Tag: overselling the microbiome

Overselling the Microbiome Award for @nytimes on thumb sucking, nail biting protecting from allergy

I am continually torn about handing out “overselling the microbiome” awards to many “stories” that are coming out recently on new scientific studies.  On the one hand, many of these studies are quite interesting.  On the other hand, a huge number of them oversell the implications of the work.  And for some reason it seems to me that studies that could indicate a positive role for microbes in some way seem to end up with more misrepresentation than other types of work.  Mind you, I truly believe the cloud of microbes living in and on various plants and animals are likely to play fundamental roles in all sorts of important functions.  But my thinking this and my thinking it is likely does not mean we should go around overstating the implications of work in this area.

And that brings me to the latest example of such overselling  … a story about thumb sucking and nail biting as covered in the New York Times: Thumb Suckers and Nail Biters May Develop Fewer Allergies

The science here is interesting  – it is based on a new paper testing for associations between thumb sucking and nail biting on the one hand and atopic sensitization, asthma and hay fever on the other.  The paper found the following: Children who suck their thumbs or bite their nails are less likely to have atopic sensitization in childhood and adulthood.

Interesting.  But a key part of this is that they discovered a correlation.  Lots and lots and lots of possible explanations for this correlation including some examined in the paper but none of which have been proven.  Some news reports do a good job of covering the topic and discussing how this is still just a correlative observation.  For example see this Washington Post article by Lateshia Beachum.  There they report on the authors comments where the authors seem to think this supports the hygiene hypothesis

“The findings support the ‘hygiene hypothesis,’ which suggests that being exposed to microbes as a child reduces your risk of developing allergies,” Hancox said in a statement.

But then immediately this is countered by some more careful thoughts

Hirsh Komarow, a staff clinician at the National Institute of Allergy and Infectious Diseases, isn’t entirely convinced about the study’s conclusions. “It’s an interesting observation, but it needs more analysis,” Komarow said.

And then he is further quoted with other possible explanations

Komarow also suggested that thumb-sucking and nail-biting could be indicative behaviors that either thwart or encourage allergic reactions. He said being part of a large family and being exposed to microbes from many siblings may affect a child’s allergic sensitization.

And there are other articles out there with a decent amount of caveating.  But sadly the New York Times article by Perri Klass is not so tempered. Here are some of what I consider to be statements without enough caveating or countering:

A new study suggests that those habits in children ages 5 to 11 may indeed increase exposure to microbes, but that that may not be all bad.

No no no.  The new study did not suggest that.  The new study is consistent with that, but it is consistent with many other explanations.

And then there is this:

These differences could not be explained by other factors that are associated with allergic risk. The researchers controlled for pets, parents with allergies, breast-feeding, socioeconomic status and more. But though the former thumb-suckers and nail-biters were less likely to show allergic sensitization, there was no significant difference in their likelihood of having asthma or hay fever.

Well it is nice that the authors of the paper tested for some other possible explanations.  But it is a giant and inappropriate leap to go from that to “These differences could not be explained by other factors that are associated with allergic risk“

And then there are multiple quotes from the authors which are not really caveated enough or at all

Robert J. Hancox, one of the authors of the study, is an associate professor in the Department of Preventive and Social Medicine at Dunedin School of Medicine, a department that is particularly oriented toward the study of diseases’ causes and risk factors. He said in an email, “The hygiene hypothesis is interesting because it suggests that lifestyle factors may be responsible for the rise in allergic diseases in recent decades. Obviously hygiene has very many benefits, but perhaps this is a downside. The hygiene hypothesis is still unproven and controversial, but this is another piece of evidence that it could be true.”

Some caveats here but not enough.  This is not “evidence that it could be true” but rather it is data consistent with that model, but also consistent with other models that have nothing to do with the hygiene hypothesis.

And then there is this:

Malcolm Sears, one of the authors of the paper, a professor of medicine at McMaster University in Hamilton, Ontario, who was the original leader for the asthma allergy component of the New Zealand study, said, “Early exposure in many areas is looking as if it’s more protective than hazardous, and I think we’ve just added one more interesting piece to that information.”

No this study did not show that early exposure from thumb sucking or nail biting has any protective benefit.  It showed a correlation between thumb sucking/nail biting and lower risk of sensitization.  It did not show any causal connection.  And even if a causal connection were found, one would still have to test for what was the mechanism and the mechanism could be many things unconnected to microbial exposure.

And then there is this

Dr. Hancox pointed out that the study does not show any mechanism to account for the association. “Even if we assume that the protective effect is due to exposure to microbial organisms, we don’t know which organisms are beneficial or how they actually influence immune function in this way.”

Yes, this is good in some ways.  But why would we assume this?  Stating this without caveats makes it seem like we should assume this.

and

Dr. Sears said, “My excitement is not so much that sucking your thumb is good as that it shows the power of a longitudinal study.” (A longitudinal study is one that gathers data from the same subjects repeatedly over a period of time.) And in fact, as researchers tease out the complex ramifications of childhood exposures, it’s intriguing to look at long-term associations between childhood behavior and adult immune function, by watching what happens over decades. 

None of these quotes are really caveating the claims.  And then the article ends with a statement that seems to indicate that this is all a proven fact

So perhaps the results of this study help us look at these habits with slightly different eyes, as pieces of a complicated lifelong relationship between children and the environments they sample as they grow, which shape their health and their physiology in lasting ways.

Yes, this study is interesting.  And yes, it might be indicative of a causative connection between exposure to microbes on thumbs and nails and reducing risk to allergy.  But no, the study did not show that there is a causative connection, just a correlation.  And thus we cannot conclude at this point that we should “look at these habits with slightly different eyes, as pieces of a complicated lifelong relationship between children and the environments.”  The correlation could be due to other factors that have nothing to do with these habits.  And this is just a massive difference.  Shame on the New York Times for not reporting on this carefully enough.

And thus I am awarding a coveted Overselling the Microbiome Award to the New York Times and Perri Klass.

Hat tip to Mark Sagoff for pointing me to the NY Times article.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Today in Overselling the #microbiome: Lick-hiker’s guide to Inner Strength

Well, thanks, I think to Christie Aschwanden https://christieaschwanden.com for pointing me to this.

Valio unveils Lick-hiker’s Guide to Inner Strength with travel presenter Ian Wright – hasan & partners

https://player.vimeo.com/video/171063576

Valio – Gefilus Trailer from hasan & partners on Vimeo.

From the Press Release

International travel presenter Ian Wright is on a mission to seek out and lick the dirtiest locations in Europe for The Lick-hiker’s Guide to Inner Strength, a campaign that promotes the virtues of Gefilus, a good bacteria product range by dairy giant, Valio.

Simultaneously almost certainly over-promoting the benefits of this one probiotic and also the risks of licking things all over the globe.

Our 25-minute documentary sees Wright’s tongue come into contact with places that harbour bad bacteria – all in the name of testing immunity, gut health, and science. These include a metro station, public toilet, telephone, kindergarten, river, €10 note, bronze statue and Tottenham Hotspur FC.

Did they really have to pick on Tottenham?

Valio commissioned hasan & partners to demonstrate the power of Gefilus, which contains the friendly Lactobacillus rhamnosus GG and vitamins. Lactobacillus rhamnosus GG is the world’s most researched lactic acid bacterium and its qualities have since been scrutinized in more than 800 scientific studies globally.

Umm – just because there are 800 papers does not mean it is necessarily good for you. I mean, published papers is a good thing. But there are also 1000s of papers on anthrax and smallpox …

Armed with bottles of good bacteria and a luminometer to count germs, the two-week tongue tour of Europe tests Wright’s taste buds and nerve to the limit. Viewers will find out if he survived the ordeal without contracting any stomach bugs and where in the world is the location with the worst bacterial score.

OK – well then. A luminometer will reveal everything you need to know about a sample of microbes. We should just use them for every microbial study everywhere (nothing against luminometers per se, but they really are not what is needed here).

Jussi Lindholm, COO of hasan & partners, comments: “Good bacteria in Gefilus products has been carefully studied and people believe in it. But seeing is believing, so the documentary is both educational and fun, designed to physically draw attention to the link between the gut, our inner strength, and our wellbeing. World traveller Ian Wright has experienced many challenges and Gefilus was probably the weirdest.”

OK. Doesn’t actually seem that weird. Just oversold …

Here is the full documentary

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Microbiomania and Fecal Transplants

Had a bit of a Tweet scream about people promoting fecal transplants to cure all sorts of ailments. Yes fecal transplants are amazing, for C. diff infections.  And yes, they are worth testing for other ailments connected to microbes and inflammation.  But worth testing is very different than “they should be used for X”.  So I posted a bit about this.  Here is a Storify summary of some of the discussion

//storify.com/phylogenomics/microbiomania/embed?border=false&template=slideshow//storify.com/phylogenomics/microbiomania.js?border=false&template=slideshow[View the story “#Microbiomania and Fecal Transplants” on Storify]

Also see this discussion on Facebook

CureZone pushing Fecal Transplants for Parkinson's, Schizophrenia ,MS, Lupus, Depression and more http://www.curezone.org/cleanse/enema/fecal_transplantation.asp #Microbiomania

Posted by Jonathan Eisen on Wednesday, December 30, 2015

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Today’s awful overselling of the microbiome – Robynne Chutkan on libido

Well, this is just plain awful Are Antibiotics Ruining Your Libido? – The Daily Beast.  In this article, Robynne Chutkan argues that people’s sex drives may be being ruined by antibiotics.  And she presents zero evidence for this other than handwaving.

Some things in this article that are inaccurate:

We’ve spent most of the last century figuring out how to eradicate our microbes, and we’re just now realizing that the vast majority are friends rather than foes that actually play a vital role in keeping us healthy.

No – the “vast majority” of microbes are not known to be our friends or to play a vital role in keeping us healthy.  Certainly, microbes and microbiomes do contribute to our health and well being.  But to say the “vast majority” are beneficial is, well, just silly.

How about this section:

Most of the patients I see suffer from manifestations of an imbalanced microbiome—a condition known as dysbiosis. Some of the signs and symptoms are localized to the GI tract, like bloating and gas; but others, including yeast infections, brain fog, fatigue, rashes, joint pain, anxiety, food cravings, allergies, and autoimmune disorders, reflect the universal role our microbes play in preventing disease

Well, based on this statement I would certainly recommend nobody see Dr. Chutkan for any of their medical treatment.  What exactly is the evidence “brain fog” is caused by dysbiosis?  Or fatigue?  Or anxiety?  Or food cravings?  (Yes, I agree that some of the other things listed have been shown to be affected by the microbiome, but each of these (e.g., allergies) is influenced by many many factors and as far as I know there are no scientific studies that show that one can look at people suffering from any of these ailments and determine if their microbiome has caused their problems or not.

And then there is the discussion of microbiomes, antibiotics and sex life:

And what’s more, a healthy, balanced microbiome is essential for a healthy, satisfying sex life.

and

But there’s another alarming, but hidden epidemic of dysbiosis that’s occurring, and it may be wreaking havoc on your sex life. It’s the common practice of taking antibiotics after intercourse to prevent urinary tract infections (UTIs).

She then goes on to discuss issues in cystitis and UTIs and infections and the vaginal microbiome.  Yes, the vaginal microbiome is important.  And yes, antibiotics and affects the vaginal microbiome, both in positive and negative ways.  So – I do think we should be concerned with overuse of antibiotics and how that affects microbiomes.  And we should be concerned with overuse in the context of UTIs.  But does that concern allow us to oversell the science?  I don’t think so.  The worst part of this whole story relates to this issue:

If you’ve been using antibiotics to prevent post-coital UTIs and you’re finding that sex is less enjoyable than it should be, your vaginal microbes might be in need of some rehab. I recommend a three-pronged approach of avoidance, encouragement and repopulation

and

It may take some time before you see meaningful results, but this approach offers the possibility of real and lasting relief, rather than an antibiotic quick fix that ultimately ends up being ruinous to your sex life. 

The problem with this is that she presents no evidence that alterations int he microbiome affect libido or sex life and no evidence that her recommended solutions (e.g., probiotics and prebiotics) help with such symptoms.  So, yes, overusing antibiotics is a risk we should limit as much as possible.  But no, lets not glorify microbiomes and overcritique antibiotics by making people worry about their sex drive and sex life without evidence.  That is not helpful and could be harmful.  For this I am giving Robynne Chutkan a coveted overselling the microbiome award.

For more on this award see here.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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A worthy cause: Help fund a "Patient Centered Probiotics Reference"

UPDATE 8/27/15 – May have had a brain cramp on this.  See comment from Richard Jefferson.  Not sure this is in fact a worthy cause.

As many know I expend a lot of energy railing against overselling of the microbiome. And one aspect of this is the misinformation that is out there regarding probiotics. Well, this looks like it might help provide an antidote to some of the BS that is out there: (function() { var d = document, fr = d.createElement(‘script’); fr.type = ‘text/javascript’; fr.async = true; fr.src = ((d.location.protocol.indexOf(‘https’) == 0)? ‘https://s-‘ : ‘http://’) + ‘static.fundrazr.com/widgets/loader.js’; var s = d.getElementsByTagName(‘script’)[0]; s.parentNode.insertBefore(fr, s);})(); This is a crowdfunding effort to create a curated resource with information on scientific studies of probiotics.

Powered by FundRazr

From their site:

In his book, “Follow Your Gut”, Dr. Rob Knight cited several examples of how your gut microbes can affect your mood, the functioning of your immune system and inflammatory diseases. He suggests that you consult your physician or pharmacist to recommend probiotics that have randomized, placebo controlled trials backing them or failing that, you can survey the latest research published in scientific journals yourself. I know this is not a simple task for the regular consumer. A master reference of probiotics that you can refer to when making decisions on what products to purchase would be a handy thing. Dr. Knight notes in his book, that “…no patient centered resource exists that compiles this data.” If someone were to go ahead and do a google search for this information, you’d have to wade through a lot of marketing material from companies trying to sell you stuff. By focusing on the peer reviewed scientific literature, we eliminate all the marketing material. The research reports are then read and summarized by our scientists (curators) who put it in our reference database in a language you don’t need to be an expert to undestand. My colleague, Dr. Stephan Schurer, of the University of Miami Medical School, and I have built databases as tools for researchers to search for new drugs. We built these by extracting & summarizing research published in scientific journals. We propose to use a similar approach to build the probiotics reference. The money we raise will go to purchasing subscriptions to the scientific journals (like Journal of Gastroenterology and Gut Pathology) so that we can download the relevant research articles. It also goes to pay the part time curators who will read the journals and enter the key information into the database and lastly it goes to the costs of hosting a website and licensing of necessary softwares. Please help us in any way you can. We greatly appreciate monetary pledges, but also we need you to tell your friends and spread the word about our project.

Definitely seems like a worth project

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Overselling the mcirobiome award: Dr Roizen’s Preventative and Integrative Medicine Conference

Just got an email announcement for “Dr. Roizen’s Preventative and Integrative Medicine Conference” in Las Vegas in December 2015.

The announcement did not start of well for me with the gender balance of the key speakers

But since I spoke at this meeting in 2013 and since there was a good gender balance at that meeting, I decided to give the benefit of the doubt and keep reading (though I note – not trying to say this 5:0 gender ratio is a good thing).

And this is when it got worse – here are the bullet points for what one should learn from attending this meeting

  • The key concept about optimal aging that Dr. Roizen learned from 56 million people who took the RealAge® test
  • Smart tips about changing you and your patient’s microbiomes and what to do for your microbiome to promote weight loss and how it inhibits aging
  • How you can affect the role of the GI tract in chronic disease
  • How to understand the clinical utility of TMAO testing for monitoring cardiometabolic risk
  • The tricks about measuring your microbiome’s effects
  • Why some choose a plant based diet and why you might not
  • What supplements do you and your patient’s need with a plant based diet to decrease inflammation and improve your microbiome
  • Clarify how a systems-based approach can effectively treat illness and promote wellness
Now – I don’t know much about Dr. Roizen or his optimal aging claims in his books (I am skeptical). But the microbiome stuff in here is silly.
Let’s start with: “Smart tips about changing you and your patient’s microbiomes and what to do for your microbiome to promote weight loss and how it inhibits aging“.  I wonder how he will give these smart tips when as far as I know there is nothing actually known about this.  How the microbiome inhibits aging?  Really? Is this going to be a summary of future research not yet done or even imagined?
What about “The tricks about measuring your microbiome’s effects.”  So – there are 1000s of scientists studying this, they mostly say it is very very very hard to study the effects of the microbiome and Roizen and crew are going to solve this with a few “tricks”?  So is he saying everyone in the field is incompetent since they can’t measure these effects but he knows how to with a few tricks?
Dr. Roizen seems like a smart person and some of what I have heard from him sounds reasonable.  These microbiome claims from him here are a clear example of “Overselling the microbiome” and buying into the hype and not staying with the science. Maybe he was not paying attention for my talk for this meeting in 2013 when I discussed overselling the microbiome

I hope he tones down his claims in the future … but for now he is a winner of a coveted “Overselling the Microbiome Award”.  For other “winners” see here.
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Some history of hype regarding the human genome project and genomics

Just taking some notes here – relates to a discussion going on online.  Would love pointers to other references relating to hype and the human genome project (including references that think it was not overhyped).  I note – see some of my previous posts about this issue including: Human genome project oversold? sure but lets not undersell basic science and various Overselling Genomics awards. 

Here are some things I have found:

White House press conference on announcing completetion of the human genome

Genome science will have a real impact on all our lives — and even more, on the lives of our children. It will revolutionize the diagnosis, prevention and treatment of most, if not all, human diseases. In coming years, doctors increasingly will be able to cure diseases like Alzheimer’s, Parkinson’s, diabetes and cancer by attacking their genetic roots. In fact, it is now conceivable that our children’s children will know the term cancer only as a constellation of stars.

Collins et al. New Goals for the U.S. Human Genome Project: 1998–2003

The Human Genome Project (HGP) is fulfilling its promise as the single most important project in biology and the biomedical sciences— one that will permanently change biology and medicine.

Human Genome -The Biggest Sellout in Human History

The Human Genome Project: Hype meets reality

NOVA: Nature vs. Nurture Revisited

After a decade of hype surrounding the Human Genome Project, punctuated at regular intervals by gaudy headlines proclaiming the discovery of genes for killer diseases and complex traits, this unexpected result led some journalists to a stunning conclusion. The seesaw struggle between our genes (nature) and the environment (nurture) had swung sharply in favor of nurture.

The human genome project, 10 years in: Did they oversell the revolution? in the Globa and Mail by Paul Taylor referring to: “Deflating the Genomic Bubble“

Also see Genomic Medicine: Too Great Expectations? by PP O Rourke

Also Has the Genomic Revolution Failed?

And Human genome 10th anniversary. Waiting for the revolution.

Science communication in transition: genomics hype, public engagement, education and commercialization pressures.

The Medical Revolution in Slate.

A Decade Later, Genetic Map Yields Few New Cures in the New York Times.

In announcing on June 26, 2000, that the first draft of the human genome had been achieved, Mr. Clinton said it would “revolutionize the diagnosis, prevention and treatment of most, if not all, human diseases.” 

At a news conference, Francis Collins, then the director of the genome agency at the National Institutes of Health, said that genetic diagnosis of diseases would be accomplished in 10 years and that treatments would start to roll out perhaps five years after that.

NNB report: Ten years later, Harvard assesses the genome map where regarding Eric Lander:

At the same time, , he said genomic research has “gone so much faster than I would have imagined.” He cited ” an explosion of work that will culminate, I think in the next five years, in a pretty comprehensive list of all the target that lead to different kinds of cancers and give us a kind of roadmap for finding the Achilles heel of cancers for therapeutics and diagnostics.”

while at the same time he blamed the press for the hype

From Great 15-Year Project To Decipher Genes Stirs Opposition in the Times June 1990

‘Our project is something that we can do now, and it’s something that we should do now,” said Dr. James D. Watson, a Nobel laureate who heads the National Center for Human Genome Research at the National Institutes of Health. ”It’s essentially immoral not to get it done as fast as possible.”

  • Note the article has many complaining about the hype in the genome project even then ..

From SCIENTIST AT WORK: Francis S. Collins; Unlocking the Secrets of the Genome

And, Dr. Collins adds, there is nothing more important in science and medicine than the project he heads

Dr. Collins predicts that within 10 years everyone will have the opportunity to find out his or her own genetic risks, to know if cancer or heart attacks or diabetes or Alzheimer’s disease, for example, lies in the future. 

From READING THE BOOK OF LIFE: THE DOCTOR’S WORLD; Genomic Chief Has High Hopes, and Great Fears, for Genetic Testing June 2000 in the NY Times

The story goes through some predictions Francis Collins made for the future in a talk.  These included:

  • BY 2010, the genome will help identify people at highest risk of particular diseases, so monitoring efforts can focus on them.
  • In cancer, genetic tests will identify those at highest risk for lung cancer from smoking. Genetic tests for colon cancer will narrow colonoscopy screening to people who need it most. A genetic test for prostate cancer could lead to more precise use of the prostate specific antigen, or P.S.A., test by identifying those men in whom the cancer is most likely to progress fastest. Additional genetic tests would guide treatment of breast and ovarian cancer.
  • Three or four genetic tests will help predict an individual’s risk for developing coronary artery disease, thus helping to determine when to start drugs and other measures to reduce need for bypass operations.
  • Tests predicting a high risk for diabetes should help encourage susceptible individuals to exercise and control their weight. Those at higher risk might start taking drugs before they develop symptoms.
  • BY 2020, doctors will rely on individual genetic variations in prescribing new and old drugs and choosing the dose. Pharmaceutical companies will take a second look at some drugs that were never marketed, or were taken off the market, because some people who took them suffered adverse reactions. It will take many years to develop such drugs and tests.
  • Cancer doctors will use drugs that precisely target a tumor’s molecular fingerprint. One such gene-based designer drug, Herceptin, is already marketed for treating advanced breast cancer.
  • The genome project holds promise for the mental health field. ”One of the greatest benefits of genomic medicine will be to unravel some biological contributions to major mental illnesses like schizophrenia and manic depressive disease” and produce new therapies, Dr. Collins said.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Overselling the microbiome award – many – for stories about placental vs. oral microbiomes

A few days ago on Twitter I was pointed to a news story about the human microbiome:

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I looked at the article and definitely agreed with Ed. So I responded

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And I pondered writing up an “overselling the microbiome award” but I got caught up in other things. And then today some people (including Jens Walter) pointed me to this New York Times article about the same topic: Study Sees Bigger Role for Placenta in Newborns’ Health – NYTimes.com. And I decided I had to write something up because too many news stories were not doing a great job with the science here.

So here goes. First, the Science news (UPDATE – NOTE this is the news part of Science magazine, not ScienceNewsOrg) story Ed Yong pointed to originally and the parts I have problems with.

  • Sentence 1: Researchers have discovered a small community of bacteria living in a most unlikely place: the placenta, the organ that nourishes a developing fetus through the umbilical cord.  No – not really.  They did not discover this.  They did a more detailed characterization of the community.
  • Sentence 2: The finding overturns the conventional wisdom that the placenta is sterile.  No – the study is another piece of evidence that argues against the “conventional wisdom”
  • Sentence 3 is OK.
  • Sentence 4.  Medical experts have long assumed that any bacteria found in the organ must have been picked up when it passed through the vagina after delivery.  Sure – some “experts” have assumed this.  But there has been growing evidence for many years that this is a bad assumption.  

I could go on and on.  Actually though I won’t.  Becuase every news story can have some limitations.  I don’t like inaccurate statements but it is a part of life I guess.  But the part that drives me batty in this story is the inclusion of a discussion about oral health.  Here are the two paragraphs that are the crux of my concern (with bold emphasizing the worst parts).

Surprisingly, the mix of bacteria in the placenta looked more like the microbiome in an adult human’s mouth than the vaginal, skin, gut, or other body microbiomes, Aagaard’s team reports today in Science Translational Medicine. The researchers think the microbes may get to the placenta from the mother’s mouth through her bloodstream, perhaps when she brushes her teeth and dislodges them into the blood. That possibility is intriguing, because there’s a well-known correlation between gum disease and preterm birth. Indeed, the array of bacteria in the placenta differed in women who gave birth early, before 37 weeks. 

“This reemphasizes the importance of oral health” during pregnancy, Aagaard says. In fact, women may need to pay attention to their teeth even before they may become pregnant, because the placenta develops early in pregnancy, she says. That may be a challenge for low-income women who can’t afford dental care, Aagaard adds. The team also found a correlation between the composition of the placental microbiome and urinary tract infections, which suggests that such illnesses or antibiotics taken to treat them could alter the microbiome in unhealthy ways.

I have read and reread the paper (which I note – is not open access – making it hard to the public to actually dig into the paper if they wanted to).  And I see no evidence presented anywhere of the importance of oral health or any causal connection between oral health and the placental microbiome or risks to pregnancies. The claims made about this here in this news story are irresponsible.  Yes, there have been some other studies about dental health and birth issues.  But nothing in this paper.  And to imply otherwise is misleading at best.  And then to go on with “That may be a challenge for low-income women who can’t afford dental care” is really not appropriate.  And to then go on about UTIs and how treating them may “alter the microbiome in unhealthy ways” is also misleading and not supported.  
Where is the critical evaluation of such claims?  Certainly the paper is very interesting.  Among the findings of interest to me: (1) that low amounts of DNA from diverse microbes is found even in the placentas from healthy pregnancies and (2) that in their analysis these microbes were most similar to those from the mouth.  But how we get from those findings (and some others) to “the importance of oral health during pregnancy” and “such illnesses or antibiotics could alter the microbiome in unhelathy ways” is, well, not in the realm of scientific research.  This is in the realm of speculation.  And speculation is fine -IF YOU TELL PEOPLE YOU ARE SPECULATING.  If you don’t tell people you are speculating I have another term for it – it is called misleading.  I assume the researchers and reporter did not intend to be misleading but that is the end result of excessive speculation without making it clear what one is doing.

Now this brings me to other articles about this study.  There are many out there.  And most seem to have eaten up this oral health connection without questioning it.  For example, consider the artilce in the New York Times yesterday:Study Sees Bigger Role for Placenta in Newborns’ Health – NYTimes.com by Denise Grady.  Some issues I have with this article:

  • Let’s start with the title “Study Sees Bigger Role for Placenta in Newborns’ Health.”  Well, no – there was nothing in this study that showed any evidence about a new connection between the placenta and newborns’ health.  
  • NYTimes: “During pregnancy, the authors of the new study suspect, the wrong mix of bacteria in the placenta may contribute to premature births.” Sure – they suspect it.  Would have been good to point out they have no evidence for this.
  • NYTimes: Although the research is preliminary, it may help explain why periodontal disease and urinary infections in pregnant women are linked to an increased risk of premature birth.  Again, may help explain – sure.  But it also may have no connection whatsoever.  There is no evidence presented in the paper connecting periodontal disease and UTIs and the placental microbiome.  So this is pure speculation.  And it should have been met with some discussion of all the other ways that periodontal disease and UTIs could lead to risk of premature birth.  Like leading to increased inflammation in the mother.  Or affecting blood flow in the mother.  Or other things.  There is actually a TON of research in this area.  Below are some of the factors that affect preterm labor, as listed by the Mayo Clinic – are we now discounting the years and years of work on this and going whole hog into proposing a new cause without any evidence?
    • Previous preterm labor or premature birth, particularly in the most recent pregnancy or in more than one previous pregnancy
    • Pregnancy with twins, triplets or other multiples
    • Certain problems with the uterus, cervix or placenta
    • Smoking cigarettes, drinking alcohol or using illicit drugs
    • Certain infections, particularly of the genital tract
    • Some chronic conditions, such as high blood pressure and diabetes
    • Being underweight or overweight before pregnancy, or gaining too little or too much weight during pregnancy
    • Stressful life events, such as the death of a loved one
    • Domestic violence or any form of abuse during pregnancy
    • Multiple miscarriages
    • Red blood cell deficiency (anemia), particularly during early pregnancy
    • Too much amniotic fluid (polyhydramnios)
    • Pregnancy complications, such as preeclampsia
    • Vaginal bleeding during pregnancy
    • Presence of a fetal birth defect
    • Little or no prenatal care
    • An interval of less than six months since the last pregnancy
    • Also, having a short cervical length or the presence of fetal fibronectin — a substance that acts like a glue between the fetal sac and the lining of the uterus — in your vaginal discharge might be linked to an increased risk of preterm labor. 
  • I note – the authors even say in their paper “Although this study is not able to address the relationship between periodontal disease and the placental microbiome, we, as a community of obstetricians, have appreciated for decades the association between periodontal disease and preterm birth”. Clearly the paper received more scrutiny that the quotes and the news stories. 
  • NYTimes: The new study suggests that babies may acquire an important part of their normal gut bacteria from the placenta. No.  Nothing in this study showed any connection between what is in the placenta and what is in the babies guts.  None.
  • NYTimes: If further research confirms the findings, that may be reassuring news for women who have had cesareans. Some researchers have suggested that babies born by cesarean miss out on helpful bacteria that they would normally be exposed to in the birth canal.  Again – there is no evidence that babies pick up microbes from the placenta.  So speculating that this may reassure women who have C- sections is way way way too premature.
  • NYTimes: “I think women can be reassured that they have not doomed their infant’s microbiome for the rest of its life,  said Dr. Kjersti Aagaard.  Wow. Now we have gone from “if further research confirms” to just flat out reassuring women who have had C-sections that there are no effects on the microbiome.
  • NYTimes: “It didn’t make a whole lot of sense to us,” she said. “It’s not like babies are hanging out in the vagina. They come shooting out pretty fast.” Also, she said, they emerge covered in a waxy substance called vernix, which most likely helps keep bacteria from latching on. Wow.  So babies come shooting out of the vegina and therefore cannot get microbes from the vagina.  This despite the massive amounts of evidence that they in fact do get microbes from the vagina and that C-section born babies get a different community (see for example this).  (UPDATE 5/26 – see UPDATE below with some comments / papers about C-sections vs. vaginal birth and how my use of “massive” here may be an overstatement itself).
I could go on and on.  But I won’t.  I am pleased the reporter talked to Martin Blaser who puts some damping on the speculation:

Dr. Martin J. Blaser, director of the human microbiome program at NYU Langone Medical Center, and the author of a recently published book, “Missing Microbes,” said that Dr. Aagaard’s study was important, but preliminary, and that it did not provide information that could be used in treating pregnant women. 

Thank you Martin.  But even with this, these articles leave me very frustrated.  The best I can do I guess is give out an award or two. So, for their reporting on the topic I am giving Denise Grady of the New York Times and Jocelyn Kaiser of Science News an Overselling the Microbiome award since they oversell the potential connection between oral health and infant health as mediated by the placenta.  And I am also giving this award to  Kjersti Aagaard, the first author of the paper, for her comments on the topic.

For more examples of “Overselling the Microbiome” awards see my page here.

UPDATE: Some other news stories where the headline alone is painful

UPDATE 2: Some articles that discussed placental microbes before this story came out

and many more

UPDATE 3: Paper on placental – mother – infant connection not even mentioned

Just found this paper from a Google Scholar search:  Probiotics Modulate Host-Microbe Interaction in the Placenta and Fetal Gut: A Randomized, Double-Blind, Placebo-Controlled Trial.  Seems like it is of direct relevance.  Abstract is below;

Abstract
Background: Early host-microbe interaction provides important maturational stimuli for the developing immune system. The role of prenatal microbial contact remains elusive. Objectives: Our aim was to investigate whether microbes in placenta or amniotic fluid affect fetal innate immune gene expression during late pregnancy and whether innate immune gene expression profiles in the placenta and the fetal gut may be modulated by dietary supplementation with specific probiotics. Methods: Altogether 43 pregnant women were randomized to receive (1) Bifidobacterium lactis, (2) B. lactis in combination with Lactobacillus rhamnosus GG (LGG) or (3) placebo for 14 days before elective cesarian section at full term in a double-blind clinical trial. Bacteria in amniotic fluid and placenta were detected by quantitative (q)PCR. The expression of Toll-like receptor (TLR)-related genes in the placenta and meconium samples was assessed by qPCR. Gene expression patterns in meconium were interpreted to reflect immune physiology in the fetal gut. Results: The study was completed by 29 mother-infant pairs. Bacterial DNA was detected in all placenta samples. Microbial DNA in amniotic fluid and placenta was associated with changes in TLR-related gene expression in the fetal intestine. Maternal probiotic supplementation significantly modulated the expression of TLR-related genes both in the placenta and in the fetal gut. Conclusions: Microbial contact in utero is associated with changes in fetal intestinal innate immune gene expression profile. Fetal and placental immune physiology may be modulated by maternal dietary intervention using specific probiotics.

This paper was not mentioned or cited as far as I can tell in the current study.

UPDATE 4: This paper also seems relevant

Microbial contact during pregnancy, intestinal colonization and human disease.  Abstract:

Interaction with colonizing intestinal bacteria is essential for healthy intestinal and immunological development in infancy. Advances in understanding early host–microbe interactions indicate that this early microbial programming begins in utero and is substantially modulated by mode of birth, perinatal antibiotics and breastfeeding. Furthermore, it has become evident that this stepwise microbial colonization process, as well as immune and metabolic programming by the microbiota, might have a long-lasting influence on the risk of not only gastrointestinal disease, but also allergic, autoimmune and metabolic disease, in later life. Modulating early host–microbe interaction by maternal probiotic intervention during pregnancy and breastfeeding offers a promising novel tool to reduce the risk of disease. In this Review, we describe the current body of knowledge regarding perinatal microbial contact, initial intestinal colonization and its association with human disease, as well as means of modulating early host–microbe interaction to reduce the risk of disease in the child.

UPDATE 5 – more misleading quotes

  • From Time’s misleadingly named article “The New Way to Predict When Pregnant Women Will Deliver“: “By focusing on oral health, we may actually be optimizing the health of the pregnancy and limiting the risk of pre-term birth,” says Aagaard. After paying so much attention to the more obvious ways to make a pregnancy healthy, it may be time to consider the less obvious – and less visible ones
  • That quote is just so inappropriate … uggh

UPDATE 6: May 24.  Some  Made a Storify with some of the Tweets related to this post.

//storify.com/phylogenomics/overselling-the-microbiome-in-placenta-story/embed?border=false&template=slideshow//storify.com/phylogenomics/overselling-the-microbiome-in-placenta-story.js?border=false&template=slideshow[View the story “Overselling the microbiome in placenta story” on Storify]

UPDATE 7: May 26 – some other papers of relevance to birth mode and infant microbiomes and placentas

A key question to me I guess is the following – how do differences between the microflora in babies born by C-Section vs. vaginal birth arise if the microbes in placentas have a big role in colonizing infants?  Perhaps the differences between C-section babies and vaginal birth babies are small — I do not know — need to dig into this more.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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?

I note – as I assume many know – I think the microbiome is critical to many human functions and phenotypes.  And screwing with it via excessive use of antibiotics seems like a very very bad idea.  The precautionary principle says to me we should avoid any antimicrobials unless absolutely necessary.  But do we really need to overstate what we know in order to effect change?  Do we need to say things like “antibiotics are extinguishing our microbiome” which is simply untrue?  I don’t think we do.  I think we can be more careful, not mislead people, and still have an impact.  And thus, I am giving out today’s “Overselling the microbiome” award to Time magazine and Martin Blaser.

UPDATE 5/1 – some links of interest

Other Overselling the Microbome Awards:

Some papers of relevance on antibioics and the microbiome

Ancestral human microbiome

UPDATE 5/3/4

Some papers that offer a more tempered view of the role of the microbiome in causing various disease:

  • Disturbed gut colonisation patterns have been associated with allergic disease, but whether microbial variation is the cause or effect of these diseases is still under investigation. We are far from understanding what constitutes a “healthy gut microbiome” that promotes tolerance. This remains a major limitation and might explain some of the inconsistency in human intervention studies with prebiotics and probiotics. Multidisciplinary integrative approaches with researchers working in networks, using harmonised outcomes and methodologies are needed to advance our understanding in this field.
  • Such data suggest that bona fide associations may exist between microbiota and obesity in humans, although causality remains to be addressed. Whether these associations will hold up to large-scale replication has yet to be determined. This situation is reminiscent of genetic association studies done in the pre-genome-wide association scan era, during which many candidate associations were found using sample sizes which at the time were considered large, but were rather small in retrospect [54]. Very few of these earlier associations have held up to replication in the modern era, where the threshold for association is more stringent and requires sample sizes orders of magnitude larger [55]. It seems reasonable to postulate that causal contributions from the gut microbiome to the development of human obesity have effect sizes on the order of common genetic variations implicated in complex diseases. If this is the case, much larger studies will be necessary before we have clear evidence of association.  
  • This review considers the nature of the evidence supporting a relationship between the microbiota and the predisposition to disease as associative, correlative, or causal. Altogether, indirect or associative support currently dominates the evidence base, which now suggests that the intestinal microbiome can be linked to a growing number of over 25 diseases or syndromes. While only a handful of cause-and-effect studies have been performed, this form of evidence is increasing. 
  • Talk by Rob Knight on “From Correlation to Causation in Human Microbiome Studies”

Update 5/4 #2.  I would also recommend people check out the Helicobacter foundation web site. which has some useful background information on the organism and the diseases it causes.

Update 5/4 #3.  Some recent papers by Martin Blaser worth looking at

UPDATE 5/4/#4. Martin Blaser on Dr. Oz show where Dr. Oz and Blaser both make some statements that are a seriously over the top.

History of studies of the affect of antibiotics on human health

Oh – and Barry Marshall – winner of the Nobel Prize for discovering how H. pylori causes ulcers and cancer – chimed in on Twitter:

//platform.twitter.com/widgets.js Other Tweets of relevance

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UPDATE 5/4 – Caesarian Section Risk notes

A related question I have been thinking about involves Caesarian sections and whether they lead to an increased risk of any ailments that might have a microbial connection (e.g., obesity, allergy, autoimmune diseases). I started digging into the literature on this for my TED talk and then again when I posted something from the Smithsonian Genomics Exhibit that suggested there were no risks associated with C-sections.

Some papers on the topic suggest there may be some risks from C-sections related to these topics but that they are very very small:

UPDATE 5/5 Diabetes

Increase in type 1 and type 2 diabetes rates in children reported – is this connected to antibiotic usage or microbiomes?

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Overselling the microbiome award: Mercola/Perlmutter on fecal transplants for severe neurological dysfunction

Well, this is pretty scary.

An automated Google Search I have picked up a hit to an article by Mercola about an interview he did with David Perlmutter: Key Dietary Strategies to Protect Yourself from Alzheimer’s : Natural Wellness Review

And the article covers many topics but one is pretty over the top.  There is a section on recommendations by Dr. Perlmutter to promote brain health.  And one of them is quoted below:

Fecal transplantation, in cases of severe neurological dysfunction where poor gut flora appears to be a contributing factor. Your microbiome is critical for multiple reasons, including regulating the set point of inflammation, producing neurotransmitters like serotonin, and modulating systems associated with brain function and brain health. This form of therapy is now the standard of care for life-threatening C. difficile infections.

Yup.  He is recommending fecla transplants to treat severe neurological dysfunction.  Not the first person to suggest a connection between microbes and neurology.  Not the first person to say that maybe trying to change the microbiome might be an interesting thing to test as a treatment for some issues.  But with no caveats here they just jump right in to using this to treat neurological dysfunction.  This is just grossly over the top and will likely mislead many many people with neurological dysfunctions into thinking fecal transplants are a known effective treatment.  I wonder if Dr. Perlmutter will start offerring home fecal transplant kits for sale on his web site (which I will not link to here).

Now, I think microbes are important.  And I think there is potential here for fecal transplants for a lot of issues.  But potential is different than proven.  By a long show.  And people like Mercola and Dr. Perlmutter should be ashamed for misleading people like this.  And thus they are today’s winners of an “Overselling the Microbiome” award.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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