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1 5 3 microbiologyresearch.org Our influential Editors and Editorial Board members are selected are members and Editorial Board Our influential Editors OUR JOURNALS HAVE EXPERT EXPERT OUR JOURNALS HAVE to the microbiology community. to the microbiology and contribution , expertise their knowledge for INTERNATIONAL EDITORIAL BOARDS EDITORIAL INTERNATIONAL . and outreach , policy, education development , professional international conferences REASONS and impact of microbiology by connecting and empowering communities worldwide, through: through: worldwide, communities and empowering connecting by and impact of microbiology Unlike commerical publishers, we invest our publishing surplus to advance the understanding the understanding our publishing surplus to advance we invest publishers, commerical Unlike WE ARE A NOT-FOR-PROFIT ORGANISATION WE ARE A NOT-FOR-PROFIT 5 TO TO PUBLISH WITH US 4 2 Find out more about our journals at about our journals Find out more

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Journal: Microbiology Today Microbiology Essential Generics: Chloramphenical Ad Chloramphenical Generics: Essential 25/11/2016 11:55 CHL25060 O65995 PIP: 106-5796 AAH: CHL600B ALLIANCE: MOVIANTO: CAPSULES CHLORAMPHENICOL 1 2 3,4 Adverse events should be reported. Reporting forms be reported. events should Adverse can be found at www.mhra.gov.uk/ and information events should also be reported to yellowcard. Adverse Essential Generics on 01784 477167. distension, pallid cyanosis, vomiting, progressing to vasomotor collapse, distension, pallid cyanosis, vomiting, progressing to vasomotor of irregular respiration and death within a few hours of the onset symptoms. Overdose: Stop chloramphenicol immediately if signs of adverse events oral develop. Treatment is mainly supportive. If an allergy develops, Baby antihistamines may be used. In severe overdosage e.g. Gray Resin Syndrome, reduce plasma levels of chloramphenicol rapidly. increase haemoperfusion (XAD-4) has been reported to substantially chloramphenicol clearance. Pack size and Price: 60 capsules £377.00 Legal Category: POM. Market Authorisation Number: PL17736/0075. Market Authorisation Holder: Chemidex Pharma Limited, 7 Egham UK. Business Village, Crabtree Road, Egham, Surrey TW20 8RB, Date of preparation: January 2016. for See Chloramphenicol Capsules Summary of Product Characteristics full prescribing information. References: 1. Martindale: The Complete Drug Reference. Chloramphenicol. [Online]. Available from: http://www.medicinescomplete.com [22nd of November 2016]. 2. Fluit, A.C., Wielders, C.L.C., Verhoef, J., and Schmitz, F.J. Epidemiology and susceptibility of 3,051 Staphylococcus aureus isolates from 25 university hospitals participating in the European SENTRY Study. Journal of Clinical Microbiology. 2001; 39(10): 3727-3732. 3. Kelly, C., LaMont. Patient information: Antibiotic- cile (Beyond the associated diarrhea caused by Clostridium diffi Basics).June 2015. 4. Bartlett J.G. Antimicrobial agents implicated cile toxin-associated diarrhea of colitis. Johns in Clostridium diffi Hopkins Med J. 1981; 149(1): 6-9. 5. Feder. H, Chloramphenicol: What we have learned in the last decade. Southern Medical Journal. 1986; (79)9: 1129-34. 6. Weigel LM et al. High-Level Vancomycin-Resistant lm. Staphylococcus aureus Isolates Associated with a Polymicrobial Biofi Antimicrob Agents Chemother. 2007 Jan; 51(1): 231–238. 7. Ensminger, P., Counter, F., Thomas, L., Lebbehuse, P. Susceptibility, resistance development, and synergy of antimicrobial combinations against cile. Current Microbiology. 1982; 7: 59-62. 8. Poilane, Clostridium diffi I., Bert, F., Cruaud, P., Nicolas-Chanoine, MH., Collignon, A. Interest cile isolates of the disk diffusion method for screening Clostridium diffi with decreased susceptibility to antibiotics. Pathologie Biologie (Paris). 2007; 55(8-9): 429-33. 9. Cattoir, V., Ould-Hocine, ZF., Legrand, P. cile clinical isolates Antimicrobial susceptibility of Clostridium diffi collected from 2001 to 2007 in a French university hospital. Pathologie Biologie (Paris). 2008; 56(7-8): 407-11. 10. Brazier, JS., Levett, PN., Stannard, AJ., Phillips, KD., Willis, AT. Antibiotic susceptibility of clinical isolates of clostridia. Journal of Antimicrobial Chemotherapy. 1985; 15(2): 181-5. 1,5 1,5 1,5 7-10 1,5 1,5 1 2 6

infections including: Oral levels comparable to i.v. levels to i.v. comparable Oral levels cile with C.diffi implicated Rarely Widely distributed throughout the body, including CSF including the body, throughout distributed Widely Typhoid Neisseria Legionella Rickettsia MRSA VRSA

E. coli

C.diffi cile C.diffi

H. infl uenzae H. infl Effective against serious Abbreviated Prescribing Information Chloramphenicol Capsules BP 250mg Presentation: Hard Gelatin Capsules. particularly Indications: Typhoid fever and life-threatening infections, uenzae, where other antibiotics will those caused by Haemophilus Infl ce. not suffi Posology: For oral administration. doses. For Adults and elderly: 50 mg/kg body weight daily in 4 divided be doubled severe infections (meningitis, septicaemia), this dose may Children: initially, but must be reduced as soon as clinically possible. Not recommended. Contra-indications: Known hypersensitivity or toxic reaction to used chloramphenicol or to any of the excipients. Should not be active for the prophylaxis or treatment of minor infections; during liable to immunisation; in porphyria patients; in patients taking drugs by breast- depress bone marrow function; during pregnancy, labour or feeding mothers. Special warnings and precautions for use: Use only if other treatments are ineffective. Use should be carefully monitored. Reduce dose and monitor plasma levels in hepatic or renal impairment; in the elderly; and in patients concurrently treated with interacting drugs. Interactions: Chloramphenicol prolongs the elimination, increasing the blood levels of drugs including warfarin, phenytoin, sulphonylureas, tolbutamide. Doses of anticonvulsants and anticoagulants may need to be adjusted if given concurrently. Complex effects (increased/decreased plasma levels) requiring monitoring of chloramphenicol plasma levels have been reported with co-administration of penicillins and rifampicin. Paracetamol prolongs chloramphenicol half-life and concurrent administration should be avoided. Chloramphenicol may increase the plasma levels of calcineurin inhibitors e.g. ciclosporin and tacrolimus. Barbiturates such as phenobarbitone increase the metabolism of chloramphenicol, resulting in reduced plasma chloramphenicol concentrations. In addition, there may be a decrease in the metabolism of phenobarbitone with concomitant chloramphenicol use. There is a small risk that chloramphenicol may reduce the contraceptive effect of oestrogens. Chloramphenicol reduces the response to hydroxocobalamin. Chloramphenicol is contra-indicated in patients taking drugs liable to suppress bone marrow function e.g. carbamazepine, sulphonamides, phenylbutazone, penicillamine, cytotoxic agents, some antipsychotics including clozapine and particularly depot antipsychotics, procainamide, nucleoside reverse transcriptase inhibitors, propylthiouracil. Pregnancy and Lactation: The use of chloramphenicol is contra- indicated as the drug crosses the placenta and is excreted in breast milk. cant effect Effects on ability to drive and use machines: No signifi on driving ability. Undesirable Effects: Reversible dose related bone marrow depression, irreversible aplastic anaemia, increased bleeding time, hypersensitivity reactions including allergic skin reactions, optic neuritis leading to blindness, ototoxicity, acidotic cardiovascular collapse, nausea, vomiting, glossitis, stomatitis, diarrhoea, enterocolitis, Gray Baby Syndrome particularly in the newborn, which consists of abdominal For further information, please contact: Essential Generics, 7 Egham Business Village, Crabtree Road, Egham, Surrey TW20 8RB, UK For further information, please contact: Essential Generics, 7 Egham Business Village, Crabtree Road, EG/CH/NOV/2016/02a 01177_Chloramphenicol Ad_Microbiology Today_AW.indd 1 Editorial

I would like to welcome everyone to the latest edition of Microbiology Today, which addresses one of the most fascinating topics in microbiology: the microbiome. Research surrounding the microbiome has always been both complex and interesting, and with recent advances in technology we have been able to generate more insight into complex communities than ever before. As research interest in this area has grown, we have seen significant interactions between microbes, environment and the host. This has given us a fresh understanding about how they impact on every aspect of life, sometimes in the most unexpected of ways. Whole Picture

he first article, written by given an overview of how improvements of questions about how exactly those Professor Julian Marchesi, outlines in sequencing technology and statistical effects come about. There is evidence that, Thow microbiome research has bioinformatics has given us a new insight as our understanding of the intricacies of developed and evolved, highlighting how into the complexity of both environmental microbiomes improves, the findings may access to a new type of information has and human microbiomes. They have then be of increasing clinical value. allowed us to ask different questions. The suggested ways in which this improved For our last piece, Professor article emphasises how an increasing understanding of the interactions and James Prosser gives a balanced outlook understanding of microbiomes has relationships within microbiomes could describing how increased accessibility the potential to impact on how we see be used to help us preserve and restore to molecular technology has and can and deal with not only human health, ecosystems across the globe. continue to influence research studies, where the focus has traditionally been, In the fourth piece, Dr Sarah but also reminding us not to forget that but also multiple microbiomes within Maddocks examines the role of the all technology has limitations. He the environment, that when combined microbiome in wound healing, outlining observes that, despite advances in together support life on Earth. how a small shift in the composition of sequencing technology and increased Dr Thorunn Helgason has written microbial populations within wounds can access to large data sets, more data the second piece, which delves into be the difference between timely and doesn’t necessarily mean improved the importance of microbiomes within delayed healing. She discusses the latest understanding. It is essential that robust soil and how they can affect food ideas around the complexity of these research questions are asked, to make production and the ability to support systems, and how the diagnosis and meaningful use of the information being human population growth. The global treatment of wounds might be influenced generated. need for more food means it is essential by these findings in the future. It is clear that this fascinating subject we understand how the microbiome Professor Paul O’Toole talks us area is likely to produce exciting new of soil can help lead to increased crop through through how variation in the findings as the research moves forward. production. Conversely, it highlights how microbiome of humans can lead to This collection of articles begins to show poor understanding and management vastly different outcomes in terms of just how significant the interactions of soil can potentially lead to poor crop human health and disease. Again, the between different microbiomes can be, production, water run-off and flooding. great strides forward in technology have and how understanding the interactions is The technology available is now being allowed questions to be asked, not only critical to understanding the impact they used to investigate which parts of the about which microbes are present, but might have. soil microbiome are integral to ‘good’ also which genes they carry and how soil, and how different land management that might affect the host. Much research Rowena Jenkins practices impact on these microbiomes. has focused on how the variation within Editor Following on from this, Dr Melissa the gut microbiome can impact a whole [email protected] Dsouza and Professor Jack Gilbert have range of disease, while still leaving plenty

Microbiology Today May 17 | www.microbiologysociety.org 49 Contents

Microbiology TODAY Articles The microbiomes of things 58 Julian R. Marchesi Mapping interactions between microbes and their surroundings.

Microbiomes and nutrient cycling 62 Thorunn Helgason Understanding the structure and function of soil to increase crop yields.

Microbiome – beyond the gut 66 Melissa Dsouza & Jack A. Gilbert Breakthroughs in microbiome research that extend beyond the human microbiome.

Microbial communities within the 70 chronic wound Sarah E. Maddocks Managing the microbiome of a chronic wound to reduce infection.

Microbiome–health associations: 74 status and perspectives Paul W. O’Toole The microbiome and the risk for health and disease. 44:2 May 2017 Features Regulars 82 Publishing 49 Editorial The latest from the Publishing team. 52 Council 2017 84 Research Visit Grants: 53 From the President supporting international collaboration 54 From the Chief Executive Some recent grant recipients share their experiences. 55 News 85 Early Career Microbiologists’ Forum 78 Annual Conference Update: Summer schools, socials and new roles 80 Focused Meetings Rebecca Hall provides a Forum update. 94 Reviews .86 Outreach – Education and Outreach Editor Rowena Jenkins and the microbiome Managing Editor Ruth Paget Two projects focusing on the microbiome. Editorial Board David Bhella, Helen Brown, Emma Denham, Lorena Fernández-Martínez, Freya Harrison, James Redfern, Alison Sinclair, 88 Policy – Connecting microbiome research Nicola Stonehouse stakeholders Address Microbiology Society, Charles Darwin House, 12 Roger Street, London WC1N 2JU T +44 (0)20 7685 2683 E [email protected] The Society’s policy work on the microbiome. Design Ian Atherton, Corbicula Design (www.corbiculadesign.co.uk) 90 Schoolzone – Teaching the human Printed by Charlesworth Press, Wakefield microbiome in schools © 2017 Microbiology Society ISSN 1464-0570 The views expressed by contributors do not necessarily reflect official policy of the Society; nor can Inspire students about the microbiome. the claims of advertisers be guaranteed. 92 Membership Q&A Introducing Daniel Morse from Cardiff University. FSC Logo 93 Latest from the Society Spider silk and antibiotics, vaccination strategies and more. Coloured scanning electron 95 Comment – micrograph of various bacteria Advances in the study of the microbiome found in a sample of human faeces. James I. Prosser Steve Gschmeissner/Science Photo Technical ingenuity to test original ideas and concepts. Library Council 2017

Executive Officers President – Professor Neil Gow School of Medicine, Medical Sciences and Nutrition, Polwarth Building, Foresterhill, Aberdeen AB25 2ZD; [email protected] General Secretary – Professor Maggie Smith Department of Biology, Wentworth Way, University of York, York YO10 5DD; [email protected] Treasurer – Professor Chris Thomas School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT; [email protected]

Chairs of Committees Communications Committee – Dr David Bhella MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH; [email protected] Early Careers Microbiologists’ Forum Executive Committee – Dr Helen Brown School of Dentistry, Cardiff University, Cardiff CF14 4XY Finance Committee – Professor Chris Thomas See ‘Treasurer’ above Policy Committee – Dr Pat Goodwin c/o Microbiology Society, Charles Darwin House, 12 Roger Street, London WC1N 2JU Professional Development Committee – Dr David Whitworth Institute of Biological, Environmental and Rural Sciences Room S22, Cledwyn Building, Aberystwyth University, Ceredigion SY23 3FG; [email protected] Publishing Committee – Professor Charles Dorman Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, College Green, Dublin 2, Ireland; [email protected] Scientific Conferences Committee – Dr Karen Robinson Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham NG7 2RD

Elected Members Professor Paul Kellam Imperial College London, Faculty of Medicine, St Mary’s Campus, Norfolk Place, London W2 1PG; & Kymab Ltd; [email protected] Professor Stephen Oliver Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA Professor David Pearce Faculty of Health and Life Sciences, Northumbria University, Northumberland Road, Newcastle-upon-Tyne NE1 8ST; [email protected] Professor George Salmond Department of Biochemistry, Hopkins Building, Tennis Court Road, Cambridge CB2 1QW Dr Mike Skinner Section of Virology, Imperial College London, Faculty of Medicine, St Mary’s Campus, Norfolk Place, London W2 1PG; [email protected] Professor Nicola Stonehouse School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT; [email protected]

52 Microbiology Today May 17 | www.microbiologysociety.org From the President

My own schedule has taken me to five symposia and the Microbiology Society Annual Conference already this year, and I have enjoyed being in the audience for a wide range of types of presentation, from fungal immunology to public health and tropical disease. The topic that has been a common denominator of every major meeting I have been to recently is the microbiome, and dozens of new papers are published each day on this topic.

round 80% of the metabolites Prosser is also key to understanding the Microbiology Today has proved to be in our bloodstream are derived future aims in this field. The microbiome immensely popular with our members Afrom the microbes in our gut and underpins so many aspects of biology for many reasons. The articles are so it is perhaps not so surprising that and so the Schoolzone article by Hannah pitched so that topics are explained to an the intestinal microbiome influences not Forrest on teaching the microbiome interested but non-specialist audience, only our local gut health, but impacts provides a useful resource for those and it also provides Society news and our human physiology, systemically introducing this topic into the biology updates that we hope keep you informed affecting our immune responses and curriculum. with all aspects of Society business. potentially even our behaviour and The microbiome was also a topic at This issue also has useful information mood. It is therefore appropriate that the forefront of the Annual Conference about our portfolio of journals, which we the Microbiology Society is undertaking in Edinburgh. We tried to ensure that aim to expand in the coming year (see a major policy review of this topic the richness of the scientific buffet at page 82) and other Society titbits from (see article by Isabel Spence and Edinburgh was accompanied by plenty of our Communications’ captain Benjamin Paul Richards, page 88). This issue local flavours, including a ceilidh, a quiz Thompson. There are also a number of Microbiology Today also contains a night and other entertainments. But with of book reviews to help guide your series of other important articles on over 900 abstracts received this year for reading of the newest tomes, treatises the microbiome in a variety of contexts. the event, it was a bumper feast and I and theses on our science, both in the Read the overview by Julian Marchesi, hope all enjoyed the variety of microbial issue and online, and I hope you will the article on the microbiome of wounds science on offer. enjoy these. Also, don’t be shy about by Sarah Maddocks, health-associated In this edition of Microbiology Today suggesting topics we might want to microbiomes by Paul O’Toole, and the you can read the second official report consider for future issues of Microbiology microbiome beyond the gut by Melissa from our newly established Early Career Today. The Microbiology Today staff Dzousa and Jack Gilbert. We know that Microbiologists’ (ECM) Forum that has ([email protected]) are environmental microbiomes are also been set up to empower our community only too delighted to hear from those critical for the major nutrient cycles that of students, postdocs and non-tenured who wish to contribute this knowledge drive the ecology of our planet (see the microbiologists. We have already received and insight. article by Thorunn Helgason) and that great input to Council meetings and we collectively the microbiomes of the world wish to grow this initiative to capture the Neil Gow represent the major metabolic engines aspirations and needs of ECMs, and to President of life. The Comment article, ‘Advances include bespoke elements that speak to [email protected] in the study of the microbiome’, by Jim this community within our main meetings.

Microbiology Today May 17 | www.microbiologysociety.org 53 From the Chief Executive

As always, the Annual Conference in Edinburgh in April was one of the highlights of my year. It was fantastic to see so many members coming together and networking, both to share scientific results, insights and challenges, and also to learn from one another, develop collaborations, solve research problems, discuss fresh ideas, admire elegantly-conducted experiments, forge new friendships and renew old ones. Bringing together the whole microbiology community is the core function of the Society, and it was heartening this year to see a record number of abstracts submitted – double the number of a few years ago.

he Annual Conference goes from as ‘Microbial Resources for Agricultural of host–pathogen interactions, and strength to strength because the and Food Security’ and ‘Antimicrobial one covering a broad range of fungal TSociety continues to put the needs Resistance and One Health’. Others will research. and wants of its members first. This focus on particular sets of interactions, And if after that, you still think year, we took on board feedback that such as ‘Arboviruses and their Vectors’. there is nothing in your field, you can previous meetings were so full of great A particular highlight this year do something about it by making an sessions that sometimes there was is the 33rd International Specialised application for a Focused Meeting, or not enough time to study the posters Symposium on Yeast, or ISSY33, which for funds to run your own Society- properly. That matters because the is organised under the auspices of the Supported Conference, or you can poster sessions at a big meeting are International Commission on Yeasts, propose a session for a future Annual often where you get a glimpse of novel, with support from the Microbiology Conference or FIS meeting. early-stage research being carried out Society. It will be held at University I try to get out and about and speak by up-and-coming stars of the future. College Cork and the theme is ‘Exploring to as many members as possible each The Divisions that organise the Society’s and Engineering Yeasts for Industrial week, and I ask you what the Society scientific programme work incredibly Application’. does well and what more you want from hard to make sure that the sessions And for members particularly us. As Council finalises the strategy for at our conferences will be stimulating interested in clinical microbiology, the next five years, one thing that is clear for any microbiologist, whatever your there is the Federation of Infection is how much you value the conference particular field. And that applies not just Societies (FIS) meeting in Birmingham programme. It is a success because to the Annual Conference, but also to in November, which is organised each you propose great ideas, because the the programme for the rest of the year, year by a range of like-minded partners, Divisions and Scientific Conferences which offers something for everyone, with the Microbiology Society playing an Committee work hard to shape those whatever kind of microbe you study, important part. ideas into a diverse and engaging wherever you work, and whatever your If you really can’t find anything programme, and because the staff particular interests. among all of these meetings to suit team are constantly on the lookout for The Focused Meetings will cover your interests, take a look at the list innovations and developments. a wide range of areas from a number of Society-Supported Conferences I look forward to seeing some of you of different angles. Some focus on – meetings that are organised by at Focused Meetings, Society-Supported particular taxa of microbes, such as members with some financial backing Conferences and FIS later in the year. the 16th International Conference on from the Microbiology Society. There Pseudomonas and the British Yeast are meetings later in the year on RNA Peter Cotgreave Group meeting on ‘The Versatility of granules in human disease, anaerobic Chief Executive Yeasts’. Others will involve a range of protists, Staphylococcus, microbiomes, [email protected] different microbes with themes such hepatitis C, the molecular mechanisms

54 Microbiology Today May 17 | www.microbiologysociety.org News

Annual Conference Prize Lecture nominations Thank you to all those who attended, presented and helped organise our 2017 Annual Conference in Edinburgh – the turn-out was fantastic and exceeded expectations once again. You can watch our summary video of the event by visiting our YouTube channel (http://microb. io/2oYhdhn). Our Conferences team is already part-way through organising Annual Conference 2018, taking place 10–13 April at the ICC Birmingham. Find out more about the upcoming programme on page 79. Microbiology Society journals This month, the Microbiology Society is celebrating 70 years of our journal, Microbiology. Society publishing is looking to the next 70 years, launching redesigned articles, implementing continuous publication, introducing journal-sponsored poster prizes, and publishing the first ICTV Virus Taxonomy Profiles. See pp. 82–83 for more information.

ECM Forum summer roadshow Nominations are still open for the Society’s Prize The ECM Executive Committee is touring the country over the summer Lectures. Our Prizes recognise significant contributions to meet Forum members and share their plans for the next few to the field of microbiology by any researcher, months. This will be a great opportunity for early career researchers regardless of background or location. Find full details to meet members in their local area. To find out more, please see our and nominate an outstanding microbiologist before website (www.microbiologysociety.org/ECM). 7 June: www.microbiologysociety.org/prizelectures. Society-Supported Conference Policy consultation responses Grants Over recent months, the Society has responded to several UK Running your own event? Why not apply for a Parliamentary and Government science policy consultations. Jointly Society-Supported Conference Grant to cover with the Society for Applied Microbiology, we responded to the House some costs of your invited speakers? Our second of Commons Science and Technology Committee’s Genomics and round of submissions closes on 12 June 2017. Genome-editing inquiry. The Society also contributed to the Royal Read more on page 84. Society of Biology’s responses to the Science and Technology Committee’s Closing the STEM skills gap inquiry (http://microb.io/2mHNf1s) and the UK Government’s Building our Industrial Strategy consultation. Focused Meetings 2018 proposals Information about our responses and opportunities to inform them is The deadline date for Focused Meeting proposals available on our website (www.microbiologysociety.org/policy), for our 2018 series is 12 June 2017. Find out in the monthly newsletter, or by contacting our Policy Officer more on page 80. ([email protected]).

Microbiology Today May 17 | www.microbiologysociety.org 55 Updated educational Grant deadlines resources Date Grant Alongside a refresh of our education website, Microbiology Online, the Society 1 June 2017 Travel Grants – for eligible members wishing to has updated some educational resources present at a conference or attend a short course to provide students and teachers with between 1 July and 30 September. the most up-to-date and relevant information. Fact files on tuberculosis, cholera, H1N1 influenza, HIV & AIDS, 1 September 2017 Travel Grants – for eligible members wishing to antibiotic resistance, and influenza have present at a conference or attend a short course all been updated to cover the latest between 1 October and 31 December. research developments in these areas. Also refreshed are some of our comics, 30 September 2017 ECM Forum Event Fund – for ECM members wishing which cover topics such as handwashing, to host a local event from 1 May onwards. brushing teeth, the discovery of yeast and antibiotic resistance. 1 October 2017 Research Visit Grants – for eligible members wishing to visit a collaborator from 1 December onwards.

International Development Fund – for eligible members wishing to contribute to microbiology development activities in low-income economy countries from 1 December onwards.

Education and Outreach Grants – for members wishing to conduct a microbiology teaching, outreach Our range of resources, aimed at primary or public engagement activity from 1 December to post-16 students, is carefully targeted onwards. to meet curriculum requirements and fit in with the specifications for science. Single copies of non-chargeable Deaths Contributions and feedback resources are free to anyone involved It is with regret that the Society The Society welcomes contributions and with teaching microbiology in the UK announces the passing of Mr John S. feedback from members. Please contact and Ireland. Classroom sets of these Page FCA, who joined the Society in 1982 [email protected] with resources, along with single copies of as an Honorary Member. your ideas. chargeable resources, are available if you Please contact mtoday@ have a School Membership of the Society. microbiologysociety.org if you wish Benjamin Thompson Download the new resources now from to notify the Society of the death of a Head of Communications www.microbiologyonline.org or contact member whose details can be included [email protected] [email protected]. in this section.

Get the latest updates, follow the Society on: +

56 Microbiology Today May 17 | www.microbiologysociety.org Looking to make an impact with your research? Publish your next article with the Society’s open access and open data journal, Microbial Genomics.

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Microbiology Today May 17 | www.microbiologysociety.org 57 Submit your article at MICROBIAL GENOMICS mgen.microbiologyresearch.org Bases to Biology The microbiomes of things

Julian R. Marchesi

Microbiomes have always been with us, and have always played fundamental roles in how systems function. It’s just that we didn’t have a specific name for them, and we have only recently started to explore them in large numbers as sequencing technology has become cheaper and more high throughput.

58 Microbiology Today May 17 | www.microbiologysociety.org Cancerous (malignant) cells divide rapidly and uncontrollably and are able to invade and destroy surrounding tissue. Maurizio de Angelis/Science Photo Library

ne of the first mentions in mentions in his abstract, “Strategies conference communication from David the literature of microbiomes for selection and direct application of Relman, and after that the usage starts Owas in the 1988 book, Fungi microbial antagonists are reviewed to increase dramatically (Fig. 1). in Biological Control Systems, edited for aerial, root and growing media/soil One current working definition of by Michael Burge, in which John M. microbiomes.” However, it seems that a microbiome is “the entire community Whipps, Karen Lewis and Roderic Joshua Lederberg has been attributed of micro-organisms (bacteria, archaea, C. Cooke reviewed mycoparasitism with creating this neologism when one lower and higher eukaryotes and and included a section heading titled searches Google, but Jonathan Eisen, viruses) within a habitat and the ‘Microbiomes, delivery systems and on his microBEnet site, has a nice surrounding environmental conditions.” disease control’ in which they explored potted history of the etymology of this This definition is derived from a recent both aerial and soil microbiomes. Later word which clarifies the situation. The discussion document that Jacques in 1992, John Whipps, in a review of next mentions come 10 years later in Ravel and I published in the journal biological disease control in horticulture, a review by Fergus Shanahan and a Microbiome, with the aim to start a

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0 1990 1995 2000 2005 2010 2015 2020 Year

Fig. 1. Numbers of articles which contain the word microbiome or microbiomes found on Scopus.

Microbiology Today May 17 | www.microbiologysociety.org 59 debate in the wider community on the Staphylococcus epidermidis terminology, as there is some confusion Streptococcus Pityrosporum viridans ovale in the literature. But how come we are now suddenly Candida albicans so excited by research into microbiomes Neisseira Corynebacterium sicca jeikeium and what they do? One of the simplest Staphylococcus hameolyticus explanations is that we now have the tools to allow us to capture, at different Trichosporon omic levels, e.g. genomes, transciptomes and metabonomes, a whole microbiome Streptococcus salivarius and its microbiota and metagenome. We can look into a system across time and across multiple samples, and for Helicobacter pylori the first time determine who’s there and what they are potentially doing, and Streptococcus thermophilus what we have found is astounding. We Bacteroides fragilis are now able to take a holistic rather than reductionist approach to try and explain how different microbiomes are Lactobacillus Lactobacillus reuteri Corynebacterium involved in ecosystem and biosystem casei aurimucosum function. One of the features of microbiome research is that it is based on a multi-disciplinary research model, Bacteroides Lactobacillus thetaiotaomicron unlike traditional microbiology, where a gasseri Ureaplasma scientist can make a career looking at a Escherichia parvum single species. In microbiome research, coli due to the large and complex datasets, the microbiologist needs, for example, biological chemists to create the data Computer illustration of the human microbiome showing the various different types of bacteria commonly for metabolite profiles, and physicists found on human skin and the linings of organs. Gunilla Elam/Science Photo Library to help make sense of it and answer the on the role of the microbiota in knowledge of how extensive the research question set in the first place. maintaining the healthy human human microbiome is. One of the For the first time we can start to try status and how they are involved in areas that most interests me is the and map the interactions between diseases. Because of ‘The Human role of the host microbiota in cancer, different microbes and the surrounding Condition’, we are very focused on any which has been referred to as the system, and this approach is throwing up new situation that potentially can lead cancer microbiome or oncobiome. some challenging notions – for example, to improving the quality and longevity The microbiota in the gut microbiome what is mammalian biology? Previously of life. To meet this need, the majority of have been implicated in playing a role we would have considered it to be the microbiome research in the last 10–15 not only in the initiation of colorectal interaction between the host’s genome years has focused on understanding cancer – by producing carcinogens or and the environment, but now we the role of the microbiota in human genotoxins which caused the ‘first hit’ need to include the metagenome of biology. Notable examples of this in the oncogenes – but also in interacting the microbiota with which we have include the now-completed Human with the developing adenoma as it co-evolved. Microbiome Project and the MetaHIT evolves into a carcinoma. Recently, the Of course, just like in microbiology, project (www.metahit.eu), both of which gut microbiota has been hypothesised research into microbiomes has focused made significant contributions to our to be responsible for host response

60 Microbiology Today May 17 | www.microbiologysociety.org to cancer treatments such as the new Julian R. Marchesi io/2lRX4Zs Last accessed 6 April 2017. immunotherapies being trialled. Sir Martin Evans Building, Cardiff Marchesi, J. R. & Ravel, J. (2015). The However, while we all have a University, Cardiff, Wales CF10 3AT UK vocabulary of microbiome research: a personal interest in understanding Sir Alexander Fleming Building, South proposal. Microbiome 3, 31. human microbiomes and how they Kensington Campus, Imperial College Relman, D. A. (2002). New technologies, influence health and disease, in the London SW7 2AZ, UK human–microbe interactions, and the search wider arena, environmental microbiomes [email protected] for previously unrecognized pathogens. are fundamental to global ecosystem J Infect Dis 186, S254–S258. functions, services and life. All of the Further reading Shanahan, F. (2002). The host–microbe major global geochemical cycles, for Eiser, J. (2015). What does the term interface within the gut. Bailliere’s Best example the nitrogen cycle, would fail microbiome mean? And where did it Pract Res Clin Gastroenterol 16, 915–931. if specific microbiomes, which are come from? A bit of a surprise. Thomas, R. M. & Jobin, C. (2015). The responsible for keystone steps within the http://microb.io/2mfKd3A Last accessed Microbiome and Cancer: Is the ‘Oncobiome’

cycle, were perturbed in such a manner 6 April 2017. Mirage Real? Trends Cancer 1, 24–35. that they failed to fulfil their evolved Lederberg, J. (2001). ‘Ome Sweet Whipps, J. M. (1992). Status of biological roles. Using a microbiome-led approach ‘Omics – A Genealogical Treasury of disease control in horticulture. Biocontrol Sci will help us understand where we need Words. The Scientist http://microb. Technol 2, 3–24. to invest our efforts to ensure that these environmental cycles continue to support an ecosystem conducive to life.

We currently stand on the verge of an exciting new era in microbiology in which we have the potential to fully define the importance of microbes in supporting microbiome function, and how we can modulate it in order to maintain the services and improve them

when we have destroyed them. “

While we all have a personal interest in understanding human microbiomes and how they influence health and disease, in the wider arena, environmental microbiomes are fundamental to global ecosystem functions,

services and life. Deep sea bacteria (blue) on the surface (yellow) of annelid worms (Alvinella sp.). “ Thierry Berrod, Mona Lisa Production/Science Photo Library

Microbiology Today May 17 | www.microbiologysociety.org 61 Microbiomes and nutrient cycling

Coloured scanning electron micrograph of multidrug-resistant Acinetobacter baumannii. Thorunn Helgason Dennis Kunkel Microscopy/Science Photo Library

Any gardener will tell you that the key to a productive and healthy crop is a ‘good’ soil. It is well understood that the sand, silt and clay content of a soil determines its nutrient cycling and water retaining properties. This reflects centuries of development in agricultural practices. Crop rotation, especially with legumes and their nitrogen-fixing bacterial symbionts, became a cornerstone of the agricultural revolution in Europe from the 18th century onwards and created significant increases in crop yields throughout the 19th century. The ‘nitrogen hypothesis’ proposes that this directly enabled the growth of the European population and, hence, the Industrial Revolution.

62 Microbiology Today May 17 | www.microbiologysociety.org n the early 20th century, development of the Haber–Bosch process (for Iwhich Fritz Haber and Carl Bosch were awarded the 1918 Nobel Prize for chemistry) made synthetic fertilisers widely available for the first time. Combined with the Green Revolution during the second half of the century, millions of people were brought out of food poverty. Agricultural production has, so far, been able to feed the world’s expanding population, but this may not last. Soils are being lost – to erosion, drought, flooding, salination and urbanisation Coloured scanning electron micrograph of multidrug-resistant Acinetobacter baumannii. – faster than they can be replaced Dennis Kunkel Microscopy/Science Photo Library by geological weathering. The steady increase in crop yields based on plant breeding technology is slowing down and cannot keep pace with population growth. Now, attention is turning to the soils: understanding their structure and function will give us ways of managing agricultural land that will maintain crop yields in the increasingly smaller spaces we have for farming.

Soil microbes and healthy soil The aim, then, is to create agricultural soils that are “good” and “healthy” in the way gardeners understand. But what is a “healthy” soil? There has been much debate recently about this among farmers, researchers and government. What we all agree on is that the soil microbiome – the living component of the soil including bacteria, fungi, protists and other single-celled organisms – is key. It plays many roles in soils, but as yet we understand rather little about them. We do know that organic matter in soils, derived from microbes, is essential. Microbes capture and bind together organic matter and mineral soil particles to create the structure on

Microbiology Today May 17 | www.microbiologysociety.org 63 Conventional 18-month ley arable wheat

which soil fertility so strongly depends. Most importantly, it appears that a soil with a diverse microbial community will have more large soil particles, called macroaggregates. Macroaggregates are water-stable particles larger than 250µm in diameter, which improve how water and nutrients are maintained within the soil. A very sandy soil is rather like a bowl full of peas: all the particles are the same size and shape, and they pack together neatly resulting in a very low water holding capacity. By contrast, a sandy soil with a substantial proportion of larger organic macroaggregates, or Soils dug from a ley strip (left) and conventional arable field (right). Note the difference in texture of the soils. a bowl of peas and grapes, is unevenly Inset: the number of earthworms extracted from each of the soil samples. T. Helgason packed, with more airspaces of varying sizes, allowing more water to fit in the Biological effects II: bowl. Fungal interactions with the soil food web Biological effects I: Like the bowl of peas and grapes, Mycorrhizal fungi influence microbial soils with thriving microbial communities (e.g. bacterial) communities and plenty of macroaggregates, i.e. soils

that have better structure, hold more Biochemical effects: water. This benefits both crops and the Release of mycelium surrounding environment: if rainfall is products (including glomalin, etc.) from taken up into the soil, then there will decomposing or living be less surface runoff and thus less hyphae flooding in other areas. And fertilisers spread on crops are available to the Physical effects I: crops for longer, increasing efficiency, Alignment of particles; and reducing downstream pollution. exerting pressure Evidence suggests that microbes are essential for the development and Physical effects II: maintenance of macroaggregates. Ψsoil Hyphal enmeshment of particles/microaggregates; Particles of sand and clay are bound altered water regime (dry–wet cycles) by bacteria, and fungal hyphae further tie these together into particles of

increasing size. Soil microfauna, protists Microaggregates 53–250 µm Particulate organic matter and earthworms are attracted to these Microaggregates <53 µm Fungal hyphae rich sources of nutrients, increasing Clay Root exudates the biological activity around them. Silt/sand Mycelium products These microscopic biological factories effectively bind nutrients within soils where plant roots can access them – Mycorrhizas and soil structure. without them, the nutrients simply wash Reproduced with permission from New Phytologist 171, 41–53; doi:10.1111/j.1469-8137.2006.01750.x

64 Microbiology Today May 17 | www.microbiologysociety.org

“

damage and erosion. Better structured Better structured soils are more fertile and less vulnerable to soils are more fertile and less vulnerable loss from drought or flood, and our food security depends on to loss from drought or flood, and our food security depends on being able to being able to reduce the threat to soil. reduce the threat to soil. The microbiome is the living community that binds the soil away. Unfortunately, typical agricultural mycorrhizal (AM) fungi – beneficial together and gives them their most useful soils have fewer macroaggregates, and symbionts that colonise plant roots. They properties. There is a case for saying the this may be limiting crop yield. grow extensive hyphal networks into industrial revolution, and by extension the the soil that again bind large particles world we live in now, was created because White Rose Sustainable together and from which the hyphae of symbiotic nitrogen fixers. Imagine what Agriculture Consortium, and the capture mineral nutrients that are moved could be done if we only understood what farm-scale experiments to the host plant in exchange for carbon. all of the microbes are doing? In 2011, researchers from the Agricultural practices such as Universities of Leeds, Sheffield and York ploughing and extended periods of bare Acknowledgements came together to develop the University ground in fields, reduce the diversity Thorunn Helgason’s work on soil of Leeds farm as a platform where large and quantity of AM fungi. We know that microbiomes is funded by the NERC Soil “scale experiments to understand the productivity tends to increase when AM Security Programme and BBSRC GFS- soil microbiome could be integrated fungi are present, most likely because Sarisa https://www.soilsecurity.org. into a working mixed arable farm. One they act as a link between the plant and of the management strategies being the rest of the soil microbiome, enabling Thorunn Helgason investigated is the use of grass/clover the plant to access nutrients and water Department of Biology, University of York, leys (or fallow) to recover soil structure in a way it cannot do without them. Heslington, York YO10 5DD and function. We can demonstrate these effects in [email protected] simple experiments, but the challenge @Luehea Grass/clover leys now is to show this at the farm scale, Planting a mixture of grass and clover to understand the mechanism that Further reading has been a traditional ley/fallow rotation drives this, and to find out what the Chorley, G. P. H. (1981). The Agricultural all over Europe since the 19th century, other microbial groups, such as nitrogen Revolution in Northern Europe, 1750–1880: but cheap synthetic fertilisers have fixers and fungal pathogens, are doing. Nitrogen, Legumes, and Crop Productivity. encouraged farmers to leave less land New DNA sequencing technologies Econ Hist Rev 34, 71–73. fallow. We are investigating how quickly that enable fast, cheap and data-rich Rillig, M. C. & Mummey, D. L. (2006). leys improve soil structure and fertility, genome sequencing have transformed Mycorrhizas and soil structure. New Phytol and early data suggests it can happen microbiology, and the study of soil 171(1), 41–53. surprisingly quickly. Soil from a ley strip microbiomes is no exception. These 50 Things That Made the Modern Economy: has a visibly ‘crumbly’ texture after 18 technologies allow us to identify these The Haber–Bosch Process BBC World podcast. months that is absent from the ploughed microbes, and observe any change in http://microb.io/2lRwwHz Last accessed strip alongside and, even without the diversity and function as the ley develops 6 April 2017. statistical analysis, we can tell the so that we can understand who is doing Food Security from the Soil Microbiome: number of earthworms has increased. what, where and why. Microbiology Society Policy Briefing note (2016). We are currently looking for the http://microb.io/2lh7zC2 Last accessed microbes that build the structure. We The 21st century and beyond 6 April 2017. expect to find bacteria that secrete sticky We urgently need to find ways to improve The White Rose Sustainable Agriculture polysaccharides, and other molecules soil structure. Climate change models Consortium. http://microb.io/2lRJ3e1 Last that attract particles together. Of predict that extreme weather events will accessed 6 April 2017. particular interest are the arbuscular become more frequent, increasing soil

Microbiology Today May 17 | www.microbiologysociety.org 65 Microbiome – beyond the gut

Melissa Dsouza & Jack A. Gilbert hese improvements have led research that extend beyond the human to the emergence of several, microbiome, and briefly consider the In recent years, vast Tlarge-scale initiatives such as challenges and opportunities awaiting the Human Microbiome Project, the this exciting field, which is still very improvements in the Tara Oceans Project, and the Earth much in its infancy. cost efficiency of high- Microbiome Project, as well as large citizen science surveys such as the Working together on the Tara Oceans throughput sequencing American Gut Project. Consequently, we Project and the Earth Microbiome have observed a tremendous increase Project technologies and the in our knowledge of microbial diversity Over the last decade, we have sophistication of statistical and microbial community dynamics experienced a resurgence of across diverse biomes, including natural history surveys of microbial bioinformatics have humans, animals, plants, air, soil, ecosystems. Empowered by rock, marine, freshwater, sediment, technological advances, programs of transformed our ability and even built environments, among research such as Tara Oceans and many others. Likewise, microbiome the Earth Microbiome Project are an to investigate microbial research has enabled the development embodiment of true, collaborative communities in a wide of surveillance programs that hold the success and the unrestrained promise of protection, restoration and ambition of multidisciplinary teams range of environments remediation of ecosystems impacted of scientists tasked with the complex by anthropogenic pollution and climate goal of constructing a catalogue of the across the globe. change. In this article, we highlight uncultured microbial diversity of this major breakthroughs in microbiome planet. The Tara Oceans researchers,

66 Microbiology Today May 17 | www.microbiologysociety.org Microbiome – beyond the gut

Melissa Dsouza & Jack A. Gilbert Coral reefs are extensive and diverse marine ecosystems. Scubazoo/Science Photo Library who spent more than three years collaboration of scientists from 20 communities of microbes, which lay collecting over 30,000 samples of water, countries. Their observations of the the foundation for predicting how they sediment and plankton, revealed their sponge core–microbiome evolution and will be influenced by climate change. findings in five reports in the May 2015 of host–microbe symbiotic interactions For example, examining the bacteria, issue of Science. Collectively, their work represent a valuable resource enabling archaea, fungi and eukaryotic microbes represents a significant leap in our further research and access to associated with forest soils across China knowledge and understanding of the biotechnologically important, symbiont- provided Ma & others with the power to numerous, previously uncharacterised, derived natural products. Similarly, understand the role of climate regions in planktonic organisms, including bacteria, an EMP-sponsored survey of the soil shaping the interactions between these protists and viruses that form vital microbiome associated with patches kingdoms. They employed co-occurrence components of marine food webs, of remnant prairie grass across the network patterns at a continental scale and that provide half of the oxygen Midwest of the United States provided to reveal complex associations that can generated each year on Earth. Likewise, a clear indication of the importance be used to predict spatial organisation, the success of the Earth Microbiome of certain bacterial taxa and functions and how changes in precipitation Project (EMP) is captured by two recent associated with this vast ecosystem, may impact soil health, stability and studies that make notable contributions and resulted in the discovery of a management. These survey projects, to the fields of microbiome evolution, new bacterial species, ‘Candidatus like the Human Microbiome Project, symbioses, and functional network- Udaeobacter copiosus’, that appears have paved the way for more specific based modelling. First, Thomas & others to be ubiquitously distributed across hypothesis testing to elucidate specific generated extensive data through the the world’s grasslands. Importantly, mechanisms of action that underpin the EMP on microbial symbiont communities large-scale studies of environmental observed ecological characteristics. They associated with 81 species of marine microbiomes have led to an improved provide the scientific community with sponges collected through an extensive understanding of what structures large, publicly available datasets that

Microbiology Today May 17 | www.microbiologysociety.org 67 are an incredible resource for the study of microbial ecology and the evolution of life.

Microbiomes to the rescue The expansion of microbiome research has created novel opportunities to develop surveillance strategies to better monitor and protect pristine environments such as the soil and aquatic ecosystems in the Antarctic. Similarly, a better understanding of microbial biochemistry and ecology is

helping us to devise new approaches to

restore and remediate sites impacted by changing climate, such as the Great Barrier Reef with warming and acidifying oceans, and the Gulf of Mexico following the recent Deepwater Horizon oil spill. Coral reefs are home

to at least 25% of all marine species making these biomes the most biodiverse marine ecosystem on the planet. Rising levels of environmental pressure due to nutrient enrichment, increased sedimentation, and climate change-induced ocean acidification and

warming have deleterious effects on “ coral reef health and biological diversity. At research institutions such as Woods Hole Oceanographic Institute and the Australian Institute of Marine Science, microbiome researchers are actively Coloured scanning electron micrograph of the purple non-sulfur bacterium Rhodobacter ferrooxidans. exploring the adaptive capacity of many Dennis Kunkel Microscopy/Science Photo Library reef organisms and their microbial symbionts to the cumulative pressures of climate change and degraded water quality. Their work is particularly critical Despite the technological advances, there still remain for the restoration and conservation of coral reefs around the world, and many challenges that need to be addressed to gain a to improve our understanding of how microbiomes can contribute to host deeper understanding of the role of microbiomes and their adaptation in the face of climate change. In 2010, the tragic explosion of the interactions within the environments and hosts they inhabit. Deepwater Horizon oil platform killed 11 workers and released 700 million litres 68 Microbiology Today May 17 | www.microbiologysociety.org“ of oil over a few months into the Gulf One of the major obstacles facing harness the power of Earth’s microbial of Mexico, producing drastic changes to microbiome research is the ecosystems. the ecology of the sediment and water. computational and bioinformatics Subsequently, multidisciplinary teams of bottleneck. Some examples of these Melissa Dsouza scientists worked tirelessly to deepen our include determining cellular functions of Argonne National Laboratory, understanding of microbial hydrocarbon the uncharacterised proteins in current Biosciences Division, 9700 S Cass degradation, its regulation, and capacity annotation databases; the development Avenue, Lemont, IL 60439, USA; in marine environments. Their research of biome-specific annotation platforms Department of Surgery, University of was the first to utilise multi-’omic- to improve interpretation; and the Chicago, 5841 S Maryland Avenue, based approaches to comprehensively development of algorithms enabling Chicago, IL 60637, USA; The Marine investigate the diversity and physiology integration of multi-’omic data. Another Biological Laboratory, Woods Hole, of the microbes that responded to this major obstacle is the lack of a global MA 02543, USA; School of Biological hydrocarbon infusion, to characterise initiative to process and integrate all Sciences, The University of Auckland, the several microbial hydrocarbon microbiome data. It is crucial that we Auckland, New Zealand degradation pathways, and to determine develop a long-term strategy that will [email protected] the impacts of dispersant application support the storage, utilisation, and on resident microbial communities and exploration of the large quantities of data Jack A. Gilbert their activities. generated worldwide by high-throughput Argonne National Laboratory, Microbiome studies have also made sequencing technologies. Ongoing Biosciences Division, 9700 S Cass meaningful contributions to a number of development of data science-related Avenue, Lemont, IL 60439, USA; different research areas, including those tools such as Qiita (http://qiita.microbio. Department of Surgery, University of investigating the effects of urbanisation me) and the Joint Genome Institute’s Chicago, 5841 S Maryland Avenue, on microbial distribution patterns and Genomes Online Database can facilitate Chicago, IL 60637, USA; The Marine microbe-driven biogeochemical cycles in the systematic review and meta-analysis Biological Laboratory, Woods Hole, lakes, rivers, and soils; those determining of data produced, thus greatly advancing MA 02543, USA the impact of microbes associated our understanding microbes and their [email protected] with controlled environments such as environments. aquaria on the health and well-being of Further reading animals in captivity; those studying the Where do we go from here? Alivisatos, A. P. & others (2015). A unified occurrence and prevalence of multidrug Challenges aside, microbiome initiative to harness Earth’s microbiomes. resistance genes in terrestrial, marine, researchers are ready to usher in new Science 350, 507–508. and freshwater environments; and others projects and collaborative ventures Bork, P. & others (2015). Tara Oceans studies exploring novel means for preventing following the announcement of the plankton at planetary scale. Science 348, microbial surface attachment and biofilm National Microbiome Initiative by the 873. formation on membrane filters designed White House Office of Science and Bourne, D. G. & others. (2016). Insights into for water purification and wastewater Technology Policy (OSTP). We are the coral microbiome: underpinning the treatment. poised to enter a new golden age of health and resilience of reef ecosystems. microbiome research wherein we Annu Rev Microbiol 70, 317–340. Challenges facing microbiome achieve a holistic understanding of Brewer, T. E. & others. (2016). Genome research microbial life; develop novel diagnostic reduction in an abundant and ubiquitous soil Despite the technological advances, and therapeutic strategies to treat bacterium ‘Candidatus Udaeobacter copiosus’. there still remain many challenges that diseases; mitigate risks associated Nat Microbiol 2, 16198. need to be addressed to gain a deeper with microbial multidrug resistance; Gilbert, J. A. & others. (2014). The Earth understanding of the role of microbiomes identify sustainable solutions for Microbiome project: successes and and their interactions within the restoring, remediating and protecting the aspirations. BMC Biology 12, 69. environments and hosts they inhabit. environment; and eventually realise and

Microbiology Today May 17 | www.microbiologysociety.org 69 Microbial communities within the chronic wound

Wound infection currently costs the NHS more than £4 billion per annum, with over 100,000 chronic wounds diagnosed each year. It is understood that all types of wounds are readily colonised by micro-organisms of either endogenous or exogenous origin.

Sarah E. Maddocks

cute wounds, such as surgical wound exceeds 1x106 colony forming site incisions, cuts, abrasions or units per gram of tissue, it is regarded as Atraumatic skin damage, often being clinically infected. become infected but resolve quickly, Traditional cultivation-dependent usually without the aid of antimicrobial methods of microbial isolation and intervention. Conversely, chronic wounds identification have largely biased are characterised by their failure to heal the recovery of certain bacterial and in a timely, predictable manner, and fungal species from chronic wounds, instead remain stuck in a non-healing namely those that thrive in isolation state for many months or even years. under laboratory conditions such as When the microbial load of a chronic Staphylococcus aureus and Pseudomonas

70 Microbiology Today May 17 | www.microbiologysociety.org Coloured scanning electron micrograph of meticillin-resistant Staphylococcus aureus (MRSA, red) on the microscopic fibres of a wound dressing.Science Photo Library aeruginosa. Next-generation molecular highlight the need to establish a better determined by location. For example, techniques and metabolic analysis of understanding of the chronic wound anaerobes are more prevalent in the chronic wound microbial populations microbiome. groin, under the arms and between have begun to reveal the true complexity the toes. In addition to this, there are of the chronic wound microbiome, with Co-occurence of micro-organisms several endogenous fungi including an estimated 300–400 different species The skin is primarily colonised genera such as Candida, Malasezzia, identified from a variety of chronic by bacteria of four major genera: Debaromyces and Penicillium to name wounds to date. Despite this advance Acinetobacteria, Bacteroidetes, Firmicutes a few. Members of these bacterial and in identification, inconsistent findings and Proteobacteria. These comprise fungal genera typically also constitute between wounds at different anatomical a mixture of aerobic and anaerobic the chronic wound microbiota, most sites, of different sizes and depth, bacteria whose predominance is likely because of their proximity to

Microbiology Today May 17 | www.microbiologysociety.org 71

“

the original site of epithelial damage. Commonly encountered, chronic The complexity of the chronic wound microbiota has given wound bacteria include Staphylococcus rise to the proposition that chronic wound infection cannot be aureus, Pseudomonas aeruginosa, Enterococcus faecalis, coagulase reduced to a single bacterial species. negative staphylococci, Proteus spp., Streptococcus spp., Citrobacter spp., that favours colonisation. Currently, the specific microbial interaction, is linked to Morganella spp., Propionibacterium spp. specific types of micro-organism that increased pathogenicity and documented and Corynebacterium spp. Common mediate impaired healing remain to be for many chronic infectious diseases fungi include Candida albicans, Candida defined, but a combination of multiple such as lung infection in sufferers of parapsilosis, Malasezzia restricta and bacterial species and the nature of the cystic fibrosis or chronic obstructive Curvularia lunata. biofilm lifestyle appears to be critical. pulmonary disorder, or periodontal The co-occurence of micro- A definitive shift from colonisation disease in the oral cavity. organisms is characterised by the to infection in the chronic wound has presence of biofilm, which is associated long been thought of as solely the The chronic wound microbiome with 60% of chronic, infected wounds. consequence of microbial load. However, Little is known about the temporal and Significantly, polymicrobial biofilm it has become progressively apparent spatial development of the chronic within the wound bed has been shown “that other elements are at play, including wound microbiome. A combination of to impair healing by disrupting the finely species diversity and pathogenicity. cooperation and competition for space tuned, sequential events necessary As wound chronicity progresses, an and nutrients invariably drives niche for wound closure to occur. This is eventual diminution of microbial species partitioning, where those best adapted concurrent with a dampening of the occurs until a small number of dominant, to the local environmental conditions pro-inflammatory immune response pathogenic micro-organisms remain will thrive at the expense of those less which is critical for innate immune and this reduction in microbial diversity well adapted. For example, bacteria clearance, and consequently maintains has been correlated with a worsening with a lower oxygen requirement are low-grade production of cytokines prognosis. Furthermore, community likely to predominate in the deeper which perpetuates the tissue damage symbiosis, because of specific or non- tissues. Population analysis using both

Coloured scanning electron micrograph of a skin wound. A fibrin mesh supports a variety of blood cells at the site of an early wound, red and white blood cells (blue) as well as platelet clots (yellow) are visible. Steve Gschmeissner/Science Photo Library

72 Microbiology Today May 17 | www.microbiologysociety.org (Gb) Glabella

(Al) Alar crease

(Ea) External auditory canal

(Na) Nare Retroauricular crease (Ra) such as temporal analysis of microbial (Mb) Manubrium Occiput (Oc) interactions, it might in future be possible to establish a sequential model for the (Ax) Axillary vault Back (Ba) development of chronic wound biofilm. (Ac) Antecubital fossa The complexity of the chronic Buttock (Bt) wound microbiota has given rise to (Vf) Volar forearm the proposition that chronic wound Gluteal crease (Gc) (Id) Interdigital web space infection cannot be reduced to a single Popliteal fossa (Pc) bacterial species. This notion challenges (Hp) Hypothenar palm Koch’s postulates and, with regards (Ic) Inguinal crease Plantar heel (Ph) to the diagnosis and management of chronic infected wounds, confers several (Um) Umbilicus problems. Not least because diagnosis (Tw) Toe web space of infection has traditionally relied upon Front Back the isolation of specific micro-organisms Bacteroidetes Proteobacteria subsequently targeted for treatment Actinobacteria Cyanobacteria Corynebacterineae Divisions selected by analysis of pure culture. Propionibacterineae Firmicutes contributing < 1% Micrococcineae Other Firmicutes Therefore, a comprehensive theoretical Other Actinobacteria Staphylococcaceae Unclassified model of the chronic wound microbiome, taking into consideration temporal Diagram showing the distribution of micro-organisms over the skin of the human body. development, spatial distribution and Darryl Leja, Nhgri/Science Photo Library synergistic bacterial interactions, has phenotypic and molecular methodology infected wounds, a robust mechanistic the potential to provide an invaluable has so far indicated a high degree understanding of community clinical tool to inform appropriate, timely of species segregation amongst the development and microbial interaction intervention to manage chronic wound chronic wound microbial populace, with remains to be established. Attempts infection. commonly co-isolated pathogens such have been made to utilise knowledge as S. aureus and P. aeruginosa found at of the oral microbiota and plaque Sarah E. Maddocks distinct regions within wound biopsies, development as a means of informing Department of Biomedical Sciences, indicating that despite sharing the same models of chronic wound colonisation Cardiff School of Health Science, Cardiff environment, they are unlikely to interact and progression to clinical infection. Metropolitan University, CF5 2YB in vivo. Despite the current scarcity Currently, these have culminated in [email protected] of evidence thoroughly describing the concept of genetically distinct, interactions between members of the co-occurring bacteria behaving as Further reading chronic wound microbiota, evidence has functional equivalent pathogroups James, G. A. & others (2008). Biofilms in highlighted specific interactions between resulting in so-called pathogenic chronic wounds. Wound Repair Regen 16, S. aureus and the opportunistic fungi biofilms — much like members of the 37–44. Candida albicans. For example, S. aureus oral microbiota. Drawing on knowledge Misic, A. M. & others (2014). The wound has been observed attached to the of oral microbial communities, it is not microbiome: modern approached to hyphae of C. albicans and this interaction unreasonable to suggest that chronic examining the role of microorganisms in is thought to promote invasion of an wound colonisation occurs in a similar impaired chronic wound healing. Adv Wound ordinarily non-motile bacterium into the manner, with initial colonisation by Care 3, 502–510. deeper skin tissues. skin microbiota followed by secondary Woods, J. & others (2014). Development and Regardless of the large body of colonisation by pathogens. By applying application of a polymicrobial in vitro wound evidence describing the composition many of the techniques traditionally biofilm model. J Appl Microbiol 112, 998–1006. of the microbial community of chronic employed in the study of oral biofilms,

Microbiology Today May 17 | www.microbiologysociety.org 73 Paul W. O’Toole Microbiome–health associations: status and perspectives

74 Microbiology Today May 17 | www.microbiologysociety.org How we got here We have known for a long time that humans and animals harbour a resident community of microbes on and in their bodies, but these micro-organisms are nutritionally fastidious and often strictly anaerobic, making their culture in the laboratory, identification and characterisation very challenging. The development of high-throughput DNA sequencing methods made it possible to apply culture-independent methods to construct inventories of organisms from any sample with sufficient numbers of cells to generate DNA for amplification by the polymerase chain reaction. Sequencing these pooled amplicons tells the investigator what bacteria are present. If there are even more cells to work with, the total pool of microbial DNA can be extracted and sequenced en masse (so-called ‘shotgun sequencing’), revealing not only what organisms are present, but also what genes they carry and what metabolism they are predicted to be capable of. Although the latter approach is much more expensive than simply profiling the sample, knowing Paul W. O’Toole Coloured scanning electron micrograph of mixed oral bacteria. Steve Gschmeissner/Science Photo Library their coding potential is usually much more biologically informative. Technical Over the last decade, there have been many exciting variations of this approach are used to advances in the understanding of the microbiome – the identify mammalian viruses, bacterial viruses (bacteriophage), fungi, yeast community of organisms present in a particular location, and protozoa, but knowledge of these microbial communities in mammals is often a sample from an animal, plant or the environment. less developed than that of the bacterial Although research on the human microbiome grabs most of microbiome. Studies of the human gut are the headlines, many of the key methodologies were taken or currently more common than studies of other body sites, but the microbiome adapted from environmental microbiologists who are used of skin, lung, oral cavity and liver, for example, are receiving increasing to dealing with very complex microbial communities that are attention. A common denominator very difficult to grow in the laboratory. to many studies is the search for links between an altered microbiome composition and a disease or disease

Microbiology Today May 17 | www.microbiologysociety.org 75 risk (Fig. 1). The list of such diseases (a) (b) linked to the intestinal microbiome

includes obesity, inflammatory bowel 20

14 15 12 10 disease, irritable bowel syndrome, type 8 10 6 4 5 2 0 2 diabetes and colorectal cancer, but 0 0 0 0 0 10 10 10 associations of microbiome alterations 10 20 20 20 20 with extra-intestinal conditions such as 30 30 30 30 cardiovascular disease, and depression/ PC2 PC1 PC2 PC1 40 40 behaviour are also being investigated. 40 40

Because there are known ways or Fig. 1. Altered microbiome in health and disease. Principal coordinates analysis with density weighting of the plausible new mechanisms whereby microbiome composition in colonic mucosal biopsies of (a) healthy controls and (b) subjects with colorectal gut bacteria can influence inflammation, cancer. B. Flemer & P. W. O’Toole. Studying the microbiome: “Omics” made accessible. Semin Liver Dis 36(4), 306–311 microbiome links to diverse conditions such as asthma, arthritis and frailty in processes such as calorie harvest Translating microbiome knowledge older people are being investigated. from the diet, fat synthesis in the liver, The clearest role for the gut inflammation, satiety, and levels and microbiome in disease is arguably

The complexity of microbiome–host kinds of bile salts made in the liver to Clostridium“ difficile-associated interactions process fatty foods. Explaining how diarrhoea. Depletion of the gut It has proven difficult to establish variations in a microbiome (composed microbiome by repeated antibiotic mechanistic links between microbiome of several hundred species, each with treatment allows a bloom of this alterations and disease, with one of several thousand genes) interact with a organism (sometimes called C-diff) the first conditions studied – obesity – multifactorial human pathophysiology which can become recurrent and proving most controversial of all. Rather was never going to be easy. Another cause colitis and diarrhoea. A normal than being able to fulfil Koch’s Postulates high profile condition with microbiome microbiome can be restored by faecal as one would for a bacterial pathogen, links, inflammatory bowel disease microbiota transplantation (FMT) in which the patient receives an enema or colonoscopic injection of a slurry A characteristic of many diseases that feature microbiome prepared with the faeces of a healthy donor. The material is donated by a alterations such as IBD, obesity, type 2 diabetes, and frailty person selected by the recipient or their physician, or in some cases is in the elderly is loss of microbiota diversity, sometimes acquired from a stool bank. FMT leads to 80%–90% cure rates in reflected in lower overall bacterial gene count. uncomplicated cases. The broadly accepted mechanism was simply the by finding the responsible organism and (IBD), is apparently not characterised microbiome restoration, coupled with using a pure culture to replicate diseases by a unifying set of depleted or over- conversion by the incoming bacteria symptoms in a model, it has not been represented micro-organisms across of primary bile acids to secondary and possible to identify single organisms or all patients and studies. Studies in twins tertiary bile acids that inhibit C. difficile definitive microbiome configurations suggest that up to half of the spore outgrowth. However, a recent that translate reproducibly from risk factors for IBD are environmental, small pilot study showed that sterile human to model systems and that so notwithstanding the accepted role of bacteriophage filtrates (not bacterial cause obesity. This is probably due to host genetic factors, it is highly cells) also led to clinical remission, “a multiplicity of mechanisms by which likely that micro-organisms contribute so even in this apparently ‘simple’ the microbiome can influence metabolic to the disease in a manner as yet disease, the microbiome involvement health, involving diverse human unclear. may be more nuanced.

76 Microbiology Today May 17 | www.microbiologysociety.org A characteristic of many diseases weight gain in obesity, predict post- and epidemiologists, to unravel how the that feature microbiome alterations prandial glucose in pre-diabetics, to microbiome modifies risk for health and such as IBD, obesity, type 2 diabetes, stratify subjects with irritable bowel disease. and frailty in the elderly is loss of syndrome, and to detect colorectal microbiota diversity, sometimes cancer (see our recent review for Acknowledgements reflected in lower overall bacterial details). Even more striking is the Microbiome work in PWOT’s gene count. This is referred to by some recent discovery that whether or not laboratory is supported by Science authors as ‘dysbiosis’ but because two cancer patients derive clinical benefit Foundation Ireland through a Centre healthy people can have very different from immunotherapy with checkpoint award to the APC Microbiome Institute microbiota, dysbiosis is hard to reliably inhibitors (monoclonal antibodies that (SFI/12/RC/2273), and a Department define. This makes routine microbiome prevent inhibition of T-cell activation) is of Agriculture, Food and the Marine profiling of healthy subjects of debatable dependent on their baseline microbiota, (DAFM) award (11/F/053) for the value. Although identifying mechanisms which also determines whether or not ELDERFOOD project. linking microbiome alterations to health they suffer from severe side effects Dedicated to the memory of the effects is still a work in progress, there that may require therapy withdrawal. late Professor George T. Macfarlane is emerging evidence for the value of These findings make profiling the gut whose pioneering work on gut microbial using microbiome markers to manage microbiome not only clinically valuable ecology and biochemistry helped to lay (perhaps even sensible routine practice), the foundations. but they also raise the prospect of rationally manipulating the microbiome Paul W. O’Toole to promote response to therapeutics School of Microbiology & APC in people who would otherwise be Microbiome Institute, Room 447 Food non-responders. A handful of drugs Science Building, University College are already known to interact with the Cork, T12 Y337 Cork, Ireland microbiome in ways that modulate their [email protected] efficacy or side-effects, so this topic warrants considerably more attention. Further reading Lynch, S. V. & Pedersen, O. (2016). The Where to now? Human Intestinal Microbiome in Health and When all the initial excitement of Disease. N Engl J Med 375(24), 2369–2379. microbiome research dies down, we O’Toole, P.W. & Flemer, B. (2016). Studying the will realise that inventories of Microbiome: “Omics” Made Accessible. Semin organisms and gene annotations are Liver Dis 36(4), 306–311. starting points, not end-points. There Ott, S. J. & others (2016). Efficacy of is a lot of microbiology research that Sterile Fecal Filtrate Transfer for Treating needs to be done on microbial genes, Patients With Clostridium difficile Infection. enzymes, metabolites, cell models, Gastroenterology 152(4), 799–811. pre-clinical models, and human Pitt, J. M. & others (2016). Resistance subjects. Fastidious organisms will Mechanisms to Immune-Checkpoint need to be cultured and grown as Blockade in Cancer: Tumor-Intrinsic and Fig. 2. Some aspects of the microbiome can be single cultures or as defined consortia, -Extrinsic Factors. Immunity 44(6), modelled by inoculating fermenter vessels with for example in artificial colon models 1255–1269. faecal samples, single isolated cultures or artificial (Fig. 2). Microbiologists will work Shankar, V. (2017). Gut microbiome profiling consortia, and applying a range of analyses including intensively in their own labs, but also tests propelled by customer demand. Nat transcriptomics and metabolomics to measure alongside bioinformaticians, metabolic Biotechnol 35(1), 9. interactions and products. M. Perez & P. W. O’Toole modellers, cell biologists, physicians

Microbiology Today May 17 | www.microbiologysociety.org 77 Annual Conference 2017 3–6 April 2017, EICC, Edinburgh, UK At the start of April, we were delighted to welcome over 1,800 of you to the EICC in Edinburgh to once again enjoy some amazing science and socialising opportunities over the course of four days.

Delegates attended our Conference from all over the globe to hear breakthrough research, and to network and build new connections. Our 2017 Conference programme included: • 29 scientific sessions • over 250 offered talks • over 600 posters • talks from over 200 invited speakers

And for the first time: • We ran two sessions dedicated to professional development. • We provided a fun platform over the lunch period with flash poster presentations. • We awarded four poster prizes, including an Early Career Microbiologists’ Forum prize, a people’s choice award, prizes from our journal Editors, and a prize selected by principal investigators.

To see for yourself what we got up to at Conference, why not check out our YouTube channel to view our videos from the event and see if you can spot someone you know! I. Atherton I.

78 Microbiology Today May 17 | www.microbiologysociety.org Keep up-to-date with events, follow the Society ICC Birmingham on Twitter: @MicrobioSoc Society-Supported Conferences Annual Conference 2018 The Microbiology Society is pleased to announce that nine meetings have been 10–13 April 2018, ICC Birmingham awarded funding in the first round of Society-Supported Conference Grants. #Microbio18 The supported conferences include national and international events that are Preparations are underway for Annual Conference 2018 and the programme is expected to attract over 1,000 delegates. looking spectacular. Session topics have now been confirmed and key speakers are Seventh Advanced Lecture Course on Human Fungal being identified to ensure that once again our Conference provide delegates access Pathogens: Molecular Mechanisms of Host–Pathogen to hot topics, new developments and leading researchers. Keep your eyes peeled for Interactions and Virulence abstract opening and updates on our website later this year. 13–19 May 2017, La Colle sur Loup, France 15th UK Meeting on the Biology and Pathology of Main symposia*: impacts on pathogenicity hepatitis C virus 19–21 May 2017, Cumbria, UK • Biological insights from studying • Synthetic ecology: from 24th International HIV Dynamics and Evolution Workshop new eukaryotic models understanding ecological 23–26 May 2017, Isle of Skye, UK • CLIMB workshop (Genome interactions to designing functional London Microbiome Meeting bioinformatics) microbial communities 7 June 2017, London, UK • Cool tools for imaging • The games microbes play The Annual Irish Fungal Society Conference 2017 • DNA repair to cover control of • The magic of mushrooms in nature 15–16 June 2017, Limerick, Ireland mutation leading to evolution, and in industry Young Microbiologists’ Conference (YMC) 2017 Beyond • Viruses and translation recombination, MutS/MutL, phase Petri dishes: Capacity Building for Applied Research variation and radioactive tolerant • Zoonosis to cover food security and 27–28 June 2017, Ilishan Remo, Nigeria organisms companion animals EMBO Conference – Anaerobic protists: Integrating • Drivers and consequences of virus parasitology with mucosal microbiota and immunology Virus workshops: diversity 31 Aug–3 Sep 2017, Newcastle upon Tyne, UK • Clinical Virology • E. coli to cover environmental The 2nd International Symposium on Stress-Associated • DNA Viruses isolates, UTI, cell biology and RNA Granules in Human Disease and Viral Infection • Negative Strand RNA Viruses strains from animals and plants 10–12 Sep 2017, Heidelberg, Germany • Phylogeny • Immunity session and immune Staphylococcus Great Britain and Ireland 2017 • Plant Viruses models 14–15 Sep 2017, Swansea, UK • Retroviruses • Microbial diversity: Community Call for Round 2 applications interactions in live hosts to cover Prokaryotic and Eukaryotic forums: Round 2 of our Society-Supported microbiome, signalling • Environmental and Conference Grant application is now • Microbial diversity: Community Applied Microbiology open! The next closing date is Monday interactions in the environment • Genetics and Genomics 12 June 2017. If you are organising a • Microbial mayhem – breaking bad conference in any field of microbiology • Microbial Infection to cover switch of commensal and meet the eligibility requirements, • Microbial Physiology, to pathogen including in don’t miss out on the opportunity to Metabolism and Molecular immunocompromised host receive up to £2,000 to cover invited • Microbial metal homeostasis: *Session titles to be confirmed speakers’ costs.

Sign up to our newsletter to ensure you are receiving regular updates about Further information and application guidelines can Conference and other Society news, and visit www.microbiologysociety.org/ be found on the Microbiology Society’s website: events for further information. www.microbiologysociety.org/proposals

Microbiology Today May 17 | www.microbiologysociety.org 79 Focused Meetings 2017

Focused Meetings are a central part of the Microbiology Society’s events programme, with each meeting on a specific microbiological theme. They offer the opportunity of a smaller scale meeting, allowing for informal networking and dedicated time on one subject. Microbial Resources for Agricultural and Food Security #AgriFoodSec17 21–23 June 2017 – Metropolitan Arts Centre, Belfast, UK The meeting will run over three days, with the All Island Phosphorus Sustainability Workshop on day one, followed by the conference on days two and three. Key workshop topics: • Industrial perspectives on phosphorus recycling • Policy, research and future directions for phosphorus sustainability • Regulatory perspectives on phosphorus management Key conference topics: • Harnessing microbial processes within the agri-food sector • Nutrients in the environment with a focus on agricultural systems • Microbial ecosystems and nutrient cycling Abstracts have closed for this meeting but registration is open. Find out more online – http://microb.io/agrifoodsec17 Dr Microbe/ iStock/Thinkstock International Meeting 2017: ISSY33 – #ISSY33 Exploring and Engineering Yeasts for Industrial Application 25–29 June 2017 – University College Cork, Ireland Four days of science, fascinating speakers, networking, posters and the magical city of Cork. Key topics: • Analysing and engineering regulatory networks in yeast • Cell factory product pitches • Engineering novel (to yeast) product pathways • Evolutionary approaches for yeast strain improvement • Exploration of yeast biodiversity for industrially relevant traits • Hybrid genomes of industrial yeasts: analysis and engineering • Metabolomics and proteomics of industrial yeasts • New synthetic pathways in yeast • New tools for yeast genome engineering Registration is open. Find out more online – http://microb.io/ISSY33 Tomás Tyner, UCC, UCC, Tyner, Tomás Ireland Antimicrobial Resistance and One Health #AMROneHealth17 29–30 August 2017 – Maynooth University, Co. Kildare, Ireland Key topics: • Antimicrobial resistance in animals • Antimicrobial resistance evolution in science and politics • Antimicrobial resistance in human health • Antimicrobial resistance in the environment Abstract submission and registration is open. Find out more online – http://microb.io/AMROneHealth17 JK1991/ iStock/Thinkstock

80 Microbiology Today May 17 | www.microbiologysociety.org Keep up-to-date with events, follow the Society on Twitter: @MicrobioSoc

16th International Conference on Pseudomonas #Pseudomonas17 5–9 September 2017 – St George’s Hall, Liverpool, UK Key topics include: • Antibiotics and biofilms • Ecology, evolution and environment • Genomics • Infections and host–pathogen interactions • Mechanisms: signalling, systems and synthetic Abstract submission and registration is open. Find out more online – http://microb.io/pseudomonas17 Edgar Lissel & Diggle Steve 2nd International Meeting on Arboviruses and their Vectors #IMAV17 (IMAV) 7–8 September 2017 – University of Glasgow, UK The meeting will run over two days. The key topics will be: • Antivirals/vaccines • Emergence from A to Zika • Vector biology & ecology • Virus discovery • Virus–host interactions and evolution Abstract submission and registration is open.

Find out more online – http://microb.io/IMAV2017 AMI Images / Library Science Photo

British Yeast Group (BYG) – The Versatility of Yeasts #BYGVOY17 11–13 September 2017 – University of Kent, UK The key topics will be: • Chromosome structure and function • Molecular biology of pathogenic yeasts • Protein folding and quality control • Synthetic and evolutionary genomics • The Cytoskeleton • Yeast metabolism Abstract submission and registration is open. Find out more online – http://microb.io/BYGVOY17 Kent Fungal Group Group Fungal Kent Kent of University Call for 2018 Focused Meeting proposals All Microbiology Society Focused Meetings are the result to put your name to a meeting and work alongside the of accepted proposals from our members, and it is our Microbiology Society to turn your vision into reality. members who provide the expertise in the wide range of The deadline for 2018 applications is 12 June 2017. fields that shape the Focused Meetings series. We deeply All forms will be reviewed by our Scientific Conferences value the relationships we have and the partnerships we Committee, who oversee our scientific programme. make when working together with our members to deliver Please send your 2018 proposals to conferences@ such fantastic events. microbiologysociety.org by the deadline. We encourage our members to submit their ideas The application form and the terms and conditions and proposals for our Focused Meetings series in 2018 can be found on the Microbiology Society website – and applications are now open. It is a great opportunity www.microbiologysociety.org/events.

Microbiology Today May 17 | www.microbiologysociety.org 81 Publishing

70 years of Microbiology

his year represents 70 years of publication for Microbiology, the Society’s oldest journal. The journal started publication Tas the Journal of General Microbiology, renamed Microbiology in 1994. The current Editor-in-Chief is Dr Tanya Parish (Infectious Zerbor/iStock/Thinkstock Disease Research Institute, USA), who has been a long-standing member of the Editorial Board. Recent journal developments include the launch of Microbe Profiles – mini reviews focusing on specific microbes from leading names in the industry – and Short Communications, a shorter body of completed research. Currently published Microbe Profiles are ‘Escherichia coli O157: H7 – notorious relative of the microbiologist’s workhorse’ (http://microb. io/2mcFeR6) and ‘Oenococcus oeni: Queen of the cellar, nightmare of geneticists’ (http://microb.io/2nRmVkr). Of the journal, Tanya says: “We have published many articles aimed at understanding the basic biology of micro- organisms. There are other changes happening in the publishing arena right now, including increased visibility and recognition for reviewers; the development of online preprint servers; and increasing use of social media to discuss research topics. At Microbiology we look forward to incorporating many of these ideas to take us into the next 70 years.“ For more information about the journal please see Microbiology’s homepage (http://mic.microbiologyresearch.org). To submit to the journal please use our online submission system (www.editorialmanager.com/mic). Article redesign and continuous publication icrobiology Society journals have launched a new article redesign that better align Mwith our journal branding. Alongside our article redesign, we have moved to continuous publication. Previously, the Society’s hybrid journals (Microbiology, Journal of General Virology, Journal of Medical Microbiology and International Journal of Systematic and Evolutionary Microbiology) were published monthly. With continuous publication, as soon as an author has approved their copy- edited and typeset proof, the Society’s production team will do a final check and then publish the article online. Each month, these will be grouped together into an online issue, which will also be printed and dispatched to subscribers. The change means that readers will see the best version of the article as soon as possible, and will lead to significant improvement of the Society’s article publication times.

82 Microbiology Today May 17 | www.microbiologysociety.org The first ICTV Virus Taxonomy Profiles are now online ast year, the Microbiology Society announced that Journal of General Virology would be publishing ICTV Virus Taxonomy Profiles – a freely available series of concise, review-type articles that provide Loverviews of the classification, structure and properties of individual virus orders, families and genera. We are pleased to say that the first Profiles are now online and include summaries on Flaviviridae, Ascoviridae, Geminiviridae and Ourmiavirus (http://jgv.microbiologyresearch.org). ICTV Virus Taxonomy Profiles are written by International Committee on Taxonomy of Viruses (ICTV) study groups, comprised of leading experts in the field. The profiles summarise the individual chapters from the ICTV’s online 10th Report on Virus Taxonomy, and will become the go-to place for researchers looking for up-to-date taxonomic information on viruses. Prizes sponsored by Microbiology Society journals icrobiology Society journals offer sponsorship for poster prizes and oral communication Mprizes for early career researchers. Past winners have received a certificate, a small cash prize and a year’s complimentary membership to the Microbiology Society. To see what some of our 2016 winners have been up to since they received their prizes, read the news story on our website (http://microb.io/2hW6QqG). We continue to award prizes and some of our 2017 winners so far include: • Dara Niketic, University of Utah – Microbiology winner at BLAST XIV Meeting. • Keenan Lacey, Trinity College Dublin – Microbiology winner at Dublin Academy of Pathogenomics and Infection Biology Meeting. • Dearbhla Lenehan, University College Dublin – Journal of Medical Microbiology winner at Dublin Academy of Pathogenomics and Infection Dearbhla Lenehan (left) and Dara Niketic (right) receiving their prizes. Biology Meeting. DAPI (Dublin Academy of Pathogenomics and Infection Biology)

Microbiology Today May 17 | www.microbiologysociety.org 83 Grants Research Visit Grants: supporting international collaboration

gata Lisik, from NUI Galway, dataset of 2,000 isolates of Pseudomonas visited Dr Hélène Agogué at the aeruginosa from around the world – The Society’s Research AUniversity of La Rochelle, France, the dataset is particularly detailed as to compare the nitrate reduction and it has associated detailed genotypic, Visit Grant scheme supports biogeography of nitrate reducers in phenotypic and patient data. As it was early career members to intertidal sediments from the French not possible to arrange to analyse and Irish Atlantic coast – accessing the data in Liverpool, the research build collaborations, samples from France to compare to visit allowed Matthew to try to assess those collected in Ireland. During her adaptation of P. aeruginosa to the cystic whether that’s on a local visit, Agata was able to learn and apply fibrosis lung, and compare this to two new research techniques, and the environmental isolate genomes. scale or internationally. results of the work will contribute to a Matthew says, “Through this With funded projects, joint publication by the two groups. collaboration I gained skills and Agata says, “Working at the experience in managing these large including those bolstering University of La Rochelle added an datasets, efficient use of computing international aspect to my research to complete the project in the time existing collaborations and that has benefited and improved that I was in Quebec, and was able to those establishing new my laboratory skills together with discuss in depth the merits of various communication, troubleshooting methodological approaches and ones, the grant scheme and lab management practice. This alternative hypotheses to the established research visit has broadened my future understanding of these infections supports the growth of career perspectives, improved my currently.” scientific skills and will benefit me in The next round of Research Visit networks of microbiologists upcoming job searches on the Irish and Grant funding opens on 1 July with a throughout the world. Read international job market.” deadline of 1 October – visits should Matthew Moore, from the University take place from 1 December onwards. about the experience of of Liverpool, visited Dr Roger Levesque To find out more see our websitewww. at the Integrative and Systems Biology microbiologysociety.org/grants. some of our recent grant Institute (IBIS) at Université Laval in Québec, Canada, in late 2016. Matthew Maria Fernandes recipients below. wanted to visit the Levesque group Professional Development Manager to access a large genome sequence

84 Microbiology Today May 17 | www.microbiologysociety.org Early Career Microbiologists’ Forum Update: Summer schools, socials and new roles

It has now been a month since the Society’s Annual Conference in Edinburgh! We hope you found the pre-Conference networking event to be a useful activity and that you made use of the ‘networking checklist’. These apply to any situation where you find yourself in a group of unfamiliar people, so keep practising!

our ECM Forum Executive Forum members to get together once you! The Programmes Representative Committee met back at the a year. role is being split to allow the Executive Yend of January with a focus on We are also developing a way to Committee to have one member on each developing the Forum and providing involve ECMs in a co-chairing scheme committee within the Society’s structure. more opportunities for its members. at the Annual Conference, with them This means that Andrew Day will This was our first meeting with the new working alongside session organisers. become the Policy Representative and Undergraduate Representative, Amiee This is a great way to push yourself out we will be holding elections for a new Allen, who is exploring ways to increase of your comfort zone, meet new people Publishing Representative, as well as for the integration of undergraduates and gain experience in how sessions at a Chair-Elect. If you think you might like into the Society. As a result, we are conferences are run. If this sounds like to put yourself forward for any of these investigating how to achieve this. something that might interest you, drop roles then the current committee is Amy Richards, your Conferences us an email and we can give you some more than happy to chat with you about Representative, is in the process of more information about what it involves it. Nominations for these will open in the designing ECM-focused meetings to and how to apply. summer so keep your eyes peeled. facilitate better networking between There will soon be nominations As always, if you have any all ECM Forum members, whilst sharing open for several positions on the questions or comments then do our collective wealth of knowledge. Executive Committee. Amiee’s term lasts get in touch via email on ECM@ We aim to roll the first event out in the for one year and so we will be looking microbiologysociety.org. summer of 2018 so keep an eye out for an Undergraduate Representative to for more information! We also replace her. If you have a keen interest Rebecca Hall discussed an annual Summer Social – in microbiology and want to network Communications Representative, a more informal event held in a with people further down the line in ECM Forum Executive Committee few areas across the UK to enable all their career then this is the role for

Microbiology Today May 17 | www.microbiologysociety.org 85 Outreach Education and Outreach and the microbiome

run an outreach activity. Three areas of microbiology research Antimicrobial resistance stood out as being particularly topical: antimicrobial resistance (AMR), and the microbiome microbiomes, and the continued need for vaccines and vaccine-related research. The group decided to give Dr David Cleary’s research and work focuses on antimicrobial three talks throughout the day to resistance and the microbiome. Using a grant, David and colleagues introduce the topics and highlight the are continuing their outreach work from last year by delivering importance of each in the context of infectious disease research. activities based around microbiology and infectious disease to The talks were designed to Jersey-based A-Level students attending a Biomedical Sciences pique the students’ interests and Summer School. underpin the learning of what, to the group, was the most important element: getting students into the

s a Research Fellow working in microbial genomics, David’s Aresearch concerns how bacteria in the airways cause acute respiratory infections or exacerbations in chronic conditions such as COPD or asthma. This involves examining the dynamics of the microbiomes of the upper respiratory tract, the focus being on how the microbiome and, in particular, the epidemiology of Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis change in response to the introduction of new vaccines. In 2016, David, along with Dr Michael Head and Dr Rebecca Brown, went to Jersey College for Girls to Participants in the Summer School at Jersey College for Girls. Dr Michael Head

86 Microbiology Today May 17 | www.microbiologysociety.org laboratory to give them hands-on experience of microbiology-related activities. Throughout the day, the Good Germs, Bad Germs group ran a laboratory session Dr Jamie Lorimer and colleagues from the University of Oxford that focused on concepts that were are running a project called ‘Good Germs, Bad Germs’ to engage highlighted in the AMR talk. The practical itself was straightforward: the public with the growing field of microbiome research, and the group gave the students a choice investigate people’s attitudes towards cleanliness. of common household cleaning products (disinfectants, hand gels) he project is led by social of bacteria present on the surface, but it as well as more natural products scientists and looks at hygiene was the cloth that was most important such as onion, garlic and various – how people think about and in re-seeding the surface after it was spices. The students then had to T practise it. Investigations are centred cleaned. Other experiments include: apply their expectations as to on the domestic kitchen microbiome each household swabbing the same what would be the most effective and participants were asked to swab five surfaces in their kitchen and an antimicrobial against Escherichia various areas of their household kitchen additional surface of their choosing; coli. before and after some kind of hygiene using a brand new chopping board and The outreach award from the intervention. The difference with this recording what it had been used for Microbiology Society will help the team project compared to other citizen science while swabbing at various intervals improve the practical session. They plan projects is that the participants were over a two-week period; swabbing to combine the general overview topics involved in the formation of the research participants’ fridges to look at the from the first event with a practical questions, known as a ‘participatory make-up of the microbiome, and drawn from the current research that approach’ to science. the effect temperature has on the will introduce the students to the use The group has run a series microbiome. In addition to these of genomics to identify AMR genes of focus groups in Oxford with 14 experiments, participants were allowed in bacterial pathogens. The general households who meet every few months to decide on their own experiments methodologies that they are adopting to design the next experiments, and for individually. Most households chose to will also provide the opportunity to the team to assess the participants’ incorporate their pet’s microbiomes in characterise the microbiome of the perceptions of microbes. These some way and to look at where their student’s nasopharynx (the bit at the perceptions include what they think pet’s microbiome signature shows up back of the nose). Their approach will be microbes are, where they come from, in their kitchen. to give students hands-on experience and what constitutes a ‘clean’ kitchen. It is hoped that the results of using some of the latest DNA sequencing Several experiments have been this project (www.goodgerms.org) technologies to generate their own data, carried out so far. In one experiment will reveal how households’ attitudes either on common bacterial species the effectiveness of various cleaning towards hygiene have changed during resident in the respiratory tract or from products, and what happened to the study. By introducing microbes and their own microbiome. The team aim the microbiome of surfaces before the concept of the microbiome to people, to then publish their output – and hope and after products were used, has this will help to inform people about that the students seeing their microflora been investigated. The results of this what good hygiene is and debunk the ‘in lights’ will inspire them to continue a experiment showed that the product idea that all micro-organisms are bad. career in research. used made little difference to the types Dr Jamie Lorimer Dr David Cleary Hannah Forrest To find out about Education and Outreach activities, visit Public Engagement Officer www.microbiologysociety.org/education-outreach [email protected]

Microbiology Today May 17 | www.microbiologysociety.org 87 Policy Connecting

microbiome Participants at the Society’s Microbiome Research Stakeholder Workshops discussed research opportunities and challenges for microbiome stakeholders research and innovation. icrobiomes aren’t just receiving microbiome research relevant to health, Hype and engagement attention from microbiologists. agriculture and food, biotechnology and Hype around microbiomes is a key MInternationally, governments, the environment. challenge, but also an opportunity to funders, regulators and other science engage policy-makers and the public policy stakeholders are also increasingly Opportunities about the importance of microbiome interested in the potential impacts, Participants identified wide-ranging research and microbiology generally. implications and innovations arising current and future opportunities for Misinformation, poorly-evidenced from microbiome research. science, society and the bioeconomy products and applications, and perceived Responding to the need for from our growing knowledge of overselling of research could risk public accessible expert information on this microbiomes, and the development confidence and safety, and affect future rapidly growing area, the Society’s and application of novel tools and investment in the field. Building the Microbiome Expert Working Group is biotechnologies to characterise, manage evidence base, clearly communicating producing a science policy report on and exploit them. Opportunities included research, and public engagement are microbiome research and its relevance precision microbiome-based diagnostics vital. to health, agriculture and food, and biotherapeutics, bioprospecting Public and stakeholder engagement biotechnology and the environment. microbiomes for natural products, was also highlighted as important and novel tools and technologies for in relation to social and bioethical Stakeholder workshops increased agricultural productivity considerations, for example, around To inform the policy report and to and sustainability or for bioenergy and synthetic biology and implications of facilitate interdisciplinary networking bioremediation. research for behaviour, lifestyle and and knowledge exchange, the Society The relevance and opportunities of health (e.g. diet, childbirth). organised five workshops in the UK and research investigating linkages between Ireland. different host and environmental Research and knowledge gaps Collectively, these multidisciplinary microbiomes for a One Health agenda The early-stage nature of microbiome workshops involved around 160 and tackling antimicrobial resistance research also means that there are participants, including researchers was also emphasised. knowledge gaps and challenges common and representatives from government, However, participants were clear to host and environmental research. research funders, industry, regulators about the early-stage nature of much Participants highlighted the inherent and science communicators. microbiome research and challenges complexity and diversity of microbiomes Discussions highlighted cross- that need to be addressed to deliver on as a broad challenge for the field, for cutting opportunities and challenges for these opportunities. example, making establishing baselines

88 Microbiology Today May 17 | www.microbiologysociety.org and biomarkers for ‘healthy’ versus microbiology, biochemistry, systems from funders, learned societies and ‘disturbed’ microbiomes challenging. biology and other disciplines, and other stakeholders that could help, Support for big data and longitudinal communication between researchers or are already helping, to progress studies will be key. working on different microbiomes. microbiome research and translation. While studies characterising Better collaboration between academia, Ideas and examples broadly included microbiome diversity are important, the industry, regulators and end-users is improving informatics and technology need for more focus on and support for also needed to facilitate translation. platforms; targeted funding and training mechanistic and functional research was Skills and expertise gaps in to meet needs; and interdisciplinary emphasised, for example, to move from bioinformatics and microbiology, and networks, meetings and initiatives to correlation to causation in microbiome the need for more integrated training strengthen collaborations and focus disease studies, and facilitate of these and other skills, were also efforts. development of robust interventions. repeatedly raised as issues. The importance of increasing Improving the reproducibility and Outputs and next steps focus on the non-bacterial members of comparability of studies, and access to Feedback from participants was microbiomes such as viruses and fungi, samples and datasets was also seen very positive, with many valuing as well as undetected microbes, was as key. Development and adoption of the opportunity for interdisciplinary also highlighted. standards and best practice for sampling, knowledge exchange and discussion. Lack of fundamental and long-term analysis and data will be important; Information and perspectives understanding about the consequences the inadequacy of metadata (e.g. gathered have been used to inform of manipulating host and environmental clinical, environmental information), for the Society’s microbiome policy microbiomes was also a concern. example, was a commonly cited issue. report, consultation responses and Development of infrastructures, including subsequent meetings with policy Knowledge integration and capacity microbiome biobanks, accessible and stakeholders. building interoperable databases and cloud- The Society will launch the Increasing interdisciplinary working computing platforms are also needed. policy report later this year when was a key theme. Microbiome research Expert Working Group members will is inherently multidisciplinary, requiring Making progress present findings to policy-makers and improved collaboration and integration of Importantly, participants suggested other stakeholders. The Society will skills and expertise across informatics, community-led activities and support also focus on other activities to disseminate the report and facilitate engagement to help progress and inform about microbiome research and microbiology. For more information about the stakeholder workshops and our Microbiome Policy Project visit www.microbiologysociety.org/ microbiome or contact the Policy team ([email protected]).

Paul Richards Policy Officer

Isabel Spence Head of Public Affairs Participants attending a Microbiome Research Stakeholder Workshop.

Microbiology Today May 17 | www.microbiologysociety.org 89 Schoolzone

Teaching the human microbiome in schools Coloured scanning electron micrograph of Every surface of the human body, inside and out, is covered in bacteria on the surface of a human tongue. Steve Gschmeissner/Science Photo Library billions of different species of micro-organisms. These micro- organisms are mainly bacteria, but also include viruses and fungi, and are collectively known as the ‘human microbiome’. The bacteria that make up the human microbiome live together in a close relationship with us and some even help the body perform vital functions.

90 Microbiology Today May 17 | www.microbiologysociety.org hese bacteria exist in unique while others can be beneficial and organisms that we interact with at communities on each person some might cause disease. The balance various stages of our life. This includes T and live in every part of our between health and disease relies any animals we touch, the food we body, from our mouths to our intestines, on the interaction and balance of eat and the antibiotics we take. When which are known as the oral or gut these bacteria in their particular teaching about the microbiome, microbiomes, respectively. Some environment. encourage students to think about bacteria in the microbiome do not Our microbiomes are influenced their own microbiome and what will have any effect on the human host, by our environment and the micro- have influenced theirs in the past month.

Classroom research activity • The physical characteristics of the environment As briefly described above, there are a number of and how this might influence what can inhabit this environments that have unique compositions of micro- environment. organisms and microbiomes. Working in small groups, pick • The functionality of each of the micro-organisms on the one of the following environments to investigate further: host and each other. • mouth • What happens if there are disruptions to the balance • nose of these micro-organisms? And what causes these • gut imbalances (i.e. drugs that may kill off a type of micro- • skin organism)? There are many aspects of these specific environments When the students have completed their research, for the students to investigate, such as: ask them to present their findings to the rest of the class • The make-up of the organisms surviving in that as a poster that could include an infographic to show a specific area. These include bacteria, viruses, fungi and visual representation of the possible number and range of eukaryotes. organisms, and the factors affecting their microbiome.

Drawing the microbiome think influences the bacteria that are food. This is their chance to get creative It is estimated that there are within their gut. with micro-organisms! Tweet your somewhere between three and 10 After brainstorming what might be pictures to the Society’s Twitter micro-organism cells to every one in their gut, get the students to draw account (@MicrobioSoc) or send human cell in the human body. These a magnified image of the inside of a picture of them to education@ micro-organisms vary in their shape their gut, depicting the different micro- microbiologysociety.org and we will and size so trying to visualise the organisms that reside there. Think share our favourites. microbiome can be difficult. about the specific types of bacteria Get your students to think about that are commonly found in the human Hannah Forrest how their gut microbiomes differ from gut and possible foreign microbes that Public Engagement Officer their classmates’. Ask them what they may be present, i.e. from recently eaten [email protected]

Microbiology Today May 17 | www.microbiologysociety.org 91 Membership Q&A This is a regular column to introduce our members. In this issue, we’re pleased to introduce Daniel Morse. D. Morse D. Where are you currently based? and what they can do. During my Who is your role model? School of Dentistry, Cardiff University, undergraduate degree, I chose further Let’s set the bar high: Sir Alexander Wales, UK. microbiology modules to deepen my Fleming, Louis Pasteur, Robert Koch and of course my PhD supervisor, Professor David What is your area of specialism? knowledge in the field. Microbiology continues to amaze me, even now. Williams. If I can be a fraction of what they Oral biofilms and infections. are and what they’ve achieved, I’ll be very What are the professional challenges And more specifically? happy! that present themselves, and how do Microbial interactions within denture- you try to overcome them? What do you do to relax? associated biofilms; the effects of My current work involves metataxonomic I have a young family, so I love to spend bacteria on candidal virulence and profiling of micro-organisms within sites time with my wife and two boys – they are pathogenicity; 3D tissue model in the oral cavity through next-generation my world. I also play guitar in a rock band, development; and biofilm infection and sequencing, looking at the microbiome. so music is an eternal love, and I like to run. subsequent host cell responses. This results in an incredibly large data What one record and luxury item would Tell us about your education to date. set, which needs a lot of analysis, you take to a desert island? I obtained my Biomedical Sciences interpretation and careful consideration Blink 182 – Take Off Your Pants and Jacket undergraduate degree from the of the results. On a ‘bigger picture’ scale, (my absolute favourite album of all time). University of the West of England. I I think the immediate future for science It reminds me of my school days, and was then recruited by a probiotic and is going to be a challenge – the potential my school friends, and just growing up antimicrobial biotechnology company in reduction in funding and the changes in and having the best time. Luxury item… Cardiff as a laboratory technician, and the worldwide view of scientific research. probably my guitar, to keep me sane. promoted to R&D Scientist leading the Additionally, as an early stage researcher Tell us one thing that your work R&D projects for both probiotics and (final stage PhD student), career options colleagues won’t know about you. antimicrobial product development. are of course on the horizon – whether During my school days, I was quite the geek I applied for a PhD studentship at I can secure a postdoctoral research – I would spend hours playing video games, Cardiff University in 2013, and started position, fellowship, eventual lectureship and represented Wales (as part of a team). in October. I have since worked on and supervision of my own students to I also used to be an online radio presenter developing polymicrobial biofilms with a keep on doing what I am doing. for a gaming radio station (cringe)! particular interest in oral acrylic biofilms What is the best part about ‘doing If you weren’t a scientist, what would (denture-associated infections), and how science’? bacteria influence candidal virulence you be? It’s amazing and so much fun. Sure, and pathogenicity in vitro and within a 3D I can’t imagine doing anything else. I would there are days where you can bang tissue model to mimic infections. love to have been an A&E doctor… Or a your head against a wall again and musician or professional gamer. Where did your interest in again, but the satisfaction of knowing microbiology come from? you are working towards making a If you would like to be featured in After choosing my first microbiology difference to scientific knowledge and this section or know someone who module as an undergraduate, it was getting hands-on in research is an may, contact Paul Easton, Head of like love at first sight! I was fascinated incredible feeling. It’s very humbling Membership Services, at p.easton@ by the world of micro-organisms – the to be able to say, “I’m a research microbiologysociety.org vast variety, how they exist and interact, scientist”.

92 Microbiology Today May 17 | www.microbiologysociety.org Podcast – Microbe Talk YouTube channel How do yeast help to give beer its taste? We took a trip Vaccines are one of the miracles of public health, but to the Institute of Food Research and had a pint with the how do they work? We went to the London School of scientists behind the National Collection of Yeast Cultures Hygiene & Tropical Medicine to speak with Dr Adam (http://microb.io/2hrjX2X). Kucharski, who told us about vaccination strategies, We also visited the bottom of the ocean, to learn about and how herd immunity protects people who can’t be the microbes that thrive there (http://microb.io/2kJSqMG), immunised (https://youtu.be/cEn1PKyBUNc). and took a trip back in time to the era of the Byzantine Also on our channel is the latest in our ‘How to’ videos, Empire to hear about the phylogeny of ancient diseases this one covering the skills you need to help you effectively (http://microb.io/2lPZB5D). network at a conference (http://microb.io/2mNtW3v). summerbl4ck on Flickr under 2.0 CC BY-NC-ND The latest from the Microbiology Society Find out what you may have missed from the Microbiology Society. This is a roundup on some of the latest from each of our channels, with details of where you can find them. Blog – Microbe Post Facebook Spider silk is certainly one of the world’s most awesome Back in February, we recorded the second of our Facebook materials, but can it be used to deliver antibiotics? We Live videos – this time from Orbital Comics in London’s spoke to Professor Neil Thomas from the University of Soho area. In the stream, we talked with Sara Kenney and Nottingham, who is looking at ways to embed antibiotics Dr Adam Roberts about Surgeon X, a comic book series set within spider silk for use as potential wound coverings against the backdrop of an antibiotic apocalypse in near- (http://microb.io/2igrG5L). future London. In our continuing series about emerging diseases, Also on our Facebook page are the latest videos from we learnt about Oropouche, a virus estimated to have our recent Annual Conference, which highlight some of the caused over 500,000 infections since its discovery in research presented at the event. 1955 (http://microb.io/2jhpSIu). Adam_C_King/Thinkstock

The Microbiology Society is producing more content than ever before – don’t miss out!

Microbiology Today May 17 | www.microbiologysociety.org 93 Microbiology Books Microbiology Books Reviews Microbiology Books

Probiotics and Prebiotics CurrentProbiotics Research and Prebioticsand Future TrendsCurrentProbiotics Research and Prebioticsand Future The Human Microbiota and Chronic Diseases: Current Research and Future EditedTrends by: K Venema, AP Carmo Trends xviEdited + 508 by: pages, K Venema, August AP 2015 Carmo Dysbiosis as a Cause of Human Pathology Edited by: K Venema, AP Carmo xvi + 508 pages, August 2015 Edited by L. Nibali & B. Henderson •xvi Containing + 508 pages, 33 chapters August 2015 Wiley-Blackwell (2016) • AnContaining invaluable 33 resourcechapters • AnEssentialContaining invaluable for 33 everyone resourcechapters working £120 ISBN 978-1118982877 •on AnEssential gut invaluable microbiota for everyone resource working •on Essential gut microbiota for everyone working See:on gut www.caister.com/probiotics microbiota See: www.caister.com/probiotics A highly popular topic, this book provides extensive See: www.caister.com/probiotics coverage of human microbiota at different anatomic sites with a clear illustration of proportions of various micro- The Bacteriocins CurrentThe Bacteriocins Knowledge and Future organisms in each site. The historical evolution of human ProspectsCurrentThe Bacteriocins Knowledge and Future Current Knowledge and Future microbiota, its relevance to environmental factors and EditedProspects by: RL Dorit, SM Roy, MA RileyEditedProspects by: RL Dorit, SM Roy, MA dysbiosis have been discussed. The effect of microbiota on xivRileyEdited + 158 by: pages, RL Dorit, July SM 2016 Roy, MA Riley human gene expression has been reviewed although, at one xiv + 158 pages, July 2016 "axiv comprehensive + 158 pages, July survey" 2016 (ASM: occasion, microbiota has been considered as ‘pathogenic’, Small"a comprehensive Things Considered); survey" (ASM:"an abundanceSmall"a comprehensive Things of Considered); survey" (ASM:"an ‘indigenous’ and Small Things Considered); "an information"abundance of (BioSpektrum) ‘probiotic’ while information"abundance of (BioSpektrum) information"See: www.caister.com/bacteriocins (BioSpektrum) microbiota is See: www.caister.com/bacteriocins always indigenous See: www.caister.com/bacteriocins (page 185). The Also of Interest possible relationship Also of Interest Also of Interest between dysbiosis • The CRISPR/Cas System: Emerging • The Technology CRISPR/Cas and ApplicationSystem: Emerging and diseases at • The Technology CRISPR/Cas and ApplicationSystem: Emerging Technology and Application different body • MALDI-TOF Mass Spectrometry in • MALDI-TOFMicrobiology Mass Spectrometry in sites – including • MALDI-TOFMicrobiology Mass Spectrometry in Microbiology cancer; chronic • Gas Plasma Sterilization in Microbiology: • Gas Theory, Plasma Applications, Sterilization Pitfalls in Microbiology: and New and metabolic • GasPerspectives Theory, Plasma Applications, Sterilization Pitfalls in Microbiology: and New Theory, Applications, Pitfalls and New diseases such as Perspectives • Antifungals:Perspectives From Genomics to Resistance rheumatoid arthritis; • Antifungals:and the Development From Genomics of Novel to AgentsResistance • Antifungals: From Genomics to Resistance inflammatory bowel and the Development of Novel Agents • Antibiotics:and the Development Current Innovations of Novel Agents and Future diseases; and • Antibiotics:Trends Current Innovations and Future • Antibiotics: Current Innovations and Future diabetes – has been Trends • Microarrays:Trends Current Technology, Innovations explored. The book concludes with a chapter on probiotics and • Microarrays: and Applications Current Technology, Innovations • Microarrays: and Applications Current Technology, Innovations prebiotics and their application in medicine, and ‘microbial and Applications therapy’ for cystic fibrosis. A comprehensive book on a popular subject with up- to-date reviews. It is clearly written and enhanced by clear illustrations. I would recommend it for researchers and students.

Azra Pachenari Middlesex University See Our Full List of Books and eBooks in See Our Full List of Books and eBooks in SeeMicrobiology Our Full List and of Molecular Books and Biology eBooks at: in For more reviews, please visit the online issue of Microbiology Microbiologywww.caister.com and Molecular Biology at: Microbiologywww.caister.com and Molecular Biology at: Today at microbiologysociety.org/microbiologytoday www.caister.com

94 Microbiology Today May 17 | www.microbiologysociety.org Comment Advances in the study of the microbiome James I. Prosser Microbiomics, the study of microbial communities in the context of their environmental characteristics, is effectively microbial ecology and the suffix ‘ome’ nicely combines the concept of ‘biomes’ with modern developments in ‘omics’ Computer artwork of a protein microarray. Alfred Pasieka/Science Photo Library approaches. he explosion in use of the term and then isolating pure cultures, Molecular techniques provided a ‘microbiome’ and the less which were identified by measuring major advance by liberating us from T explosive, but still dramatic, many physiological characteristics. reliance on laboratory cultivation. increase in community studies result These physiological data allowed 16S rRNA genes, amplified from largely from development of molecular us to explore relationships between extracted DNA, enabled identification techniques to characterise microbial isolated organisms and environmental by comparison of sequences with those communities. Until the early 1990s, we characteristics, providing a basis for in burgeoning databases, assessment typically studied natural communities development, and experimental testing, of diversity and comparison of by incubating solid growth medium, of ideas, explanations and ecological communities. Findings were remarkable. inoculated with environmental samples, concepts. We discovered considerable diversity,

Microbiology Today May 17 | www.microbiologysociety.org 95 even in familiar cultivated microbial but they are only as good as their ability discovering extremely high sequence groups, and abundant microbes in to answer scientific questions and test diversity or groups with no cultivated high-level taxonomic groups with hypotheses. representatives. These discoveries were no cultivated representatives. This This introduces what I believe to unexpected and raised new ecological approach was extended to functional be a major limitation to advances in questions, but this study exemplifies genes and was greatly facilitated by microbiomics. Many of the promises the point that discoveries do not require decreasing sequencing costs. It is made for microbiomics and ‘omics’ unstructured surveys. It can even be worth remembering that no technique techniques are reminiscent of those argued that important discoveries are is perfect and molecular community made for early molecular techniques 25 more likely to arise from question- and analysis has bias and limitations. Some years ago. Our limited ability to deliver hypothesis-driven research. cells lyse more easily than others, on these promises results from an The field of microbiomics is some genes are easier to amplify, etc., apparent reluctance to ask important, enormously exciting and provides but this tremendous technical advance critical scientific questions or to propose intellectually interesting and stimulating generated many surveys and sequence ideas, hypotheses and explanations for scientific challenges that are lists. This is now the standard approach unexplained natural phenomena. Most important within and beyond microbial to community analysis but in some studies are not question- or hypothesis- ecology. We have never before had senses it represented a backward driven, and microbiomics is dominated such powerful techniques to study step. Ironically, this is partly because by descriptive and correlation-based microbial communities, but we must genome sequencing of cultivated studies. Correlation-based studies think carefully if they are to be fully microbes demonstrated considerable attempt to gain information on links exploited. We will only make significant lateral transfer of genes, particularly between phylogeny and function by advances in scientific understanding those of ecological importance. We looking for correlations between of the links between communities therefore have only limited information 16S rRNA gene sequences and and their environments if we begin by on relationships between (16S rRNA- environmental characteristics. It is identifying interesting phenomena and based) phylogeny and function, which is relatively easy to obtain such data questions, and suggest explanations the basis of evolutionary and ecological but the environmental characteristics and potential answers that can be theory, and the valuable link between measured are usually those that are tested experimentally, thinking carefully environmental and physiological cheap and easy to measure, rather about which techniques are required. characteristics was broken. than those of ecological relevance. Important scientific questions are Microbial ecologists attempted These studies also assume, implicitly, unlikely to be answered by hoping that technical solutions to this problem. a relationship between phylogeny, explanations will ‘fall out of the data’ Sequencing of transcripts and physiology and environmental and microbiomics will advance faster, proteomics, respectively, indicate characteristics. As a consequence, they and deliver its promise, only when we which genes are stimulated and are usually descriptive and situation- can match technical ingenuity with translated following environmental specific and are rarely based on intellectual effort, creativity and the change. Increases in gene abundance important scientific questions. They can confidence to develop and test original tell us which organisms are growing. be used to generate hypotheses and ideas and concepts. Stable isotope probing indicates which explanations, but these are rarely tested. organisms assimilate a particular Hypothesis-based studies also James I. Prosser substrate. Sequencing all genes lead to discoveries. Our first molecular Institute of Biological and Environmental (metagenomics) indicates potential studies of soil ammonia oxidisers Sciences, University of Aberdeen, function, but relies on the (dangerous) tested the hypothesis that soil pH Cruickshank Building, St Machar Drive, assumption that gene presence is linked selects different groups of these Aberdeen, AB24 3UU to activity and ecosystem function. It is organisms. Sequence data answered [email protected] easy to be seduced by these techniques this question but we could not avoid

96 Microbiology Today May 17 | www.microbiologysociety.org

1 5 3 microbiologyresearch.org Our influential Editors and Editorial Board members are selected are members and Editorial Board Our influential Editors OUR JOURNALS HAVE EXPERT EXPERT OUR JOURNALS HAVE to the microbiology community. to the microbiology and contribution , expertise their knowledge for INTERNATIONAL EDITORIAL BOARDS EDITORIAL INTERNATIONAL . and outreach , policy, education development , professional international conferences REASONS and impact of microbiology by connecting and empowering communities worldwide, through: through: worldwide, communities and empowering connecting by and impact of microbiology Unlike commerical publishers, we invest our publishing surplus to advance the understanding the understanding our publishing surplus to advance we invest publishers, commerical Unlike WE ARE A NOT-FOR-PROFIT ORGANISATION WE ARE A NOT-FOR-PROFIT 5 TO TO PUBLISH WITH US 4 2 Find out more about our journals at about our journals Find out more

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Journal: Microbiology Today Microbiology Essential Generics: Chloramphenical Ad Chloramphenical Generics: Essential 25/11/2016 11:55 CHL25060 O65995 PIP: 106-5796 AAH: CHL600B ALLIANCE: MOVIANTO: CAPSULES CHLORAMPHENICOL 1 2 3,4 Adverse events should be reported. Reporting forms be reported. events should Adverse can be found at www.mhra.gov.uk/ and information events should also be reported to yellowcard. Adverse Essential Generics on 01784 477167. distension, pallid cyanosis, vomiting, progressing to vasomotor collapse, distension, pallid cyanosis, vomiting, progressing to vasomotor of irregular respiration and death within a few hours of the onset symptoms. Overdose: Stop chloramphenicol immediately if signs of adverse events oral develop. Treatment is mainly supportive. If an allergy develops, Baby antihistamines may be used. In severe overdosage e.g. Gray Resin Syndrome, reduce plasma levels of chloramphenicol rapidly. increase haemoperfusion (XAD-4) has been reported to substantially chloramphenicol clearance. Pack size and Price: 60 capsules £377.00 Legal Category: POM. Market Authorisation Number: PL17736/0075. Market Authorisation Holder: Chemidex Pharma Limited, 7 Egham UK. Business Village, Crabtree Road, Egham, Surrey TW20 8RB, Date of preparation: January 2016. for See Chloramphenicol Capsules Summary of Product Characteristics full prescribing information. References: 1. Martindale: The Complete Drug Reference. Chloramphenicol. [Online]. Available from: http://www.medicinescomplete.com [22nd of November 2016]. 2. Fluit, A.C., Wielders, C.L.C., Verhoef, J., and Schmitz, F.J. Epidemiology and susceptibility of 3,051 Staphylococcus aureus isolates from 25 university hospitals participating in the European SENTRY Study. Journal of Clinical Microbiology. 2001; 39(10): 3727-3732. 3. Kelly, C., LaMont. Patient information: Antibiotic- cile (Beyond the associated diarrhea caused by Clostridium diffi Basics).June 2015. 4. Bartlett J.G. Antimicrobial agents implicated cile toxin-associated diarrhea of colitis. Johns in Clostridium diffi Hopkins Med J. 1981; 149(1): 6-9. 5. Feder. H, Chloramphenicol: What we have learned in the last decade. Southern Medical Journal. 1986; (79)9: 1129-34. 6. Weigel LM et al. High-Level Vancomycin-Resistant lm. Staphylococcus aureus Isolates Associated with a Polymicrobial Biofi Antimicrob Agents Chemother. 2007 Jan; 51(1): 231–238. 7. Ensminger, P., Counter, F., Thomas, L., Lebbehuse, P. Susceptibility, resistance development, and synergy of antimicrobial combinations against cile. Current Microbiology. 1982; 7: 59-62. 8. Poilane, Clostridium diffi I., Bert, F., Cruaud, P., Nicolas-Chanoine, MH., Collignon, A. Interest cile isolates of the disk diffusion method for screening Clostridium diffi with decreased susceptibility to antibiotics. Pathologie Biologie (Paris). 2007; 55(8-9): 429-33. 9. Cattoir, V., Ould-Hocine, ZF., Legrand, P. cile clinical isolates Antimicrobial susceptibility of Clostridium diffi collected from 2001 to 2007 in a French university hospital. Pathologie Biologie (Paris). 2008; 56(7-8): 407-11. 10. Brazier, JS., Levett, PN., Stannard, AJ., Phillips, KD., Willis, AT. Antibiotic susceptibility of clinical isolates of clostridia. Journal of Antimicrobial Chemotherapy. 1985; 15(2): 181-5. 1,5 1,5 1,5 7-10 1,5 1,5 1 2 6

infections including: Oral levels comparable to i.v. levels to i.v. comparable Oral levels cile with C.diffi implicated Rarely Widely distributed throughout the body, including CSF including the body, throughout distributed Widely Typhoid Neisseria Legionella Rickettsia MRSA VRSA

E. coli

C.diffi cile C.diffi

H. infl uenzae H. infl Effective against serious Abbreviated Prescribing Information Chloramphenicol Capsules BP 250mg Presentation: Hard Gelatin Capsules. particularly Indications: Typhoid fever and life-threatening infections, uenzae, where other antibiotics will those caused by Haemophilus Infl ce. not suffi Posology: For oral administration. doses. For Adults and elderly: 50 mg/kg body weight daily in 4 divided be doubled severe infections (meningitis, septicaemia), this dose may Children: initially, but must be reduced as soon as clinically possible. Not recommended. Contra-indications: Known hypersensitivity or toxic reaction to used chloramphenicol or to any of the excipients. Should not be active for the prophylaxis or treatment of minor infections; during liable to immunisation; in porphyria patients; in patients taking drugs by breast- depress bone marrow function; during pregnancy, labour or feeding mothers. Special warnings and precautions for use: Use only if other treatments are ineffective. Use should be carefully monitored. Reduce dose and monitor plasma levels in hepatic or renal impairment; in the elderly; and in patients concurrently treated with interacting drugs. Interactions: Chloramphenicol prolongs the elimination, increasing the blood levels of drugs including warfarin, phenytoin, sulphonylureas, tolbutamide. Doses of anticonvulsants and anticoagulants may need to be adjusted if given concurrently. Complex effects (increased/decreased plasma levels) requiring monitoring of chloramphenicol plasma levels have been reported with co-administration of penicillins and rifampicin. Paracetamol prolongs chloramphenicol half-life and concurrent administration should be avoided. Chloramphenicol may increase the plasma levels of calcineurin inhibitors e.g. ciclosporin and tacrolimus. Barbiturates such as phenobarbitone increase the metabolism of chloramphenicol, resulting in reduced plasma chloramphenicol concentrations. In addition, there may be a decrease in the metabolism of phenobarbitone with concomitant chloramphenicol use. There is a small risk that chloramphenicol may reduce the contraceptive effect of oestrogens. Chloramphenicol reduces the response to hydroxocobalamin. Chloramphenicol is contra-indicated in patients taking drugs liable to suppress bone marrow function e.g. carbamazepine, sulphonamides, phenylbutazone, penicillamine, cytotoxic agents, some antipsychotics including clozapine and particularly depot antipsychotics, procainamide, nucleoside reverse transcriptase inhibitors, propylthiouracil. Pregnancy and Lactation: The use of chloramphenicol is contra- indicated as the drug crosses the placenta and is excreted in breast milk. cant effect Effects on ability to drive and use machines: No signifi on driving ability. Undesirable Effects: Reversible dose related bone marrow depression, irreversible aplastic anaemia, increased bleeding time, hypersensitivity reactions including allergic skin reactions, optic neuritis leading to blindness, ototoxicity, acidotic cardiovascular collapse, nausea, vomiting, glossitis, stomatitis, diarrhoea, enterocolitis, Gray Baby Syndrome particularly in the newborn, which consists of abdominal For further information, please contact: Essential Generics, 7 Egham Business Village, Crabtree Road, Egham, Surrey TW20 8RB, UK For further information, please contact: Essential Generics, 7 Egham Business Village, Crabtree Road, EG/CH/NOV/2016/02a 01177_Chloramphenicol Ad_Microbiology Today_AW.indd 1 Advertisement Feature

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