Important & neglected aspect of lab studies of animals : effect of habitat change on microbiome

By Aaron Logan via Wikipedia 

Very very interesting paper came out recent from some colleagues at UC Davis: PLOS ONE: Routine Habitat Change: A Source of Unrecognized Transient Alteration of Intestinal Microbiota in Laboratory Mice

Abstract: The mammalian intestine harbors a vast, complex and dynamic microbial population, which has profound effects on host nutrition, intestinal function and immune response, as well as influence on physiology outside of the alimentary tract. Imbalance in the composition of the dense colonizing bacterial population can increase susceptibility to various acute and chronic diseases. Valuable insights on the association of the microbiota with disease critically depend on investigation of mouse models. Like in humans, the microbial community in the mouse intestine is relatively stable and resilient, yet can be influenced by environmental factors. An often-overlooked variable in research is basic animal husbandry, which can potentially alter mouse physiology and experimental outcomes. This study examined the effects of common husbandry practices, including food and bedding alterations, as well as facility and cage changes, on the gut microbiota over a short time course of five days using three culture-independent techniques, quantitative PCR, terminal restriction fragment length polymorphism (TRFLP) and next generation sequencing (NGS). This study detected a substantial transient alteration in microbiota after the common practice of a short cross-campus facility transfer, but found no comparable alterations in microbiota within 5 days of switches in common laboratory food or bedding, or following an isolated cage change in mice acclimated to their housing facility. Our results highlight the importance of an acclimation period following even simple transfer of mice between campus facilities, and highlights that occult changes in microbiota should be considered when imposing husbandry variables on laboratory animals.

I personally think that we as a community are going to have to come to grips with the fact that the microbial communities in / on research organisms (of all kinds) may have a profound effect on experimental results.  This may explain many of the differences seen in experiments between facilities or over time within a facility.  In general, I think either controlling the microbes more carefully in lab experiments (e.g., using defined flora) or at least monitoring them is going to be very important to best interpret studies of plants and animals in the lab (or for that matter – in the field too).  Anyway -this paper is a tiny window into one of the ways that controlling for microbiomes may be important in lab studies.

Citation: Ma BW, Bokulich NA, Castillo PA, Kananurak A, Underwood MA, et al. (2012) Routine Habitat Change: A Source of Unrecognized Transient Alteration of Intestinal Microbiota in Laboratory Mice. PLoS ONE 7(10): e47416. doi:10.1371/journal.pone.0047416

A soothing microbiome music video of sorts

For all you microbiome geeks out there here is a music video of sorts from Antonio Gonzalez Peña in Rob Knight’s lab.

Diabetes and the microbiome – some hype and some caution – in the same stories

A new paper is getting some press on a link between type II diabetes and the microbiome.  The paper is here.  The abstract of the paper reads:

Assessment and characterization of gut microbiota has become a major research area in human disease, including type 2 diabetes, the most prevalent endocrine disease worldwide. To carry out analysis on gut microbial content in patients with type 2 diabetes, we developed a protocol for a metagenome-wide association study (MGWAS) and undertook a two-stage MGWAS based on deep shotgun sequencing of the gut microbial DNA from 345 Chinese individuals. We identified and validated approximately 60,000 type-2-diabetes-associated markers and established the concept of a metagenomic linkage group, enabling taxonomic species-level analyses. MGWAS analysis showed that patients with type 2 diabetes were characterized by a moderate degree of gut microbial dysbiosis, a decrease in the abundance of some universal butyrate-producing bacteria and an increase in various opportunistic pathogens, as well as an enrichment of other microbial functions conferring sulphate reduction and oxidative stress resistance. An analysis of 23 additional individuals demonstrated that these gut microbial markers might be useful for classifying type 2 diabetes.

Seems pretty reasonable.  All they say there is that they found associations between bacteria and diabetes.  That is interesting but they do not seem to present any evidence about a causal connection.  Perhaps people who get type II diabetes end up then having their microbiome shift.  Perhaps a shift in the microbiome causes type II diabetes.  Or perhaps something else (e.g., excessive inflammation) causes both type II diabetes and microbiome shifts.  Who knows.

But alas a bit of hype crept into some of the the news stories.  And it seems that the scientists behind the study are responsible for some of this hype.  For example, consider the article Changes in Intestinal Bacteria Linked to Type 2 Diabetes – US News and World Report.  One quote is a bit much for me:

“I think our study provides many targets for disease prevention and treatment through gut microbiotia in the near future,” said study senior author Jun Wang, executive director of the Beijing Genomics Institute in Shenzhen, China.

Fortunately the reporter who wrote this story does a very good job of providing cautious interpretations.  See for example:

“There’s no way right now that you can say there’s a cause-and-effect relationship. It could be that the patients with diabetes were treated with drugs that changed their gut flora. Or maybe they ate differently? This is an interesting hypothesis — that gut bugs could influence diseases states — but it’s far from proven,” said Dr. Stuart Weinerman, associate chief of the division of endocrinology at North Shore University Hospital/Long Island Jewish Medical Center in New Hyde Park, N.Y.

Also see stories like Gut bacteria could cause diabetes from Science Codex.  The title alone makes me want to cry.  Some quotes as well as discussion in that article also seem, well, not cautious enough.

The research, which was recently published in the scientific journal Nature, also demonstrated that people with type 2 diabetes have a more hostile bacterial environment in their intestines, which can increase resistance to different medicines.

Definitely not buying this “hostile” environment claim.  Fortunately as with the US News story, there is some caution presented

“It is important to point out that our discovery demonstrates a correlation. The big question now is whether the changes in gut bacteria can affect the development of type 2 diabetes or whether the changes simply reflect that the person is suffering from type 2 diabetes.”

 So – the stories seem to actually be doing an OK job with the correlation vs. causation issue I have complained about many times.  And though some of the scientists may be pushing a bit of overinterpretation the reporters and even the press releases have some decent cautionary statements.

I can’t keep up so here are some unfiltered links on obesity and microbiomes

I just can’t keep up.  These seem like they might be worth reading.  But no time to blog about them.  So here are some possible things to look at if you care about obesity and its possible connection to the microbiome.


News stories:

And I am sure there is a lot more ….

Overselling the microbiome award: MedicalDaily on Effects of Sugary Drink

There is a news article of possible interest in Medical Daily: Sugary Drinks Increase Bad Bacteria in Gut, Risk of Diabetes : Consumer News  This article reports on a paper in Obesity Reviews.  Alas the paper is not freely available. But the PhD thesis from one of the authors is.  The thesis is fascinating – I have read much of it now and skimmed other parts and it has the article as Chapter 2.  There are a few differences in the abstract – for example the Obesity Reviews paper does not start off with “The saying “you are what you eat” is no longer pure folklore but is scientifically substantiated by recognition of host-microbe interactions promoting digestion, absorption and metabolism.” which is in the thesis chapter.  But my guess is the published article is very similar to the thesis chapter.

The news article really goes overboard in hyping what appears to be little more than a correlation.  Among the issues I have:

  • Title:  Sugary Drinks Increase Bad Bacteria in Gut, Risk of Diabetes
    • Whew.  It is a doozy.  No evidence that the bacteria found are “bad” as far as I can tell.  No evidence that sugary drinks specifically cause the increase.  The paper is a review paper outlining a lot of prior work and some theories hypothesizing connections between fructose and sweeteners and the microbiome and obesity.  But I don’t see any evidence of specific increases in bad bacteria in the gut.
  • Byline: Sugary drinks help bad microbes grow in the human gut. This increase leads to many health complications like obesity and metabolic syndrome, raising risk of diseases associated with metabolic syndrome like diabetes.
    • Wow.  Even worse than the title.  Sugary drinks help the bad microbes grow.  And this leads to many health complications.  No evidence is presented for this.

In this case it is certainly much better to go to the source than to read the news story since the source (the PhD thesis and presumably the review paper) is quite thorough and interesting.  It has some fascinating ideas about sugar and sugar substitutes and their potential effects.

Mind you, I think microbes play a role in obesity too.  But the simple “sugary drinks CAUSE growth of bad bacteria which CAUSES health problems” well, if only it were so.  So for their overselling the effects of sugar and the microbiome without evidence I am giving the Medical Daily a highly coveted “overselling the microbiome award“.

Yes Virginia, even the cervix has a #microbiome ……….. or does it?

Just read over the following paper: PLoS ONE: The Cervical Microbiome over 7 Years and a Comparison of Methodologies for Its Characterization

It is interesting and has lots of tidbits worth looking at in more detail including

  • An analysis of methods for classifying sequence reads as to which organism they likely come from
  • comparison of amplification and sequencing methods
  • long time period covered in the sampling
  • and much more
But what struck me more than anything is that, well, they referred to the microbial community that they were sampling as the “cervical microbiome.”  And though what they discuss here is fascinating in many ways, I am beginning to wonder if every site on the human body (or sites on other organisms) should have its own microbiome.    Or, another way of looking at this is – where do we draw the line between niches?  Is there a eyebrow microbiome?  A left elbow microbiome?  A testicle microbiome?  Certainly, I view the microbes that live in and on people as part of an ecosystem.  But I think just as biomes in the world around us should be defined by – well – something bigger than just GPS coordinates – so too microbiomes should probably be a bit bigger than just the microbes found in a particular body site.  Starting to wonder if we are going to see a proliferation of microbiomes just as we have seen a proliferation of OMIC words.  Ooh — this could give me something new to give an award for.  

Best #human #microbiome item of week: #MinaBissellToo #Cancer #TED

From Science Friday.

My wife just told me about a fascinating Science Friday episode that I missed today: Building Organs, On One Microchip At A Time : NPR.  The discussion was with Dr. Donald Ingber from Harvard who has been designing mock organ systems with microchips.

Of particular relevance to microbiome studies are the following sections

“One example was that we put human intestinal cells that have been studied and cultured for years, and the pharmaceutical companies actually use them for looking at absorption in dishes, but everybody knows they’re not very good. They don’t really mimic gut function. When we put them in our chip and when we give them peristaltic-like undulating stretching rhythmically and we trickle flow over them like in your gut, they start forming villi, which are like the finger-like projections that increase surface area for absorption in your intestine. 

And what really surprised me is that the proliferative cells, the cells that are dividing rapidly, are in the crypt, the bottom – like between your fingers, at the bottom of these fingers, which is exactly like in your intestine. Plus, they put out mucus on the top of it, which protects it, and now we can put microbes on top. If you put microbes – if you put bacteria on cells in a dish, we call it contamination, and you have to throw it out and sterilize it. But we put microbes on the top and they’re perfectly happy. They’re symbiotic. And this is important because – and I don’t know if your show highlighted it, but over the last few months there’s been a lot of news that the microbiome – the microorganisms that live in our body can be very important for various diseases. And so we now have ways to study that. And the microbiome in the human is different than the mouse. And so this is very exciting for new opportunities.”

And then later

And I think other groups are looking at, you know, viral infections, for example. With our gut-on-a-chip, we’re hoping to study Crohn’s disease. Where it’s known in Crohn’s disease, there are three major contributors. One is inflammation, and we could add white blood cells, for example. The other is the microbiome, the microbes living in the gut. The other is peristaltic-like motions – again, mechanics. And so we can control all three of those.

Now I am sure there is some excessive enthusiasm for the power of their chip system here.  But it is fascinating and certainly will have many uses for testing models of function of host-microbe interacting systems.

The part I find most fascinating has nothing per se to do with the gut – what is most interesting is the concept that mechanical forces are fundamentally important to cell and organ function, development and regulation.  Here is one portion of what Ingber said:

We, you know, we actually – I’ve worked for 35 years in a strange – from a strange perspective in biology in that I’ve been – I was convinced that mechanical forces, that the forces due to breathing-like motions and stretching, you know, your muscles and the pulsations of blood through your vessels, that the stretching and the relaxing, the mechanical stresses are as important for regulating cell and tissue function as chemicals in genes. This is now getting more accepted in biology, but because of that, I felt that we had to create microenvironments that could mimic that – we had to develop microchips that can mimic that microenvironment. And what we ‘re finding consistently is that cells that people used before that they didn’t think were very good are now recapitulating organ-like functions. 

And as I said at a meeting yesterday, you know, there are no bad cells, just like there are no bad kids. There are bad families. There are bad neighborhoods and so forth. But – and so you have to give it the right microenvironment. We’ve also – I guess another surprising thing in the lung – and this was surprising – is that not only did we mimic complex functions such as the entire inflammatory response if we put a bacteria in the airspace in our little breathing lung on a chip, we saw in human, white blood cells stick to the vessel migrate across and engulf them. And that is something we hope for. 

But when we started to do things like we looked at toxicities of airborne particulates like in smog, we found that they were absorbed across the airspace to the vessel, which was great, but we found that breathing motions, physiological breathing motions increase the efficiency of that by tenfold. Now that no one’s even thought of before, nor have I. And so that was a prediction. And then we went back to animal models where we could control ventilation and we found exactly the same thing.

I have been thinking a lot about mechanical focuses and biology recently – especially since Mina Bissell came to visit UC Davis last year.  I wrote about her visit here: Mina Bissell, another of my science heroes, returns to #UCDavis (and also about her last visit before that here — The Tree of Life: A eureka moment – but not of the good kind).  Mina has been focused on how mechanical forces are critical to cancer development.  The best way to learn about Mina’s obsession is to watch one of her talks such as one that was recently posted at TED.

In the era of genomics and other ones the importance of mechanical forces and local environment has been ignored by many.  But it shouldn’t be.  When I was a graduate student at Stanford, one professor there – Paul Green – was completely obsessed by mechanical forces and their effects of biological systems.  Sadly – Paul – who was an amazing teacher and person – died of pancreatic cancer just as I was finishing my PhD.  But every time I see something about mechanical forces I think of him and I think he would have really enjoyed this Science Friday as well as Bissell’s work.

The human #microbiome project (HMP): new papers and news stories

Just collecting here the new papers from the Human Microbiome Project and some news stories discussing them.

Main papers in Nature

PLoS Collection (all free)

Other paper out in Nature on the topic though not from the HMP

Some news stories:

Some previous posts of mine in this general area

Some other good recent posts or articles worth looking at on the topic
Related links
And of course – a gratuitous embed of my recent TEDMED talk

Dubious Press Release from Cedars-Sinai linking Irritable Bowel Syndrome (IBS) and Bacteria in Gut

Quick one here.

Not impressed with this press release from Cedar-Sinai: Dr. Pimentel links IBS and gut bacteria – Cedars-Sinai (see other variants of it here: Daily Disruption – Cedars-Sinai Study Links Irritable Bowel Syndrome (IBS) and Bacteria in Gut and here: Irritable bowel syndrome clearly linked to gut bacteria).

Among the things that bug me here:

  • They don’t include a link to the paper or even provide a citation
  • They claim that culturing microbes is the “gold standard” for connecting bacteria to the cause of this disease.  AND they imply this is the first method to use culturing to study the disease.  Both notions are wrongheaded.  
  • They confuse cause of IBS and symptoms.  They say that b/c antibiotics help reduce symptoms, therefore, bacteria cause the disease.  Really?  So then fevers must cause things like malaria and flu because ibuprofen helps reduce symptoms right?
  • At some point it might be nice to mention that the MD behind the new study has also been pushing the idea that IBS is caused by bacterial overgrowth for many years both in a book and via a testing company though it is unclear what his association with the company is.  I note – ads for the book claim ” In addition, Dr. Pimentel presents a simple treatment protocol that will not only help you resolve your IBS symptoms, but will also prevent their recurrence.”  So – apparently he already had a cure BEFORE the new study was even done.  I general I am skeptical of papers that show evidence for something coming from someone who apparently already “knew” the answer.

Of course, I am not saying IBS is NOT caused by bacterial overgrowth as they claim.  But I can say this – PRs like this make me skeptical that anything new was done in this current publication.

Can’t wait for this meeting on Microbial Communities as Drivers of Ecosystem Complexity

I truly can’t wait for this meeting: Keystone Symposia Conference | Microbial Communities as Drivers of Ecosystem Complexity – Program

Organizers: Jacques Ravel, Vincent B. Young, Mitchell Sogin and Trina McMahon. March 25 – 30, 2011 • Beaver Run Resort  •  Breckenridge, Colorado

The current program is listed below.  Still time to register.  Oh, and it is in Breckenridge, CO, which is kind of nice.  If you are interested in microbial communities, especially molecular studies of said communities, this could be the place to be …

  • Norman R. Pace, University of Colorado at Boulder, USA 
    Molecular Analysis of Microbial Communities – Historical Perspective
  • Mitchell Sogin, Marine Biological Laboratory, USA Long-Tailed Microbial Communities
  • Susan Lynch, University of California, San Francisco, USA Microbial Community Analysis Using the PhyloChip
  • Jonathan A. Eisen, University of California, Davis, USA Phylogenetic and Phylogenomic Approaches to Metagenomic Analysis
  • Joseph Petrosino, Baylor College of Medicine, USA Sequencing Technologies Applied to Studying Microbial Ecology
  • Patrick D. Schloss, University of Michigan, USA Developing and Validating Tools for Computational Microbial Ecology
  • Rob Knight, University of Colorado, USA Quantitative Insights into Microbial Ecology
  • Jed Alan Fuhrman, University of Southern California, USA Integrating Molecular and Environmental Data to Evaluate Community Patterns
  • John Heidelberg, University of Southern California, USA Metagenomic Analysis of Marine Microbial Communities
  • Peter J. Turnbaugh, Harvard University, USA Metagenomic Analysis of the Human Gut
  • Susannah Tringe, DOE Joint Genome Institute, USA Bioenergy Metagenomics
  • Stanislav Dusko Ehrlich, Institut National de la Recherche Agronomique (INRA), France A Human Gut Microbial Gene Catalogue Established by Metagenomic Sequencing
  • Trina McMahon, University of Wisconsin-Madison, USA Functional Genomics of Polyphosphate Accumulating Bacteria: ‘Eco-Systems’ Biology for Wastewater Treatment
  • Gregory J. Dick, University of Michigan, USA Talk Title to be Determined
  • Robert L. Hettich, Oak Ridge National Laboratory, USA A Proteogenomic Approach for Characterizing the Molecular Activities of Gut Microbiomes
  • Brendan Bohannon†, University of Oregon, USA Environmental Microbial Ecology
  • Claire Horner-Devine, University of Washington, USA Biogeography of Microbial Communities
  • Thomas Schmidt, Michigan State University, USA Ecologic Strategies of Environmental Microbes
  • Margaret Riley, University of Massachusetts Amherst, USA Antibiotic-Induced Changes in the GI
  • Jacques Ravel, University of Maryland School of Medicine, USA The Temporal Dynamics of the Vaginal Microbiota
  • Forest Rohwer, San Diego State University, USA RNA Virus Communities Associated with Human
  • Zoe G. Cardon, Marine Biological Laboratory, USA Soil Microbial Ecology
  • David A. Stahl, University of Washington, USA Metabolic Modeling of a Mutualistic Microbial Community
  • Jay P. Tiesman, Procter & Gamble, USA Microbial Community Analysis from a Systems Biology Perspective
  • Edward F. Delong, Massachusetts Institute of Technology, USA Systems Biology of Planktonic Marine Microbial Communities
  • David A. Relman, Stanford University, USA Perturbation of the Human Microbiome: Unrest at Home
  • Julie Segre, NHGRI, National Institutes of Health, USA The Skin Microbiome
  • Vincent B. Young, University of Michigan, USA Integrating Human Microbial Ecology in a Clinical Setting