Today’s YAMMM (Yet another mostly male meeting): pharma-nutrition #PN2015

Just got pointed to (by Elisabeth Bik) an announcement for a meeting: Home : Pharma-Nutrition 2015 with a focus on “Linking the Microbiome with Nutrition and Pharma”.  And alas, the list of confirmed speakers is as follows:

  • Keynote Speaker
    • Martin J. Blaser, NY University Medical Center, New York, NY, USA
  • Speakers
    • Gregor Reid, University of Western Ontario, London, ON, Canada 
    • Alain van Gool, Radboud University, Nijmegen, The Netherlands 
    • David Hafler, Yale, New Haven, CT, USA 
    • John F. Cryan, University College Cork, Cork, Ireland 
    • André Marette, Laval University, Montreal, QC, Canada 
    • Charles R. Mackay, Monash University, Clayton, Victoria, Australia
    • Alan L. Landay, Rush University Medical Center, Chicago, IL, USA

Yay.  All men.  How wonderful.  Because, you know, there are no women working on the microbiome and nutrition right?  Ugg.

Seems like they are still working on getting more speakers.  I will send this blog post to the organizers and see what they say.  But suffice it to say I am very disappointed in them.  Oh, and shockingly, the two organizers are men: Johan Garssen and Alan Landay.

These YAMMMs (Yet Another Mostly Male Meeting) really have got to be killed.  People should not got to them.  People should not speak at them.  And the organizers should not be allowed to run other meetings unless they can explain themselves and provide evidence that they will work to not have this happen again.


I found the program committee for the meeting.  Alas the gender ratio there is lame too.

  • John F Cryan, University College Cork, Cork, Ireland
  • Alain van Gool, Radboud University Medical Centre, Nijmegen, The Netherlands
  • David Hafler, Yale School of Medicine, New Haven, CT, USA
  • Charles R Mackay, Monash University, Melbourne, Australia
  • André Marette, Laval University, Sainte-Foy, QC, Canada
  • Gregor Reid, Lawson Health Research Institute, London, ON, Canada

And a bit strangely – all of the people on the program committee are speakers.  No bias there.

Microbiome topic of the day: radiation therapy and the microbiome

Just saw this interesting story in the Observer: Cancer scientists to classify gut bacteria to prevent the side-effects of radiotherapy | Science | The Observer.  It discusses an effort to give more consideration to protecting and / or repopulating the microbiome in relation to radiation therapy.  I think this is critically important.  I want to note – people should give some credit to DARPA for being ahead of their time on this issue.  I went to a workshop in 2004 organized by Brett Giroir and Manley Heather.  The topic was “Radiation Protection” and one of the points of discussion was the gut microbiome and the effect of radiation on it.

Anyway – since that meeting I have been following this topic on and off.  And I do think thinking about the microbiome in relation to radiation therapy (and any radiation exposure) is critically important.

Simple microbiome quiz and then mapping function from PGED

Just did this: Map-Ed Genetics: Pin Yourself on Our World Map! (the microbiome one – there are two right now – the other is personal genomics – and others coming).  Best part is browsing the map of other participants afterwards.

Love these QTL experiment where microbe relative abundance is the quantitative trait being studied

Just got pointed to this very interesting paper by one of the authors: Genome-wide mapping of gene–microbiota interactions in susceptibility to autoimmune skin blistering : Nature Communications : Nature Publishing Group.  I really really love this new approach of doing QTL experiments where the quantitative trait being measured is the relative abundance of various microbes.  The first paper of this kind I know of that did such a QTL analysis was Benson et al. 2010 in PNAS in mouse.  There have been a few others using this approach (e.g., Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits) and I am sure we will see many many more.  Basically this approach allows one to identify genes / polymorphisms / regions of the genome in a host that influence the relative abundance of specific microbes.  And such information will be critical in understanding the interactions of microbial communities with hosts.

Lies, damn lies, and press releases – trouble with recent PR about autism and microbiomes

Uggh.  Just saw a bunch of stories about autism and the microbiome.   Many of the comments in the news stories I read seemed, well, not so good.  So I decided to sniff around.  Seems that many of the comments and stories are based on a new PLOS One paper and the comments and press release from the group behind the paper.

Here is the press release I found: Clues about autism may come from the gut.  From Arizona State University.   So I read it.  But I had a hard time getting past paragraph 2:

In new research appearing in the journal PLOS ONE, a team led by Rosa Krajmalnik-Brown, a researcher at Arizona State University’s Biodesign Institute, present the first comprehensive bacterial analysis focusing on commensal or beneficial bacteria in children with autism spectrum disorder (ASD).

This did not sound true and sounded a bit overblown as I could have sworn I had seen other “comprehensive” studies of the microbiome in children with ASD. So first I decided to look at the paper.  And – thanks a lot – there was no link in the PR or the stories I had seen.  So I had to go to PLOS One and do a little searching and I found it:

Reduced Incidence of Prevotella and Other Fermenters in Intestinal Microflora of Autistic Children

Kang D-W, Park JG, Ilhan ZE, Wallstrom G, LaBaer J, et al. (2013) Reduced Incidence of Prevotella and Other Fermenters in Intestinal Microflora of Autistic Children. PLoS ONE 8(7): e68322. doi:10.1371/journal.pone.0068322

So – first I asked – did they make the same claim in the paper or was this just in the PR?  Usually such things are just in the PR but amazingly they have this claim in the paper too, with lines like:

“previous studies describing the relationship between autism and gut microbes have either mostly focused on the emergence of harmful bacteria or mainly paid attention to already-known beneficial bacteria”

So I decided to then look at Pubmed and Google Scholar for other papers on autism and the microbiome. Here are some that I found:

Not all of these are what one would call comprehensive.  But some of them are at least approaching the scale of what was done here.  And surprisingly, not all of them are cited in the new study.  In particular, the papers by Gondalia et al including one on “Molecular Characterisation of Gastrointestinal Microbiota of Children With Autism (With and Without Gastrointestinal Dysfunction) and Their Neurotypical Siblings” is not references despite it doing some similar things.  I guess, if you don’t cite other comparable studies, and pretend they don’t exist, then that makes one’s work seem a but more novel right?  Weird not to cite that work though – not sure why that happened.  And certainly some of the other studies, even though they are cited, seem like they could be referred to as comprehensive.  I mean – Ian Lipkin’s study did metagenomics not just PCR based sequencing.  Isn’t metagenomics sort of more comprehensive than PCR?  
Anyway – let’s just say this is not the first “comprehensive” study of autism and the microbome.
Moving on in the press release I encountered another painful statement.

The work also offers hope for new prevention and treatment methods for ASD itself, which has been on a mysterious and rapid ascent around the world.

Just what exactly does this new study say about prevention or treatment?  Actually, as far as I can tell – nothing.  So this is a bonus overselling statement just for the PR
Oh but then the PR just get’s worse:

Their new study is the first to approach autism from a different angle, by examining the possible role of so-called commensal or beneficial bacteria.

Seriously?  We have gone from trying to claim this is the first comprehensive study of the microbiome and autism to now saying it is the first?  Fu#*(@@# ridiculous.
Other lines that are troubling are encountered further on including
  • The authors stress that bacterial richness and diversity are essential for maintaining a robust and adaptable bacterial community capable of fighting off environmental challenges.”.  Hmm.  What is the difference between richness and diversity? And what is the evidence that they are essential for such functions?
  • The species is a common component in normal children exhibiting more diverse and robust microbial communities.”  Again – what makes that robust?
  • Michael Polan’s recent New York Times Magazine story on the microbiome points to the fact that he is proud that his gut microbiome is rich in Prevotella regarding it as a possible sign of a healthy non-Western diet.  Really?  They brought Michael Pollan (with a mis-spelling that might be on purpose so that Pollan does not see this) into their PR?  Uggh
Anyway – I kind of wanted to give them an overselling the microbiome award for some of their statements.  But in the end I would rather give them an “Overselling ourselves” award.  It is a shame too.  I think continuing to explore possible connections between autism and the microbiome will be important.  Making misleading statements about what you have done and not citing / properly referencing other work will not help.

YAGGP? – Yet another gratuitous genomics plot?

After my talk at Future of Genomic Medicine 2013 meeting last week a few people asked if I would post these slides on my blog. So here they are:

As part of my talk last week I started off showing this slide:

Such figures are part of many genomics talks 

But this was not about sequencing growth / improvements.  Instead it was about hits for the word “microbiome” in Pubmed.

Of course, there are more papers today than ever so it is important to do some sort of control search.  

So I chose to search for “Elvis” in an homage to an old story on protein sequences:

The results clearly prove that studies of the microbiome are on the rise …

SimplyThick food thickener, necrotizing enterocolitis, and microbiomes

Wow.  I have not heard anything about this issue until this NY Times article: Warning Too Late for Some Babies –  The article summarizes some recent FDA and other medical warnings about a product called SimplyThick.  This product has been connected to cases of necrotizing enterocolitis (NEC) in premature infants.  NEC is a horrible horrible ailment with an incredibly high death rate.  I am familiar with NEC mostly because some colleagues at UC Davis are involved in clinical trials to use probiotics and prebiotics as a preventative therapy for NEC (see more on the project here: Premie NEC — Foods For Health Institute and UC Davis Medicine – Helping Premature Infants Thrive).  NEC seems to have some general connection to “microbiome health” although it is not entirely clear (to me at least) whether the connection is correlative or causal in any way.  The NY Times article simple serves to remind me that we seem to know very very little about the connection between diet and general microbe-related health in infants (or for that matter, adults).  We desperately need to accelerate the pace at which we determine / study how foods, food additives, and diet affect our microbial communities …

Lesson of the week from this article is captured in this quote

“You try not to put anything in a baby’s intestine that’s not natural.” If you do, he added, “you’ve got to have a good reason.”

I am not by any means convinced that everything has to be “natural” (I am not sure I even know what that means) but stuffing preemies full with some food thickener simply because it has been marketed to speech pathologists as something to use seems like a pretty bad idea.

Overselling the microbiome: University Bern press release uses slight of hand to make mouse study seem to be about people

Interesting new paper came out recently on “Sex Differences in the Gut Microbiome Drive Hormone-Dependent Regulation of Autoimmunity.”  It is alas in Science so it is not available openly.

Anyway there are some news stories about the article where you can get the gist of it.  Best one is probably the blog post by Christine Gorman: Transplanted Bacteria Turn Up Testosterone to Protect Mice against Diabetes.  The story is pretty interesting.

For those who do not know I have been a bit obsessed about the connection between diabetes and the microbiome for a while.  See my Ted talk for example where I discuss my own personal connection to this issue.

But the science is not what I want to talk about here.  What I want to talk about is how science press releases can just be awful.  The one for this paper is like some sort of con artist’s scheme.  Here it is on Science Daily: Good bacteria in the intestine prevent diabetes, study suggests.  First, they lure you in with a headline that, well, fails to mention that the study was in mice.  And then they keep trying to lure you with some lines about humans and their microbes.  In fact, the first two and half paragraphs I think are pretty deceptive.

All humans have enormous numbers of bacteria and other micro-organisms in the lower intestine. In fact our bodies contain about ten times more bacteria than the number of our own cells and these tiny passengers are extremely important for our health. They help us digest our food and provide us with energy and vitamins. These ‘friendly’ commensal bacteria in the intestine help to stop the ‘bad guys’ such as Salmonella that cause infections, taking hold. Even the biochemical reactions that build up and maintain our bodies come from our intestinal bacteria as well as our own cells.  

Pretty important that we get along with these little bacterial friends… definitely. But as in all beautiful relationships, things can sometimes turn sour. If the bacteria in the intestine become unbalanced, inflammation and damage can occur at many different locations in the body. The best known of these is the intestine itself: the wrong intestinal bacteria can trigger Crohn’s disease and ulcerative colitis. The liver also becomes damaged when intestinal bacteria are unbalanced. 

Research groups led by Professor Jayne Danska at the Sick Children’s Hospital of the University of Toronto and Professor Andrew Macpherson in the Clinic for Visceral Surgery and Medicine at the Inselspital and the University of Bern have now shown that the influence of the intestinal bacteria extends even deeper inside the body to influence the likelihood of getting diabetes. In children and young people, diabetes is caused by the immune cells of the body damaging the special cells in the pancreas that produce the hormone insulin.

Yup – lots and lots of stuff about people.  Which is fine.  I like people.  But the thing is. The paper is about mice.  So lines like “have now shown that the influence of the intestinal bacteria extends even deeper inside the body to influence the likelihood of getting diabetes” are kind of misleading because so far there has been no mention of mice and that line is they only true for mice, not people.  And then they wrap up this section with another line about people, clearly trying to imply that the “have now shown …” part is relevant to people.

And then, finally, they turn to mice.

By chance, 30 years ago, before the development of genetic engineering techniques, Japanese investigators noticed that a strain of NOD laboratory mice tended to get diabetes. These mice (also by chance) have many of the same genes that make some humans susceptible to the disease. With the help of the special facilities of the University of Bern and in Canada, these teams have been able to show that the intestinal bacteria, especially in male mice, can produce biochemicals and hormones that stop diabetes developing.

And then they go back to people.

Diabetes in young people is becoming more and more frequent, and doctors even talk about a diabetes epidemic. This increase in diabetic disease has happened over the last 40 years as our homes and environment have become cleaner and more hygienic. At the moment, once a child has diabetes, he or she requires life-long treatment. 

“We hope that our new understanding of how intestinal bacteria may protect susceptible children from developing diabetes, will allow us to start to develop new treatments to stop children getting the disease,” says Andrew Macpherson of the University Bern.

Wow.  So in a press release about a paper that is about mice, there are three sentences about mice and the rest are about people.  The thing is, in case you don’t know – mice are not the same as people.  Just saying.  And for trying to overplay the connection of their work to humans, I am giving the writer’s of this press release my coveted Overselling the Microbiome Award.

Past posts about this award include:

The kitten microbiome – new related paper and Mendeley collection

Saw this new paper today: Dietary format alters fecal bacterial populations in the domestic cat (Felis catus) – Bermingham – 2013 – MicrobiologyOpen – Wiley Online Library

And was reminded on the Kitten Microbiome project. It was conceived as a (sort of) joke but studying the microbes in our domestic companion animals is a good thing and could be very interesting in many ways.

So I created a Mendeley group on cat / kitten microbiome studies:

Oh, and while I was at it I created a group for the Dog Microbiome.

Not sure these should really be completely separate (i.e., there could be a collection on the domestic animal microbiome) but am keeping them separate for now.

Guest post: uBiome puts microbiome science in the hands of the people

It is a fascinating time to be doing microbiology. One of the latest occurrences is the spread of work on the human microbiome and even more recently the launching of several crowdfunding / citizen science efforts in this area. (Full disclosure – I am a collaborator on one of these efforts – the American Gut Project).  Another one of these efforts is a startup called uBiome. After seeing the announcement of their launch I asked Zac Apte, one of the founders, if he would be interested in writing a guest post for my blog on what they are doing. And, well, he agreed. And it is below (the post title “uBiome puts microbiome science in the hands of the people is from him too – I added the pic).

uBiome puts microbiome science in the hands of the people

Most people think “germs” is a dirty word. That’s what we’re taught since preschool. But the truth is that microbes aren’t just good or bad — it’s a lot more complicated than that. We are surrounded by microbes (on and inside of us) that form a complex ecosystem that supports and nourishes our health.

uBiome ( is a citizen science startup focused on allowing people direct access to this cutting ed research. By amassing a large set of microbiome samples along with health and lifestyle data, we will perform a microbiome-wide association study, examining specific traits as well as diseases such as diabetes, heart disease, hypertension, and depression in the context of the human microbiome.

We hope participants will join our community and track themselves in the long term — as you change your diet or exercise regime, begin taking a new medication, such as an antibiotic, or simply as you age. Now is a great time for a first data point.

Finally, we’re not just polling people for their poop. We’re also polling them for their creativity in scientific research. When our first dataset goes live, we’re going to ask our citizen scientists to form their own cohorts and we’ll empower them (statistically speaking) to test their own hypotheses. That’s our vision.

Our team has expertise in metagenomics as well as roots in population genetics, computer science, and network mathematics. We also have a team of scientific advisors which includes inventor and MacArthur Genius award winner Dr. Joseph DeRisi, biotechnology pioneer and inventor of the recombinant Hepatitis B vaccine Pablo Valenzuela, as well as doctors, bioinformaticians, and researchers.

We really appreciate Jonathan Eisen reaching out to give us this opportunity to say hello on the Tree of Life blog — and we look forward to engaging with you!

By Zac, Will and Jessica – the uBiome team