Invisible You: the Human Microbiome Exhibition

In an earlier post, I described plans for an exhibition at the Eden project here in Cornwall that would combine art and the biology of the microbes that live on and in our body. Supported by the Welcome Trust, that exhibition has now become a reality. Located in the Core building (and included in the normal Eden Project ticket), it consists of a variety of art installations that are widely different, but that all focus on the importance of the invisible ‘bugs’ we carry around on our bodies. For example, Rebecca Harris’ ‘Symbiosis’is a textile map of the human body depicting microbes as embroidered knots and Rogan Brown creates bacteria out of layers of cut paper:IMG_7972

IMG_7968There is much more to discover, including music and poetry. The opening week has/had a number of demonstrations/workshops too. I will blog about two of these later. It has been a great experience for Will and myself to be involved in this project, and we urge everyone to go take a look at the Invisible You exhibition!

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Society for General Microbiology Meeting 2015 Birmingham

Five of us from the ECEHH coastal pathogens research group based at the Penryn campus in Cornwall attended the Society of General Microbiology Annual Conference held this year in the International Convention Centre in Birmingham. This was a great opportunity to catch up with colleagues and friends, to network, stay informed about the latest developments in our field of research (and broader topics of interest) and of course to showcase our own research.

Will Gaze gave an excellent presentation in the Antimicrobial Resistance session on the first morning of the conference on his work on class 1 integrons as markers of antibiotic resistance. On the second day of the conference, Mik Vos presented “Rates of lateral gene transfer in prokaryotes: high but why?” in the session on the Building Blocks of Microbial Evolution, which generated some interesting discussion in Q&A session following. The rest of the coastal pathogens group that attended the conference presented posters:

“Human recreational exposure to antibiotic resistant bacteria in coastal bathing waters” by Anne Leonard, Lihong Zhang, Andrew Balfour, Ruth Garside & William Gaze

“No effect of transformation on the evolution of resistance to bacteriophages in the Acinetobacter baylyi model system” by Amy Mcleman, Pawel Sierocinski. Elze Hesse, Angus Buckling, Gabriel Perron, Nils Huelther Pal Jarle Johnsen & Michiel Vos

“Investigating co-selection for antibiotic resistance in the environment” by Aimee Murray, Lihong Zhang, Jason Snape & William Gaze

“Dissemination of CTX-M bearing coliforms in the UK aquatic environment” by Lihong Zhang, Andrew Balfour, Aimee Murray, Anne Leonard & William Gaze.

Upcoming conferences where we will be presenting our research:
3rd international symposium on the environmental dimension of antibiotic resistance (May 2015, Wernigerode, Germany)

Anne Leonard

see Aimee and Michiel working thwir magic below….

Aimee SGM Mick SGM

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Antibiotic resistance risk for coastal water users

Recreational users of coastal waters such as swimmers and surfers are at risk of exposure to antibiotic resistant bacteria, according to a new study  by Anne Leonard, Lihong Zhang, Andrew Balfour, Ruth Garside and Will Gaze published this week.

We assessed the amount of water ingested during different water sports and combined this with water sampling data to estimate people’s exposure to bacteria resistant to antibiotics. Using data gathered across England and Wales in 2012, we estimated that over 6.3 million water sport sessions resulted in one type of resistant bacteria being swallowed.

The research focused on the prevalence of Escherichia coli and specifically considered those resistant to an important class of antibiotics known as third-generation cephalosporins – or 3GCs. We considered surfers, sea swimmers, divers and kayakers and found that while only 0.12% of E. coli found in coastal waters and rivers running into beaches were resistant to 3GCs, this number was enough to present a potential risk of exposure to water users. Surfers and sea swimmers were among those at highest risk of exposure due to their tendency to swallow more water. The project was led by microbiologist Dr William Gaze, who believes these findings represent just part of the story:

“We know very little about how the natural environment can spread antibiotic resistant bacteria to humans, or how our exposure to these microbes can affect health. People are exposed to antibiotic resistant bacteria in many ways, through person-to-person contact, via food and as a result of international travel. Our research establishes recreational use of coastal waters as an additional route of exposure. With millions of people visiting beaches in England and Wales each year, there is a risk of people ingesting 3GC resistant E. coli, and it looks like water-users’ exposure to all resistant bacteria could be even higher.”

The study also showed that people’s risk of exposure to resistant bacteria is closely related to water quality at a given beach, demonstrating the importance of the EU Bathing Water Directive, which aims to ensure good water quality standards. Antibiotic resistant bacterial infections pose a serious threat to human health and the study’s authors are currently working to investigate the link between recreational exposure in the sea, colonisation in the body and infection. We hope that our findings will increase the understanding of the health risks that water users might face. Another of the study’s authors, Anne Leonard, said:

“Although this research has established that coastal waters are a potential source of exposure to antibiotic resistant bacteria, we’re not recommending that people stop visiting the beach. Exercise and enjoyment of the natural environment has many established benefits for health and wellbeing, and this kind of research will help us ensure people can still make the most of our coastal resources.”

A number of media have reported on the study, including Vice, the Daily Mail, New Jersey.com and the Süddeutsche Zeitung. Finally, first author Anne Leonard summarizes the research in a short video:

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twitter

Two weeks ago I visited collaborator Adam Eyre-Walker at the University of Sussex in Brighton. Adam and I have been working on a paper exploring what selective forces underly the rate with which bacteria take up new genes, using insights from theory developed to explain the rate at which point mutations occur. The manuscript is close to submission and I hope to post about it sometime soon. Adam also has a blog, where he writes both about population genetics (primarily the fitness effects of mutations) and the sociology of science (primarily scientific publishing): recommended reading! It was great to catch up and also to meet the people in his group. Our converation in the pub turned not to blogs but to twitter, as Adam mentioned his recent tweets describing his experience with PLoS ONE asking him for his personal bank statements to prove he really did qualify for a publication fee waiver, which garnered quite some attention. I have always been  suspicious about twitter, mainly associating it with every man and his dog spouting uninteresting opinions about everything and anything all the time.anabodiodicsThere seems to be an element of truth in this assessment. Idiocy, in-jokes and self-promotion aside, of course there are also plenty of interesting tweets. In Adam’s experience, twitter is a good tool to promote his research, as well as an effective way of finding out about interesting new papers and events in his field (something collaborator Britt Koskella told me before). I realize that twitter can be a very efficient medium to keep updated on specific interests. It might actually be a little bit too good at its job by offering an endless source of procrastination. For instance, scrolling for just a minute through Adam’s twitter feed I found a cool clip on false positives, an interesting discussion of Adam’s analysis of lab size and productivity and a witty comment on The Sun’s page 3. Considering that I have the attention-span of a prawn anyway, I have not yet signed up…

Michiel

P.S. A nice post by Beryl Lieff Benderly on the pro’s and cons of using twitter in science can be found here.

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Pitch: a Guide to the Bacteria and Archaea

Background: inspired by a post by Jonathan Eisen on his blog ‘the tree of life’, I wrote a little post on ‘a Field Guide to the Bacteria’ last year. Both our posts were about the rather megalomaniacal (in a good way) idea of sampling, sequencing and identifying bacteria from the environment in ‘real time’. So rather than walking through the field with binoculars identifying birds, walking (anywhere) with a small sequencing device+computer and identifying microbes. This is obviously quite futuristic, but I have been thinking about a guide book to bacteria (from now on read ‘bacteria’ to mean both bacteria and archaea) that would be perfectly feasible. I think it is a very cool idea, but it would be great to have some of your feedback to see if it is actually worth pursuing. I am starting with the premise that a) bacteria cannot be identified in the field and b) a guide on bacteria cannot be in any way, shape or from be representative of actual diversity (in contrast to say most regional bird guides). More positively, I also think that c) bacteria can be beautifully illustrated and d) that they have very diverse and interesting life-styles that would make for some good reading. Applying a ‘traditional’ natural history format focusing on species diversity could be a very good way of bringing the sophistication of bacteria to the attention of the general public.

The pitch: a guide book where 100 bacterial species are represented by a page of text and an opposing page with a Scanning Electron Microscopy (SEM) picture. The format will be like any other guide book, utilizing pictograms to signify key characteristics (e.g. genome size, metabolism and habitat) and a short text segment on general biology as well as a segment on how the species impacts on us humans. Using 100 species would allow covering a lot of bacterial variation: many different taxonomic groups, many different habitats and niches and many different types of metabolism. Examples would include oceanic species, soil species, gut species, phyllosphere species, pathogenic species, hotspring species, food fermenting species, endosymbiotic species, photosynthesizing species, lithotrophic species, multicellular species, tiny species, ‘giant’ species, magnetic species, halophilic species, Bacteroidetes, Actinobacteria, Chloroflexi, etc etc. Each species would serve to highlight one specific, interesting behaviour.

The illustrations: beautiful SEM colour illustrations will be essential. Hands down the most beautiful SEM pictures of bacteria I have seen so far are those of award-winning ‘micronaut‘ Martin Oeggerli. Martin uses highly sophisticated post-processing colouring for an ‘acrylic finish’. See below for a fantastic image of a consortium of gut bacteria (including a plant fibre and the eukaryotic parasite Giardia on the far right):06-intestinal-bacteria-670

The format: there is some precedent: MicrobeWiki features illustrated descriptions of selected bacterial species (example page here). Although this is a great resource, it is not comparable to the coffee table book I have in mind. There is a case to be made to not produce a book, but build an app instead. This might be cheaper to do and also allow reaching a wider audience. Also, it will be relatively easy to add many more species to the app when the project is succesful. And it will allow linking to relevant websites, such as those hosting genome sequences etc (the downside to this is that the app needs curating to prevent dead links and just having a multi-FASTA file with millions of A’s and T’s and C’s and G’s pop up by itself is not that helpful to the average reader and would need a lot of extra context).  Of course, the two formats are not mutually exclusive. I still think a book is nicer though.

An example page: because a picture is worth a 1000 words, my sister Leonie helped me to produce an example page using my favourite bacterium Myxococcus xanthus. The SEM is by Juergen Berger at the MPI and was used a cover for Current Biology for one of my papers with Gregory Velicer (although beautiful, I think the colours are a bit artificial, soil is not blue!). I am not sure about the pictograms yet. Most conventional guides have a little map with a distribution range coloured in. I do not think that will be very helpful for most bacterial species, as they are generally very widely distributed and they definitely do not migrate (my thoughts on bacterial biogeography are summarized in this paper and this other paper). A pictogram of the habitat would be very useful however. Likewise, a pictogram summarizing genome information (genome size, chromosome and plasmid number and shape (circular or lineair) and number of genes) would be essential. More tricky but absolutely necessary would be a clear pictogram summarizing metabolism (and whether the species is aerobic or anaerobic). There are many other small interesting pieces of information that could be summarized in such a standard way. BOOK

The contributors: this will have to be a team effort. Here’s who would be needed:

  • the scientific community. PI’s that work on an interesting model system would be asked to a) write two pages on what is cool about their model system (+ provide a list of basic information needed to produce the pictograms) and b) send a sample to an SEM facility. In return they will have an outlet to educate the public about their favourite organism by being featured in a book and they will have permission to use a beautiful picture of their bug in their future talks. I know (of) many labs that I could ask to contribute and I do not see any problems there.
  • an SEM wizard. The production of SEMs and, as importantly, the post-processing of images would need to be done by a single person/facility to guarantee continuity and consistency. The quality of the images would be vital to the project.
  • an editor. That would be me. As with the images, the text needs to have a consistent format and style. Editing text provided by other scientists would be much less work than writing copy on 100 species myself from  scratch. I like writing; this should be doable.
  • a graphic designer. The book needs to look slick. The pictograms need to be informative and beautiful at the same time.
  • a  couple of expert microbiologists. Guides usually have a background section at the start featuring more general information about habitats, morphology and life history. This will be a must for this guide, as most readers will know comparatively little about the featured organisms. For instance, having an expert on metabolism on board to briefly explain this complicated topic to the lay person would make the guide much more valuable. The same goes for genome sequencing. Hopefully Jonathan Eisen would want to write the foreword.

How to get there: I am not sure! I guess there are three ways of securing money to make this happen: approaching publishers, crowdfunding and outreach grants. I do not have a good idea about the costs involved and the sales needed to cover them. I would greatly appreciate your comments on the book idea itself and about financing!

Michiel

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Is every bacterium everywhere?

I posted some excerpts from a paper in progress a while back (How many species of bacteria are there? and Bacteria vs. Animals). Here another post on the question “Is every bacterium everywhere?” (then I will stop and just link to the published version!).

Through the narrow sea strait between the Indonesian islands Bali and Lombok, past Borneo and Sulawesi on towards the Philippines runs the Wallace line, named after the co-conceiver of the theory of evolution through natural selection Alfred Russell Wallace. The fauna west of this invisible line is Asiatic, and includes for example tigers and orang-utans, whereas the fauna east of this line shares Asiatic and Australian characteristics, missing most of the Asiatic megafauna species. To understand why such biogeographic boundaries exist, it is necessary to look into the geological past. During the last Ice Ages, seawater levels were dramatically lower and the islands on the Asiatic side of the line were connected to each other as well as to mainland Asia. However, deep waters separated this landmass from more easterly islands such as Lombok and Sulawesi. Without land bridges, these islands could only be colonized by animals capable of surviving journeys over sea or through the air. The debate on whether there exist equivalents of the Wallace line for bacteria is well over a century old (1) and has still not been resolved. One important reason for this lack of progress is that biogeographic patterns change depending on the taxonomic or genetic resolution used (2). For example: different monkey species occur on both sides of the Wallace line and so when only the broad classification ‘’primate’ would be used, no biogeographical patterns would be apparent. Only when looking at the level of species, patterns would emerge, for instance showing that the Crab-eating macaque is the only primate species occurring on either side of the Wallace line. Moreover, it is likely that high resolution sequencing data would reveal subtle genetic differences between populations of a species inhabiting different islands on one side of the Wallace line. As the methods used to differentiate bacteria are often relatively crude, biogeographic differences thus could be overlooked.

 
One other problem with the study of bacterial biogeography is that different researchers use different definitions of the term ‘biogeography’. In its broadest sense, biogeographic patterns could be said to exist when finding different species in different geographical locations. In a narrower sense, biogeographic patterns are recognized only in the subset of cases where geographically distinct, but environmentally very similar locations harbour different species. In this latter case, barriers to dispersal must have prevented a single species to colonize all suitable habitats (3). In its broad definition, bacterial biogeography is uncontroversial: different environments select for different bacteria. In its narrower definition, things are not so clear. The very small sizes of bacteria combined with their large population sizes are likely to make dispersal by water or wind highly effective, and presumably not much hindered by potential barriers such as seas, mountain ranges or just sheer distance. Indeed, there are no known cases of bacteria that are restricted to one geographical location, whereas there are many documented cases of bacterial species (be it in forest soils, hot springs or the open ocean) that occur globally. This is not to say that there is no geographic structuring within these species: isolates that are geographically more distant often are on average also genetically more distant. To some extent, the differences must be due to chance, with different populations experiencing different mutations with small effects on fitness that persist without spreading to other geographic populations. To a large extent, these genetic differences must be due to adaptation to local differences in habitat. It is hard to figure out which ecological differences between locations are relevant to bacteria as there are many and they can be subtle (some could even be related to the biogeographic differences in animals and plants). The effects of habitat on bacterial diversity are therefore likely to be underestimated (2).

 
1. O’Malley MA. 2007. The nineteenth century roots of ‘everything is everywhere. Nat Rev Microbiol 5:647-651.
2. Hanson CA, Fuhrman JA, Horner-Devine MC, Martiny JB. 2012. Beyond biogeographic patterns: processes shaping the microbial landscape. Nature Reviews Microbiology 10:497-506.
3. Martiny JB, Bohannan BJ, Brown JH, Colwell RK, Fuhrman JA, Green JL, Horner-Devine MC, Kane M, Krumins JA, Kuske CR, Morin PJ, Naeem S, Ovreas L, Reysenbach AL, Smith VH, Staley JT. 2006. Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4:102-112.

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Self-funded PhD positions available

Advertised on the site FindAPhD: an advert describing opportunities to work with Will Gaze or myself at the European Centre for Environment and Human Health. Just to make it abundantly clear: this is and advertisement for a SELF-FUNDED PhD position, so you have to apply for a grant yourself first. This blog gives you a bit of a taste of what we do, but we are relatively flexible in accomodating project ideas (after all, you have been awarded the money, not us!). So come join us in lovely Cornwall!

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