Quick post - new paper of interest on "The Infinitely Many Genes Model ..."

This paper seems of potential interest: The Infinitely Many Genes Model for the Distributed Genome of Bacteria by Franz Baumdicker, Wolfgang R. Hess, and Peter Pfaffelhuber

Abstract:

The distributed genome hypothesis states that the gene pool of a bacterial taxon is much more complex than that found in a single individual genome. However, the possible fitness advantage, why such genomic diversity is maintained, whether this variation is largely adaptive or neutral, and why these distinct individuals can coexist, remains poorly understood. Here, we present the infinitely many genes (IMG) model, which is a quantitative, evolutionary model for the distributed genome. It is based on a genealogy of individual genomes and the possibility of gene gain (from an unbounded reservoir of novel genes, e.g., by horizontal gene transfer from distant taxa) and gene loss, for example, by pseudogenization and deletion of genes, during reproduction. By implementing these mechanisms, the IMG model differs from existing concepts for the distributed genome, which cannot differentiate between neutral evolution and adaptation as drivers of the observed genomic diversity. Using the IMG model, we tested whether the distributed genome of 22 full genomes of picocyanobacteria (Prochlorococcus and Synechococcus) shows signs of adaptation or neutrality. We calculated the effective population size of Prochlorococcus at 1.01 × 1011 and predicted 18 distinct clades for this population, only six of which have been isolated and cultured thus far. We predicted that the Prochlorococcus pangenome contains 57,792 genes and found that the evolution of the distributed genome of Prochlorococcus was possibly neutral, whereas that of Synechococcus and the combined sample shows a clear deviation from neutrality.

Wish they had gone beyond these two cyanobacteria ... but still seems of possible interest. Baumdicker, F., Hess, W., & Pfaffelhuber, P. (2012). The Infinitely Many Genes Model for the Distributed Genome of Bacteria Genome Biology and Evolution, 4 (4), 443-456 DOI: 10.1093/gbe/evs016

Dueling microbial diversity talks at #UCDavis on May 2 #symbioses #microbiology

Here is a storification of the dueling microbial diversity talks that happened at UC Davis on Wednesday May 2.

Crowdsourcing some facts for my upcoming #Tedmed talk on #microbes on #humans

OK all I am looking for some help here is finding out some latest pieces of information about the microbes that live in and on people for my Tedmed talk next week Some things I could use

• 1. What is the number of species of microbes found on one person across their entire body (gut, skin, mouth, etc)? 

•  2. What is the number of species of known human pathogens (that are microbes) 

•  3. What human ailments are now thought to be possibly caused by disturbances in the microbiome? 

•  4. How many viruses (kinds and numbers) are found in the human microbiome? 




•  5. What is a good source of open (e.g., creative commons) images of the microbes found in / on people? 

 I am going to post these each as a comment below so people can respond to each one ... Thanks

This is both crazy and completely brilliant: The Microbial Academy Of Sciences

Oh My God.  This is so wild and crazy I can't just write OMG - I have to write the whole thing out: The Microbial Academy Of Sciences: What Bacteria Can Discover That We Can't | Co.Exist: World changing ideas and innovation

The article describes an art exhibition in San Francisco in which one part involves giving microbial cultures access to images from space.  The reason for this is possibly captured in this quote

"Because cyanobacteria can perform photosynthesis," Keats says, "they’ll be able to detect patterns of starlight just as human scientists do with their eyes. The difference will not be in their methodology, but rather in the conclusions they reach."

and even better

But in all those eons, bacteria have never been given observatory access, to study the cosmos for themselves. … My observatory is built to address that unfortunate oversight, providing the resources for colonies of bacteria to research a theory of everything, reconciling cosmic and quantum observations in their own bacterial way."

I know some hard core scientists may object to this and some of the other lines by the artist but I personally think this is brilliant (in a devious way but brilliant nevertheless).   Everyone out there should read this article by Morgan Clendaniel.  And I for one and going to try to go to the exhibit ASAP.  I personally cannot believe I have not heard of this yet since it seems to have opened in January ...

Want more research funding? Time to give your study organism a better nickname

People who work on pathogens, especially really nasty ones, have built in marketing and fundraising tools. They have nicknames (for the organism, the disease, or both): Good ones. Like "black death" "flesh eating bacteria" "bone break fever" any "wasting disease" any "hemorrhagic fever" "male killer" and more. Now - there are a few non pathogens with good nicknames, like "Conan the bacterium" for Deinococcus radiodurans. But I think we really need to work on better nicknames for non pathogenic microbes. So here are a few proposals:

Any halophilic archaea -> "salt monsters"
Prochlorococcus -> The carbon eater
Rhizobium -> The fixer
Any methanogen -> Fartilicious
Myxococcus xanthus -> The stalker
Nanoarchaeum -> The Hobbit
Tetrahymena thermophila -> The hymenator

Come on everyone.  Let's get some better nicknames.

Full list of 2012 American Academy of Microbiology Fellows Announced

Just got this email and well, I thought I would share.  I would share even if I was not on the list since, well, I love microbes and microbiology.  Note the list is also available on the AAM Web site here.

The American Academy of Microbiology is honored to welcome these new Fellows, elected in recognition of their records of scientific achievement and original contributions that have advanced microbiology:

• James B. Anderson, Ph.D., University of Toronto, Mississauga, ON, Canada
• Dan I. Andersson, Ph.D., Uppsala University, Sweden
• Raul Andino, Ph.D., University of California, San Francisco
• Brenda J. Andrews, Ph.D., University of Toronto, BC, Canada
• Charles Barlowe, Ph.D., Dartmouth Medical School, Hanover, NH
• Joel B. Baseman, Ph.D., University of Texas Health Science Center, San Antonio
• Ruth L. Berkelman, M.D., Emory University, Atlanta, GA
• Robert E. Blankenship, Ph.D., Washington University, St. Louis
• James B. Bliska, Ph.D., Stony Brook University, NY
• Kerry S. Bloom, Ph.D., University of North Carolina, Chapel Hill
• Jef D. Boeke, Ph.D., D. Sc., Johns Hopkins School of Medicine, Baltimore, MD
• Charles M. Boone, Ph.D., University of Toronto, BC, Canada
• Stephen Buratowski, Ph.D., Harvard Medical School, Boston, MA
• George Church, Ph.D., Harvard Medical School, Boston, MA
• Daniel G. Colley, Ph.D., University of Georgia, Athens
• Patricia A. Conrad, Ph.D., D.V.M., University of California, Davis
• Ross E. Dalbey, Ph.D., Ohio State University, Columbus
• Roger J. Davis, Ph.D., Howard Hughes Medical Institute and University of Massachusetts Medical School, Worester
• Piet A.J. de Boer, Ph.D., Case Western Reserve University School of Medicine, Cleveland, OH
• Mark R. Denison, M.D., Vanderbilt University Medical Center, Nashville, TN
• Shou-Wei Ding, Ph.D., University of California, Riverside
• Jonathan Eisen, Ph.D., University of California, Davis
• Luis Enjuanes, Ph.D., National Center of Biotechnology-Spanish National Research Council (CNB-CSIC), Campus Universidad Autonoma, Madrid, Spain
• Tom Fenchel, Ph.D., D. Sc., University of Copenhagen, Denmark
• Robert L. Garcea, M.D., University of Colorado, Boulder
• Reid Gilmore, Ph.D., University of Massachusetts Medical School, Worcester
• Douglas T. Golenbock, M.D., University of Massachusetts Medical School, Worcester
• Robert M. Goodman, Ph.D., School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ
• Daniel E. Gottschling, Ph.D., Fred Hutchinson Cancer Research Center, Seattle, WA
• Glenda Gray, M.B. B.Ch., F.C. Paeds., Perinatal HIV Research Unit, Baragwanath Academic Hospital, Soweto and University of the Witwatersrand, Johannesburg, South Africa
• F. Ulrich Hartl, M.D., Dr. Med., Dr. Med. Habil, Max Planck Institute of Biochemistry, Martinsried, Germany
• Regine Hengge, Ph.D., Freie Universität Berlin, Germany
• John E. Heuser, M.D., Washington University, St. Louis and Kyoto University, Japan
• Wolf-Dietrich Heyer, Ph.D., University of California, Davis
• Edward A. Hoover, D.V.M., Ph.D., Colorado State University, Fort Collins
• Barbara J. Howlett, Ph.D., The University of Melbourne, Australia
• Philip Hugenholtz, Ph.D., University of Queensland, St. Lucia, Australia
• James M. Hughes, M.D., Emory University School of Medicine, Atlanta, GA
• Eric Hunter, Ph.D., Emory University, Atlanta, GA
• Regine Kahmann, Ph.D., Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
• Albert Z. Kapikian, M.D., NIAID, NIH, Bethesda, MD
• Patrick Keeling, Ph.D., University of British Columbia, Vancouver, Canada
• Karla Kirkegaard, Ph.D., Stanford University, CA
• Eugene V. Koonin, Ph.D., NCBI, NLM, NIH, Bethesda, MD
• Thomas M. Kristie, Ph.D., National Institutes of Health, Bethesda, MD
• Nirbhay Kumar, Ph.D., Tulane University, New Orleans, LA
• Ching Kung, Ph.D., University of Wisconsin, Madison
• Jean-Paul Latge, Ph.D., Institut Pasteur, Paris, France
• Jeffrey G. Lawrence, Ph.D., University of Pittsburgh, PA
• Jared R. Leadbetter, Ph.D., California Institute of Technology, Pasadena, CA
• Maxine L. Linial, Ph.D., Fred Hutchinson Cancer Research Center, Seattle, WA
• Alison McBride, Ph.D., NIH, Bethesda, MD
• Xiang-Jin Meng, M.D., Ph.D, Virginia Polytechnic Institute and State University, Blacksburg, VA
• Hiroaki Mitsuya, M.D., Ph.D., National Cancer Institute, NIH, Bethesda, MD
• Edward Mocarski, Jr., Ph.D., Stanford University School of Medicine, CA
• Jens Nielsen, Ph.D., Dr. Technology, Chalmers University of Technology, Gothenburg, Sweden
• Victor Nizet, M.D., University of California, San Diego
• Paul A. Offit, M.D., Children's Hospital of Philadelphia, PA
• Joseph S. Pagano, M.D., University of North Carolina, Chapel Hill
• Julian Parkhill, Ph.D., The Sanger Institute, Cambridge, United Kingdom
• Robin Patel, M.D., Mayo Clinic, Rochester, MN
• John T. Patton, Ph.D., NIAID, NIH, Bethesda, MD
• Martin Polz, Ph.D., Massachusetts Institute of Technology, Cambridge
• Markus Ribbe, Ph.D., University of California, Irvine
• Naomi Rosenberg, Ph.D., Tufts University, Boston, MA
• Eric J. Rubin, M.D., Ph.D., Harvard School of Public Health, Boston, MA
• Peter Sarnow, Ph.D., Stanford University School of Medicine, CA
• Christa M. Schleper, Ph.D., University of Vienna, Austria
• Olaf Schneewind, M.D., Ph.D., University of Chicago, IL
• David M. Serwadda, M.B.ChB., M. Med., M.P.H., Makerere University School of Public Health, Kampala, Uganda
• Eric J. Snijder, Ph.D., Leiden University Medical Center, Netherlands
• Roger E. Summons, Ph.D., Massachusetts Institute of Technology, Cambridge
• Michele S. Swanson, Ph.D., University of Michigan Medical School, Ann Arbor, MI
• Rudolf K. Thauer, Dr. rer. nat., Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
• Kenneth L. Tyler, M.D., University of Colorado School of Medicine, Denver
• Rytas Vilgalys, Ph.D., Duke University, Durham, NC
• Peter R. Williamson, M.D., Ph.D., NIAID, NIH, Bethesda, MD
• Thomas A. Wynn, Ph.D., NIAID, Bethesda, MD
• X. Sunney Xie, Ph.D., Harvard University, Cambridge, MA
• Arturo Zychlinsky, Ph.D., Max Planck Institute for Infection Biology, Berlin, Germany

We hope that you will join us in welcoming the new Fellows at the Fellows Luncheon and Meeting at the General Meeting in San Francisco on June 19th. 

Sincerely yours,

Bonnie L. Bassler, Ph.D. 

Chair, Board of Governors 

American Academy of Microbiology

Hmm ... City of Davis definition of microorganism needs work

From City of Davis Guide to Composting

MICROORGANISM microscopic plants and animals.They exist in soil for the purpose of breaking down organic matter into basic mineral elements.They include bacteria, fungi, actinomycetes, algae, protozoa, yeast, germs, ground pearls, and nematodes.

Gonna have to get them to work on this ...

Microbial metaomics discussion group this week: metatranscriptomics and biogeography

A visiting student at my lab Lea Benedicte Skov Hansen will be leading our "metaomics" discussion group this week.  We will be discussing a combination of metatranscriptomics and biogeography and the papers of the week are:

Metatranscriptomics paper:

Microbial community gene expression in ocean surface waters. Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW, Delong EF. Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3805-10. Epub 2008 Mar 3.



Some related papers of potential interest from DeLong

• Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyre.
• Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea.
• Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean.
• Microbial metatranscriptomics in a permanent marine oxygen minimum zone.
• Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities.

We are also discussing:

Drivers of bacterial beta-diversity depend on spatial scale. Martiny JB, Eisen JA, Penn K, Allison SD, Horner-Devine MC.
Proc Natl Acad Sci U S A. 108(19):7850-4.  (NOTE I am an author on this one - but the meat of the ideas/work was done by Jen Martiny, Claire Horner-Devine and others).

Related papers of possible interest by Jen Martiny and Claire Horner-Divine include:

• Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems.
• Patterns of fungal diversity and composition along a salinity gradient.
• The biogeography of ammonia-oxidizing bacterial communities in soil.
• Phylogenetic clustering and overdispersion in bacterial communities.
• Microbial biogeography: putting microorganisms on the map.
• An ecological perspective on bacterial biodiversity.
• A taxa-area relationship for bacteria.
• A comparison of taxon co-occurrence patterns for macro- and microorganisms.

Will let everyone know how the discussions go.  

Interesting 2011 pub on origin of multicellularity in cyanobacteria

Just a quick one here.  There is an (openaccess) publication I thought people might find interesting: The origin of multicellularity in cyanobacteria.  Schirrmeister BE, Antonelli A, Bagheri HC. BMC Evol Biol. 2011 Feb 14;11:45.

In particular it has some very nice figures on phylogeny of cyanobacteria and the evolution of phenotypes in the group.

Figure 1. Phylogenetic tree of 1,254 cyanobacterial species. 

Figure 4. Phylogenetic tree of a cyanobacterial subset. 

Some of the same authors also have a paper on the need for better phylogenetic sampling of genome data in the group:


Evolution of cyanobacterial morphotypes: Taxa required for improved phylogenomic approaches. Schirrmeister BE, Anisimova M, Antonelli A, Bagheri HC. Commun Integr Biol. 2011 Jul;4(4):424-7. Epub 2011 Jul 1.

Though I note, I am a bit annoyed and surprised they did not cite my "Phylogeny driven genomic encyclopedia" paper in this pub ...

First "Guardians of microbial diversity" award to Rob Dunn #microbiology #GMDs

Nice piece by Rob Dunn: Eating off the floor: How clean living is bad for you | Guest Blog, Scientific American Blog Network

For this I am awarding him the first of what will be many "Guardians of Microbial Diversity" awards here (we can just call these the GMDs). Not only will he get an award - I am going to send him a GMD gift from the various GMD doodads I am putting together.

Congratulations Rob.  Now off to design some more diverse GMD doodads. 

Notes on #UCDavis Citizen Microbiology Meeting #UCDCitSci

We had a meeting at UC Davis on "Citizen Microbiology" from 1/23-1/24. It was a small meeting funded via my microBEnet project which itself is supported by a grant from the Alfred P. Sloan Fundation. The meeting was held at UC Davis - participants stayed at the new Hyatt on campus. We met in the new Conference Center. Participants at the meeting were me, David Coil (post doc in my lab), Paula Olsiewski (from the Sloan Foundation), Holly Bik (post doc in my lab), Darlene Cavalier (founder of ScienceForCitizens.Net), Dan Smith from Argonne National Lab, Denneal Jamison from UC Davis, Holly Menninger from NC State, Noah Feirer from CU Boulder, Josh Neufeld from Waterloo, Jason Bobe from The Personal Genome Project, Tom Bruns form UC Berkeley, Madhu Katti from Fresno State, Chris House from Penn. State, and Patrik D'haeseleer (from Lawrence Livermore National Lab).
Below is a "Storification" I made of the tweets and links from the meeting.

Draft post cleanup #12: RecA is cool (and interesting)

Yet another post in my "draft blog post cleanup" series.  Here is #12:

I have been interested in RecA and related proteins for many many years.  In particular I have been interested in structural and functional evolution of RecA and its relatives.  This all started when for my second scientific paper I helped a post doc in the lab where I was doing my PhD do some structure-function-evolution studies (with a little help from Chris Lee, then in Mike Levitt's lab, and my brother, then in Don Wiley's lab).

For my first talk at a scientific meeting I discussed using RecA as a marker for phylogenetic studies (and had a slide where I had text saying RecA was cool).  Over the years I have continued to try and study RecA or at least use it for studying microbial diversity in some way.  See for example

• The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species 
• The phylogenetic relationships of Chlorobium tepidum and Chloroflexus aurantiacus based upon their RecA sequences
• Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radio resistance 
• Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp. 
• Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees)

Anyway - in this context I was excited to see a new paper on RecA-structure-function-evolution studies: PLoS Genetics: Separation of Recombination and SOS Response in Escherichia coli RecA Suggests LexA Interaction Sites from Olivier Lichtarge and others.  In the paper they use Lichtarge's Evolutionary Trace method to study RecA.

The paper is worth a look and if you are interested in structure-function-evolution types of studies and need a good protein to work on, I would suggest you look at RecA and its relatives ... They are Cool.

Oh and for the fun of it -- I have found some of my slides from that talk in 1995.  Here they are

Draft post cleanup #8: Don't let a hospital kill you - CNN.com

Yet another post in my "draft blog post cleanup" series.  Here is #8 from 5-1-2008
------------------

Saw an interesting article today on CNN.Com: Don't let a hospital kill you - CNN.com.  It has some useful suggestions for how to protect yourself from infection in a hospital.  In many cases we have an excessive fear of germs which can be a bad thing.  But in hospitals, staying clean is almost certainly a good idea ...

Transfaunation and Fecal Transplants: What Goes Around Comes Around, Literally and Figuratively

In 2006 when I had just moved to UC Davis from TIGR, I was on a Southwest flight from Sacramento to (I think) Arizona. The person sitting next to me and I did the normal chit chat - what do you do? where are you going? etc. And the conversation became fascinating. The person sitting next to me was Mike Lagrone - a farrier (I forget people's names frequently ten minutes after meeting them - but his name I remember even today, so he clearly made an impression). He travelled around the West helping take care of people's horses. (I note - I think more information about him is here Mike Lagrone | EquiMed - Horse Health Matters).

Anyway - we ended up talking about microbes and animals and I told him about a project my lab was working on on tracking the microbes after ileal transplantation in people (see our paper on this here - the result of a collaboration between Amber Hartman in my lab and the lab of Michael Zasloff's at Georgetown). We then discussed probiotics and he then told me an amazing story about how the old school farriers used a special method to treat horses if they were sick with some sort of gastrointestinal distress (e.g., colic). They would make the sick horse "poo tea" by taking feces from healthy horses and making it into a tea of sorts and then they served this to the sick horses. Anyway - the flight ended and he told me I should talk to some of the old school people in the Vet School at UC Davis and they might know more about it.

And then a few months later I had an interesting conversation with someone from the UC Davis Vet School - Jonathan Anderson - about horses. And as part of the conversation I told him of the discussion with Mike Lagrone and Jonathan told me there was a method called "transfaunation" which was analogous to the poo tea treatment - and was used for cows and horses and possibly other animals. Jonathan suggested I talk to Dr. Nicola Pusterla at UC Davis about this ... but alas I never did.

And so - the seed of "transfaunation" and "poo tea" faded. And some things that should not have been forgotten were lost. History became legend. Legend became myth. And for four and a half years, the idea passed out of all knowledge.

But like the ring of power, transfaunation and poo tea could not be suppressed forever.  And magically, people began to talk about it over the last four years.  The human microbiome became hot.  Fecal transplants became a topic of conversation (with a little help from Carl Zimmer).  Even Colbert covered the topic.  And the final straw for me to get me to write about Mike Lagrone was when a few days ago my mom showed me an article in Scientific American by Maryn McKenna entitled "Swapping Germs: Should Fecal Transplants Become Routine for Debilitating Diarrhea?"  I knew then that the time had arrived for me to write about Mike Lagrone.  So I have.

I note, one reason I wanted to write up the story of meeting Mike Lagrone was because I personally had not noticed much in the coverage of human fecal transplants discussing the animal side of things.  This seemed a bit odd as transfaunation and poo tea and such are clearly closely connected in concept to fecal transplants in people.  A little digging (well, actually, a few Google searches) showed that many in fact have made the connection.  See for example these stories/articles:

• News story discussing both fecal transplants and transfaunation and poo tea. 
• The Treatment For Clostridium Difficile? Transplant!
• Don't poo-poo it!
• Endoscopic Fecal Microbiota Transplantation: “First-Line” Treatment for Severe Clostridium difficile Infection?

To help those who might be interested in the animal side of "fecal transplants" I have made a mini-Mendeley collection of papers on the topic:

Transfaunation and Fecal Transplants is a group in Biological Sciences on Mendeley.

It is interesting to me how what goes around comes around (literally and figuratively).  This is probably a very ancient methodology - trying to move microbes from healthy individuals to sick ones to help treat them for various GI ailments.  And lets not even start talking about coprophagia which almost certainly has some "microbial colonization" component.  Thus, I conclude that, though fecal transplants in people may seem gross, it certainly makes a lot of sense that it could provide some benefits.  Not saying we know how to do it best or that it can cure everything - but it certainly seems worth pursuing in more detail.

Stay tuned - it seems very likely we will here much more about this in people over the next few years.  For some of the latest on the human side of things see
Fecal Transplants: They Work, the Regulations Don’t - also by Maryn McKenna.

Seems that medicine is catching up to what animals (and their caretakers) have known for some time ...

Carl Zimmer on "Who Owns Your Microbes"?

There was an interesting piece by Carl Zimmer in the New York Times a few days ago: Our Microbiomes, Ourselves - NYTimes.com

In the piece Zimmer discusses the issue of who owns your microbiome. This can be considered an extension of the concept of "Who owns your cells?" such as has been discussed in the context of Rebecca Skloot's HELA book.

My favorite line(s):

Monitoring the bacteria flushed into the sewer system of a town, for instance, might reveal a lot about the entire town’s health. But a regulation requiring permission from every resident of the town would stop the study dead in its tracks

Personally I think none of us own our microbes - since we get them from the world around us and likely share them with millions of others. It would be akin to saying we own genes found in all humans. But there very well may be some person specific alleles in microbes that could in a way be akin to person specific cell lines. Not sure.

Anyway - I think I am going to name all my microbes as a first step in protecting my rights to them ...

The Rare Biosphere, 2011 report from American Academy of Microbiology

I had posted this to twitter a while ago but not here. There is a report that came out from the American Academy of Microbiology from a Workshop in which I participated. The report is on "The Rare Biosphere, 2011" and it discusses some of the issues associated with the long tail of rare organisms that might exist, especially microbes.  It is worth a look.

From their page:

The microbial world represents the last truly unexplored frontier in the diversity of life on Earth. New environmental sampling technologies have revealed a wealth of rare microbial species in the soil, ocean, even our own bodies that were effectively cloaked from previous sampling methods by more abundant species. Dubbed the rare biosphere, these microbial species, while individually rare, collectively account for more than 75% of the biomass of some microbial communities, yet little is known about them. This rare biosphere represents a treasure trove of genetic novelty that may possess numerous unique bioprocesses and biomaterials. These rare species may play keystone roles in microbial communities and act as a reservoir of genetic diversity. But how can scientists effectively study the rare biosphere? In April 2009 the American Academy of Microbiology convened a colloquium to explore this question. Based on that colloquium, this report analyzes the current state of study of the rare biosphere and identifies where gaps in knowledge exist. The report concludes that the Herculean task of studying the rare biosphere requires an international collaborative effort and additional environmental sampling, coupled with a focus on advancing sequencing and data analysis technologies. With less than 1% of microbial species able to be grown in the laboratory, the prospects of new discoveries in the rare biosphere seem as vast as microbial diversity itself.

You can get a PDF of the report here.

Yes, Colbert did indeed discuss Fecal Transplants #microbeRule

See Cheating Death - Chicken Pox Lollipops & Fecal Transplants - The Colbert Report - 2011-08-12 - Video Clip | Comedy Central

The Colbert Report	Mon - Thurs 11:30pm / 10:30c
Cheating Death - Chicken Pox Lollipops & Fecal Transplants
www.colbertnation.com
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NPR Piece on Discovery of Hydrothermal Vent Oasis

Very nice to see this: The Deep-Sea Find That Changed Biology : NPR

It discusses the story of the discovery of the first hydrothermal vent oases back in 1977. I note this is near and dear to my heart. I worked as an undergraduate and then after graduating in Colleen Cavanaugh's lab at Harvard on chemosynthetic symbioses. And then amazingly I got to go on the 2002 deep sea cruise celebrating the 25th anniversary of the discovery of the vents. On that cruise Rosebud (mentioned in this article) was discovered.

And I am still fascinating by the deep sea - (with Colleen Cavanaugh's lab esp. Irene Newton and w/ Tanja Woyke via JGI we sequenced the first chemosynthetic symbiont genome a few years ago). Hat tip to Eileen Choffness for pointing this story out.

Submit Ideas and Vote on Ideas for Presentation Topic Ideas for Special Session at the ASM General Meeting in SF 2012

Calling all microbiology fans - The American Society for Microbiology (ASM) is doing something very different for the 2012 General Meeting in San Francisco that might be of interest.  There will be a special session, organized by the Communications Committee (of which I am a member) where everyone/anyone can propose topics and then these get voted on to determine the winners (see Your Topics, Your Votes, Your Choice).

From the web site

Submit your scientific presentation topic for ASM2012 and then vote and comment on your colleagues’ ideas. The people who submit the top 5 entries will receive a travel subsidy of $800 (or $1200 for international submitters) and will present their topics at the General Meeting in San Francisco, on Tuesday, June 19 at 2:30 p.m., PT.

The submission deadline closes Feb. 1, 2012 at noon, GMT. The top 5 voted topics will then be approved by March 1, 2012.

The rules of the system are as follows (also from the web site)

• All scientists are encouraged to submit, especially undergraduates, graduate students, post-docs and technical staff.
• Registered site users get 10 votes to allocate among topics, with a maximum of 3 votes per topic. However, votes can be reallocated up to the Feb. 1, 2012 deadline.
• Topics must be submitted with a title. A 3 to 5 sentence description is strongly encouraged. You may also include links to additional or background materials by inserting an http:// before a URL in the description field.
• While multiple topics may be submitted. Only one topic per submitter will be selected. In other words, if a submitter gets 3 topics in the top 5 by Feb. 1, 2012, that person will only be allowed to present on one topic at the meeting.
• The submitter must be the presenter.
• No pseudoscience allowed. If you see an entry that looks suspicious, please flag the idea as inappropriate at the end of the topic's description. ASM reserves the right to remove improper submissions and comments.
• Topics must be presented within a 30 minute time slot, 10 minutes of which will be allotted for questions and answers.
• Speakers for invited sessions at ASM2012 are not eligible to participate in this session.

So - please consider submitting ideas and voting on ideas and spreading the word.

Journal club today on bacteria in toilets - posting some notes here

I am heading a journal club discussion today of the following paper: PLoS ONE: Microbial Biogeography of Public Restroom Surfaces

I am going to use this page/post to put up some notes for the discussion.  Fortunately I have a good guide in this - Rob Dunn wrote a nice commentary/review for Scientific American blogs: Public bathrooms house thousands of kinds of bacteria

Stay tuned/come back to this page as I will be posting some more notes. Any suggestions for other things to look at/discuss would be welcome.

Notes (I note - I am copying much of the text from the paper not rewriting it.)
What was sampled?

Ten surfaces (door handles into and out of the restroom, handles into and out of a restroom stall, faucet handles, soap dispenser, toilet seat, toilet flush handle, floor around the toilet and floor around the sink) in six male and six female restrooms evenly distributed across two buildings on the University of Colorado at Boulder campus were sampled on a single day in November 2010. 

How did they collect samples?

Surfaces where sampled using sterile, cotton-tipped swabs as described previously [14], [15]. As the 12 restrooms were nearly identical in design, we were able to swab the same area at each location between restrooms. In order to characterize tap water communities as a potential source of bacteria, 1 L of faucet water from six of the restrooms (each building having the same water source for each restroom sampled) was collected and filtered through 0.2 µm bottle top filters (Nalgene, Rochester, NY, USA). 

How did they get DNA?

Genomic DNA was extracted from the swabs and filters using the MO BIO PowerSoil DNA isolation kit following the manufacturer's protocol with the modifications of Fierer et al. [14]. 

How did they get sequence data?

A portion of the 16 S rRNA gene spanning the V1–V2 regions was amplified using the primer set (27 F/338R), PCR mixture conditions and thermal cycling conditions described in Fierer et al. [15]. PCR amplicons of triplicate reactions for each sample were pooled at approximately equal amounts and pyrosequenced at 454 Life Sciences (Branford, CT, USA) on their GS Junior system. A total of 337,333 high-quality partial 16 S rRNA gene sequences were obtained from 101 of the 120 surface samples collected, averaging approximately 3,340 sequences per sample (ranging from 513–6,771) (Table S1) in 4 GS Junior runs, with the best run containing 116,004 high-quality reads. An additional 16,416 sequences (ranging from 2161–5084 per sample) were generated for five of the six water samples collected for source tracking analysis. Each sample was amplified with a unique barcode to enable multiplexing in the GS Junior runs. The barcoded sequencing reads can be separated by data analysis software providing high confidence in assigning sequencing read to each sample. Sequence data generated as part of this study is available upon request by contacting the corresponding author.

How did they analyze the data?

All sequences generated for this study and previously published data sets used for source tracking (see below) were processed and sorted using the default parameters in QIIME [16]. Briefly, high-quality sequences (>200 bp in length, quality score >25, exact match to barcode and primer, and containing no ambiguous characters) were trimmed to 300 bp and clustered into operational taxonomic units (OTUs) at 97% sequence identity using UCLUST [17]. Representative sequences for each OTU were then aligned using PyNAST [18] against the Greengenes core set [19] and assigned taxonomy with the RDP-classifier [20]. Aligned sequences were used to generate a phylogenetic tree with FastTree [21] for both alpha- (phylogenetic diversity, PD)[22] and beta-diversity (unweighted UniFrac) [23] metrics. The unweighted UniFrac metric, which only accounts for the presence/absence of taxa and not abundance, was used to determine the phylogenetic similarity of the bacterial communities associated with the various restroom surfaces. The UniFrac distance matrix was imported into PRIMER v6 where principal coordinate analysis (PCoA) and analysis of similarity (ANOSIM) were conducted to statistically test the relationship between the various communities [24]. In order to eliminate potential biases introduced by sampling depth, all samples (including those used in source tracking) were rarified to 500 sequences per sample for taxonomic, alpha-diversity (PD), beta-diversity (UniFrac) and source tracking comparisons.

Sourcetracking

To determine the potential sources of bacteria on restroom surfaces and how the importance of different sources varied across the sampled locations, we used the newly developed SourceTracker software package [25]. The SourceTracker model assumes that each surface community is merely a mixture of communities deposited from other known or unknown source environments and, using a Bayesian approach, the model provides an estimate of the proportion of the surface community originating from each of the different sources. When a community contains a mixture of taxa that do not match any of the source environments, that portion of the community is assigned to an “unknown” source. Potential sources we examined included human skin (n = 194), mouth (n = 46), gut (feces) (n = 45) [26] and urine (n = 50), as well as soil (n = 88) [27] and faucet water (n = 5, see above). For skin communities, sequences collected from eight body habitats (palm, index finger, forearm, forehead, nose, hair, labia minora, glans penis) from seven to nine healthy adults on four occasions were used to determine the average community composition of human skin [26]. The mouth (tongue and cheek swabs), gut and urine communities were determined from the same individuals although the urine-associated communities were not published in the initial report of these data [26]. While urine is generally considered to be sterile, it does pick up bacteria associated with the urethra and genitals [28], [29]. The average soil community was determined from a broad diversity of soil types collected across North and South America [27].

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Notes on Sourcetracking

Abstract to paper:

Contamination is a critical issue in high-throughput metagenomic studies, yet progress toward a comprehensive solution has been limited. We present SourceTracker, a Bayesian approach to estimate the proportion of contaminants in a given community that come from possible source environments. We applied SourceTracker to microbial surveys from neonatal intensive care units (NICUs), offices and molecular biology laboratories, and provide a database of known contaminants for future testing.

Some lines from paper

We developed SourceTracker, a Bayesian approach to identifying sources and proportions of contamination in marker-gene and functional metagenomics studies. Our approach models contamination as a mixture of entire source communities into a sink community, where the mixing proportions are unknown.

SourceTracker's distinguishing features are its direct estimation of source proportions and its Bayesian modeling of uncertainty about known and unknown source environments.

SourceTracker outperformed these methods (NAIVE BAYES AND RANDOM FORESTS) because it allows uncertainty in the source and sink distributions, and because it explicitly models a sink sample as a mixture of sources.

SourceTracker also assumes that an environment cannot be both a source and a sink, and we recommend research into bidirectional models.

Based on our results, simple analytical steps can be suggested for tracking sources and assessing contamination in newly acquired datasets. Although source-tracking estimates are limited by the comprehensiveness of the source environments used for training, large-scale projects such as the Earth Microbiome Project will dramatically expand the availability of such resources. SourceTracker is applicable not only to source tracking and forensic analysis in a wide variety of microbial community surveys (where did this biofilm come from?), but also to shotgun metagenomics and other population-genetics data. We made our implementation of SourceTracker available as an R package (http://sourcetracker.sf.net/), and we advocate automated tests of deposited data to screen samples that may be contaminated before deposition.

Who was there?

A total of 19 phyla were observed across all restroom surfaces with most sequences (≈92%) classified to one of four phyla: Actinobacteria,Bacteroidetes, Firmicutes or Proteobacteria (Figure 1A, Table S2). Previous cultivation-dependent and –independent studies have also frequently identified these as the dominant phyla in a variety of indoor environments [10]–[13]. Within these dominant phyla, taxa typically associated with human skin (e.g. Propionibacteriaceae,Corynebacteriaceae, Staphylococcaceae and Streptococcaceae) [30]were abundant on all surfaces (Figure 1A). The prevalence of skin bacteria on restroom surfaces is not surprising as most of the surfaces sampled come into direct contact with human skin, and previous studies have shown that skin associated bacteria are generally resilient and can survive on surfaces for extended periods of time [31], [32]. Many other human-associated taxa, including several lineages associated with the gut, mouth and urine, were observed on all surfaces (Figure 1A). Overall, these results demonstrate that, like other indoor environments that have been examined, the microbial communities associated with public restroom surfaces are predominantly composed of human-associated bacteria.

Figure 1. Taxonomic composition of bacterial communities associated with public restroom surfaces.

(A) Average composition of bacterial communities associated with restroom surfaces and potential source environments. (B) Taxonomic differences were observed between some surfaces in male and female restrooms. Only the 19 most abundant taxa are shown. For a more detailed taxonomic breakdown by gender including some of the variation see Supplemental Table S2.

doi:10.1371/journal.pone.0028132.g001

Comparative analysis

Comparisons of the bacterial communities on different restroom surfaces revealed that the communities clustered into three general categories: those communities found on toilet surfaces (the seat and flush handle), those communities on the restroom floor, and those communities found on surfaces routinely touched with hands (door in/out, stall in/out, faucet handles and soap dispenser) (Figure 2, Table 1). By examining the relative abundances of bacterial taxa across all of the restroom samples, we can identify taxa driving the overall community differences between these three general categories. Skin-associated bacteria dominate on those surfaces (the circles in Figure 2) that are routinely and exclusively (we hope) touched by hands and unlikely to come into direct contact with other body parts or fluids (Figure 3A). In contrast, toilet flush handles and seats (the asterisk-shaped symbols in Figure 2) were relatively enriched in Firmicutes (e.g.Clostridiales, Ruminococcaceae, Lachnospiraceae, etc.) andBacteroidetes (e.g. Prevotellaceae and Bacteroidaceae) (Figure 3B). These taxa are generally associated with the human gut [26],[33]–[35] suggesting fecal contamination of these surfaces. Fecal contamination could occur either via direct contact (with feces or unclean hands) or indirectly as a toilet is flushed and water splashes or is aerosolized [36]–[38]. From a public health perspective, the high number of gut-associated taxa throughout the restrooms is concerning because enteropathogenic bacteria could be dispersed in the same way as human commensals. Floor surfaces harbored many low abundance taxa (Table S2) and were the most diverse bacterial communities, with an average of 229 OTUs per sample versus most of the other sampled locations having less than 150 OTUs per sample on average (Table S1). The high diversity of floor communities is likely due to the frequency of contact with the bottom of shoes, which would track in a diversity of microorganisms from a variety of sources including soil, which is known to be a highly-diverse microbial habitat [27], [39]. Indeed, bacteria commonly associated with soil (e.g. Rhodobacteraceae, Rhizobiales, Microbacteriaceae and Nocardioidaceae) were, on average, more abundant on floor surfaces (Figure 3C, Table S2). Interestingly, some of the toilet flush handles harbored bacterial communities similar to those found on the floor (Figure 2, Figure 3C), suggesting that some users of these toilets may operate the handle with a foot (a practice well known to germaphobes and those who have had the misfortune of using restrooms that are less than sanitary).

Figure 2. Relationship between bacterial communities associated with ten public restroom surfaces.

Communities were clustered using PCoA of the unweighted UniFrac distance matrix. Each point represents a single sample. Note that the floor (triangles) and toilet (asterisks) surfaces form clusters distinct from surfaces touched with hands.

doi:10.1371/journal.pone.0028132.g002

Table 1. Results of pairwise comparisons for unweighted UniFrac distances of bacterial communities associated with various surfaces of public restrooms on the University of Colorado campus using the ANOSIM test in Primer v6.

doi:10.1371/journal.pone.0028132.t001

Figure 3. Cartoon illustrations of the relative abundance of discriminating taxa on public restroom surfaces.

Light blue indicates low abundance while dark blue indicates high abundance of taxa. (A) Although skin-associated taxa (Propionibacteriaceae, Corynebacteriaceae,Staphylococcaceae and Streptococcaceae) were abundant on all surfaces, they were relatively more abundant on surfaces routinely touched with hands. (B) Gut-associated taxa (Clostridiales, Clostridiales group XI, Ruminococcaceae,Lachnospiraceae, Prevotellaceae and Bacteroidaceae) were most abundant on toilet surfaces. (C) Although soil-associated taxa (Rhodobacteraceae, Rhizobiales, Microbacteriaceae and Nocardioidaceae) were in low abundance on all restroom surfaces, they were relatively more abundant on the floor of the restrooms we surveyed. Figure not drawn to scale.

doi:10.1371/journal.pone.0028132.g003

Comparisons 2 (Gender)

While the overall community level comparisons between the communities found on the surfaces in male and female restrooms were not statistically significant (Table S3), there were gender-related differences in the relative abundances of specific taxa on some surfaces (Figure 1B, Table S2). Most notably, Lactobacillaceae were clearly more abundant on certain surfaces within female restrooms than male restrooms (Figure 1B). Some species of this family are the most common, and often most abundant, bacteria found in the vagina of healthy reproductive age women [40], [41] and are relatively less abundant in male urine [28], [29]. Our analysis of female urine samples collected as part of a previous study [26] (Figure 1A), found that Lactobacillaceae were dominant in urine, therefore implying that surfaces in the restrooms where Lactobacillaceae were observed were contaminated with urine. Other studies have demonstrated a similar phenomenon, with vagina-associated bacteria having also been observed in airplane restrooms [11] and a child day care facility [10]. As we found that Lactobacillaceae were most abundant on toilet surfaces and those touched by hands after using the toilet (with the exception of the stall in), they were likely dispersed manually after women used the toilet. Coupling these observations with those of the distribution of gut-associated bacteria indicate that routine use of toilets results in the dispersal of urine- and fecal-associated bacteria throughout the restroom. While these results are not unexpected, they do highlight the importance of hand-hygiene when using public restrooms since these surfaces could also be potential vehicles for the transmission of human pathogens. Unfortunately, previous studies have documented that college students (who are likely the most frequent users of the studied restrooms) are not always the most diligent of hand-washers [42], [43].

Source Tracking


Human sources:

Results of SourceTracker analysis support the taxonomic patterns highlighted above, indicating that human skin was the primary source of bacteria on all public restroom surfaces examined, while the human gut was an important source on or around the toilet, and urine was an important source in women's restrooms (Figure 4, Table S4). 

Soil not an apparent source:

Contrary to expectations (see above), soil was not identified by the SourceTracker algorithm as being a major source of bacteria on any of the surfaces, including floors (Figure 4). Although the floor samples contained family-level taxa that are common in soil, the SourceTracker algorithm probably underestimates the relative importance of sources, like soils, that contain highly diverse bacterial communities with no dominant OTUs and minimal overlap between those OTUs in the sources and those found in the surface samples. As soils typically have large numbers of OTUs that are rare (i.e. represented by very few sequences) and the OTU overlap between different soil samples is very low [27], it is difficult to identify specific OTUs indicative of a soil source. 

Other potential sources:

The other potential sources we examined, mouth and faucet water, made only minor bacterial contributions to restroom surface communities either because these potential source environments rarely come into contact with restroom surfaces (the mouth – we hope) or they harbor relatively low concentrations of bacteria (faucet water) (Figure 4). While we were able to identify the primary sources for most of the surfaces sampled, many other sources, such as ventilation systems or mops used by the custodial staff, could also be contributing to the restroom surface bacterial communities. More generally, the SourceTracker results demonstrate how direct comparison of bacterial communities from samples of various environment types to those gathered from other settings can be used to determine the relative contribution of that source across samples. Although many of the source-tracking results evident from the restroom surfaces sampled here are somewhat obvious, this may not always be the case in other environments or locations. We could use the same techniques to identify unexpected sources of bacteria from particular environments as was observed recently for outdoor air [44].

Figure 4. Results of SourceTracker analysis showing the average contributions of different sources to the surface-associated bacterial communities in twelve public restrooms.

The “unknown” source is not shown but would bring the total of each sample up to 100%.

doi:10.1371/journal.pone.0028132.g004

Conclusion

While we have known for some time that human-associated bacteria can be readily cultivated from both domestic and public restroom surfaces, little was known about the overall composition of microbial communities associated with public restrooms or the degree to which microbes can be distributed throughout this environment by human activity. The results presented here demonstrate that human-associated bacteria dominate most public restroom surfaces and that distinct patterns of dispersal and community sources can be recognized for microbes associated with these surfaces. Although the methods used here did not provide the degree of phylogenetic resolution to directly identify likely pathogens, the prevalence of gut and skin-associated bacteria throughout the restrooms we surveyed is concerning since enteropathogens or pathogens commonly found on skin (e.g. Staphylococcus aureus) could readily be transmitted between individuals by the touching of restroom surfaces.

Supporting Information Top

Table S1.

Public restroom surfaces sampled and comparison of alpha-diversity metrics for each restroom surface. Note that all alpha-diversity values were determined from 500 randomly selected sequences from each sample.

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Table S2.

Average taxonomic composition of bacterial communities associated with female (F) and male (M) public restroom surfaces. Numbers in parentheses indicate the standard error of the mean (SEM). Taxonomy was determined using the RDP-classifier for 500 randomly selected sequences from each sample.

(DOC)

Table S3.

Results of ANOSIM test comparing the bacterial communities associated with male and female restroom surfaces.

(DOC)

Table S4.

Results of SourceTracker analysis showing percentage of microbial community contributions of different source environments to restroom surfaces. Values are the average of ten resamplings with the standard error of the mean reported in parentheses.

(DOC)