for a grant to support their attendance Technician Meeting Grants Seminar Speakers Fund at one SGM meeting each year. All associate members who are Small grants to cover the travel and Grants contribute to travel, registration technicians are eligible to apply for other expenses of up to two speakers and accommodation expenses. The a grant to support their attendance on microbiological topics in annual student need not be presenting their at one SGM meeting each year. departmental seminar programmes. research so it is an ideal introduction to Applicants need not be presenting scientific meetings at little or no cost to Student Society Sponsored work at the meeting. Some themselves or their supervisor’s budget. Lectures microbiology technicians who are not Applicants must be Student Members These cover the travel and other members of SGM may also apply for resident and registered for PhD in expenses of up to two speakers on a grant to attend a Society Meeting. an EU country. Closing date for the microbiological topics per society each Closing date for the Edinburgh Edinburgh meeting: 28 March 2008. year at student society meetings. meeting: 20 March 2008. President’s Fund for Research International Visits IUMS-SGM Fellowships Up to £3,000 is available to support Studentships These provide funding for young early-career microbiologists who are Elective Grants microbiologists from developing planning a short research visit to Funding for medical/dental/veterinary countries to pursue, or complete, part another laboratory (minimum visit students to work on microbiological of an on-going research programme 4 weeks, maximum visit 3 months). projects in their elective periods. The in a laboratory in a developed country Closing dates for applications: 20 closing dates for applications in 2008 and/or acquire theoretical or technical March and 26 September 2008. are 20 March and 26 September. knowledge in their particular area of Retired Member Grants research. See www.iums.org/outreach/ Contribute toward accommodation outreach-fellowships.htm for details. Education & development and the Society Dinner at one SGM International Development Fund meeting a year. Closing date for the National The Fund exists to provide training Edinburgh meeting: 28 March 2008. Education Development Fund courses, publications and other help to Scientific Meetings Travel Grants Small grants to members for microbiologists in developing countries. This scheme aims to support early- developments likely to lead to an Applications for 2008 are invited. career microbiologists wishing to improvement in the teaching of any Closing date: 26 September 2008. aspect of microbiology relevant to present work at a scientific meeting The Watanabe Book Fund in the UK or overseas. Graduate secondary or tertiary education in the Members who are permanently research assistants and lecturers, and UK. Up to £1,000 is also available to resident in a developing country postdoctoral researchers (within 3 years support science promotion activities. may apply for funding to acquire of first appointment in all cases), and GRADSchool Grants microbiology books for their libraries. postgraduate students are eligible to Postgraduate Student associate These annual awards are available as apply. Retrospective applications members who are not eligible for a result of a generous donation from are not considered. a free place on a UKGrad (www. Professor T. Watanabe of Japan. The SfAM/SGM Short Regional grad.ac.uk) personal development following awards were made in 2007: Meeting Grants course (National GRADSchool) may Edgar Sevilla–Reyes (Mexico) and Wasu Contribution of up to £2,000 towards now apply for a grant from SGM to Pathom–aree (Thailand). Applications the costs of running a regional cover full course fees. Retrospective for 2008 are invited. Closing date: microbiology meeting. applications are not considered. 26 September 2008. microbiology today feb 08 7 microshorts

Lucy Goodchild takes a look at some stories New treatment for African that have hit the headlines recently. sleeping sickness The standard treatment for human African trypanosomiasis, or African sleeping sickness, is highly toxic and kills a large percentage of patients every year. The disease-causing parasites have Bird ‘flu Hope Probiotics to treat viral also started to become drug-resistant. Clinical trials in Uganda of a new drug combination have been successful, offering hope to over 15,000 people who are infected every year. The combination of transmitted for diarrhoea nifurtimox and eflornithine caused no treatment-related deaths and it was successful in all patients. Every year, more than half a million infants worldwide die as a Although eflornithine must be administered intravenously and is a strain on health services, this is to foetus dengue result of diarrhoea caused by rotavirus. Probiotic bacteria, beloved the best treatment available for the next decade, while new drugs are being developed. Scientists at Peking University, of yoghurt advertisers, could soon be used to treat these infections. http://ntds.plosjournals.org/perlserv/?request=get-document&doi=doi/10.1371/journal.pntd.0000064 Beijing, China, studied the fever Even in industrialized countries rotavirus disease costs $1 billion bodies of people who had died per year. Researchers from the Karolinska Institute and the from H5N1 avian influenza patients University of Linkoping in Sweden, and the Nestlé Research Center Dental flora cause alopecia and found that the virus infects Dengue fever is caused in Switzerland tested the effect of Lactobacillus rhamnosus in animal Alopecia areata, or localized alopecia, affects 1 in 1,000 people. It is a dermatitis that causes bald organs other than the lungs by the most prevalent models. 59 % of the animals given probiotics before infection did patches, and was thought to be an autoimmune condition. Scientists at the University of Granada and can even be transmitted mosquito-borne virus that not develop diarrhoea, compared with just 7 % in those without have found that the bald patches, which can occur on the scalp, beard and even eyebrows, are caused from placenta to foetus. They infects humans. Despite around probiotics. Hyperimmune bovine colostrums (HBC), an antibody by ‘infection outbreaks on the teeth’. Many people experience recurrences after regrowth because the detected genetic material from 100 million people being used to treat rotavirus infections, is expensive. If probiotics are hair follicles are not destroyed. Patches are usually on a line projected from the dental infection. The the virus as well as antigens in infected, there is currently no used, the required dose of antibodies can be reduced by 90 %, researchers advise people exhibiting alopecia areata to visit the dentist. the lungs, trachea, lymph node treatment available. Scientists which will be particularly beneficial in developing countries. http://prensa.ugr.es/prensa/research/index.php T-cells, neurons and placental at the Novartis Institute for www.biomedcentral.com/bmcmicrobiol/ cells. Viral genetic material Tropical Diseases and the m False-colour scanning electron micrograph of Trypanosoma brucei, was also found in the intestinal Genome Institute of Singapore the cause of African sleeping sickness, amongst red blood cells. Eye HIV helper identified of Science / Science Photo Library mucosa. In an infected foetus, have monitored the genetic More than 90 % of HIV-1 HIV particles and help them the lungs, circulating immune responses of the dengue c Alopecia areata. Dr P. Marazzi / Science Photo Library infections result from sexual penetrate target cells. SEVIs cells and liver all contained virus to analyse host–virus intercourse, but factors are so effective that they can evidence of viral presence. interactions and identify Crohn’s disease clue influencing the infectiveness enhance infection rates by Scientists are unsure about potential drug targets. Three of the virus in semen have several orders of magnitude; in ‘Sticky’ Escherichia coli is known to be present in patients with whether an infected foetus pathways have been noted. been poorly understood some cases over 100,000-fold. Crohn’s disease. Scientists have identified a bacterium that would survive if its mother Researchers hope to develop until now. Researchers at the The researchers have published releases a molecule containing mannose, which in turn prevents survived infection, but they drugs that inhibit these University Clinic of Ulm have their study in Cell and plan to macrophages from killing E. coli in the intestine. Mycobacterium said ‘this study has shown the pathways, in order to halt virus discovered that prostatic acidic explore how the fibrils allow paratuberculosis, which causes a disease called Johne’s disease in capacity for human vertical replication. phosphatase (PAP), a molecule the viruses to enter their target cows, is transmitted to humans in dairy products. Researchers at that is plentiful in semen, cells. Future findings could transmission of the H5N1 virus’. http://ntds.plosjournals.org/perlserv/ the University of Liverpool suggest that this weakens the body’s builds a sort of ferry for virus lead to drugs that block the http://multimedia.thelancet.com/pdf/ ?request=get-document&doi=doi/ immune response to intestinal bacteria, resulting in symptoms like press/H5N1.pdf 10.1371/journal.pntd.0000086 particles to help them infect process, which could be added bleeding and diarrhoea. The team is planning to carry out clinical cells. Amyloid fibrils (known to microbicide gels that are trials using antibiotics to target M. paratuberculosis in patients with as semen-derived enhancers being developed. m False-colour transmission Crohn’s disease. of virus infection, SEVI) Cell electron micrograph of Dandruff fungus www.liv.ac.uk/newsroom/press_releases/2007/12/crohns-disease.htm are formed, which capture 14 December 2007 rotavirus particles, a cause of genome sequenced viral diarrhoea. CNRI / Science Photo Library Scientists from Procter & Gamble have sequenced the genome Melanin may be of Malassezia globosa, the fungus that causes dandruff. As much as 50 % of people are affected by dandruff and similar disorders b False-colour scanning antimicrobial electron micrograph showing caused by fungi. Researchers looked at the most common type, two human skin scales from In humans, the skin pigment melanin helps to protect the body which was stored at a fungus bank in Holland, and identified new a mild case of dandruff. Dr against harmful UV rays producing the painfully familiar sunburn. targets for dandruff treatment. M. globosa uses 50 enzymes to digest Jeremy Burgess / Science Photo Scientists know that, in invertebrates, melanin encapsulates the products of the skin’s sebaceous glands, leading to the telltale Library invading parasites and fungi, which appear as black-brown spots symptoms of itching and flaking. The fungus is also involved in on the shell. However, its effect on bacterial infections has eczema, atopic dermatitis and psoriasis. Experts hope the research, c Endoscope view of ulceration been hotly debated. Writing in J Biol Chem, scientists say melanin which has been published in the Proc Natl Acad Sci USA, will lead and inflammation in the ileum protects crayfish from bacterial infections. The bacteriumAeromonas to treatments for a closely related pathogenic plant fungus that of a 42 year-old woman with hydrophila is dangerous in crayfish; researchers found that effective Crohn’s Disease. David M. infects crops like wheat and corn. Martin MD / Science Photo melanin production is crucial to the survival of those infected. Proc Natl Acad Sci U S A (2007) 104, 18370–18735 Library J Biol Chem (2007) 282, 21884–21888; doi:10.1074/jbc.M701635200

8 microbiology today feb 08 microbiology today feb 08 9 addresses

council07–08 Officers Members President – Prof. Robin Weiss Prof. Mike R. Barer Division of Infection and Immunity, University College London, 46 Cleveland Street, Infection, Immunity and Inflammation, University of Leicester, London W1T 4JF Medical Sciences Building, PO Box 138, University Road, Leicester LE2 4FF t–0207 679 9554;–f–0207 679 9555;–e–[email protected] t–0116 252 2933;–f–0116 252 5030;–e–[email protected] Treasurer – Prof. Colin R. Harwood Dr David J. Blackbourn School of Cell and Molecular Biosciences, University of Newcastle Medical School, University of Birmingham, Cancer Research UK Institute for Cancer Studies, Framlington Place, Newcastle upon Tyne NE2 4HH Edgbaston, Birmingham B15 2TT t–0191 222 7708;–f–0191 222 7736;–e–[email protected] t–0121 415 8804;–f–0121 414 4486;–e–[email protected] General Secretary – Dr Ulrich Desselberger Prof. Neil A. R. Gow Dept of Medicine, University of Cambridge, Level 5, Addenbrooke’s Hospital, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Cambridge CB2 2QQ Aberdeen AB25 2ZD t–01223 763403;–e–[email protected] or [email protected] t–01224 555879;–f–01224 555844;–e–[email protected] Scientific Meetings Officer – Prof. Hilary M. Lappin-Scott Prof. Iain M. Hagan Dept of Biosciences, University of Exeter, Geoffrey Pope Building, Paterson Institute for Cancer Research, Wilmslow Road, Manchester M20 4BX Exeter EX4 4QD t–0161 446 8193;–f–0161 446 3109;–e–[email protected] f–01392 263434;–e–[email protected] Dr Richard M. Hall International Secretary – Prof. George P. C. Salmond Biological Reagents and Assay Development (BR&AD), GlaxoSmithKline R&D, Dept of Biochemistry, University of Cambridge, Tennis Court Road, Building O, New Frontiers Science Park – North Site SC1, H31/1-047 (Mail Code H31111), Downing Site, Cambridge CB2 1QW Third Avenue, Harlow, Essex CM19 5AW t–01223 333650;–f–01223 766108;–e–[email protected] t–0127 962 7172;–f–0127 962 7014;–e–[email protected] Education Officer – Dr Susan J. Assinder Dr Kim R. Hardie Academic Development Unit, Deiniol Building, Deiniol Road, Bangor, University of Nottingham, Centre for Biomolecular Sciences, University Park, Gwynedd LL57 2UX Nottingham NG7 2RD t–01248 382604;–f–01248 370731;–e–[email protected] t–0115 846 7958;–f–0115 586 7950;–e–[email protected] Editor, Microbiology Today – Dr Matt Hutchings Dr Paul A. Hoskisson School of Biological Sciences, University of East Anglia, Norwich Research Park, Strathclyde Institute of Pharmacy & Biomedical Sciences, University of Strathclyde, Norwich NR4 7TJ 204 Geroge Street, Glasgow G1 1XW t–01603 592257;–e–[email protected] t–0141 548 2819;–e–[email protected] Editor-in-Chief, Microbiology – Prof. Charles J. Dorman Dr Catherine O’Reilly Dept of Microbiology, Moyne Institute, Trinity College, Dublin 2, Ireland Dept of Chemical and Life Sciences, Waterford Institute of Technology, Cork Road, t–+353 1 608 2013;–f–+353 1 679 9294;–e–[email protected] Waterford, Ireland Editor-in-Chief, JGV – Prof. Richard M. Elliott t–+353 51 302858;–f–+353 51 378292;–e–[email protected] Centre for Biomolecular Sciences, School of Biology, University of St Andrews, Prof. Petra C. F. Oyston North Haugh, St Andrews, Fife KY16 9ST TL Molecular Bacteriology, Dstl, B07A Microbiology, Porton Down, Salisbury SP4 0JQ t–01334 463396;–e–[email protected] t–01980 613641;–f–01980 614307;–e–[email protected] Editor-in-Chief, JMM – Prof. Charles W. Penn Prof. Rick E. Randall School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT School of Biology, Biomolecular Sciences Building, University of St Andrews, t–0121 414 6562;–f–0121 414 5925;–e–[email protected] North Haugh, St Andrews, Fife KY16 9ST t–01334 463397;–f–01334 462595;–e–[email protected] Prof. Bert K. Rima School of Biology and Biochemistry, Medical Biology Centre, The Queen’s University of Belfast, 97 Lisburn Road, Belfast BT9 7BL t–028 9097 5858;–f–028 9097 5877;–e–[email protected] groupconveners Cells & Cell Surfaces – Dr Ian R. Henderson Fermentation & Bioprocessing – Prof. Chris J. Hewitt Division of Immunity and Infection, University of Birmingham Medical School, Dept of Chemical Engineering, Loughborough University, Loughborough LE11 3TU Edgbaston, Birmingham B15 2TT t–01509 222503;–e–[email protected] t–0121 414 4368;–f–0121 414 3599;–e–[email protected] Food & Beverages – Dr Cath D. Rees Clinical Microbiology – Prof. Dlawer Ala’Aldeen University of Nottingham, School of Biological Sciences, Sutton Bonington Campus, Molecular Bacteriology and Immunology Group, Division of Microbiology, Loughborough LE12 5RD School of Molecular Medical Sciences, University Hospital, Nottingham NG7 2UH t–0115 951 6167;–f–0115 951 6162;–e–[email protected] t–0115 823 0748/0771 (secretary);–f–0115 823 0759;–e–[email protected] Irish Branch – Dr Evelyn Doyle Clinical Virology – Prof. Judy Breuer School of Biology and Environmental Science, Ardmore House, ICMS Centre for Infectious Disease, Barts and the London Medical School, University College Dublin, Belfield, Dublin 4, Ireland 4 Newark Street, London E1 2AT t–+353 1716 1300;–f–+353 1716 1183;–e–[email protected] t–0207 882 2308;–f–0207 882 2181;–e–[email protected] Microbial Infection – Dr Nick Dorrell Education & Training – Prof. Joanna Verran Pathogen Molecular Biology Unit, Dept of Infectious and Tropical Diseases, Dept of Biology, Chemistry and Health Science, Manchester Metropolitan University, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT Chester Street, t–0207 927 2838;–f–0207 637 4314;–e–[email protected] Manchester M1 5GD Physiology, Biochemistry & Molecular Genetics – Prof. Maggie C. M. Smith t–0161 247 1206;–f–0161 247 6325;–e–[email protected] Molecular & Genetics, University of Aberdeen, Institute of Medical Sciences, Environmental Microbiology – Prof. Geoffrey M. Gadd Foresterhill, Aberdeen AB25 2ZD Division of Environmental and Applied Biology, Biological Sciences Institute, t–01224 555739;–f–01224 555844;–e–[email protected] School of Life Sciences, University of Dundee, Dundee DD1 4HN Systematics & Evolution – Prof. Niall A. Logan t–01382 344765;–f–01382 348216;–e–[email protected] Dept of Biological and Biomedical Sciences, Glasgow Caledonian University, Eukaryotic Microbiology – Dr Alastair Goldman Cowcaddens Road, Glasgow G4 0BA t–0141 331 3207/8510 (admin assistant);–f–0141 331 3208;–e–[email protected] Molecular Biology & Biotechnology, University of Sheffield, Firth Court, Sheffield S10 2TN Virus – Prof. Rick E. Randall t–0114 222 2779;–e–[email protected] School of Biology, Biomolecular Sciences Building, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST t–01334 463397;–f–01334 462595;–e–[email protected]

10 microbiology today feb 08 c Adam and Eve, 1526 (oil on panel, 117x80 cm) by Lucas Cranach I (1472–1553). Did the microbes of hunter–gatherers in Eden differ from those of modern humans? Courtauld Institute of Art Gallery, Life on us London This issue of Microbiology Today thanks to our diet of solanacaeous vegetables (tomatoes, potatoes, peppers and so on), all of which came from the Americas. It is ironic that the post-Columbian exchange takes a look at some of the microbes resulted in the introduction of novel foods (Solanaceae and Zea mais) from the New World to the Old, whereas almost who share our bodies. SGM President all the pathogens such as smallpox, measles, yellow fever and tuberculosis made the transatlantic journey in the other direction. Since human numbers and activity affect the global Robin Weiss wonders just how ecosystem, it would seem sensible from a microbial point of view to adopt the attitude ‘if you can’t beat them, join them’. human we are. Humans certainly provided the SARS coronavirus with a brief world tour before it retreated to its fruit bat reservoir ore than 30 years ago, Michael Andrews with occasional forays into civet cats. wrote an entertaining book entitled Zoonoses in turn raise the question, how similar is our The Life That Lives On Man (London: microbial flora to that of our closest living relative, the Faber & Faber, 1976), concerning chimpanzee? It would be interesting to compare, say, the oral human ectoparasites such as fleas, lice, flora of chimpanzees to that of humans. Considering virus- mites and ticks, and the diseases they es, many of the ubiquitous, endemic not highly pathogenic Mcarry: plague, typhus and lyme disease. This issue of Micro- viruses have co-evolved with the human host, e.g. herpes- biology Today is devoted to the microbes that live on or in us. viruses. In contrast, most of the highly pathogenic, epidemic Humans are mobile ecosystems that harbour numerous viruses came to humans from diverse animal sources, long bacteria, viruses, fungi and single-cell eukaryotes. Even our after we left the forest for the savannah and eventually spread own genome has been repeatedly colonized by retroviral out of Africa. Many of them, such as measles, smallpox and genomes constituting some 8 % of human DNA sequences influenza, became part of the human microbial scene only (see Voisset & Griffiths, p. 30), and that’s not counting other during the last 12,000 years or so, when we domesticated transposons and parasitic DNA. livestock, and when other animals, such as dogs, cats, rats Articles on the skin (Farrar & Bojar, p. 14, oral cavity and mice, chose to colonize human settlements. Thus while (Spratt, p. 22), large bowel (Tannock, p. 26) – a veritable we share >98 % host DNA sequence similarity with the chemostat for Escherichia coli – illustrate what a wonderful chimpanzee, the microbial and viral species that live in or on habitat we provide for microbes. Relatively few of them are us are only ~50 % shared with the great apes. routinely pathogenic, but in specially susceptible hosts such Does life on us represent a harsh and challenging environ- as the immunocompromised individual, viruses and fungi ment? It may sometimes seem so, given our modern habits of that we carry for decades without ill effects can suddenly washing with soap, brushing our teeth, taking antibiotics and run wild. There is also the danger of MRSA leaving its separating drinking water from sewage. But, as the articles commensal niche in our nostrils to invade surgical wounds in this issue illustrate, we still abound with microbes. One with devastating effects (as Foster describes on p. 18). interesting human ecological niche (not explored here) is the As an ecosystem, it has become clear that we are only vagina. Together with the uterine cervix, it is home to the part human, because a significant amount of our biomass is symbiont Lactobacillus acidophilus and frequently to the more microbial. In demographic terms, microbes outnumber our irritating Candida and Gardnerella, not to mention sexually own cells. While there are 1014 human cells in the average transmitted papilloma viruses, herpes simplex virus type II, adult, there are probably ~1015 bacteria and >1017 viruses Chlamydia, Gonococcus, Trepanema, Haemophilus ducreyi and associated with the human body. In terms of genetic diversity Trichomonas. The lactobacilli help to maintain the vaginal and complexity, the microbial metagenome of humans may mucosal surface at pH 4.2, but after ejaculation of semen, be greater than the 3×109 base pairs of human DNA. this can rise to pH 8.0. This sudden shift from an acid to an Are the microbes that live on us on to a good thing? Yes, alkaline milieu might strike an environmental microbiologist if we consider that for a large mammalian host, our current as dramatic, although I would not go as far as calling sexually population of 6 billion is substantial, and widely distributed. transmitted microbes extremophiles! Even viruses that do not actually infect us may find that humans serve as a useful vector for dispersal. At the Professor Robin A. Weiss September 2007 SGM meeting we were reminded by Mya Division of Infection and Immunity, University College Breitbart that the most prevalent virus to be found in human London, 46 Cleveland Street, London W1T 4JF (t 0207 faeces is pepper mild mottle virus. This curious finding is 679 9554; e [email protected])

12 microbiology today feb 08 microbiology today feb 08 13 Human skin may s a microbial habitat, human skin is some- Staphylococci implants. S. epidermidis is by far the most common cause what inhospitable. Resident micro-organisms Over 40 species of Staphylococcus are currently recognized, of of such infections. The most significant virulence factor must be able to withstand a much drier which at least ten can be found on human skin. Staphylococcus of coagulase-negative staphylococci is the production of not be the most ideal and nutritionally limited environment than epidermidis is the most prevalent member of the human skin extracellular polysaccharide or ‘slime’. This is produced that found, for example, in the gut. As a microflora on most body sites. Other common skin residents in large amounts by around 50 % of S. epidermidis isolates habitat for micro- consequence, there are relatively few microbial belonging to this genus include S. hominis, S. haemolyticus and enables the bacteria to adhere to and colonize medical Agroups capable of colonizing human skin. The dominant and S. capitis. These are all coagulase-negative staphylococci. devices. It also contributes to antibiotic resistance and micro-organisms belong to the genera Staphylococcus, The coagulase-positive and more infamous S. aureus is not interferes with removal of invading bacteria by the immune organisms, but as Mark Propionibacterium and Corynebacterium. Skin commensals usually considered a resident of human skin but is found in system. Consequently, staphylococcal infections of medical can colonize both the skin surface and hair follicles. The the nose of approximately 30 % of the population. When devices are difficult to treat. Farrar and Richard distribution and density of these micro-organisms varies found on skin it is most likely to be a transient colonization. greatly over the body and is influenced mainly by nutrition Staphylococci are found in the highest numbers on the face Propionibacteria Bojar report, the skin and humidity. For example, total bacterial numbers per cm2 and chest, and in some individuals in the armpit. Propionibacteria are most prevalent and found in the greatest of skin in the armpit or on the face can reach 107, whereas on As pathogens, cutaneous staphylococci are most commonly numbers in lipid-rich areas of human skin, i.e. the face, chest the forearm numbers may only reach 102. On the whole our associated with infections of catheters and prosthetic and back. In the laboratory, propionibacteria are routinely microflora is more resident microflora exists without any detriment to human isolated under anaerobic conditions. However, they are health and may actually play a protective role in preventing aerotolerant and growth has been shown to be increased species-rich than we colonization by pathogens. However, occasionally our . Inflammatory acne vulgaris on the back. M.D. Farrar in the presence of low concentrations of air, making them microflora can cause problems, some of which will be c Coloured scanning electron micrograph of clusters of Staphylococcus microaerophilic. Propionibacterial numbers on the face and think. addressed in this article. epidermidis bacteria. David Scharf / Science Photo Library back can reach 107 per cm2 of skin. Propionibacterium acnes Skinmicrobes

14 microbiology today feb 08 microbiology today feb 08 15 is the dominant member of the genus through the use of ribosomal RNA on skin. Other members of cutaneous Molecular typing has shown there to sequencing, the microbial diversity of propionibacteria include P. granulosum, numerous habitats has been shown to P. avidum which is found in more humid be many more bacterial species present be greatly underestimated. Recently, areas such as the armpit, P. propionicum such techniques have been applied and P. lymphophilum. Propionibacteria on human skin than previously thought to human skin. This has shown there have been associated with the common to be many more bacterial species skin disease acne vulgaris for over Corynebacterium bovis, C. jeikeium and described, Malassezia spp. are also present on human skin than previously 100 years. Although propionibacteria C. xerosis. Corynebacteria are also lipophilic. Members of this genus, in thought. This is mostly due to previous do not cause this disease, they are found in lipid-rich areas and many particular M. globosa and M. restricta, studies relying solely on culture thought to be a significant factor in the are lipophilic. Recent sequencing of are thought to be involved in the techniques. However, a note of caution development of inflammation.P. acnes the genome of C. jeikeium has shown pathogenesis of seborrheic dermatitis, should be applied; to date, molecular has been the main focus of research it to have a nutritional requirement for a severe form of dandruff. Although studies have looked at samples at only into propionibacteria and acne due to monounsaturated fatty acids, which their role is not exactly clear, disease a single point in time. This makes it its higher densities, but involvement it cannot synthesize. Corynebacteria is believed to develop due to an difficult to distinguish those organisms of other propionibacteria and even are of great interest to the personal inappropriate immune response to the that are true residents from transiently members of other genera cannot be hygiene industry as they are thought organism. colonizing micro-organisms and en- discounted. Skin propionibacteria to be major contributors to underarm vironmental contaminants. If we are are becoming an increasing cause of body odour. Secretions from sweat and Other skin residents to truly understand the diversity of infections in immunocompromised other skin glands can be metabolized Other micro-organisms are found the human skin microflora, more individuals, particularly following to odorous compounds by this group on human skin and are recognized long-term studies are required where surgical procedures. Endocarditis, eye of organisms. Many deodorant pro- as commensals, although they are multiple samples are taken from infections and tissue infections have ducts contain antibacterial agents that found in much lower numbers than individuals over a period of time. all been reported. Publication of the aim to reduce bacterial numbers and the groups described above. True However, those studies carried out to genome sequence of P. acnes in 2004 therefore reduce the potential for commensals include members of the date are important as they have shown has helped to accelerate research, but odour formation. Corynebacteria may genera Micrococcus, Brevibacterium, the skin to be a potential habitat for a the actual role of this organism in also cause opportunistic infections. Kytococcus and Dermacoccus (both diverse range of micro-organisms. acne and the factors involved in the C. jeikeium is recognized as a significant formerly classified as micrococci), transition from harmless commensal nosocomial pathogen and is resistant and the Gram-negative Acinetobacter. Mark D. Farrar to inflammatory stimulus are still to several antibiotics, including erythro- All these can be regularly isolated, Senior Research Fellow unknown. mycin, tetracycline, kanamycin and albeit in low numbers, from human m Coloured transmission electron micrograph chloramphenicol. skin. Less prevalent and probably Richard A. Bojar of a section through Propionibacterium Corynebacteria acnes bacteria. Kwangshin Kim / Science considered transients rather than true Principle Research Fellow Corynebacteria are related to propi- Photo Library Malassezia spp. commensals are species of Streptococcus onibacteria, but grow under aerobic From there being just one recognized and Peptostreptococcus. Skin Research Centre, Faculty of conditions. This genus is less well m Transmission electron micrograph of a species several years ago, molecular Biological Sciences, University of characterized than Staphylococcus budding Malassezia cell. M.D. Farrar typing has led to the description of 13 Is the skin microflora more Leeds, Leeds LS2 9JT, UK (t 0113 or Propionibacterium, but ribosomal species in this genus, 11 of which have diverse than we thought? 3435616 or 0113 3435615; c Biopsy section of a human hair follicle RNA typing is helping to distinguish showing Gram-positive micro-organisms been found on human skin. As with With advances in molecular typing e [email protected]; species. Skin residents include within the follicle. M.D. Farrar some of the bacterial groups already and classification of micro-organisms [email protected])

16 microbiology today feb 08 microbiology today feb 08 17 e afraid, be very afraid? use of antibiotics and non-ideal clinical controversially associated with a rare Staphylococcus aureus is practices. In some countries such as but often fatal pneumonia. In the last most well known as its Denmark and Sweden the incidence of few influenza pandemics,S. aureus antibiotic-resistant form, MRSA is much lower due to a variety of infection was a common complication. MRSA, a scourge of mod- measures, including stringent screening Perhaps if bird ‘flu jumps the species ern medicine and a major and isolation of MRSA carriers. barrier then S. aureus might find a world Bpublic enemy. MRSA (meticillin-resist- of susceptible hosts awaiting infection. ant S. aureus) is quite rightly feared Can things get worse? CA-MRSA strains also produce high as it causes considerable death and Up to now MRSA has been primarily levels of a newly discovered set of cyto- suffering in the UK, and around the associated with nosocomial (hospital- lytic peptides, able to lyse human world. To an extent this is a calamity acquired) infections. However, recently neutrophils, our main cellular defence of our own making as a result of over the spread of community-acquired against S. aureus. MRSA (CA-MRSA) is particularly dis- But enough of scaremongering, we turbing, as these organisms are becom- can always rely on the drugs, can’t we? ing endemic in the wider population. For several years vancomycin has been A number of these strains produce used as a fallback drug when others Panton–Valentin leukocidin, which is have failed. Recently, resistance even to this has appeared, which has led to the spectre of VRSA (vancomycin- resistant S. aureus). Whilst not a common problem, this highlights the inevitability of development of resistance to all new drugs.

False-coloured transmission electron micrograph of MRSA. Biomedical Imaging Unit, Southampton General Hospital / SPL

MRSA is constantly in the news. Simon Foster questions how well we are coping with living with this public enemy. S. aureus: a ‘superbug’

18 microbiology today feb 08 microbiology today feb 08 19 It can’t be that bad? c S. aureus abscess. Emma Nickerson, Mahidol University It is all too easy to fear and loathe S. aureus and with such c Open incision to drain pus from a thigh in a case of S. aureus antipathy, to gloss over the special relationship which has pyomyositis. Emma Nickerson, Mahidol University evolved between us and one of our most faithful microbes. We all have a high titre of circulating antibodies against nature of the bacterium. Some people actually carry the S. aureus and so we must be challenged subclinically on a same strain of S. aureus for years and such a long-term regular basis. Getting a serious S. aureus infection is actually commitment to a relationship is laudable. Carriage cannot remarkably difficult and mostly requires immense effort be looked upon, however, as an easy life for S. aureus as it not on our part via injury, surgery, indwelling medical devices, only has to survive and proliferate in a rather harsh physical etc. S. aureus is an opportunist pathogen for which many environment, but also resist human innate defences and of the diseases it causes are distinctly inopportune for the compete with other microflora. Understanding the basis for bacterium. Endocarditis and other deep-seated infections carriage is beginning to not only define the roles for several give little chance for reintroduction into the environment. S. aureus components, but also give us clues as to the host Superficial and minor skin lesions are the primary infections environment. Surface components such as wall teichoic acids caused by S. aureus and the flow of golden pus gives relief to and the proteins ClfB and IsdA are required for nasal carriage the host and the prospect of dispersal to the pathogen. and act as adhesins to nasal squamous cells. ClfB and IsdA, That is not to say that the interaction between S. aureus like many other S. aureus surface proteins bind to more than and the human host during infection is not exquisite and one human ligand and so their true in vivo target cannot as highly evolved. S. aureus has a myriad of surface and secreted yet be defined (if a single target actually exists). TheisdA components able to react in the most intricate ways with gene is only expressed under conditions of iron deprivation almost every facet of the human immune and other bodily and so the nose must be iron-limited. aureus, suggesting that our resident age of approaches for the present, and Tarkowski, A. & Foster S.J. (2007). The systems. The organism is also extraordinarily adaptable in We also control S. aureus on our surfaces via the flora is battling it out for the prize of the future, that will at least alleviate Staphylococcus aureus surface protein IsdA being able to cause a wide range of different infections. S. production of bactericidal fatty acids and peptides. IsdA a human host. Thus S. aureus, whilst some of the burden. S. aureus cannot mediates resistance to innate defenses aureus has a large arsenal of virulence determinants, including is required for resistance to these factors and survival on it is a formidable foe, can be beaten by be eradicated from the human environ- of human skin. Cell Host Microbe 1, toxins, enzymes and adhesins. Apart from a very few specific live human skin. It is interesting that patients with atopic other lowly microbes. ment and it does not seek to eradicate 199–212. syndromes (such as toxic shock) it is impossible to label dermatitis often have altered fatty acid metabolism resulting us. By understanding more of the Lina, G., Boutite, F., Tristan, A., individual components as primary virulence determinants. in reduced levels of anti-staphylococcal fatty acids and Man against microbe basis of our interaction with S. aureus Bes, M., Etienne, J. & Vandenesch, It is more the skilful wielding and interplay of a variety of this correlates with enhanced S. aureus colonization. In The golden age of antibiotic discovery we are beginning to discover possible F. (2003). Bacterial competition for determinants drawn from its repertoire that allows S. aureus fact, application of anti-staphylococcal fatty acids results in is over and the inevitable rise in breakpoints to reduce the incidence of human nasal cavity colonization: role of to succeed so well across different infections. This in itself reduced colonization in these patients. Thus by harnessing resistance levels does not bode well infections and also to treat those once staphylococcal agr alleles. Appl Environ requires extraordinary powers of regulation in response to our own defence mechanisms we may reduce the prevalence for the future. S. aureus soon acquires established. Although S. aureus can be Microbiol 69, 18–23. the host environment. Many regulators have been identified of S. aureus carriage. The interaction of S. aureus and our skin resistance to new drugs, including a killer, with associated suffering, one but how these interact, particularly in response to the host fatty acids is even more intense, as at sub-growth inhibitory Takigawa, H., Nakagawa, H., Kuzukawa, linezolid and daptomycin. However, cannot but admire the tenacity and environment has remained largely elusive. concentrations the fatty acids are able to inhibit virulence M., Mori, H. & Imokawa, G. (2005). antibiotics will always remain a key tool versatility of one of the most intimate determinant production and so potentially allow survival of Deficient production of hexadecanoic in our armoury against S. aureus and it cohabitees of the human body. acid in the skin is associated in part with Living in harmony? the organism but render it benign. is essential that industry is encouraged the vulnerability of atopic dermatitis The primary niche for S. aureus is as a commensal living in The nose and skin are also inhabited by a range of other to keep new compounds flowing into Simon Foster patients to colonization by Staphylococcus our noses, on our skin and in the nasopharynx. In fact 20 % flora (see the article by Farrar & Bojar on p. 14) and it is the clinic. Alternative approaches such Department of Molecular Biology aureus. Dermatology 211, 240–248. of the human population are permanent carriers and 60 % interesting to note that nasal carriage by Staphylococcus as vaccines and therapeutic/prophylac- and Biotechnology, University of are transient carriers, which attests to the highly successful epidermidis or corynebacteria does not coincide with S. Wang, R., Braughton, K., tic antibody development have contin- Sheffield, Firth Court, Western Kretschmer, D., Bach, T.-H.L., ued apace, but all Phase III trials so far Bank, Sheffield, S10 2TN, UK Queck, S.Y., Li, M., Kennedy, A.D., Although S. aureus can be a killer, one cannot but admire have ended in failure. MRSA is high on (t 0114 2224411; Dorward, D.W., Klebanoff, S.J., the UK political agenda and the favour- e [email protected]) Peschel, A., DeLeo, F.R. & Otto, M. ed approach for control rests on cleaner (2007). Identification of novel cytolytic the tenacity and versatility of one of the most intimate hospitals. In truth, there is no one mea- Further reading peptides as key virulence determinants sure that will remove the MRSA problem. Clarke, S.R., Mohamed, R., Bian, L., for community-associated MRSA. cohabitees of the human body. It is by a concerted and integrated pack- Routh, A.F., Kokai-Kun, J., Mond, J.J., Nat Med 13, 1510–1514.

20 microbiology today feb 08 microbiology today feb 08 21 Microbial life in the mouth b A healthy human mouth. BananaStock / JupiterImages The variety of surfaces in the oral he oral cavity forms the top principally found only in this habitat. The soft tissues in the presence of sex hormones in the gingival crevicular fluid section of the gastrointestinal oral cavity lack significant plaque accumulation due to the (serum-like exudate that bathes the tooth/gum interface) is tract and provides a large rapid rates of epithelial cell turnover, the exception being the thought to drive this. Few changes have been observed with cavity offers a home to a whole range number of diverse surfaces on dorsum of the tongue which is associated with a significant further increases in age, except to note that loss of teeth and which a wide variety of complex and characteristic microbiota. The hard non-shedding therefore habitat will influence the microbiota. of microbial communities, as Dave biofilms is able to form. These surfaces of the oral cavity, i.e. teeth; provide a far more stable Tsurfaces include soft shedding tissues of substratum for the colonization of bacteria. Dental plaque Spratt describes. the buccal mucosa, papillae and crypts In a healthy mouth the only non-shedding surface available of the tongue and hard non-shedding Acquiring the oral microbiota for colonization is enamel (a hard, highly calcified tissue) of surfaces of the teeth. Dental plaque Colonization of the oral cavity begins at birth. Neonates the tooth surface. This surface is covered with a conditioning is the term commonly used for the are usually sterile, despite encounters with the maternal film or pellicle, derived from the saliva, within seconds of biofilm formed on teeth; however, the resident microbiota during birth. The acquisition of the cleaning and it is this surface which is rapidly colonized by term plaque has now been extended oral microbiota is via passive transmission from a variety of the bacteria in saliva (up to 108 per ml). The colonization to encompass biofilms on all the sources including food, milk, water and particularly saliva can be split into two broad processes, the initial attachment oral surfaces. These biofilms consist from the mother. However, the majority of these bacteria are of bacteria to the pellicle and the secondary attachment of of a complex microbial community present only transiently and only a limited range actually other cells to those already present. The process is far from embedded in a matrix of polymers of colonize. Streptococci predominate the primary colonization, random and cell-to-cell recognition of genetically distinct bacterial and salivary origin. especially Streptococcus salivarius and S. mitis. The richness partner cell types plays an important role in development More than 700 bacterial taxa have and diversity of the microbiota increase rapidly with age and of micro-colonies and subsequent biofilm architecture. been recorded in the oral cavity by the time the infant has teeth (6–18 months) numerous Co-aggregation interactions are thought to contribute or (although only 100–200 occur in any species are present. The microbiota becomes more complex perhaps drive plaque development. Early plaque accumu- particular mouth) and this rich and during puberty (12–16 years) and notable increases are lation is facilitated by intrageneric co-aggregation among diverse flora contains bacterial species observed in Gram-negative anaerobes and spirochaetes. The Streptococcus and Actinomyces species, as well as intergeneric

22 microbiology today feb 08 microbiology today feb 08 23 co-aggregation between these species. The partnerships recession of the gums. This is clinically and microbiologically Periodontitis refers to a group of between dental plaque bacteria are highly specific and lead distinct from crown caries. The disease has been shown to more advanced and related diseases to complex biofilms. These processes are likely to benefit the have a definite progression, each with its own characteristic defined as ‘an apical extension of individuals involved and may have nutritional or protective microbiology. In brief, initially the lesion is described as gingival inflammation to involve the roles. The plaque is therefore rich and diverse and contains ‘soft’ and consists of a highly demineralized tissue replete tissues supporting the tooth (perio- numerous microenvironments with a variety of gradients with bacteria (increased numbers of lactobacilli and Gram- dontal ligament and bone)’ and present, including nutrients, oxygen, redox potential and pH. positive pleomorphic rods, Actinomyces israelii and A. results in a periodontal pocket. By far The plaque is not only heterogeneous in nature but differs gerencseriae, but fewer streptococci). The progression of the the most common is chronic perio- depending on location on the tooth surface and indeed with lesion leads to a change in appearance and is categorized as dontitis which is the major cause of time. Mature plaque is therefore an extremely complex and ‘leathery’, consisting of a re-mineralized surface overlaying a tooth loss in adults. The microbiota highly dynamic community. heterogeneous mix of bacteria, de-mineralized tissue and re- present in the periodontal pocket is mineralized tissue. A further progression is to a ‘hard’ lesion extremely diverse, with up to 100 Unknown quantities which is fully re-mineralized and inactive with respect to culturable species from a single pocket. It has been estimated that only about 50 % of the oral caries (reduced numbers of S. mutans). Since such a rich microbiota is pres- microbiota can be cultivated. While this is a high percentage ent, trying to identify the particular spe- Root canal infections. Structures present in the mouth not compared to some other microbial systems, it still means cies responsible for disease initiation normally exposed to the microbiota are usually sterile, for that we have very little knowledge about half of the oral and progression is a very complex example, the endodontium – the pulp and root canal system microbiota. Culture independent techniques have clearly and difficult undertaking (especially within teeth. The root canals of teeth are complex systems made inroads in determining the richness of this proportion as probably only half of the taxa of interconnecting channels containing the blood vessels (mainly via comparative 16S rRNA gene sequencing) of the are culturable). However, the World and nerve tissue leading from the tooth apex to the pulp microbiota. However, it has only been very recently that Workshop on Clinical Periodontology chamber. Endodontic infections are therefore defined as techniques have allowed the metagenome and functions of has designated three species as aetio- infections of the pulp and periapical tissues. Bacteria and the whole community to be studied. logic agents of periodontitis in a sus- bacterial products can gain access to the pulp chamber, often ceptible host: Aggregatibacter (formerly Oral infections as a consequence of caries (demineralization of enamel and Actinobacillus) actinomycetemcomitans, Small alterations in an environment can lead to ecological dentine). The resulting inflammation will lead to pulpal Porphyromonas gingivalis and Tanner- shifts and subsequent population changes, and in certain necrosis and progress to resorption of bone supporting the ella forsythia (formerly Bacteroides specific cases this may predispose to a more ‘pathogenic’ tooth, finally leading to tooth loss. The bacteria associated forsythus). Numerous other types of microbial community. This concept is termed the ‘ecological with individual lesions are surprisingly limited given periodontitis exist and the microbiology plaque hypothesis’ and can be used to understand the the number of taxa potentially able to colonize and the of each is thought to be different. microbial aspects of a range of oral infections. large number of taxa associated with periodontal lesions. The oral microbiota is also responsible Dental caries and periodontal disease are some of the most This reduced diversity implies special selective pressures for a number of other oral problems prevalent infectious diseases of humans and are due to the operating within the root-canal system. Root-canal infections including oral malodour, thrush, angu- accumulation of dental plaque on the tooth surface and at are invariably polymicrobial in nature and typically 4–12 lar cheilitis, denture-associated erythe- the tooth gum interface respectively. bacterial isolates can be cultured. This microbiota is often matous candidosis, Candida leukoplakia diverse with respect to growth atmosphere, nutritional needs Dental caries. This is the localized demineralization of and median rhomboid glossitis. and virulence determinants and may be regarded as an ‘infec- the tooth tissue by various acids produced by bacterial tion team’. For example, primary colonization and adherence fermentation of dietary carbohydrates and is arguably In summary to dentine is carried out by streptococci which additionally the most common, chronic infectious disease in humans. Life on us and especially our oral micro- utilize oxygen, thus making the environment more anaerobic Approximately 90 % of all dentate adults in the UK have biota is complex, dynamic, rich and and therefore suitable for the colonization and growth of at least one restored tooth as a result of caries with a mean diverse. Changes in the community strict anaerobes. Commonly, isolates from infected root frequency of seven per person. Caries can be simply and structure brought about by environ- canals include streptococci, Actinomyces spp., Prevotella spp., conveniently split into two categories: coronal (crown) mental alterations cause a range of Peptostreptococcus spp. and Fusobacterium nucleatum. caries and root-surface caries. Coronal caries can occur on diseases, the ecology and pathology of all surfaces of the crown where the plaque biofilm is allowed Periodontal diseases. This broad group of diseases affects which remain, largely, unknown. to develop and mature. Demineralization occurs due to a the periodontal tissues (gums and supporting bone). The shift in the microbiota brought about by an increase in the most common of the periodontal diseases is gingivitis; this is Dave Spratt m Top. Mouth of a person reflecting a history of poor oral care: the gums are inflamed (gingivitis) and the lower incisor teeth are surrounded by deposits of tartar. Science Photo Library amount and frequency of dietary fermentable carbohydrates. usually brought about by poor oral hygiene. The microbiota Senior Lecturer, Microbiology Unit, The increase in acids, such as lactic acid, reduce the pH and their extracellular products present at the gum margin Division of Microbial Diseases, UCL m Lower left. False-coloured scanning electron micrograph of a cavity (lower centre) in a human to a level which only favours the growth of acid-loving cause a reversible (with good oral hygiene) non-specific Eastman Dental Institute, 256 Gray’s incisor. Cavities are caused by dental plaque (brown), a film of bacteria embedded in a microbes such as Streptococcus mutans, which is additionally inflammation of the gums. The plaque microbiota shifts from Inn Road, London WC1X 8LD, UK glycoprotein matrix. Steve Gschmeissner / Science Photo Library highly acidogenic. Root surface caries, as the name implies, a streptococci-dominated community to one dominated by (t 0207 915 1107; f 0207 915 1127; m Lower right. False-coloured scanning electron micrograph of Streptococcus mutans bacteria occurs on root cementum or dentine and is secondary to Actinomyces species. e [email protected]) (pink) in dental plaque. Manfred Kage, Peter Arnold Inc. / Science Photo Library

24 microbiology today feb 08 microbiology today feb 08 25 There are about as many I have finally cum to the konklusion that a good reliable set ov bowels iz worth more to bacterial cells in our bowel A lifelong a man than enny quantity of brains. Josh Billings (Henry Wheeler Shaw, as there are human cells in American humorist, 1818–1885) our body. Gerald Tannock ne can empathize, if not completely commitment concur, with the sentiment expressed in the quotation attributed to the fictional, takes a look at the amazing poorly educated, but commonsensical character Josh Billings. Constipation community of bacteria that and diarrhoea are both unpleasant con- to bowel Oditions reflecting bowel dysfunction, the latter often due helps to set the very young to the activities of pathogenic microbes. Little appreciated, however, are the legions of bacteria that normally reside in the large bowel of humans and which constantly toil to digest on a fit and healthy life. bacteria complex molecules derived from the diet (such as fibre) and alimentary secretions (such as mucins in mucus). In doing so, the bacteria produce short-chain fatty acids, gases, indoles, phenols and amines as fermentation products. The bowel bacteria, sometimes referred to as commensals because they share the banqueting table that we lay in the large bowel, form a complex community about which relatively little is yet known. Hundreds of bacterial species are probably able to inhabit the human bowel, but not more that 50 % of the bacterial cells, based on comparisons of microscopic and plate counts, have been cultivated so far in the laboratory. Much of our knowledge of the taxonomy of these bacteria has been gained by the use of nucleic acid-based analytical methods, most of which target 16S rRNA gene sequences that form a cornerstone of bacterial phylogeny. From the application of these methods, which are culture-independent, we know that four bacterial phyla dominate the bowel community (Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria) and that there are about 10,000-fold more bacterial cells in the average large bowel than there are human beings on Earth.

Early days Our lifelong commitment to feeding this large bacterial mass starts soon after birth when the bowel is apparently adventitiously inoculated with bacteria of environmental and maternal origins. Soon, a regulated and predictable succession of bacterial groups occurs in the bowel. Alone among mammalian species, the bowel community of human infants is dominated by Actinobacteria belonging to the genus Bifidobacterium which, by the time the baby is aged 3–6 months, comprise, on average, at least 40 % of the total bacterial community of stool, regardless of alimentation. These bacteria are especially endowed with the ability to c A false-coloured 3D CT scan of the abdomen of a 53-year-old patient, showing healthy intestines. detect and hydrolyse oligosaccharides, such as those found Zephyr / Science Photo Library in human milk, using tightly regulated catabolic pathways.

26 microbiology today feb 08 microbiology today feb 08 27 b Bifidobacterial cells viewed by scanning electron microscopy. Bar 1 µm. G. Tannock

Thus, during the first few months of Impact on allergies in stool collected from infants born in in relation to the normal in order to discover the means to ecology in general, and the bacteriology of the bowel in life, while immunological germinal Allergies (eczema, hayfever, asthma) countries with low or high prevalence heal. Thus medical knowledge focuses on the pathogenesis of particular. foci develop in the bowel mucosa, the are more common today among the of allergies, however, have revealed diseases and the derivation of intervention strategies. These The standing objection to botany (microbial ecology) bowel of infants is colonized by large inhabitants of affluent countries than differences. The exposure of infants to are noble causes, but while we know much about diseases, one has always been, that it is a pursuit that amuses the fancy numbers of bifidobacteria. they were 60 years ago, yet remain different kinds of bacteria in different wonders whether we really understand ‘health’. Defining the and exercises the memory, without inspiring the mind, or uncommon in poorer nations. What geographical regions of the World functional roles of bifidobacterial species in early life might Benefits for the bowel has changed in affluent countries that could be influenced by ethnicity and be illuminating in the contexts of both disease and health. advancing any real knowledge; and, where the science is mucosa could be responsible for this pheno- maternal diet, as well as the factors Francis Xavier believed that a Jesuit education until the carried no further than a mere systematic classification, the Commensals interact with the bowel menon? Doubtless there are thousands mentioned above. The bifidobacterial age of 7 prepared a child to live a useful Christian life in charge is but too true … Not that system is by any means mucosa, at least in experimental of possible correlations, including red species detected in the stool of allergic no matter what circumstances they later ended up in. to be thrown aside – without system the field of Nature animals, and in so doing influence herrings such as an increase in the babies compared to healthy infants has Modern educationists also understand that there are optimal would be a pathless wilderness – but system should be the expression of mammalian genes. number of telephones per head of also been reported to differ. The varying periods during childhood in which the ability to process subservient to, not the object of, pursuit. The up- or down-regulation of gene population, but there may be bacterio- compositions of bowel communities in certain information (visual, sound, numbers, language) Gilbert White, curate of Selborne, 1778 transcription as a result of bacterial logical possibilities worthy of investi- human populations are meaningless, can be acquired. While the commitment to maintaining a exposure may be transient, but the gation. The kinds of bifidobacteria that however, unless functional links to dis- bowel community is lifelong, critical beneficial interactions Gerald W. Tannock succession of bacterial types to which babies are exposed to now may differ ease or health can be made. Fortunately, with commensals may occur during early childhood. Later, Department of Microbiology & Immunology, University the infant bowel mucosa is exposed compared to 60 years ago. This might preliminary observations point to a the presence of bowel bacteria may be incidental or, with of Otago, 720 Cumberland Street, PO Box 56, Dunedin, could, in some instances, have long- be because of better hygiene, different differential response of immune cells increasing age and the development of chronic diseases, even New Zealand (t +64 3 479 7713; f +64 3 479 8540; lasting physiological, including obstetrical practices and the relatively to bifidobacterial species residing in malign. e [email protected]) immunological, ramifications as a common use of antibiotics in modern the bowel of infants, opening extensive Whatever your quantity of brains, you may find that the result of molecular communications paediatrics. We cannot investigate this opportunities for the investigation of bowel community, together with its activities, an exciting and Further reading between bacterial and human cells. possibility because we do not have bifidobacterial–eukaryotic cell cross- important field of research. The study of bowel commensals Gore, C., Munro, K., Lay, C., Bibiloni, R., Morris, J., Woodcock, This conditioning of the bowel mucosa bowel samples collected from infants talk in relation to health and disease. should concentrate on community function and interactive A., Custovic, A. & Tannock, G.W. (2007). Bifidobacterium during infancy, which may have born long in the past. Even if we did, mechanisms, avoiding subversion by the wiles of high pseudocatenulatum is associated with atopic eczema: a nested lifelong consequences, is integral to the the accuracy of the assay results might Bowel commensals and throughput sequencers and the creation of phylogenetic case-control study investigating the fecal microbiota of infants. J concept of ‘biological Freudianism’: the be compromised by the storage of the health catalogues. Note could be taken of the advice given by the Allergy Clin Immunol (published ahead of print). biological (bacteriological) past is alive samples over decades. Comparisons Medical science continues to be more naturalist and putative ‘father of ecology’, whose comments Tannock, G.W. (2005). Commentary: remembrance of microbes in the physiological present. of the bifidobacterial species present concerned with defining the abnormal concerning botany are equally relevant to modern microbial past. Int J Epidemiol 34, 13–15.

28 microbiology today feb 08 microbiology today feb 08 29 etrovirus infection represents perhaps the most (ERV) and they are replicated and inherited in a Mendelian b Common Gibbon (Hylobates lar). Many HERV integrations are also How many of our genes are actually present in the same genomic locus in other primates, a feature which intimate of all host–pathogen relationships. fashion along with all other nuclear DNA. has been used to date the time of germ-line infection. HERV-W is The replication of these viruses requires the Over the course of evolution, retroviruses have invaded the common to Old World primates (e.g. chimpanzees, gibbons and insertion of a DNA copy of their genome into germ-line of our ancestors on numerous occasions such that African green monkeys) but is absent from New World primates human in origin? David Griffiths and (e.g. squirrel monkey) and is therefore thought to have entered the chromosomal DNA of the infected cell. This human ERVs (HERVs) now comprise ~8 % of our genome. the germ-line around 25–40 million years ago, the divergence time process, known as integration, is essentially These can be divided into around 30 different families, each estimated from fossil records. Art Wolfe / Science Photo Library Cécile Voisset explore the fascinating irreversible and provides a means for stable, usually lifelong, representing a different ancestral infection event. The timing . False-coloured TEM of an ultrathin section showing a group of R HERV-K particles budding from a cultured human teratocarcinoma infection of the host. Moreover, if a retrovirus infects a sperm of their introduction into the genome ranges from over cell. HERV-K is the only HERV family known to encode assembled or egg cell, or their germ cell precursors, its genetic material 30 million years ago up to less than 1 million years ago, virions. These non-infectious particles are well characterized in cell impact of endogenous retroviruses in can become permanently fixed in the germ-line DNA of any depending on the family. Since HERVs represent ancient lines derived from testicular tumours. Some recent studies have resulting offspring. In this way, the retrovirus can persist infections, they are not closely related to retroviruses cur- suggested that HERV-K has been capable of re-infecting the human germ-line relatively recently (<100,000 years), raising the question in the host and its descendents for millions of years. Such rently circulating in humans, such as HIV. Instead, they have of whether a relative of this virus stills circulates as an infectious and on our bodies. inserted sequences are known as endogenous retroviruses greater sequence similarity with ERVs of animals. virus today. Klaus Boller, Paul-Ehrlich-Institut, Langen, Germany

Human endogenous retroviruses: from ancestral pathogens to bona fide genes

30 microbiology today feb 08 microbiology today feb 08 31 b Coloured TEM of a section through a demyelinated nerve in multiple sclerosis. The axon (blue) has only its Schwann cell (brown) surrounding it. The Schwann cell would normally produce the myelin sheath. A nerve’s myelin sheath helps it conduct electrical impulses and when the myelin sheath is lost, nerve function is impaired. Steve Gschmeissner / Science Photo Library

Consequences of endogenization for the virus Research on other HERV proteins has time that they entered our germ line, Because retrovirus infection is frequently pathogenic, any focussed on their potential role in cancer their infectious counterparts may have new introduction of ERVs is likely to be highly detrimental because a number of malignancies are been pathogenic viruses. As noted for the host. Therefore, to become fixed in a genome, a accompanied by increased production above, there are no HERVs closely newly endogenized retrovirus would probably be inactivated of HERV RNA and proteins. Some related to the infectious retroviruses to prevent its expression, for example through mutation or members of the HERV-K family, which currently infecting humans, although truncation of genes encoding viral proteins or by cellular integrated into our genome relatively ERVs related to lentiviruses have mechanisms such as the silencing of ERV gene expression by recently (~1–5 million years ago), can recently been described in rabbits. DNA methylation. In this way, endogenization of retroviruses express non-infectious particles. These Could it be possible in the future that leads ultimately to their inactivation and a reduction in patho- defective viruses are expressed in mel- HIV will be tamed by endogenization? genicity. Contemporary HERV families therefore consist of anoma, testicular tumours and myelo- numerous heterogeneous elements, ranging from full-length proliferative diseases, but whether David J. Griffiths defective proviruses to isolated long terminal repeats (LTRs) they are actively involved in triggering Principal Research Virologist, derived from recombination events. (LTRs are regions of the or promoting tumour development Moredun Research Institute, retroviral genome containing gene promoter and enhancer appears doubtful. It is perhaps more Pentland Science Park, Bush elements.) However, inactivation of ERVs may take many likely that they are up-regulated as Loan, Penicuik, Midlothian generations and the immediate effect of germ-line integration a result of other genetic lesions in EH26 0PZ, UK (t 0131 445 5111; can therefore be increased pathogenesis, which could the tumour cell. An exception may e [email protected]) potentially lead to the extinction of the host. In humans, be teratocarcinoma where a HERV-K the effects of HERV acquisition on our ancestors millions protein called Rec has been directly Cécile Voisset of years ago can only be a matter of speculation. However, implicated in activating transcription Postdoctoral Fellow, Inserm an epidemic of neoplastic disease currently afflicting koalas factors involved in cellular proliferation. U613, Faculté de Médecine et des in Australia represents a modern example of retrovirus As with syncytin-1 and MS, additional Sciences de la Santé, 29200 Brest, endogenization in action and provides a rare opportunity to research is necessary to determine its France (t +33 2 98 01 83 71; study this process and its effect on the host. direct border between maternal blood and foetal tissues, and in the aetiology of multiple sclerosis importance in tumour development. e [email protected]) While the vast majority of HERVs are defective, many are its formation and maintenance is crucial for a healthy preg- (MS). MS is a chronic inflammatory nevertheless transcribed as RNA in various tissues and in a nancy. Dysregulation of syncytin-1 expression could impair disease of the central nervous system, An infectious HERV? Further reading few instances HERV proteins or particles may be produced. placental morphogenesis and has also been linked with pre- characterized by the loss of the myelin In some species, such as pigs and Antony, J.M., van Marle, G., Opii, W., Butterfield, D.A., Mallet, F., Yong, V.W., The abundance of HERVs raises the question of what effect eclampsia. Syncytin-1 induces the formation of cell-to-cell sheath that surrounds and protects chickens, a few ERVs have escaped Wallace, J.L., Deacon, R.M., Warren K. their presence has had on the evolution of our genome fusion by interacting with its specific receptors, the amino neurons. The pathogenic mechanisms deleterious mutation and remain cap- & Power, C. (2004). Human endogenous and whether they have any function today. These topics acid transporters ASCT1 and ASCT2. In non-placental involved in MS are still unclear, but able of infectious transfer. In humans retrovirus glycoprotein-mediated have proved to be rather controversial, but recent work tissues, syncytin-1 expression is usually kept silent through inappropriate expression of syncytin- no such virus has yet been described. induction of redox reactants causes has provided some tantalizing evidence supporting roles in promoter methylation because inadvertent cell fusion 1 in astrocytes has been proposed to However, recent work by laboratories oligodendrocyte death and demyelination. normal human physiology and also in disease. could be deleterious for tissue organization and integrity. exacerbate the inflammatory events in France and the USA has recon- Nat Neurosci 7, 1088–1095. Syncytin-2, which has been characterized only recently, is within the brain and spinal cord by structed infectious forms of HERV-K Bannert, N. & Kurth, R. (2004). HERVs as bona fide human genes also expressed in cytotrophoblastic villous cells and may inducing inflammatory mediators such that represent the consensus sequence Retroelements and the human genome: Among the rare HERV-encoded proteins, syncytin-1 and serve a similar function in placental development. The as interleukin-1β (IL-1β) and reactive of the most recently acquired HERV-K new perspectives on an old relation. syncytin-2 are particularly interesting examples of how HERVs encoding the syncytin proteins are only present in oxygen species. These factors are viruses. The original HERVs are defect- Proc Natl Acad Sci U S A 101 (Suppl. 2), new functional genes may be acquired from HERVs in the primates; however, unrelated ERV envelope proteins in mice cytotoxic for oligodendrocytes, the cells ive for replication but the consensus 14572–14579. human genome. Syncytin-1 and syncytin-2 are glycoproteins and sheep have also been implicated in facilitating placental involved in myelin formation. What sequences, in which the effects of indi- Bieda, K., Hoffmann, A. & Boller, K. encoded by the envelope genes of specific proviruses of the cell fusion. Given the divergent placental structures between triggers the expression of syncytin-1 vidual mutations have been ‘averaged (2001). Phenotypic heterogeneity of HERV-W and HERV-FRD families, respectively. Of note, the these species and humans, this is a startling example of in the astrocytes is unknown but it has out’, are infectious. These viruses there- human endogenous retrovirus particles other viral genes in these proviruses are highly mutated, parallel evolution where unrelated retroviruses have been co- been shown that cytokines detrimental fore provide important tools for further produced by teratocarcinoma cell lines. suggesting that the genes encoding these envelope proteins opted to serve a conserved host function. to MS, such as tumour necrosis factor, analysis of the function of this ancient J Gen Virol 82, 591–596. may have been positively selected by providing some benefit interferon-g, IL-6, and IL-1 can activate virus and its potential role in disease. Boller, K., Schönfeld, K., Lischer, S., to humans. The key biological function of these two proteins Are HERVs still pathogenic? the syncytin-1 promoter, while the MS- Fischer, N., Hoffmann, A., Kurth, R. & is their ability to mediate the fusion of cellular membranes Although individual HERV proteins, such as syncytin-1 and protective cytokine interferon-β inhi- The future for HERVs Tönjes, R.R. (2008). Human endogenous to produce multinucleate cells or syncytia. Importantly, it 2, may serve a physiological role for the host, expression bits syncytin-1 expression. Why this HERVs have been with us and our retrovirus HERV-K113 is capable of appears that this function has been co-opted by the host to of HERVs has also frequently been linked with diseases, should occur in some individuals and ancestors for millions of years and it is producing intact viral particles. J Gen serve an important physiological function. notably autoimmune diseases and cancer. However, due not others is also unclear but common only recently that their abundance has Virol 89, 567–572. Syncytin-1 is expressed predominantly in placental cyto- to the ubiquity and abundance of HERVs, it has proved herpes virus infections of the central been recognized and their functional Stoye, J.P. (2006). Koala retrovirus: a trophoblast cells where it participates in their fusion to form difficult to confirm or refute a role for them in pathogenesis. nervous system have been proposed as significance begun to be elucidated. genome invasion in real time. Genome Biol the syncytiotrophoblast. This is a fused cell layer that forms the Nevertheless, recent evidence has implicated syncytin-1 a potential initiating factor. Whatever their function today, at the 7, 241.

32 microbiology today feb 08 microbiology today feb 08 33 meetings

Postgraduate Conference Postdoc and beyond – Meetings on the web Spring08 Edinburgh International Grants planning for a research career IrishBranch For up-to-date information on future These will be available, subject to the 2 April Spring08 Conference Centre Society meetings and to book online Are you a PhD student or first postdoc usual conditions. See www.sgm.ac.uk/ Regulatory mechanisms in see www.sgm.ac.uk nd wondering how to plan for your future? 31 March–3 April 2008 162 Meeting grants/pg.cfm host–pathogen interactions At this event short talks on strategies Meetings organization Offered poster to improve your chances of a career in National University of Ireland, The SGM meetings programmes are Plenary Registration presentations research will be followed by Q&A, a Galway – 27–28 March 2008 organized by the committees of the buffet and wine. Entry is free, but by Abstract submission – 29 February special interest groups, co-ordinated Bacterial secretion Registration is through the SGM Delegates whose offered posters have ticket only, so make sure you tick the Organizer Conor O’Byrne by the Scientific Meetings Officer, systems: commonality website (www.sgm.ac.uk/meetings). been accepted should note that an box on the booking form. If applying (e [email protected]) Professor Hilary Lappin-Scott. Registration fees per day (incl. lunch, area of 90 cm x 90 cm only is available and diversity for a PG conference grant, attending For details of Irish Branch activities Suggestions for topics for future refreshments, abstracts book, conference on the poster boards for their display. symposia are always welcome. 31 March–1 April 2008 the workshop qualifies you for over- contact Evelyn Doyle (e evelyn. literature, welcome reception) See p. 10 for contact details of night accommodation on Wednesday. [email protected]). Earlybird (up to 29 February 2008) Microscence Noticeboard Conveners. Hot topic Ordinary Members* £45 At the meeting, a board will be set Social events Administration of meetings is carried Student/Associate Members* £25 up with notices of job, postdoctoral out by Mrs Josiane Dunn at SGM Microbes and climate Monday 31 March Non-members £115 positions, studentships, courses, Headquarters, Marlborough House, change Welcome Reception Retired/Honorary Members Free conferences, etc. Contributions are Basingstoke Road, Spencers Wood, 2 April Full (after 29 February 2008) welcome and may be brought to the Get to know your fellow delegates OtherEvents Reading RG7 1AG (t 0118 988 1805; over a glass of wine on the first f 0118 988 5656; e meetings@sgm. Ordinary Members* £55 meeting or sent beforehand to Janet evening of the conference. ac.uk). Programme Booklet Student/Associate Members* £35 Hurst ([email protected]) Ceilidh & Supper (entry by ticket only) A booklet giving full details of the Non-members £125 Federation of Infection Offered papers & posters programme is enclosed with this Retired/Honorary Members £10 Special events Tuesday 1 April Societies Conference Many Groups organize sessions for issue of Microbiology Today. Any *Please note: to qualify for earlybird Communicating microbiology Society Dinner (at the Hub) Cardiff – 1–3 December 2008 the presentation of short oral papers changes will be posted on the rates, 2008 membership fees must be 31 March – Workshop A 3-course meal with inclusive wine e [email protected] or allow intercalated papers within SGM website. paid by the deadline of 29 February. 1 April – Display and pre-dinner drink. their symposia. Offered posters are Microbes: then, now and welcome at all Society meetings. hereafter Offered posters Fuels and chemicals from Other symposia IUMS Istanbul Each poster should be associated Autumn08 Trinity College Dublin renewable feedstocks Innate immunity systems Meetings of the three divisions either with the Plenary topic or with Fermentation & Bioprocessing rd Cells & Cell Surfaces/Microbial of the International Union of a Group. The subject content of the 8–11 September 2008 163 Meeting Group Infection Groups Microbiological Societies 2008 latter should be relevant to the remit Organizer: G.M. Stephens Organizers: I. Henderson & 5–9 August of a Group (see website for details); Bacterial adhesion within the it does not have to relate to the topic Plenary Bacterial biofilm structure and A. Cunningham XII International Congress of food and beverages industry of the Group Symposium taking Behaviour of biofilm organization Biofilm infection of medical Bacteriology and Applied Food & Beverages Group place at a particular meeting. General P.B. Rainey New Zealand devices Microbiology bacteria: from cooperation Organizers: C.E. Rees & Offered Posters will not be accepted. P. Stoodley USA Clinical Microbiology Group XII International Congress of and communication to T.G. Aldsworth Abstracts K. Sauer USA Organizers: D. Mack & M. Tunney Mycology control Sealed membranes: the Titles and abstracts for all J. Webb Southampton 10–15 August 8–9 September 2008 Infective endocarditis structural basis of transport and presentations are required in a Organizers: G.M. Gadd, H.-C. Flemming Germany Clinical Microbiology Group energetic processes VIV International Congress of standard format and should be P.S. Handley, P.R. Langford, T. Tolker-Nielson Denmark Organizers: S. Lang & D.R. Ready Physiology, Biochemistry and Virology submitted through the SGM website. H.M. Lappin-Scott, M.M. Tunney, Biofilm communication, resistance Industrial bioremediation: from Molecular Genetics Group Deadlines Deadlines for submissions are published in Microbiology Today and M. Upton & J. Verran and control contamination to clean-up Organizers: F. Sargent & G.M. Fraser Abstract submission: 31 January 2008 on the web. For further information Environmental Microbiology Group / Contact details of organizers are Early registration: 1 April 2008 S. Molin Denmark contact the Events Administrator. Speakers Irish Branch M.R. Parsek USA included in the meeting programme www.iums2008.org Biofilm basics Organizers: R. Howarth, C. Whitby on the SGM website. Deadline for Abstracts Book P. Kolenbrander USA J. Verran Manchester & E.M. Doyle receipt of titles and abstracts for Molecular Biology of The full text of the abstracts book D.A. Spratt London H.M. Lappin-Scott Exeter Packaging of nucleic acids offered presentations: 9 May 2008. Archaea for the Federation of Infection A. Mc Bain Manchester G. Seymour New Zealand Eukaryotic Microbiology Group A poster to promote the meeting is St Andrews – 19–21 August 2008 Societies Conference 2007 is M. Upton Manchester M. Givskov Denmark Organizers: M.L. Ginger & enclosed with this issue. Please display www.biochemistry.org/meetings available as a PDF file at www.sgm. ac.uk/meetings/past.cfm A.H. Rickard USA P. Gilbert Manchester S.K. Whitehall it in your department. Biochemical Society / SGM

34 microbiology today feb 08 microbiology today feb 08 35 schoolzone

Schools Membership costs only £10 a year. Benefits include b Artwork of a cross-secion through human skin. BSIP Estiot / Science Photo Library

Microbiology Today, advance copies of new teaching resources Second, pilosebaceous follicles Body odour and discounted fees on SGM INSET courses. To join see (each containing a sebaceous gland During puberty hair starts to grow and a single hair) become blocked, www.sgm.ac.uk/membership. Enquiries: [email protected] in your armpits and, as if this isn’t often due to the over-proliferation bad enough, body odours start or go to www.microbiologyonline.org.uk for full details of of skin cells called keratinocytes. wafting around. BO is caused by Sebum and bacteria become trapped resources and activities. volatile waste products released by in the follicle and the bacteria cause bacteria such as Corynebacterium In recent months science teacher Gemma Sims has been working an inflammatory immune response, jeikeium that feed off the dead cells, resulting in a spot. at the SGM to produce multimedia microbiology resources for Epidermis sebum and sweat that stick to the skin We all produce sebum and have and hairs. The problem can easily be the new Biology A-levels coming on stream in England and bacteria on our skin, so why are alleviated by daily washing and the Wales this September. Most of her efforts have been devoted some people more prone to acne use of deodorants (which are often to explaining the microbial science that students will need to Dermis than others? The answer is not clear, antibacterial). Sebaceous but influential factors may include understand to follow the courses, but the resource also aims gland genetics (something you can blame to have ‘added value’ and put microbes into the your parents for), hormones (girls Fungi often find it is linked to their Fungi can also colonize the skin, context of real life. Further information about the periods) and stress. generally causing no harm, but some whole teaching pack will be available in the May The good news is that acne is species can cause infections such as issue of Microbiology Today. treatable and usually goes away in ‘athlete’s foot’. This can cause itchy time (only 10 % of acne sufferers and cracked skin, but can easily be The following article is a taster for a resource we Pilosebaceous Sweat still have it after the age of 25). Ask treated with an antifungal cream. The follicle are developing for Key Stage 4 and 5 Personal, Social gland your pharmacist about an effective fungi are spread by direct contact and they particularly like the warm, moist, Health and Economic Education (PSHE). ‘What your over-the-counter cream called Nerve benzoyl peroxide and, if this does sweaty bits between your toes, so mum might not know and probably hasn’t told you’ will not help, your doctor can prescribe a make sure you dry them thoroughly, deal with some of the health issues that affect teenagers. variety of suitable medications. wear clean socks and avoid sharing towels. The fungus Malassezia globosa lives on the scalp and can The skin Acne myths cause dandruff, but don’t worry, an Acne antifungal shampoo will soon clear it d Acne is not caused by poor hygiene Microbes 12 up. Ask your pharmacist for advice The skin is home to 10 bacterial (‘blackheads’ contain the pigment cells, the most common being about suitable products. melanin, not dirt). Propionibacterium acnes. Just before and puberty: puberty your body starts to release d Acne is not linked to any specific The vagina foods, e.g. chocolate. sex hormones. One of their effects Before puberty the vagina is alkaline is to stimulate the production of an d Wearing makeup is OK (and is and contains bacteria such as oily substance called sebum from sometimes necessary for your self a teenager’s enterococci and coliforms, but during sebaceous glands below the surface confidence), but make sure you puberty the environment of the vagina of the skin. In some people this can use non-greasy (‘non-comedonal’) changes. Secretions of sticky mucus lead to the most common skin products and that you remove it fully. encourage the growth of the bacterium guide disease: acne. Adults may tease To squeeze or not to squeeze? Lactobacillus acidophilus which feeds on you about your zits, but acne is no If there is an obvious white ‘head’ that glycogen and produces acidic waste. laughing matter. 80 % of adolescents Being a teenager can be so horrible that many adults fungi and protozoa. They live in your gut, mouth, skin, resembles an erupting volcano then a This results in a vaginal pH of 4 which suffer from it and it can cause scarring (especially teachers and parents) have wiped its ghastly vagina, upper respiratory tract and urethra, and each of gentle squeeze is fine. But remember, deters other bugs, but if the natural and serious emotional distress. memories from their minds. It is easy to feel lonely and us has our own unique collection. They help digestion, your hands can be a source of infection flora of the vagina is disrupted (e.g. Inflammatory acne, with its unsightly isolated, but don’t worry, you are not alone: there are over synthesize vitamins, boost immunity and occupy niches (wash them first) and incorrect after taking antibiotics), less welcome pustules is by far the worse type. 10 times the numbers of microbes living in and on you than that would otherwise be filled by pathogens. Puberty is a squeezing can push the sebum further visitors can thrive. Vaginal thrush, there are human cells in your body. You are home to time of change, both physically and emotionally, and this But what causes it? into the follicles, exacerbating the for example, is caused by the fungus a complex community of bugs such as bacteria, viruses, affects your microbes too… Three factors conspire: first, there is an inflammation and leaving a scar. Candida albicans. Symptoms include over-production of sebum. a burning or itching sensation and a

36 microbiology today feb 08 microbiology today feb 08 37 thick yellowy-white discharge. It is bladder. You also need to urinate Judged by the students’ comments extremely common (75 % of women frequently (but not much comes out), and from the highly reproducible get it) and it can be easily treated by your urine may be dark or bloody Summer in the city data obtained during the 3 weeks, the over-the-counter antifungal drugs. and you could have a fever and pain To foster the interest of young people in science and to encourage summer school was a great success. The volume and consistency of in your lower back or pelvis. The The young scientists enjoyed learning mucus changes throughout the immune system usually clears the their study of microbiology, 15 talented A-level students were invited about fungi, carrying out a project that menstrual cycle, and each woman infection, but your pharmacist can to take part in a three-week Summer School at The University of would help and inform other scientists is different. If you notice secretions give you medication to ease the and, perhaps most importantly, Manchester. Sue Crosthwaite describes the event. which are different for you, especially symptoms and drinking cranberry meeting like-minded students. To keep if they are accompanied by an juice really does work (there is Students investigated the ‘one astonishing pictures of enormous their interest burning, the SGM sent unpleasant odour, itchiness or pain, evidence that it prevents bacteria gene–one enzyme’ model organism fermenters in which Aspergillus niger is each of the students an information then see your doctor immediately. sticking to the walls of the urethra). Neurospora crassa, a key eukaryotic grown for the production of citric acid. pack on careers in microbiology, and a These could be symptoms of thrush, If it is your first attack of cystitis or if microbe that plays an important This was followed by a memorable copy of the latest issue of Microbiology bacterial vaginosis, a sexually symptoms last more than 3 days, you role in elucidating gene function. By talk given by Dr Christian Heintzen Today. transmitted infection or a forgotten must see your doctor. If not treated monitoring and recording the growth, (Manchester) centred around the use The project was supported by the tampon (yes, it does happen!). the infection could move up to the morphology and colouration of 100 of model organisms in basic research, National Institute of General Medical bladder or kidneys. Neurospora strains for which genes of in particular the use of Neurospora Sciences (USA), Leica Microsystems UK The urinary tract unknown function are deleted, the for the study of circadian clocks. A Ltd and The University of Manchester. The urethra (the tube that carries Preventing cystitis students contributed to a community highlight was a visit from Professor urine from the bladder) contains Girls effort that aims to characterize Nick Read (Edinburgh) whose Sue Crosthwaite bacteria such as staphylococci, phenotypically all available Neurospora presentation on The Dynamic Hypha (e susan.k.crosthwaite@ d After a poo, wipe from front to back enterococci and corynebacteria. knockout strains. Excitement included some stunning movies of manchester.ac.uk) (to avoid spreading faecal bacteria); Sometimes other bacteria invade, grew when several of the strains modern molecular imaging techniques causing the condition cystitis d Don’t let yourself become displayed interesting and unexpected and the use of laser tweezers in the (urethritis). Sorry girls, but you are dehydrated – drink 2 litres of water phenotypes. The students captured study of cell–cell communication. more likely to suffer than males. per day; images of the colonies as well as high m The thrush fungus, Candida albicans. Dr Jayne Brookman’s Bioscience for Women have a shorter urethra and d Avoid perfumed hygiene products Eye of Science / Science Photo Library magnification pictures of the hyphae, Business talk on fungal disease, which because its opening is close to the that can irritate the urethra; which occasionally revealed stunning incorporated some particularly b changes in morphology. All the anus it is easily infected by faecal d Urinate after sex (as soon as is False-coloured transmission electron unsavoury images of the symptoms bacteria. To put it bluntly, the micrograph of Escherichia coli. Dr Linda data were uploaded to The BROAD of fungal infections, was especially polite!) to ‘flush out’ any bacteria. Stannard, UCT / Science Photo Library symptoms feel like you are weeing Institute database, from where they well-received! The lectures concluded concentrated sulfuric acid while a Boys now can be accessed worldwide. with a talk from Dr Eileen Paul herd of elephants tap dance on your d You can get cystitis too, but it is Taking it further The practical work was accompanied (Northbank Communications) on less common. It could be linked Eady, A. & Bojar , R. (2001). Spotting by lectures on various topics revolving the role communicating science to dehydration or a problem with the onset of puberty – the secret’s in the around fungal biology. Dr Geoff to different sectors of society can the urinary system. Go to the skin. Microbiology Today 28, 178–181. Robson (Manchester) introduced play in promoting the success of doctor! (www.sgm.ac.uk/pubs/micro_today/ the students to the use of microbes biotechnology and life-science-based pdf/110104.pdf) in biotechnology and showed some industries. Conclusion Spinney, L. (2007). Bugs R Us. New Scientist 2617, 34–38. Despite the fact that your microbes can cause embarrassing and irritating Websites In brief conditions, most of the time their General health: presence is beneficial. If you are www.nhsdirect.nhs.uk Education Show Science in School concerned about any health matter, www.embarrassingproblems.co.uk Birmingham NEC, 28 February–1 March 2008 The latest issue of this quarterly European magazine, don’t suffer in silence and hope it will Acne: SGM will be showcasing some new resources at the supported by the EU, is now available. go away: talk to someone! Your GP, www.stopspots.org Education Show this year. Representatives from member It is published by EIROforum and based at the European pharmacist or school nurse will know Cystitis and urinary problems: schools must be sure to visit Stand U29, where a warm Molecular Biology Laboratory in Heidelberg. The content what to do and the links on the right www.cobfoundation.org welcome will await. There will be something for everyone, includes teaching materials, cutting-edge science, education may be useful. Sex and sexual health: with a completely new version of The World of Microbes for projects, interviews with scientists, resource reviews and www.brook.org.uk KS 2 and 3 available to take away and demonstrations of the much more. The print version is in English, but multilingual Gemma Sims www.ruthinking.co.uk multimedia A-level microbiology teaching pack. To register versions are available online. Subscriptions are free at (e [email protected]) www.mariestopes.org.uk for the event, see www.education-show.com www.scienceinschool.org

38 microbiology today feb 08 microbiology today feb 08 39 gradline

Gradline aims to inform and entertain members in the early for another few months or years, but postdoctoral research SGM and you is not a permanent career and has a fairly short shelf life. SGM is committed to supporting career development of stages of their career in microbiology. If you have any news For this reason careful career planning is essential for early career microbiologists and offers a range of activities. contract researchers. If you work in a poorly funded area, For many years we have been closely involved with the or stories, or would like to see any topics featured, contact you may not have the cushion of a well-resourced lab and Life Science Careers Conferences. In recent years SGM has it is even more important to develop a clear career strategy. Jane Westwell (e [email protected]). taken a lead role in organizing the conferences and carries Roberts money has funded a range of activities for contract out much of the background work. In addition to this, last researchers in universities. Some supervisors recognize their November Jane Westwell and Lucy Goodchild from the responsibility to research staff in their teams; others may be External Relations Office travelled to University of Leeds, less encouraging. Whatever your situation, you owe it to KCL and University of Bristol where the events took place. yourself (and it is your right) to take every opportunity to develop your career. Undergraduate and postgraduate students from all branches of bioscience had the chance to listen to speakers The Career Word from a variety of career pathways. Talks included R&D UKGrad in the pharmaceutical industry, teaching in schools, IP A major initiative to support UK-based postgraduate management, planning for an academic career, clinical You are busy with your research and the Roberts money was directed researchers is UKGrad (www.grad.ac.uk). One of its most sciences and CVs, interviews and job hunting. Refreshment if you focus all your energy onto the towards centrally funded activities, successful activities is the long-running programme of and lunch breaks gave an opportunity to network with the work in hand the future will look after the rest was allocated to institutions personal development courses for postgraduate students, speakers, learned societies and employers. Some delegates itself – right? … Well not really, unless with research council funded staff commonly known as GRADschools. There are two types of took part in a CV clinic where they received feedback you have a fairy godmother who and postgraduate students. Your course: those organized on a regional basis and tailored to on their CV in a one-to-one session with an experienced specialises in careers and, to be honest, university almost certainly offers the needs of local students who can attend free of charge reviewer. The SGM exhibition stand was laden with copies they are fairly thin on the ground. postgraduate skills training that was and, alternatively, national GRADschools that are organized of Microbiology Today and our careers information sheets. developed in response to the Roberts by the central office and take place at a number of locations Luckily, universities, funding bodies, Regular attendees at the SGM Spring meeting will know Review. Do you take full advantage throughout the UK. The courses last 3 or 4 days and offer learned societies and professional that we always arrange a skills development session for of the courses and workshops that a chance to take a step back from your research and focus associations all recognize the need to early career microbiologists. 2008 will be no different and are on offer? Or do you reluctantly on transferable skills such as networking, communicating support scientists early in their careers we will be running a session entitled Postdoc and beyond – traipse along to one or two of them and team-working. The courses give vital breathing space and between them they provide a planning for an academic career. We will focus on three main to keep your supervisor quiet? Maybe and participants have a chance to reflect on their experience whole range of activities to support themes: getting published, getting funded and getting that the programme in your university and to start to think about career options. Most students early-career scientists. We take a look elusive lectureship. After the presentations the speakers is not well publicised – if not, it is return to their research feeling revitalized and with increased at a few here that are particularly will be glad to answer questions from the audience and a good idea to check out what is motivation. relevant to microbiologists. we expect that the usual lively discussion will follow. The available. A quick survey of university Students who are funded by a research council or the evening will end with drinks and a buffet. websites, revealed workshops on Wellcome Trust are entitled to a funded place on a national As you can see, there is plenty of opportunity to attend R is for Roberts… a range of topics including science GRADschool. The SGM is aware that this leaves a large courses and workshops tailored to the needs of 21st century …or more precisely the late communication skills, getting the number of microbiology researchers with no obvious means research microbiologists. These are only a starting point; Sir Gareth Roberts who led a most out of conferences, managing of financing a place. As a result, the Society launched the there are also a number of websites offering advice, shared government-commissioned review of your supervisor and surviving your GRADschool grant scheme and since 2007 we have been experiences and points of view. University career advisory UK science and published a report in viva. These workshops may not seem offering postgraduate student members of the society grants services are often undervalued by postgrad and postdocs, 2002. The Roberts review identified, directly relevant to your current to cover the full fees of a national GRADschool course. but can be an excellent resource. among other things, a mismatch situation and perhaps you view them Eligible students must have been members of the SGM for between the actual skills of graduate as a distraction from your research. more than three calendar months, in the final or penultimate There is lots of support and advice out there just waiting to and postgraduate scientists and the However, a PhD does not guarantee year of their studentship and be funded by organizations be used so why not make time for yourself in 2008 to think skills employers wanted. The report you a job and you can improve your other than the Wellcome Trust or a research council. We about where you are heading in your career. recommended a range of measures employability by recognising and allocated a handful of grants in 2007 and are hoping to Jane Westwell, External Relations Office to improve this situation. In response developing your transferable skills see an increase in uptake in the coming year. It is a golden the Government made £20 million to present alongside your valuable opportunity to attend a fabulous course, if you are eligible to Useful websites funding (Roberts money) available to research experience. apply for a grant you have nothing to lose – go for it! www.biocareers.org.uk – microbiology careers website implement a programme of activities. As a postdoctoral researcher, in www.grad.ac.uk – UKGrad, resources for postgraduate The emphasis for postgraduates an established and well-funded GRADschool participant comment: students including information on GRADschools being on employability and on career laboratory, it is easy to drift from one ‘I was able to put my own research into perspective. I found planning for postdoctoral scientists. contract to another. Sometimes last- www.npc.org.uk – National Postgraduate Council working and exchanging ideas with fellow students really So much for the brief history lesson – minute funding comes through and sciencecareers.sciencemag.org – articles, advice on all rewarding.’ how does this affect you? Some of you can put off the inevitable decision aspects of science careers

40 microbiology today feb 08 microbiology today feb 08 41 Science vs science communication – a fine balance Gemma Walton is a postdoc at University of Reading. She has a keen interest in science communication and public engagement but hasn’t yet made the decision to abandon research. In the meantime she takes every opportunity to have fun with the communication activities and gain useful experience.

You appeared on TV – how did suppliers to actually putting the Q that come about? display together on set-up day. The My PhD supervisor was approached visitors were from all walks of life – by the BBC to help with a programme from school children to retired in The Truth About Food series. He professors. We had a lot of interest suggested I do it since I had some with many people wanting to know Profile spare time after completing my thesis. more about their guts. The great thing about promoting this topic is that Name Gemma Walton What was it like being everyone can relate to it. Age 27 Q on TV? What transferable skills did you Present occupation Research Fellow It was amazing! I was involved in gain from this? (gut microbiology), University of the design of an experiment which Q Reading essentially was feeding pre- and The obvious ones are organization and Education University of Reading, PhD probiotics to a bunch of cowboys to communication skills, but I would Food Bioscience (looking at whether look at their effect on gut health. I had say that I really developed my project prebiotics may offer some protection to fly out to Colorado for some of the management skills. Co-ordinating against colorectal cancer through filming; everyone was really friendly, the timely production of the display changing the bacteria within the material, freebies and accompanying colon and their metabolic activities); so I was very much at ease and it was great to see what goes on behind literature was a massive task although Coventry University, BSc Biological my colleagues made a big contribution Sciences. the scenes on a production. Back in Reading they did some more filming in too. What appeals to you about the lab. Fiona Bruce interviewed me; Have you taken up any training Q communicating science? she was also very friendly and down- Q opportunities? It’s a great way to help people to to-earth, making it a great experience. During my PhD, I attended a Life understand why things happen. It’s I had plenty of opportunity to develop Science Careers Conference to find about taking concepts that people may communication skills, especially in the out more about career options. I also not grasp and trying to relate them to US where pre- and probiotics are not took part in Royal Society science life in a way that can be understood. well known. communication training course prior How do you balance your research What else have you been involved to the summer exhibition. Q commitments with science Q with? What aspect of your work gives communication activities? In 2007, our research group was Q you the most job satisfaction? In a way the two can go hand in selected to display our research at In terms of my research getting hand. The communications I have the Royal Society Summer Science results in projects is very satisfying. done to date have related to my Exhibition. I was heavily involved But I do also really enjoy science research field – you have to find a little in putting the stand together – from communication tasks. Being able to extra time to do these; but it’s working with designers, editing do both of these things in one job is an enjoyable part of the work. the publicity leaflets, liaising with great.

42 microbiology today feb 08 hotoffthepress

Science writer Meriel Jones takes a look at some recent A novel amniotic pathogen they consider that any difference over 3 % is significant. The similarity between the two strains and the closest named papers in SGM journals which highlight new and exciting Lawson, P.A., Moore, E. & Falsen, E. (2008). Prevotella bacterium was 95.3 %. These bacteria were members of the amnii sp. nov., isolated from human amniotic fluid. Int J Syst Bacteroides–Prevotella–Porphyromonas group and the two isolates developments in microbiological research. Evol Microbiol 58, 89–92. were especially close to members of the genus Prevotella. Many Researchers from Göteborg, Sweden, and Oklahoma, USA, species of Prevotella have been isolated from people, from the have identified a novel species of bacterium from human mouth and from both healthy and infected tissues in the pelvic amniotic fluid. The bacteria were first recovered in 1999 from region. The rRNA sequence of the two isolates and the range Alcohol hand rubs increase growth of Acinetobacter fluid that was described as turbid and ill-smelling. Similar of sugars and other chemicals that they were able to synthesize were different from all known Prevotella species. The closest Edwards, J., Patel, G. & Wareham, D.W. (2007). Low concentrations of bacteria were found again in amniotic fluid in 2006 and the relative was Prevotella bivia which was first identified in the commercial alcohol hand rubs facilitate growth of and secretion of extracellular authors have now worked out exactly what sort of bacteria they endometrium and has frequently been detected in patients with proteins by multidrug-resistant strains of Acinetobacter baumannii. J Med Microbiol are. The cells will only grow in the absence of oxygen, which pelvic inflammatory diseases. 56, 1595–1599. makes working with them rather difficult. The researchers first tried out the standard biochemical identification tests used with In addition to these two bacterial strains, the researchers The medical profession continues to be haunted by serious bacterial infections anaerobic bacteria, then commercial bacterial identification kits realised that several studies that had simply isolated DNA acquired within hospitals. If the bacteria can survive antibiotics, as in the so-called and finally they analysed the fats within the bacteria and the from the vagina of healthy women had recovered the same multidrug-resistant strains, treatment can be very difficult. The classic measure sequence of one gene. DNA sequence. It therefore looks like Prevotella amnii may be of good hand hygiene can reduce infection rates by 10–50 %, so hospitals have A comparison of the sequence of the rRNA gene from the present all the time among the bacteria that inhabit the healthy introduced ways for staff to clean their hands frequently without suffering from two isolates proved they were highly related to each other vagina. However, in some circumstances its numbers increase chapped skin. These include using alcohol-based hand rubs (ABHRs) dispensed because the genes were 99.5 % similar. This gene is chosen and it can become a pathogen. The fact that the researchers from a pump adjacent to patients’ beds. These are solutions of ethanol or for taxonomic studies because it changes very slowly over have now discovered ways to identify this species means that isopropanol, often in combination with an antiseptic and moisturiser which time. As a result, although researchers cannot give a precise routine hospital laboratories can be more confident in their are less irritating to skin than soap. correlation between a species definition and rRNA similarity, identification of new opportunistic bacterial pathogens. Although studies have shown that ABHRs reduce infection rates, they are not effective against all bacteria. One example is the spores of Clostridium difficile that Something in the air can cause very serious gastrointestinal infections. Now, Justin Edwards, Geeta Patel and David Wareham from Barts and The London NHS Trust and the MRC Ogata, N. & Shibata, T. (2008). Protective effect of Clincal Sciences Centre of Imperial College London have found evidence that low low-concentration chlorine dioxide gas against influenza A concentrations of ABHRs enhance in vitro growth of Acinetobacter baumannii, an virus infection. J Gen Virol 89, 60–67. opportunistic pathogen of critically ill patients. ’Flu, caused by the influenza A virus, is a continuing A. baumannii has emerged in recent years as an important cause of ventilator- health problem. It infects around one-fifth of the world’s associated pneumonia and blood infections in patients with burns, population yearly, causing symptoms that range from very immunosuppression and critical illness. Many strains also turn out to be resistant minor to a severe illness. Indeed, ’flu is a factor in the death to many antibiotics so that treatment is extremely difficult. The bacteria have a of around half a million people every year. Some pandemic remarkable ability to persist on surfaces in the hospital environment and are spread strains have caused more severe mortality, such as the 1918 by the hands of hospital staff so that hand hygiene is the key factor in preventing pandemic that killed 20–50 million people worldwide. these infections. Measures to counteract ’flu include vaccination, which only has short-term and partial success, and antiviral drugs, wondered whether even this low level could be useful against The researchers therefore tested whether low concentrations of commercially which all have drawbacks, such as toxicity to the sufferers the ’flu virus. available ABHRs could affect the growth of multidrug-resistant A. baumannii. and the emergence of resistant influenza strains. Depending on the growth medium, the presence of 0.01–1 % ABHR resulted in They arranged for small groups of mice to inhale a ’flu aerosol increased growth of A. baumannii. In contrast, a hand-cleaning product that was The ’flu virus is spread in the air as patients cough and for 15 minutes, counted the number of virus particles in the free of alcohol and relied on strong detergents to kill bacteria did not support sneeze. Researchers at the Taiko Pharmaceutical Co. Ltd lungs of the mice and recorded their health 16 days later. The the growth of A. baumannii at all. in Japan have been wondering whether there is a way to air breathed by half of the mice also contained about 0.03 deal with the virus when it is in this airborne form, so p.p.m. ClO gas. This gas reduced the number of virus particles m A hospital hand wash. How effective The researchers then investigated the proteins secreted by A. baumannii as it 2 reducing the opportunities for infection. There are many by over 1000-fold 3 days later and all the mice were alive are alcohol-based hand rubs against grew because previous work has shown that low concentrations of ethanol increase chemicals that are very effective at killing viruses, but 16 days later. In contrast, seven out of the 10 mice that had Acinetobacter baumannii? Mark Thomas / the virulence as well as the numbers of A. baumannii. They discovered that OmpA Science Photo Library most are also toxic to people. The researchers investigated inhaled the viral particles alone had died. The ClO gas had to was a major secreted protein, along with another protein with an unknown role. 2 chlorine dioxide (ClO ) gas, which has a well-known and be present at the same time as the virus in the air; breathing c OmpA is well known and may help the cells take up ethanol as a food source when 2 A crowded public space. Could the very effective antimicrobial action when dissolved in water. it even 15 minutes later completely cancelled the protective addition of chlorine dioxide to the air in other nutrients are in short supply. It may also help the bacterial cells sense each It has been used to disinfect public supplies of drinking effect. The reason was that the gas damages proteins on the public buildings help to prevent the spread other and form films on surfaces. of influenza? Jupiter Images water since the 1950s and is also used in food industries. Air outer surface of the virus that are essential for attachment to

The findings of this paper are certainly interesting, but their clinical significance containing low levels of ClO2 is considered safe to breathe, mammalian cells to start an infection. The authors suggest that

remains unclear. However, if low concentrations of ABHRs do indeed exist in the with the US Occupational Health and Safety Administration ClO2 gas could therefore be used to disinfect the air in places clinical environment, this work may have implications for those hospitals currently setting an upper limit of 0.1 parts per million (p.p.m.) for such as airports, hotels, offices and schools without the need to

experiencing outbreaks of A. baumannii. ClO2 in the workplace. Norio Ogata and Takashi Shibata close the buildings and thus disrupt the flow of normal life.

44 microbiology today feb 08 microbiology today feb 08 45 b A 19th-century tuberculosis ward. This is the Haskoy Hospital for Women in Constantinople (present-day Istanbul), then the capital of the Ottoman Empire. Tuberculosis (TB) is a bacterial infection, usually of the lungs, that was a widespread cause of death before a vaccine was developed in the 20th century. In the late 19th century it was discovered that the disease was contagious, and hospitals were created to quarantine patients and prevent the spread of the disease. This photograph, by the Abdullah Brothers, was taken in the period from 1880–1893.Library of Congress / Science Photo Library Export blockade Researchers in the USA have now devised a system to identify and study these elusive proteins by turning an antibiotic McCann, J.R., McDonough, A., Pavelka, M.S. & Braunstein, resistance mechanism against the bacterial cells. The trick M. (2007). β-Lactamase can function as a reporter of is to use a test where the exported protein, in this case β- bacterial protein export during Mycobacterium tuberculosis lactamase, is essential for the bacteria to survive. β-Lactamase infection of host cells. Microbiology 153, 3350–3359. is an enzyme that many bacteria use as protection against the Tuberculosis continues to kill millions of people slowly every antibiotic penicillin. Since penicillin interferes with synthesis year. It is caused by the bacterium Mycobacterium tuberculosis. of the bacterial cell wall, the β-lactamase must be outside the Few drugs are effective against this species and the bacteria cell to provide protection. M. tuberculosis is normally resistant have very effective strategies to thrive within the body. For to penicillin so the researchers created a sensitive strain by example, they colonize macrophages, a type of human cell that removing the protective gene, called blaC. They then linked the usually destroys invading bacteria. To do this the bacterium β-lactamase gene to any gene where they suspected that the secretes proteins to ensure survival through interference with encoded protein might be exported. Mammalian cell cultures the body’s defence systems. M. tuberculosis has at least four were infected with the bacteria and penicillin was added. If systems to export proteins from the cells. The one that is the cells really did export the protein, the β-lactamase was probably responsible for most protein secretion is the general exported as well and protected the bacteria from the antibiotic. secretion pathway (Sec), but the twin-arginine translocation If the protein was not exported, the bacteria died. pathway (Tat) is also important. The pathways recognize signals on the proteins to identify which ones to export, The idea was tested with several β-lactamase genes using but also appear to export proteins that lack conventional proteins known to be exported by the Tat and Sec pathways signals. M. tuberculosis secretes proteins when grown alone in to come up with a reliable system. Shortened versions of laboratory cultures, but a different set appears to be made and the Escherichia coli TEM-1 β-lactamase gene as well as M. exported during infection of the host. Researchers think that tuberculosis BlaC worked well with several export signals. The vaccines or drugs to prevent export of these proteins could be cultured mammalian cells were very like macrophages, so the very effective therapies. Unfortunately, it has proved difficult researchers think that they now have a way to identify the to even identify them since it is difficult to collect bacterial most interesting category of proteins, namely those that are proteins from infected human tissues. exported by M. tuberculosis during intracellular growth.

46 microbiology today feb 08 goingpublic

The Society has a broad programme of activities to promote FIS 2007 Press briefing at the Science Media Centre Microbiology microbiology to the public, the media, opinion-formers and The Federation of Infection Societies Microbes and climate change in social media holds an annual conference. In Climate change has been at the top of the public agenda for a while and we had www.micropodonline.com 2007, SGM was the conference’s policymakers. 2007 has seen some great successes, as Lucy become increasingly concerned that the important role of microbes was hardly host society, and was responsible for ‘New media’ is increasing in mentioned. To redress this, we decided to run a press briefing on the topic. Goodchild reports. Contact Lucy at [email protected] publicizing the research to the media. popularity all the time. Podcasts The microbial aspect of climate change is notoriously complex, so we first had to break pop up every day and every At first glance, there was a plethora of it down into manageable chunks. We split the briefing into four sections, based on other person has a blog. There is Microbiology in the Media brilliant news stories. Research covered climatically important gases: microbial methane production, carbon dioxide and ocean a small group of websites new and existing superbugs, which acidification, nitrous oxide and microbes, and oceanic dimethyl sulphide production. dedicated to microbiology, SGM September 2007 meeting, Edinburgh always make the front pages. However, The briefing was held on 10 December 2007 at the Royal Institution in London. The with Microbiologybytes and For every SGM meeting, the public pork to the self-assembly of the we encountered two problems. The national news media were invited, as were press officers from contributing universities. Microbeworld leading the way. affairs office produces press releases Clostridium difficile protein coat and its first was selecting relatively few stories The speakers – James Chong (University of York), Ian Joint (Plymouth Marine However, there was no such to get the research presented to the applications in nanotechnology. The from so much newsworthy research Laboratory), Mark Trimmer (Queen Mary, University of London) and Michael Steinke website dedicated to providing public. The plenary session this time press releases were produced in close and the second was finding authors (University of Essex) – gave exceptional presentations; everybody was enthralled. Four microbiology news, information was ‘Food, fluids, fingers, faeces and collaboration with the authors and willing to participate. Medics seem to journalists attended, from Science, the Daily Mail, the Press Association and BBC Radio and entertainment for the flies: food- and water-borne pathogens’, sent to our extensive list of reporters be strangely reticent in this respect. 4. We had chosen a ‘busy news day’ for our briefing, so the turnout was less than we so we knew there would be some a week before the meeting. We also Despite all our efforts, only four general public… until now. had hoped. newsworthy stories. made them available to journalists scientists agreed to press releases. I have been working with Dr However, the coverage was exciting. During the briefing, we had enquiries from the We selected over 30 abstracts to on EurekAlert and AlphaGalileo, two I was unable to attend the conference, Lucy Harper, Communications Guardian and the Telegraph, both unable to attend but interested in the stories. The be the subjects of press releases. online science news centres. so yet again I made sure my contact Officer at the SfAM, to develop a speakers were interviewed immediately after the briefing for Radio 4’s Farming Today, After asking the authors whether The meeting started on Monday 3 details were clear on the press releases. brand new portal brimming with which aired the following morning at 5.45am, and the Daily Mail ran a fantastic piece they would like to be involved, September 2007. As I was the main Although I had received a taster during news, views, information and on methanogens. The stories were a hit online, and were chosen as blog topics in just 15 abstracts remained. Topics contact for the press releases on site, SGM’s September meeting, nothing fun – all with a microbiological several languages. Perhaps most exhilarating was the subsequent appearance of a £1 ranged from Hepatitis E in European I made sure I had my mobile by my could have prepared me for the theme. Our aim is to engage with million anaerobic digester on a farm in The Archers, exactly what Dr Chong had been side from the beginning. Sure enough, response. One of the press releases, the public about microbiological talking about! media calls began to pour in. We had about a new strain of community- issues, covering bird ‘flu, home enquiries from all over the world about acquired MRSA, was selected for hygiene and giant fungi among NEW MRSA IS the research being presented and a promotion by the Press Association. Science and the Parliament 2007 many others. On Tuesday 27 November 2007, the variety of publications were interested The Royal Society of Chemistry (RSC) hosts ‘Science and the Parliament’ annually, to Micropod was launched on day before the conference was due to ON THE LOOSE in the stories, from Grocer magazine encourage scientists and politicians to debate key scientific issues. The 2007 event 17 December with the theme start, the phone began to ring first thing through to BBC online and Nature. focussed on ‘Energy and Climate Change – The Science Behind the Energy Debate’. ‘The microbiology of Christmas’. in the morning. The pace increased I was kept rather busy over the next SGM has a stand at the event every year, and this year Executive Secretary Ron Fraser In the first podcast, we asked and before long I was answering few days and the calls kept coming for and I attended the event at Our Dynamic Earth in Edinburgh. residents of Reading, ‘will you be three phones. We had calls from UK NEW ‘KILLER weeks after the meeting. eating turkey this Christmas?’ We broadsheets and tabloids, as well as Since microbes and climate change had featured so heavily in our activities in 2007, we I am still keeping tabs on the discussed the many and varied television channels. The journalists were very excited about this event; it gave us the opportunity to bring the subject to MRSA’ ALERT coverage of the meeting. The Society life. SSERC very kindly lent us a digital microscope and laptop to allow delegates to see microbiological aspects to the wanted to speak to the author, Dr was mentioned in hundreds of places, festive season and I interviewed Marina Morgan from the University of the display and helped us to set up. We showed a mix of algae and protozoa, which is both in print and online. Some of my astrobiologist Lewis Dartnell Exeter. Marina was on her way to the lively and exciting, to highlight the climatic importance of photosynthetic microbes. favourite coverage included articles about life in the snow. Our first conference in Cardiff, but she took all Even before the delegates arrived, people were transfixed. Staff at Our Dynamic Earth in Le Monde, De Standaard, www. blogs were about bird ‘flu and were creeping over hesitantly and asking is ‘that happening right now?’ They were thepoultrysite.com, United Press the calls nonetheless and was exactly fascinated by the protozoa, and surprised to hear about the role of algae in climate the festive increase in STIs. International and Ten to the Minus what the press were looking for. change. Many people commented that they were pleased to see us acknowledging the This year’s topics will include Nine. On the first day of the conference, news cameras appeared and the importance of microbes in climate change. hygiene and cleanliness, bugs in story made almost all of the national The Scottish Government will consider a Climate Change Bill this year and we hope that space and GM. So far, we have newspapers, as well as many regional micro-organisms will be taken into account, both as an important aspect of modelling an editorial board of four people, ones. Dr Chris talked about it on and as a key to tackling greenhouse gas emissions. but we are looking for additional This Morning on TV and I was happy helpers. If you are interested to hear a news bulletin on Marina’s SGM could not carry out these promotional activities without input and help from in getting involved and you are research while I was on my way to members. If you would like to be included in our database of experts, contact Lucy, willing to attend the occasional the airport. With Marina’s help, we or click on the link for the form at the bottom of the SGM website noticeboard page virtual meeting (just doing our certainly reached a wide audience with (www.sgm.ac.uk/noticeboard.cfm). bit to save the planet), please the research! drop us a line.

48 microbiology today feb 08 microbiology today feb 08 49 reviews

If you would like your name to be added to our database of consulted and their life stories. I feel Manual of Clinical for the beginner, although one notable Reviews on the web that cogent comments of the experts Microbiology, 9th edn, exception to this was the short chapter Reviews of the following books are book reviewers, please complete the book reviewer interests in these pages should have joined their vols 1 and 2 on the taxonomy and classification available on the website at www.sgm. comments in the essays, and that brief of viruses. Nonetheless, it is the very ac.uk/pubs/micro_today/reviews.cfm form at www.sgm.ac.uk. A classified compendium of reviews biographical details would have been Edited by P.R. Murray, E.J. Baron, J.H. intensity of the information provided that Genomics and Evolution of Microbial better at the end of the book. For seven Jorgensen, M.L. Landry & M.A. Pfaller gives this book its strength. For those Eukaryotes from 1996 to the present is also available on the website. essays, which concern diseases caused Published by American Society for seeking a ready source of information on Listeria, Listeriosis, and Food Safety, by animal parasites such as flukes and Microbiology (2007) matters relating to the practice of clinical 3rd edn hookworms, a microbiologist needs US$209.95 pp. 2,488 microbiology, this surely should be one Enzyme-mediated Resistance to advances. The book is a comprehensive to have a textbook of parasitology or ISBN 1-55581-371-0 of the first ports of call. Despite the invertebrate zoology handy. A glossary Antibiotics Mechanisms, Dissemination, study of the history of hygiene. It is While the size and weight of each density of the text, the judicious use of and a few life cycle diagrams would and Prospects for Inhibition written beautifully and is not only of these two volumes are a strong headings, subheadings and tables makes have made these chapters easier for Molecular Genetics of Bacteria, 3rd edn accessible but also utterly fascinating. disincentive to carrying them around the retrieval of specific information fairly microbiologists. The writing is informal Modern Soil Microbiology, 2nd edn The notes are informative and useful in one’s briefcase, they assuredly straight forward. This is also helped by and colloquial, which is not always but do not detract from the story. This deserve a place on the shelf of every an extensive and detailed subject index. Adenovirus Methods and Protocols, helpful – in one chapter I was more is a must read for anybody interested in medical microbiology department. A number of the chapters also contain Vols 1 and 2, 2nd edn than usually surprised by the prescience history and especially for those who have The first volume deals broadly with helpful diagrams, with several in Bacterial Pathogenomics of Darwin, and had to remind myself an interest in public health. bacteriology and related subjects such colour. The latter are particularly Exploitation of Fungi that ‘Darwin’ is the given name of one as antibiotic susceptibility testing, while valuable when showing features such Gene Cloning and Manipulation Lucy Goodchild, SGM of the experts – nor did I need frequent as the appearance of bacterial colonies volume 2 covers virology, fungi and Virology Principles and Applications information along the lines of ‘The taxi parasites. Despite the use of the word growing on agar plates, Gram-stained fare to Chelsea was £10’. The index of Hospital Acquired Infections Power ‘clinical’ in the book’s title, a number of films or pathological material. Although the book is strangely constructed and Strategies for Clinical Practice Parasites and Infectious chapters are more ‘academic’, covering it was not available for me to review, a not very helpful. Amazingly, considering Crash Course: Infectious Diseases Disease Discovery detailed molecular and biochemical CD-ROM with close to 500 illustrations that the author is the editor of a scientific Master Medicine. Microbiology and by Serendipity, and information on the mechanisms of from the book is also available for journal and the distinguished publishers Infection, 3rd edn Otherwise resistance to antibiotics, antivirals, purchase through the publisher. have over 400 years experience of The Microbiology Bench Companion antifungals and antiparasitic agents. In Despite the fact that there were over Clean: A History of book production, typos are numerous. By G.W. Esch addition to detailed information on 250 contributors to these two volumes, Advances in Food Diagnostics Personal Hygiene and I suspect from a text comment that Published by Cambridge University a comprehensive range of pathogens, the text appears remarkably cohesive. Superantigens: Molecular Basis for Their Purity the typos and the occasional less Press (2007) the initial chapters deal with the Indeed, in the Preface the Editor-in-Chief Role in Human Diseases £23.99/US$45.00 pp. 355 well-organized chapter are the result By V. Smith complementary and important issues candidly reveals that he and the other Encyclopedia of Infectious Diseases: ISBN 0-52167-539-0 of an excessive rigidity with respect to Published by Oxford University Press of laboratory management, design, Editors had their work cut out trying to Modern Methodologies deadlines, and a final rush to complete (2007) The 15 chapters or essays in this information technology and storage of achieve consistency. However, they are Methods for General and Molecular the book. £16.99 pp. 457 book vary greatly. Some tell stories, micro-organisms. Other general chapters to be congratulated on achieving their Microbiology, 3rd edn ISBN 978-0-19-929779-5 for example how the cause of malaria In spite of the above criticisms the book of value to those working at the bench objective. Interestingly, approximately Virulence Mechanisms of Bacterial 30 % of the authors for this edition were Clean tells the story of hygiene from was discovered, and how a toad and its is valuable for some well-told stories cover disinfection and sterilization, Pathogens, 4th edn from outside the USA. This is a welcome ancient Egypt to the modern world. fluke parasite, water-loving creatures, and the thoughts of the author and his and the control of laboratory-acquired Microbial Biodegradation: Genomics and development in terms of moving away Virginia Smith documents the changes in survive in a desert. Other chapters experts. It is appropriate for purchase infections. Furthermore, in the current Molecular Biology discuss important issues. Why is from a purely American perspective of practices and investigates the motivations by libraries of universities and institutes climate where there is much media The Cyanobacteria: Molecular Biology, vaccination highly effective for some the field and is likely to broaden the behind these changes. It is so easy to see with microbiology departments; coverage and political interest in Genomics and Evolution diseases but has no prospect of success the subject of healthcare-associated potential readership of the book. hygiene and cleanliness as a necessity, this would also permit individual Models of Exacerbations in Asthma and with others? Did the elimination of a infections, it is reassuring to note that especially with the rise in antibiotic- microbiologists to peruse and consider In summary, this book is highly COPD highly debilitating disease (hookworm) whether they wanted a copy. there are two short but well-written and recommended to those involved in the resistant infections like MRSA, but this Animal Viruses: Molecular Biology has not always been the case. Prior to from an area lead to an increase in focussed chapters on infection control field of clinical microbiology, be their Finally, what about the ‘serendipity’ Coronaviruses: Molecular and Cellular the public acceptance of germ theory, prosperity, or did improvement in epidemiology and laboratory procedures specialty bacteriology, virology, mycology featuring in the subtitle? Having started Biology hygiene and cleanliness had several living conditions eradicate the disease? for the epidemiological analysis of micro- or parasitology. The price makes it by considering it to be a major factor Sex in Fungi: Molecular Determination roles. In ancient Egypt, the focus was How can medication be delivered to organisms. unlikely that many individuals will an impoverished and ill-educated in discovery, in the end the author and Evolutionary Implications on cosmetics and beauty, and in Rome, The format of the book, which comprises purchase personal copies, although given population? settles for 5–10 %, with well-planned Methods for Computational Gene the new Galenic medicine advocated dense text in a fairly small font, will the amount of information contained investigations being the major route to in each volume, there is a case to be Prediction cleanliness to avoid illness. Religious Many of the essays are interesting and discovery. A conclusion perhaps not not attract the casual reader. Indeed, I made that the book is good value for Acinetobacter: Molecular Biology asceticism followed, compelling people lucidly written. The book is, however, a too far from the aphorism on genius would not feel generally inclined to money. With this in mind I would Antimicrobial Susceptibility Testing to remain clothed and avoid washing to very unusual one and has shortcomings. attributed to Thomas Carlyle – 1 % recommend it to first-year microbiology strongly recommend that microbiology Protocols remain morally pure. Hygiene was not The essay section of about 240 pages inspiration and 99 % perspiration. students or those just starting in the simply influenced by disease, but also by comes after a prologue of over 100 pages field of clinical microbiology as there are departments purchase copies for their staff. Segmented Double-stranded RNA religion, fashion, politics and technical describing meetings with the 18 experts Michael Carlile, Bridgwater other more accessible tomes available Alan Johnson, Health Protection Agency Viruses: Structure and Molecular Biology

50 microbiology today feb 08 microbiology today feb 08 51 Human activity is a big factor in global warming and politicians around the world are trying to agree some control measures. But as Dave Reay reveals, they cannot afford to ignore the role played by microbes in climate change. commentmicrobes as climate engineers ‘The Anthropocene’ is the name given into the atmosphere each year as a these microbially mediated feedbacks by Nobel Laureate Paul Crutzen to the result of microbial methanogenesis. on further climate warming in the 21st epoch we now live in. Ours is an age This amount would be far greater if it century is potentially huge. where global climate is increasingly was not for the significant proportion The role of microbes as climate determined by humankind, one where used by methanotrophic bacteria before engineers is evident, as is their potential our species continues to alter the it can escape into the atmosphere. to exacerbate the problems of enhanced

composition of the atmosphere and the The CH4 that does escape is still not global warming driven by our burning energy balance of the planet. Arrogant free from their attentions; high affinity of fossil fuels. But all is not lost in organisms that we are, it is easy to view methanotrophs utilize atmospheric the world of climate microbiology.

this as something entirely novel in CH4 at a rate of ~30 million tonnes In the abundance and diversity of

Earth’s history – evolution’s newest top each year. Along with additional CH4 microbial life on our planet may lie consumers breaking the environmental release from gas hydrates and microbial the roadmap by which we can better shackles and dictating global climate. methanogenesis in the oceans, the navigate the Anthropocene. Through In truth of course, micro-organisms world’s termite population produces a better understanding of microbial

have been at it for billions of years. an additional 20 million tonnes of CH4 decomposition of organic matter, there From the first molecule of oxygen every year courtesy of the methanogenic is the potential to alter land-management released by a cyanobacterium in bacteria in their guts. Aside from practices to conserve or even enhance the turbulent oceans of a young energy-related sources like fossil fuel soil carbon storage. By inducing

Earth, to the methanogen-made CH4 extraction, most human-induced increased primary production in the

belched from the warm bogs of the CH4 emissions come from ruminant oceans, by adding iron or reactive Carboniferous, microbes have long livestock, rice cultivation and landfill, nitrogen, there exists the possibility

helped determine the composition of adding around 150 million tonnes to of sequestering more CO2 from the Earth’s atmosphere and its climate. the atmosphere annually, all derived atmosphere. Already the methanotrophs Both natural and human-induced from the methanogens that thrive in in landfill cover soils are playing a vital

fluxes of CO2, CH4 and N2O are these carbon-rich environments. role in intercepting the vast quantities of

dominated by microbiology. In the sea, N2O has a sobering global warming CH4 produced below, cyanobacteria are

CO2 uptake by phytoplankton provides potential of 298 (this is the warming being explored as providers of hydrogen the pump for the annual drawdown produced per kg of a gas over a 100- fuel, and vats of phytoplankton are of 90 billion tonnes of carbon from year time horizon relative to 1 kg of being grown as the feedstock for

the atmosphere, with microbial CO2). Again, it is microbes that biofuels. decomposition and respiration returning dominate global emissions. For every Microbes will continue as climate much of this to the atmosphere. On tonne of reactive nitrogen that human engineers long after humans have land, the huge amount of carbon activities add to the biosphere, between burned that final barrel of oil. Whether stored in soils and vegetation is under 10 and 50 kg end up being emitted they help us to avoid dangerous climate

continual attack from microbes, the into the atmosphere as N2O. change in the 21st century or push us balance between primary production, It is not only via reactive nitrogen even faster towards it is dependent on respiration and decomposition resulting that we are changing microbial just how well we understand them. in the uptake of around 120 billion greenhouse gas emissions. Through Dave S. Reay tonnes of carbon each year, and the loss our post-industrial emissions, we have School of GeoSciences, Crew of about 119 billion tonnes. enhanced global warming. Average Building, West Mains Road, For CH , the flagella-print of micro- temperatures have risen by 0.7 °C in 4 University of Edinburgh EH9 3JN organisms on the atmosphere is even the last 100 years, with a projected (t 0131 650 7723; f 0131 662 more apparent. The world’s wetlands increase in the 21st century of between 0478; e [email protected]) pour over 100 million tonnes of CH4 2 and 4.5 °C. From enhanced soil m The author measuring methane emissions carbon decomposition rates to elevated Please note that views expressed in Comment do not from a peatbog in northern England. D Reay wetland methanogenesis, the impact of necessarily reflect official policy of the SGM Council.

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