Treponema are not "ancient" but absence from some human's guts is very interesting

So I saw some Tweets today that caught my attention, discussion news stories about "ancient" bacteria being missing from some human's gut microbiomes:

Uhh? http://t.co/psM91dMi50 pic.twitter.com/JBvXvhq66T
— Nick Loman (@pathogenomenick) March 25, 2015

There are no "ancient bacteria". when we actually see the paper i'm sure it will be a doozy. http://t.co/qewzlRHcLX
— Pat Schloss (@PatSchloss) March 25, 2015

These refer to a sadly inappropriate headline in Science



What is wrong with this?  Well, there are no "ancient" bacteria around today.  They are all modern.  I am not even sure what they were trying to say.  Just a really bad evolution argument I guess.  I pondered giving Science a Twisted Tree of Life Award which I give out for exactly this kind of thing -  but decided first to dig into the science here and gloss over the bad evolution headline.

And it turns out - what the news story is about is in fact interesting - a new paper out in Nature Communications:  Subsistence strategies in traditional societies distinguish gut microbiomes.

The paper is freely available and has some really interesting material in it.  They key to me - at least related to this "ancient" bacteria claim is the following part of their abstract:

As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2–2.5 MB, coverage depth × 26–513) and functional potential characterization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine. Gut Treponema are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialized societies.

And then some further detail in the paper:

Although Spirochaetes have been previously reported from the gut microbiome of non-human primates and ancient human populations, they have only been observed in high abundance among extant human populations with non-Western lifestyles, such as a traditional community in Burkina Faso and a hunter-gatherer community in Tanzania. As such, they may represent a part of the human ancestral gut microbiome that has been lost through the adoption of industrial agriculture and/or other lifestyle changes. 

So they don't go into the full detail here but what I think they are saying is that they infer that human ancestors had Spirochaetes (based on the finding of it in non human primates and some human populations).  And thus they further infer that human populations (e.g., the people they studied in Oklahoma) that do not have these Spirochaetes have "lost" them.

I note - I think this terminology of "loss" they are using is not quite right here in a way.  Saying that these Spirochaetes have been lost implies to me that they are heritable.  But they do not in fact show that.  It could be that these are related to diet or environment in some way - something shared by some human populations and non human primates, for example.  And thus the absence from some "Westernized" populations could be more of an environmental thing than a "loss" in the past.

Please make it stop - overselling the microbiome award for rugby, exercise, microbiome stories

Update added 11/2/14 - for all my posts on Overselling the Microbiome go here. 

Well, I think today's lesson is, many people, including many scientists and science reporters, just do not get that there is a difference between correlation and causation.  I know - this is like beating a dead horse since many write about this issue.  But it just needs to be called out every time until it stops.  And today's fun comes from stories and the original research articles about how exercise supposedly alters the gut microbiome.

I was pointed to this just a few minutes ago on Twitter:

Seems like more appropriate title would b "rugby players have different diets" http://t.co/nzNsnHCYtA @phylogenomics

— Bernat Olle (@bernatolle) June 10, 2014

In this Tweet Bernat Olle points to a "news" story in Medpage Today: Exercise Boosts Gut Microbiome Diversity by Kristina Fiore.   Well, so of course I started digging around.  And, not surprisingly, the study that this is based on shows absolutely no causal connection between exercise and the gut microbiome.  The study is in the journal "Gut": Exercise and associated dietary extremes impact on gut microbial diversity.  And here is what they did:

• They selected subjects - 40 "elite" rugby players.
• They identified healthy male "controls" with similar age and size and from similar place. 
• Then they collected faecal and blood samples from participants and did surveys about their nutrition and clinical data.
• Among many measurements, they did 16S sequencing from the fecal samples
• Then they did some bioinformatics and found differences between the rugby players and the controls in many features including microbiomes.

And amazingly, from this they report, in their abstract

The results provide evidence for a beneficial impact of exercise on gut microbiota diversity but also indicate that the relationship is complex and is related to accompanying dietary extremes.

No overselling here - Martin Blaser on the Daily Show discussing Missing Microbes and the human microbiome

Martin Blaser does a good job on the Daily Show discussing the human microbiome and his new book Missing Microbes.

The Daily Show
Get More: Daily Show Full Episodes,Indecision Political Humor,The Daily Show on Facebook

Overselling the microbiome award: Time Magazine & Martin Blaser for "antibiotics are extinguishing our microbiome"

Well, alas, Time magazine turned what could have been a story about the spread of antibiotic resistance into what appears to be a promotion for Martin Blaser's new book: Antibiotic-Resistant Bacteria Are Now In Every Part of the World | TIME.com.

The article starts of OK - reporting on the new WHO report on antibiotic resistance.  But then it gets into the microbiome and what antibiotics supposedly do to it.  Some quotes:

"But even more concerning, say experts like Dr. Martin Blaser, director of the human microbiome program at the New York University Langone Medical Center and author of Missing Microbes, is how these antibiotics are affecting the makeup of both good and bad bacteria that live within us – our microbiome. The first big cost of antibiotics is resistance,” he says. “But the other side of the coin is [the fact that] antibiotics are extinguishing our microbiome and changing human development.”

Extinguishing our microbiome?  Really?  The evidence simply does not support such a claim.  I personally think antibiotics may be contributing to messing up the microbiome in many people and that this in turn might be contributing to the increase in a variety of human ailments (e.g., I mentioned this issue in my TED talk and many many times here and elsewhere).  But "extinguishing"?  Not even close.  In fact, many of the published sutdies done so far suggest that the human microbiome is pretty resilient in response to antibiotics.  Really serious overselling of the impact of antiobitcs by Blaser.

And "changing human development?"  Not sure what the evidence for that is either.  Most likely this refers to the role the microbiome plays in immune system development but I am not aware of strong evidence that antibiotics lead to changes in human devleopment.

They then quote Blaser again:

If I prescribe a heart medicine for a patient, that heart medicine is going to affect that patient,” says Blaser. “But if I prescribe an antibiotic, that antibiotic will affect the entire community to some degree. And the effect is cumulative.

Yes antibiotics can affect more than one person because microbes (and resistance) can spread.  But "the effect is cumulative"?  I do not think that has been shown.

Finally, Time (well, Alice Park, the author) states (in relation to limiting overuse of antibiotics)

That may also help to protect our microbiomes, which in turn could slow the appearance of chronic diseases such as obesity, cancer and allergies.

What?  Now antibiotics cause obesity?  And allergies?  And cancer? Sure - there is good reason to think that antibiotic usage plays a role in obesity and allergies.  The evidence is not yet completely overwhelming but it is certainly a reasonable notion.  But how did cancer get thrown in here?

Human microbiome story of the month: OpenBiome fecal bank for fecal transplants

Wow - fascinating story by David Glenn in the Chronicle of Higher Education: Student-Led Project Banks on Promise of Fecal Transplants - Research - The Chronicle of Higher Education.  The article tracks the story of Carolyn Edelstein and Mark B. Smith and James Burgess who have created a feces bank called OpenBiome to provide materials for fecal transplants.


Some related posts of mine:

• Transfaunation and Fecal Transplants: What Goes Around Comes Around, Literally and Figuratively
• Just in time for #ASM2013 - FDA adding regulations for fecal transplants #microbiome
• More (you know you wanted it) on fecal transplants and the microbiome
• Must read microbiome paper of the month: defined microbioata treatment of Cdiff infections
• Got poo?: Clinical trial on fecal transplants (aka fecal bacteriotherapy) to treat C. difficult infections
• Fecal transplants taken up by American Hospital Association in letter to HHS about Medicare/Medicaid
• Yes, Colbert did indeed discuss Fecal Transplants #microbeRule

Simple but important paper on the personal microbiome

Figure 1.

Quick post.  Just saw this paper:

PLOS ONE: The Personal Human Oral Microbiome Obscures the Effects of Treatment on Periodontal Disease:

Schwarzberg K, Le R, Bharti B, Lindsay S, Casaburi G, et al. (2014) The Personal Human Oral Microbiome Obscures the Effects of Treatment on Periodontal Disease. PLoS ONE 9(1): e86708. doi:10.1371/journal.pone.0086708

It has multiple things of interest (certainly to me - as we are doing some work on the oral microbiome). But I do not have time right now to dig through all of it.  I want to just point out one very important line in it:

Our results highlight how understanding interpersonal variability among microbiomes is necessary for determining how polymicrobial diseases respond to treatment and disturbance

This is consistent with what has been a gut feeling of mine (and something I say in lots of interviews and talks) but for which I did not have any obvious citation in mind.  Now I do.

Quick ego-post - link to interview of me by National Geographic Weekend show

Quick post here.  Was interviewed for National Geographic Weekend by Boyd Matson a few days ago and the show was just posted online: January 19, 2013: Waging War Against Whalers, Paragliding Above Pakistan and More – News Watch.  Scroll down to find the link to my part ..

Possibly interesting new microbiome study but can't get past misleading quote

Just got done reading: Restoring helpful bacteria of the gut and intestines may treat patients with RCDI, find scientists.  A lot in the story is interesting.  And it discusses work by friends / colleagues of mine.  But I just don't feel like writing about the work because the end of the article rubs me the wrong way.  Here is the whole paragraph that bothers me:

"This study helps underscore the importance of the microbiome in maintaining health and demonstrates that good bacteria play an integral role in immune defenses against disease," says E. Albert Reece, M.D., Ph.D., M.B.A., Vice President for Medical Affairs at the University of Maryland and the John Z. and Akiko K. Bowers Distinguished Professor and Dean of the University of Maryland School of Medicine. "These findings also provide a potential therapeutic model for other diseases that have been linked to changes in the human intestinal microbiota, such as obesity and diabetes."

What is wrong with this?  Well, #1 - the 1st sentence implies a bit too much to me that this study is novel in demonstrating that "good" bacteria play a role in immune defense.   When of course this has been shown for many many years.  But let's let that slide.  Not a big deal.

It is the last line that irks me:  "These findings also provide a potential therapeutic model for other diseases that have been linked to changes in the human intestinal microbiota, such as obesity and diabetes."

Hmm.  Obesity and diabetes in humans have not been shown to be caused by changes in the microbiome.  And therefore it is inaccurate to imply that one could take the fecal transplant for C. difficile model (which is what this current work is about) and extended it to obesity and diabetes.  You could say he is careful with words here by saying "linked to" not "caused by" but I think the clear implication here is that he is promoting fecal transplants as a therapy for obesity and diabetes.  And he should be more careful (especially as Dean of the University of Maryland School of Medicine).  I beg of people out there.  Please please please.  Microbiome studies have enormous potential.  In so many areas.  But we risk turning microbiome work into the next medical snake oil if we are not careful with our words.

Mini journal club: staged phage attack of a humanizes microbiome of mouse

Doing another mini journal club here.  Just got notified of this paper through some automated Google Scholar searches: Gnotobiotic mouse model of phage–bacterial host dynamics in the human gut

Full citation: Reyes, A., Wu, M., McNulty, N. P., Rohwer, F. L., & Gordon, J. I. (2013). Gnotobiotic mouse model of phage–bacterial host dynamics in the human gut. Proceedings of the National Academy of Sciences, 201319470.

The paper seems pretty fascinating at first glance. Basically they built on the Jeff Gordon germ free mouse model and introduced a defined set of cultured microbes that came from humans.  And then they stages a phage attack on the system and monitored the response of the community to the phage attack.

Figure 1 from Reyes et al.

They (of course) also did a control - in this case with heat killed phage.  And they compared what happened to the live phage.  I love this concept as they are able to control the microbial community and then test dynamics of how specific phage affect that community inside a living host.  Very cool.

Overselling the microbiome award: VIB press release saying "Intestinal flora determines health of obese people"

Some really cool new papers are out on the human microbiome today.  But alas that is not what I am here to talk about.  I am here, once again, to complain about overselling the microbome.  There is a headline from a press release from one of the institutes involved in one of the new studies that really irks me: "Intestinal flora determines health of obese people".  As far as I can tell from reading the paper under discussion in this PR, nothing showed that the flora "determined" the health of obese people.  Yes, the flora had really interesting correlations with health status.  But "determines health" implies that the flora were the causal component of the health of obese people.  And as far as I can tell this was not shown.  What was shown was that the microbial communities - and some metrics of those communities like richness - can help predict risk of individuals for various health related ailments.

Now, mind you, the person discussed in this PR Jeroen Raes is completely brilliant and one of my favorite people in science in many ways.  And also it is important to point out that the paper does not make these claims.  The paper says things like

Our classifications based on variation in the gut microbiome identify subsets of individuals in the general white adult population who may be at increased risk of progressing to adiposity-associated co-morbidities

Because it is there? (Why Larry Smarr freezes his feces)

Hat tip to ...

Why Professor Larry Smarr (@lsmarr) freezes his own faeces | @BBCNews VIDEO http://t.co/fVZrQNXaYo #DigitalHealth #QuantifiedSelf #QS

— Paul Sonnier (@Paul_Sonnier) August 12, 2013

Perhaps this meeting should be renamed "Of Microbiomes and Men" ....

Well, just got an email inviting me to participate in a meeting on microbiomes. The full invite is at the bottom of this posting.  Alas, at first glances it seems this meeting, has, well, some gender issues.

Confirmed Keynote Speakers: both male.

• Mark Adams, Ph.D., Scientific Director, J. Craig Venter Institute, San Diego
• Sarkis K. Mazmanian, Professor of Biology, California Institute of Technology

Confirmed other speakers: all seven male

• Pierre Belichard, Co-founder and CEO, Enterome
• Adam Godzik, Ph.D., Bioinformatics and Systems Biology, Professor & Program Director, Sanford-Burnham Research Institute
• JunHua Li, Team Leader of Reference Metagenomics, BGI Research
• Victor Nizet, MD, Professor & Division Chief, Department of Pediatrics, UCSD School of Medicine, San Diego
• Steve Orndorff, NuMe Health
• Andrei Osterman, Ph.D., Professor, Bioinformatics & Systems Biology, Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute
• Bernd Schnabl, MD, Assistant Professor, Division of Gastroenterology, UCSD School of Medicine, TSRI California Campus

I suppose one could say "Well, they are still working on their agenda ... maybe they will have some female speakers."  So I decided to dig around a little bit more. They provide a link to the outline agenda here. Alas that is even worse.  There we find out who some invited speakers are who have not yet accepted

• David Odelson, R&D Program Director, Life Technologies
• Peter B. DiLaura, President & CEO, Second Genome
• Chris Christofferson, Morganthaler Ventures 
• Lou Tartaglia, Third Rock Ventures
• Mike Grey, Pappas Ventures
• Justin L. Sonnenburg, Assistant Professor, Microbiology & Immunology, Stanford School of Medicine, Palo Alto, CA

So that is 9 confirmed speakers and six invited speakers - all of whom are male.  Great.  Here is a suggestion.  DO NOT GO TO THIS MEETING.

Thoughts on Citizen Microbiology and upcoming session at #ASM2013

I am sitting on a Southwest Airlines flight heading to Denver for the American Society for Microbiology 2013 meeting. At 3 PM today I am scheduled to co-chair (with David Coil from my lab) a session on “Citizen Microbiology” (well the full title is Citizen Microbiology: Enhancing Microbiology Education and Research with the Help of the Public). The schedule of the session is at the bottom of this post but it promises to be very interesting and exciting (no bias here at all).

As far as I know, this is the first session ever on “Citizen Microbiology” at a large meeting of any kind. We held a small workshop at UC Davis in January of 2012 on Citizen Microbiology but that was quite small. I note - I use a very broad definition for Citizen Microbiology including basically any project that engages the public in some way to participate in a research project relating to microbes. This is the perfect time to have such a session at a large meeting and the ASM General Meeting is an ideal setting. There are a series of converging forces that makes this timing ideal including:

There is a growing appreciation of microbes and the role they play on the planet. Some of this appreciation is broad - covering all microbes - all the time - everywhere. But much of it is due to a growing interest in the microbes closer to us - those that live in and on us (the human microbiome) - those that live in and on plants and animals and other organisms we care about - and those that live in the places where we spend much of our time (the microbes of the built environment). I mean - come on - everyone is talking about fecal transplants now in public - in cover stories of the NY Times Magazine and in Ted talks.

• Technological and scientific advances have made it possible to better sample the microbes found in any particular location. Clearly, DNA sequencing technology and associated analytical tools are a central component of these advances, but other factors are important too. 
• The world is becoming more and more digital which makes the sharing of information (which is key to Citizen Science) easier and better. And social media has made it easier to communicate and discuss actions like Citizen Microbiology. 
• Citizen Science is growing by leaps and bounds in other areas (e.g., check out http://www.scistarter.com). 
• Crowdsourcing (not the same thing as Citizen Science - more on this another time perhaps) is also growing in leaps and bounds. 
• Crowdfunding is providing new ways to fund scientific activities. 
• Sensors of all kinds are getting cheaper and easier to use and are being deployed widely. 
• Many people are becoming more and more interesting in recording information about themselves and sharing it with others. 
• The “open science” movement is making the literature, software, methods and data and more available to everyone with no or few restrictions thus allowing for more people in diverse environments to become engaged in research. 
• Microbiology education and outreach is spreading with some great journalists and diverse other sources of information including hundreds of microbiology blogs and many other forms of social media being used. 

These are but a few of the reasons why I believe the time is right for Citizen Microbiology. But there are also what I would call somewhat negative reasons why the time is right too. These include 

• Germophobia is rampant and fueled by media hype and marketing forces. 
• We have done, and continue to do, serious harm to our microbial world. Antibiotics are overused. Antimicrobials are in everything. More and more children and missing out on vaginal birth. And so on 
• Although our understanding of the importance of microbes is everywhere, there are also many who are overselling what we know - claiming that probiotics will cure all ailments for example. 
• Some information about microbes that is out there on the web is, well, less that ideal 
• The ethics of engaging the public in studies of microbes are not fully appreciated by some and not completely understood by most. 

So this is both an exciting and a critical time for microbes and microbiology. And I hope that this session will not only help launch the field of Citizen Microbiology, but will help get everyone to think about the bigger issues and how to move the field forward in the right directions. For there is so much we need to do and think about including

• Ethics 
• Funding 
• Openness and sharing 
• Visualization 
• Analysis tools 
• Communication 
• Outreach 

And of course - the people at the session are not the only ones engaged in Citizen Microbiology or related activities (see a list we made a while back here). If you are doing a project please post something about it here. And if you are not doing a Citizen Microbiology project - well - why not? Get your act together.

Anyway - got to put away the computer as we land in Denver soon and I will rush off to the conference center, hopefully on time, to chair this exciting session. And I hope to see you there or have you follow online (check out the Twitter hash tag #ASM2013). And keep your eyes open for more excitement in this area.

-------------------------
Today’s session at ASM 2013:

(Division W Lecture) Authentic Research for Novice Scientists: Phage Discovery and Genomics by Undergraduate Students
Graham Hatfull;
Univ. of Pittsburgh, Pittsburgh, PA.

Understanding Human Influence on Microbial Distribution Patterns in the United States: A Citizen Science Approach
G. Barguil Colares1, J. Marcell1, D. Smith1,2, J. A. Eisen3, J. Gilbert1,2;
1Argonne Natl. Lab., Lemont, IL, 2Univ. of Chicago, IL, 3UC Davis, Davis, CA.

The Home MIcrobiome Project: Learning the Lessons of Citizen Science and Communication
J. A. Gilbert, D. Smith;
Argonne Natl. Lab., Lemont, IL.

The New National Lab: How Citizen Science is Transforming American Research
Darlene Cavalier;
Sci. Starter, Sci. Cheerleader, Philadelphia, PA.

Sequencing the Human Microbiome with Citizen Science
Z. Apte1, J. Richman2, W. Ludington3;
1uBiome, Inc, San Francisco, CA, 2Oxford Univ., Oxford, UNITED KINGDOM, 3Univ. of California, Berkeley, Berkeley, CA.

The American Gut Project: Challenges and opportunities for crowdsourcingmicrobial ecology
Antonio Gonzalez Peña;
Univ Colorado at Boulder, Boulder, CO.

Public Science in Private Places: A Study of the Microbial Ecology of One Thousand Houses in Fifty States and Five Countries
Rob Dunn;
NC State Univ., Raleigh, NC.

---

UPDATE: Notes from the Session Added 5/23

Here are some notes from the meeting:
Meeting Report: ASM 2013 in Denver, Day 1
ASM 2013, Day 1: From Oceans to Guts
Citizens doing Science, or Science on Citizens? (ASM 2013: Post 1)
Symbionticism: ASM 2013 LINKS
Storify by SPONCH

My storify embedded below

Excellent piece in the NY Times Magazine by @michaelpollan "Some of my best friends are germs" #ASM2013

Quick post here.  There is a really nice piece on in the New York Times Sunday Magazine by Michael Pollan on the human microbiome: Say Hello to the 100 Trillion Bacteria That Make Up Your Microbiome.  In it he discusses how he had his microbiome typed by the American Gut Project  and he discusses browsing through the output.  He also discusses a diversity of issues in the microbiome and work of various folks.  People featured include Justin Sonnenburg, Rob Knight, Burce German, Catherine Lozupone, Stanley Falkow, Jeffrey Gordon, Michael Fischback, Maria Gloria Dominguez-Bello, Martin Blaser, Ruth Ley, Andrew Gewirtz, Patrice Cani, Erica Sonnenburg, and Stephen O'Keefe.  The article does a really good job of highlighting why the microbiome is important yet does not oversell what we know at this point.

I note - Pollan came to UC Davis as part of his research for the article a little while back.  Below are some pics of him getting a tour of the UC Davis LEED Platinum brewing facility.  Anyway the article is definitely worth a look.  And just in time for the ASM 2013 Meeting which I am about to head to this AM.

Just in time for #ASM2013 - FDA adding regulations for fecal transplants #microbiome

Well, I guess this could be good news or bad news or both.  The FDA has sniffed the winds of microbiome studies and decided that it wants some more regulation on fecal transplants (aka fecal bacteriotherapy).  See for example Fecal Transplant: FDA Wants Regulation.  Fecal transplants are spreading like crazy these days and every where I go in real life and online I hear and see more about them.   For more on fecal transplants see some of my previous posts such as More (you know you wanted it) on fecal transplants and the microbiome and Fecal transplants in the news and Transfaunation and Fecal Transplants: What Goes Around Comes Around, Literally and Figuratively.

I guess the FDA feels like they have to do something given the spread of FT.   Given how many scam artists and oversellers of the microbiome are out there I think some sort of increased protection or regulation is probably a good thing.  But I am not sure what the best way to do this is.  Clearly some are unhappy with the FDA sticking their noses into fecal transplants (e.g., see here).  But given how little we know about FTs other than as treatment for Clostridium dificile infections it seems like one could make a reasonable argument for more regulation or caution.  It seems strange though that we can do just about anything and everything we want to kill all the microbes around us with very little regulation and yet attempting to manipulate the microbes in and on us or add a few here and there is being regulated more.

What do others think?  Do we need more regulation from the FDA on fecal transplants?

UPDATE - some links to other discussions of this:

• The kibosh (from Controversies in hospital infection prevention)
• Fecal transplants to treat C. diff now need FDA approval
• FDA halts US poop transplants pending further review (Raw Story). 
• FDA: Fecal Transplants Need Investigational New Drug Application ... (JWatch blog)
• Oversight for Fecal Transplants | The Daily Scan | GenomeWeb
• Many Years Young: Fecal Transplant: FDA Wants Regulation
• FDA Declares Stool a Drug -- Not kidding! @ TigerDroppings.com
• Fecal Transplant: FDA Wants Regulation - Digestive Health Center - Everyday Health - EverydayHealth.com

No need to oversell the human microbiome with studies like these ...

I know I complain all the time about news stories and people "overselling the microbiome".  Mind you, I believe microbial communities are likely to be found to have very very important roles in the biology of the plants and animals and other organisms on which they live, but I worry about overhyping the possibilities.  But thankfully, there are some good researchers at work out there documenting just what the microbiome can and does do.  And the results continue to be promising.

Here is the one that caught my eye most recently: BBC News - 'Weight loss gut bacterium' found about this PNAS paper.  While the study is in mice and it is what one could call "limited" in some ways, it is really fascinating and has much promise.  Basically, they isolated a new bacterium (with the awkward name of Akkermansia muciniphila, and did a series of experiments in mice looking at the role this bacterium can play in many mouse gut properties.  But most interesting, treatment of mice with this bacterium (and only when the bacterium was alive) led to a reduction in high fat induced metabolic disorders and obesity.  I am still re-reading the paper but the result seems solid.  And exciting.

So - there is no need to oversell the microbiome when the results coming in sell themselves ...

UPDATE 30 minutes after posting

Of course, I should have checked to see if Ed Yong wrote anything about this.  And he did: The Mucus-Lover that Stops Mice from Getting Fat.  Read his post.  It is excellent.  With ALL sorts of links and background and other detail.

Yes, the human microbiome has truly arrived: on Wait Wait Don't Tell Me

So cool.  Yesterday on "wait wait ... don't tell me" Kai Penn (actor) was enticed to play the game "Ahhh! Get It Off Me!" in regard to microbes: Not My Job: Kal Penn Takes A Quiz On The Microbiome : NPR

Hat tip to Jenna Lang for pointing me to this.

Via @nprnews: Not My Job: Kal Penn Takes A Quiz On The Microbiome n.pr/10hVj0J @jessicaleegreen @phylogenomics
— Jenna Morgan Lang (@jennomics) April 27, 2013

Quick post: interesting article in Smithsonian on the human microbiome by Richard Conniff

Just q quick post here.  There is an interesting article about the human microbiome worth checking out: Microbes: The Trillions of Creatures Governing Your Health.  By Richard Conniff in Smithsonian Magazine. It also comes with some related videos and pictures. See for example and And it references my "Overselling the microbiome" award ...

When a scientific team recently suggested that changes in gut bacteria could protect against stroke, Jonathan Eisen of the University of California at Davis lambasted them for “absurd, dangerous, self-serving claims that completely confuse the issue of correlation versus causation.” Eisen, a specialist in microbial genomics, now regularly presents “overselling the microbiome” awards on his blog. He says he doesn’t doubt the ultimate importance of the microbiome: “I believe the community of microbes that live in and on us is going to be shown to have major influences.” But believing that “is different from actually showing it, and showing it doesn’t mean that we have any idea what to do to treat it. There is danger here.”

And it even discusses a fecal transplant-like treatment called RePOOPulate. What could be better? Anyway - definitely worth checking out.

Microbes and obesity - more connections

A couple of recent papers on weight-loss surgery and microbes have gotten a lot of attention to the idea that obesity and microbes have a more than just coincidental connection.

Some of the news stories on the topic are below. A few of them are a bit over the top but the new work seems pretty sound so this is definitely worth a look.

• Fox: After weight-loss surgery, new gut bacteria keep obesity away
• National Post 'Weight loss bacteria' found in gut may play key role in fighting ...
• BBC: Bacteria find 'key to treating obesity without surgery'
• CBS: Gut bacteria may be key to weight loss
• LA Times Bacteria may provide some of gastric bypass surgery's boost
• NY Times: Bacteria in the Intestines May Help Tip the Bathroom Scale, Studies Show
• Nature via Scientific American: Gut-Microbe Swap Helps with Weight Loss

First multiple "Overselling the microbiome award": the Daily Mail article on Germs

At the recent "Future of Genomic Medicine" meeting, George Church gave me some grief over my "Overselling the microbiome award" because he thinks (rightly) that some people also undersell the microbiome.

So I set out today to find an example to give out such an award.  And within seconds I bumped into this: Germs: There are bugs that cure infections, protect against stroke and even keep your skin clear | Mail Online in the Daily Mail.

 Wow.  And not in a good way.  Oh well, so much for the underselling award.  Just the title made me cringe.  And so so so so many of the details are so so bad.

Where to start.  I guess from the beginning.

".The secret lies in the balance of the bugs, which exist in a fragile ecosystem. Knock one out and the system goes haywire."

Umm.  No.  Not that I know of.  Knock one out?  What evidence is there for this?  None.

"Imbalances in gut bacteria, for instance, have been linked with diabetes, obesity, autism, eczema, psoriasis, asthma and inflammatory bowel conditions such ulcerative colitis and Crohn’s disease"

".... may even ... cause ... multiple sclerosis "

Holy crap.  That sounds awesome.  Except that there are all correlations so far with no known causative role at least in humans.

Then they list some of the other good things microbes apparently have been proven to do:

"ANXIETY-BUSTING GUT BACTERIA"
"It seems that the type of bugs you have in your body can affect mood."

Though at least in this section they do refer to a mouse study but clearly imply this is true in humans too.  It may be.  But I am unaware of any studies proving it.

"BUGS ARE GOOD FOR YOUR SKIN"
"It's a common misconception that the cleaner the skin, the better — and the bacteria that live on our skin have an important role."

I am all for not killing all microbes willy nilly but their is certainly one part of the body that you probably do want to wash a lot - your hands.  So As long as they don't say "Don't wash your hands" this could be OK.

So what do they say next:

‘If you wash your hands repeatedly, they dry out — this is partly because you wash away all the oils but also because you remove a large number of the bacteria that help maintain the skin’s condition,’ says Professor Mark Fielder, a medical microbiologist at Kingston University.

Oh FFS now they are basically telling people to not wash their hands.

"SHARE A KISS... AND BACTERIA"
‘Every time you kiss, for example, you exchange a million bacteria. 'So your gut microbiology becomes close to that of your loved ones.’

Sounds great.  I could not find any references on the topic but sounds great.

"SOME TYPES MAY PREVENT STROKE"
Wherein the tell a story based on a press release which had led me to post the following: "Award: Ridiculous, absurd, offensive overselling of the microbiome from Chalmers & Gothenburg".  Any idea if I think this is an accurate press release?

TRANSFUSION TO BEAT INFECTIONS
Wherein they discuss fecal transplants for C. difficile infections, which seem to work quite well and I have written about a lot (e.g. Transfaunation and Fecal Transplants: What Goes Around Comes Around, Literally and Figuratively).  But then they kill their positive mojo on the topic by writing:

Lawrence Brandt, a professor of medicine and surgery at New York’s Albert Einstein College of Medicine, believes the treatment could work for other, non-gastro conditions, such as obesity and Parkinson’s.

Seriously?  Fecal transplants for Parkinson's?

And it goes on and on including:
"SOME BACTERIA KEEP YOU SLIM"
"BUGS THAT HELP MEDICINE WORK"
"COULD THEY WARD OFF CANCER?"
"KEY TO BABIES’ IMMUNITY"

I mean - I really really do think the microbiome plays roles in many many parts of our lives.  But those who promote it this much are the snake oil sellers of the modern era.  A slight of hand here and soon they will be selling us some specific brand of probiotic or way to protect our microbiomes.  So for this article the Daily Mail is getting my first multiple "Overselling the microbiome award."  They could get 3 or 4 just from this article if not more.  But I will just give them two.  And I will keep searching for an underselling the microbiome recipient.