Today’s misleading overselling the #microbiome – U. Chicago on Alzheimer’s and gut microbes

Well, this is disappointing if not disturbing

A new paper is out that has some interesting findings but the paper itself, and the press release form the authors (at University of Chicago) really goes overboard in misstating the findings.

Here is the paper in Scientific Reports. I purposefully am not putting the title of the paper here in the post yet, because amazingly, even the title is misleading.

But here is what a summary of what they showed, based on their results section, which seems interesting and sound

  • Antibiotic treatment of a variety of mice showed alterations in the GI microbiome and in various inflammatory markers circulating in the blood
  • Male mice treated with this antibiotic regime showed reduced Aβ plaque deposition but increased soluble Aβ levels
  • Reactive gliosis surrounding Aβ plaques is reduced in male mice treated with this antibiotic regime 
This is not all they report as they also discuss various controls and other observations about these mice and their brains and their responses to the antibiotic treatment.  
But what they do not report on is any evidence of anything other than a correlation between the GI microbiome changes and the inflammatory markers and the reduced Aβ plaque deposition.  They even state this VERY BRIEFLY in their paper

We are fully cognizant of the fact that the findings reported herein are purely correlative and do not elucidate precise mechanism(s). 

Yet then through other papers parts of the paper they misstate what they find and somehow, almost magically, turn this correlation into evidence for a causative connection.  For example in the abstract

These findings suggest the gut microbiota community diversity can regulate host innate immunity mechanisms that impact Aβ amyloidosis.

No. These findings are consistent with that.  They are also consistent with, for example, the antibiotics affecting microbes in the brain which in turn could affect inflammatory markers.  Or microbes on the skin.  Or in the blood.  Or elsewhere.  I don’t see any evidence here for a causative connection between the gut microbes (which are certainly affected by these antibiotics) and the plaque.

Yet even worse is that this misrepresentation of a causative connection makes it into the title of the article

Antibiotic-induced perturbations in gut microbial diversity influences neuro-inflammation and amyloidosis in a murine model of Alzheimer’s disease

No no no no no no no no.  No evidence that the perturbations in the gut microbes are directly influencing anything in the brain.  It is a good model.  But they need to be more careful with their wording.

And sadly, this gets even worse in the press release about the paper: Antibiotics weaken Alzheimer’s disease progression through changes in the gut microbiome | EurekAlert! Science News

What?  This “through changes in the gut microbiome” is just completely misrepresenting what was shown in the paper.

Here are some misleading parts of the PR

The study, published July 21, 2016, in Scientific Reports, also showed significant changes in the gut microbiome after antibiotic treatment, suggesting the composition and diversity of bacteria in the gut play an important role in regulating immune system activity that impacts progression of Alzheimer’s disease.

Nope. Nope. and Nope.

Thankfully there are a few caveats in the PR too but that does not balance misleading statements.  The worst is saved for the end

“There’s probably not going to be a cure for Alzheimer’s disease for several generations, because we know there are changes occurring in the brain and central nervous system 15 to 20 years before clinical onset,” he said. “We have to find ways to intervene when a patient starts showing clinical signs, and if we learn how changes in gut bacteria affect onset or progression, or how the molecules they produce interact with the nervous system, we could use that to create a new kind of personalized medicine.”

Basically, saying there will be a cure for Alzheimer’s. And then saying if we learn HOW (not if) gut microbes affect onset or progression, then we can better cure or treat this disease.  This is just too bold and misleading for my taste.  Nice paper.  Interesting work and implications. But it is misleading to say they have shown any causative connection between gut microbes and Alzheimer’s in this paper and also very misleading to start to talk about how they will use this to lead to treatments or cures.

Oh, and did I mention this was in mice not humans?  So how do they get from a correlative study in mice to how gut microbes affect progression of Alzheimer’s in humans?  Really this is not OK, even to hint at.

And of course, which such misleading material in their own paper and in their PR it is not surprising that some of the reporting on this is going awry.

See the Daily Express for example

And the Business Standard
And I am sure many more to come.  Scientists have to be more careful with discussing and presenting the implications of their work.  I love the microbiome field and the possible implications to me are enormous for the role of the microbiome in various areas of biology.  But misrepresenting ones findings, especially when it comes to human diseases, is dangerous and bad for science and bad for the microbiome field.  The author’s of the paper and the people behind the PR at the University of Chicago should publish a correction of the PR and also publish a correction of their paper to correct the misleading representations. And for their misleading material in their paper and in the PR I am giving them a coveted “Overselling the Microbiome” award.

Some responses

Minor correction made


And scarily, one of the authors of the paper, Rudy Tanzi is using the paper to promote his book and his claim that Alzheimer’s can be prevented through manipulation of the microbiome

UPDATE 2 — July 24 – 8:50 AM

I have written to the author of the PRs at U. Chicago to ask for a correction to be made

UPDATE 3 — July 24, 9 AM

So many people posting links to the misleading articles where all that comes through (e.g., on Twitter) is the headline including the misleading information about the gut. Am responding to many of them but not all.

Fortunately, Argonne National Lab responded quickly

UPDATE 4 — July 24 11:30 AM

I also will contact the author of this article on ScienceNews: Antibiotics might fight Alzheimer’s plaques  because it also has some misleading statements about the gut microbiome connection

Image caption:

PLAQUE FIGHTER  A long dose of antibiotics reduced Alzheimer’s-related plaques (shown here in a human brain) in the brains of mice, results that suggest gut bacteria can influence the disease

1st sentence does better

A long course of antibiotics reduced the levels of a hallmark of Alzheimer’s disease in the brains of mice, possibly by changing the species of bacteria in the gut

But then it reverts

This microbial shift in the gut appeared to affect the brain.

And continues with more

Sisodia and colleagues don’t know how bacteria signal from the gut to the brain to affect A-beta, although their study raises one possibility. 

And then this

If a similar relationship between gut bacteria and Alzheimer’s does exist in people,

UPDATE 5 — July 24 11:45 AM

Sent an email to the author.

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.

Overselling the microbiome award: Dr. Raphael Kellman at MindBodyGreen

Well this article by Dr. Raphael Kellman has just lots of overstatements about the microbiome: Why The Microbiome Is Your Key To Glowing Skin & Healthy Weight

For example, he writes:

Have you and your boyfriend or girlfriend ever gone out for a feast of delightfully unhealthy proportions only to then find yourselves picking fights with one another once you’re back home and digesting?  Fueling your body with unhealthy bacteria, and then feeding it with more unhealthy bacteria, is a sure-fire way to destabilize your mind-body connection. Instead, focus on supporting the positive bacteria in your belly with fermented foods like yogurt, sauerkraut, and kefir and watch your spirits soar.

This implies that somehow the microbome has some role in such situations and in mediating the relationships between two people.  And it implies that that can be fixed with fermneted foods.  And this is without any shred of evidence …

Then there is a discussion that makes the microbome sound like the master controller of all that is human:

Our bodies are cohesive entities, yes, but within each there are several languages spoken. 

The microbiome works like a translator for all of these systems, deciphering and decoding so that one process can communicate with the other for more efficiency and effectiveness (helping our systems to work as a team instead of independently alongside one another).

And then there is evidence free claims about fatigue and the microbiome

I’ve found that this kind of unexplained fatigue is often linked to a lack of diversity in the microbiome and can be remedied, despite what conventional medicine says

Whenever someone critiques “conventional” medicine and then presents no evidence for their claims, one should be wary, very wary.

And it ends with

Your inner ecology, your microbiome, is influential on your physical health, and that shows through glowing skin, a balanced weight and a youthful essence.  

So – if you want to be youthful and glowing and have good sex and relationships and get rid of your fatigue and fix your automimmune disorders and obesity and connect all of your systems together, all you have to do is fix your microbiome.  Simple.  Oh and how do you do that?  Why funny you asked, because I am selling this new book on the Microbiome Diet to solve all your problems.  Ridiculous.  And dangerous.

And thus I am giving out an Overselling the Microbome award to Dr. Kellman.

Overselling the microbiome award: CBC Fresh Air & JA Tetro on kissing microbiomes

Well, so there I was, enjoying a relatively peaceful and quiet Valnetine’s day.  When I noticed a Tweet directed to me from one of my favorite scientist’s out there

So I decided to check it out.  I clicked on the link and got to a CBC Fresh Air news story on Soundcloud:

▶ Kissing and romance and bacteria with Jason Tetro Feb 14/15 by CBC Fresh Air

I plugged in my headphones (was not sure if my kids should hear it) and listened away.  And what I heard was excrutiatingly painful.  The CBC Fresh Air reporter was discussing kissing and the microbiome with JA Tetro.  And Tetro made some of the most misleading, ridiculous overstatements about the microbiome I have heard in many years:

  • He basically implied or specifically said that, in humans, attraction to partners and relationship success was determined by finding a partner with similar microbiomes to oneself.  
  • Furthermore he discussed how maintaining similar microbiomes (e.g., via consuming the same probiotics or fermented foods) would help maintain attraction and how things like travel away from a partner might lead to repulsion.  
  • He said things like tha our immune systems determine if a partner is right for you from kiss-based comparison of a partner’s microbiome to one’s own.  
  • And that if the microbiome in a kissing partner is a match this leads to bliss and addiction and that salive is the first line of defense when it comes to relationships.  
  • He even went so far as to say that this is all about “trying to find your mother because our microbiomes come from our mother.”  

I could do on and on.  It was the worst, most misleading, innacurate material I have probably ever heard about microbiomes.  Tetro and CBC Fresh Air should be ashamed.

Sadly, I found some other misleading, inaccurate material from Tetro about the same topic in an article about kissing microbiomes from a few months ago: Swapping spit and testing chemistry: How kissing, germs help you pick your partner where Tetro is quoted

Tetro says that when you kiss your date, his or her germs make their way into your mouth’s ecosystem. And if it’s a match, you’ll want to keep smooching. 

“This study does one amazing thing, it shows you that kissing is the best way to find a mate for the long term. It might sound really gross but if the bacteria from the other person harmonizes with your bacteria, your immune system is all good. You feel a sense of calm and happiness, maybe even addiction,” he explained. 

“But if the bacteria don’t align with your microbes, you actually feel disgust and revolt. Your immune system is rejecting that person as a possible mate.”


“This study proves that when it comes to finding the right mate, the old game of spin the bottle actually has a base in science,” he said. 

More completely inaccurate, made up material with no basis in science.  As far as I can tell, this is basically made up.  Sure there may be a theory behind this.  But to present it as established facts about the microbiome is ridiculous.

This is all a shame really since the paper which the CBC Fresh Air story is referring to is actually a perfectly fine paper and the authors of the paper do not seem to be pushing these over the top ridiculous ideas.  And for this terrible story I am giving CBC Fresh Air and JA Tetro an “Overselling the microbiome award“.

I note before I finished writing this up I looked around and the discussion on Twitter about the article and saw that Bik and others had tried to get Tetro to tone down his claims but he refused. See for example Tweets below:










// and many more — but the gist was — Tetro presented not a single reference to back up his claims and did not seem to understand that what he did was misleading – to present personal ideas as though they were supported by research. So I felt the need to write a post providing some counter to his claims.

As an aside, the ridiculousness about kissing and microbomes did spawn one good thing: someone sent me this satire post amid the Twitter discussion: Love Transplants

BREAKING NEWS: Global chocolate distributor, Venus Inc., released a statement earlier today detailing their newest product line focused on manipulating the natural human microbiome to increase and sustain romantic relationships.

UPDATE 1: More from Tetro on kissing and the microbiome

Uggh. Was pointed to some more bad material from Tetro on kissing and the microbiome.  This time in Shape Magazine.

Question from Shape: 

Is it true that if the microbes aren’t in sync, kissing can make someone feel ill? Why is this? 

Answer from Tetro:

It’s due to the immune response, which is involved in everything from prevention of infection to allergies. For example, studies have shown a kiss from someone who has recently eaten peanuts can induce an allergic reaction for peanut allergy sufferers. This is due to the rapid nature of the immune system. When we kiss deeply, some 80 million bacteria are transferred. With that much, the immune system will react. If the bacteria are recognized and liked, then the response is one of happiness, joy and even addiction. But if they are not aligned, then like an allergic response, the person will feel uneasy and even defensive. When that happens, it’s best to move on.

Again.  This stuff about if the bacteria are recognized then the response is one of joy, happiness and addiction appears to be completely made up.

Another question from Shape:

Can people be a match, but over time fall out of interest with each other because microbes change?

Answer from Tetro:

Absolutely. Depending on the way people live, eat, exercise and perform hygiene, the microbiota can change over time. If this happens in one and not another, this could lead to a problem and possibly an eventual demise. To prevent this, the best way to help is to keep the microbiomes aligned using bacteria common to both. The best way to do this is though the use of probiotics.

So – is Tetro trying to sell probiotics?  WTF?  This also appears to be completely made up.

UPDATE 2: Oh wait, more awful material from Tetro – this time in Glamour.

We’ve found that microbes actually drive the majority of our how our bodies work, from general health to mental health to romantic health,” says Jason Tetro, microbiologist, probiotic company Bio-K+ advisory board member, and author of The Germ Code.

Microbes “drive the majority of how our bodies work”.  Really?  So our genes don’t matter?  Or our history?  Oh FFS.  This is just more off the deep end. And some other doozies like

“If you like the bacteria on someone’s body, you’ll like how he smells. If you experience that quasi-allergic reaction to his scent, it’s a sign your bacteria aren’t harmonizing,” says Tetro. Barely any of it has to do with how his actual body smells; it’s mostly chalked up to the scent his bacteria is giving off.

And much of the rest of the article is not quoting Tetro but the ideas clearly come from him.  I am intrigued about the part at the beginning saying he is on the Bio-K+ advisory board.  This appears to be the Bio-K+ probiotics company.  I wonder if this has anything to do with Tetro saying things like this, about probiotics:

And if you make it past a kinda queasy kiss and end up having sex with the guy, you can expect more of the same physical reaction (perhaps unless he’s been taking probiotics in between when you first kissed and had sex. Science suggests they can potentially change someone’s microbes to match yours, says Tetro). 

Perhaps all this ridiculousness is just marketing for Bio-K+?  I wonder if they provide relationship probiotics?  Uggh.  This just gets worse and worse the more I dig.

UPDATE 3: Even more from Tetro this time from the Globa and Mail: Why women’s germs are important to the health and happiness of us all

While ancient cultures never used kissing as a means to find a mate – it was simply an act of food sharing – modern society views this touching of lips and sharing of saliva as a part of the ritual of selecting a spouse. When the microbes of the mouth meet the immune system of a potential partner, a reaction happens. If the microbes are seen as friendly – similar to the rearing women – then there will be a sense of harmony and happiness

If, however, the germs are foreign to the system, inflammation will incur as well a sense of unease, ruining any chance for a long-term relationship. As a result, those with the most closely resembled microbiomes will find themselves making the best mates.

And then

Further research into the links between the female microbiome and society will no doubt unveil even more fruitful facts. For now, as we prepare to honour women the world over on March 8, we can all take a moment to be thankful for women for their beneficial microbes, for making the human species happy and healthy.

Again, there is no scientific basis for these claims.  There is no literature out there showing microbes exchanged via kissing lead to any of these responses.  There certainly is no literature showing that somehow the immune system examines the microbes and if there is a match (to one’s mother) then this leads to harmony and happiness.  And there is no literature on the opposite occurring when there is not a match.  This is just completely made up.  Presented as though it is established in the scientific literature.

UPDATE 4: Some papers on kissing and microbiomes and related topics

Just thought I would add some links to papers on kissing and microbiota and related topics.  I have scoured the literature on this in the past and again now and find nothing – absolutely nothing – that supports the outlandish claims of Tetro.

Key paper: Shaping the oral microbiota through intimate kissing.  The most recent and most detailed paper on the topic.  Open access from the journal Microbiome.  This is a pretty good paper by Kort et al.  It has some background references worth looking at too. Here are their conclusions:

This study indicates that a shared salivary microbiota requires a frequent and recent bacterial exchange and is most pronounced in couples with relatively high intimate kiss frequencies of at least nine intimate kisses per day or in couples sampled no longer than 1.5 h after the latest kiss. The microbiota on the dorsal surface of the tongue is more similar among partners than unrelated individuals, but its similarity does not clearly correlate to kissing behavior. Our findings suggest that the shared microbiota among partners is able to proliferate in the oral cavity, but the collective bacteria in the saliva are only transiently present and eventually washed out, while those on the tongue’s surface found a true niche, allowing long-term colonization.

Other papers of possible interest – and there are pretty few – most of which are on kissing and pathogens

UPDATE 5: Some reasonable stories about the kissing / oral microbiota paper:

UPDATE 6: Some other ridiculous stories about kissing and microbiomes – with completely different – but equally bogus claims – compared to the ones described above. For example, some discuss the idea that a match for oral microbiomes would be ones that are most different from one’s own – the exact opposite of Tetro’s claims.  Though this at least has some logical basis, there is no evidence for it.  None.

UPDTAE 7: Sadly the ridiculous ideas from Tetro spread to other places

How Bacteria Affects Your Love Life –

UPDATE 8: April 29 2015. More ridiculous microbe claims from Tetro

Here is a painful quote from a new article by Tetro: “Almost all bacteria love milk and use the various components for nutrition and growth”.  Where does this come from?  So – anaerobic thermophiles from Yellowstone love milk?  Intracellular symbionts of aphids love milk? Photoautotrophs love milk? WTF.

Really shameful overselling the microbiome from the American Society for Microbiology regarding lupus

Well, this press release is from October:Study Suggests Altering Gut Bacteria Might Mitigate Lupus But I just discovered it and it definitely deserves an award.  An Overselling the Microbiome Award.  The PR, sadly and amazingly from the American Society for Microbiology which should know better, discusses a paper from the ASM Published journal Applied and Environmental Microbiology.  The PR does an OK job discussing what was in the paper – a study of the microbiome in mice including those that are a model for lupus.  The researchers characterized the microbiome is mice with and without the lupus model disease and also compared over time and between sexes.  And they found some interesting correlates of microbial patterns that are found during flare ups of lupus for example and also in drug induced worsening of symptoms.  But they never showed ANY causal connection between any of the mcirobes and the lupus like disease.  And the never showed ANY benefit of treating the lupus-like symptoms in the mice.  Yet amazingly they go over board in making such claims including


No – the study did not suggest that at all.  The authors suggested that, yes.  And the study is consistent with that.  But it is also consistent with altering gut bacteria having NO EFFECT on lupus.  So this title is simply deceptive.

In the text other statements are like this:

These results suggest that the gut bacteria may contribute to lupus.

Stunningly, the PR includes some really inappropriate comments including:

Nonetheless, Luo suggests that people with lupus should eat Lactobacillus-containing probiotics, such as live culture yogurts, to reduce lupus flares.

Seriously?  Shame on ASM for allowing this garbage to be in the PR. No evidence at all is presented that this is helpful.

Also in the PR:

More generally, “The use of probiotics, prebiotics, and antibiotics has the potential to alter microbiota dysbiosis, which in turn could improve lupus symptoms,” says co-principal investigator Husen Zhang. Ultimately, says Luo, fecal transplant might prove valuable as a treatment for lupus.

Again, shame on ASM.  No evidence is presented for this either.

And then the PR ends with

“We were inspired in part to perform this research by a study on type 1 diabetes, which found that that disease is dependent on gut microbiota,” says Zhang. “Like type 1 diabetes, lupus is an autoimmune disease that is even more prevalent [than type 1 diabetes] in women.”

What?  I know of no research that shows that type 1 diabetes is dependent on gut microbiota.  I really don’t even know what to say here.

This is one of the worst Press Releases I have ever seen in terms of misleading statements about microbiomes.  And ASM should be embarassed about it.  And ASM should retract it.  And ASM should never ever put out something like this again.  And for this, I am awarding a coveted “Overselling the Microbiome Award” to ASM for putting out this inappropriate press release.  If any with lupus goes out and gets even remotely worse from taking such probiotics, prebiotics, or antibiotics, ASM will bear some of the responsibility for their problems.  Shameful.

UPDATE 1: Jan 2, 2015

I did some searching for “probiotics” and “lupus” and found some much more tempered claims from other places. For example in “Lupus Studies Point to Gut Microbes, Epigenetics

 “The long-standing anecdotal patient reports of certain diets worsening or improving flares might be more real than we thought. They should be studied more systematically, now that we know that almost any dietary component acts on the gut microbiota, [which] in turn has profound effects on the immune system,” Dr. Kriegel said. He also warned that patients should not assume that the various “probiotic” products now available to consumers would have a beneficial effect in lupus. “Probiotics could theoretically even worsen a disease state, since it is possible that physiologic immune responses against benign commensals could fuel autoimmune responses via cross-reactivity (as we hypothesize) or other mechanisms,” he said.

Dr. Kriegel concluded, “I think the best will be to wait until we have a better understanding of which commensals or commensal-derived products might be driving which autoimmune disease and then target those with a diet that is known to modulate these strains or products. Ideally, the field will also develop eventually novel types of antibiotics or vaccinations against certain commensals. Such approaches would allow us, in the future, to more specifically modulate the gut microbiota in autoimmunity.” 

Now that is responsible commenting on lupus and the microbiome.  Too bad ASM allowed complete BS to get into this PR instead of more reasonaed statements.

See also


Rediscovering some critical terms of use in microbial discussions: #microbiomania and #microbophobia

Earlier this week I was trying to come up with a short term to use when referring to the “Overselling of the Microbiome” and related hype. And I came up with one I really really like: microbiomania. The term just captures the essence of hype about microbiomes to me I guess.

So – of course – the first thing to do was to see if anyone else used this term.  And the number one thing I looked at was domain names.  Nope.  Microbiomania.Com and Microbiomania.Org are now mine.  And then I started to search the interwebs. And surprsingly there was not much (in English at least).  But some links showed up to books in Google Books with passages from > 100 years ago.  And this is when the digging got to be fun.  Here are some of the things I found.

1. A section from “The Medical Era

When copying this section of the search results I discovered Google Books has an embed tool for Google Books though not sure how well it works: here is a try

Anyway – the text of this section of the book reads:

The Paris correspondent of the Chicago Tribune in a recent letter says We hear very little now of microbist or anti microbist theories Dr Koch’s so called discovery is regarded with skepticism though not refuted The truth is his assertions are generally held to be not proven Dr Peters the favorite pupil of the great surgeon Dr Trousseau denounces what he calls microbiomania as a social danger and declares that the micro bians doctrine is vain sterile and objectionable in every way as both needlessly alarming and wrongly reassuring 

So I guess there were some folks who did not like the Koch and his silly theories about germs.

2. The Eclectic Medical Journal Volume 48

OCR text:

Microbiomania For five or six years past says Semolla you could not open a journal without encountierng an alleged discovery of one or more pathogenic bacilla and it is not necessary for me to tell you that the surest means of attaining celebrity is to discover in such and such a malady a new bacillus or a minute micrococcus I can not tell you what ridiculous puerilities have been brought forth by the imagination of physicians who are incapable of serious work and according to the rules of experimental medicine mount every new idea as though it were a triumphal car and think that in celebrating and exaggeraring its praises they manifest their love of progress 

Pretty awesome stuff I think.

3. The Louisville Medical Journal also comes up with a hit to microbiomania

Here is the attempt at an embed:

and the OCR interpreted text reads

and microbophobists The feeling against the theory of the microbial origin of cholera is very strong and was expressed by Prof Peter both at the Academy and the School of Medicine in these terms It is a pure satisfaction of natural history to say with the German School that there exists a microbe producer I say that there is a microbe product The parasitic doctrines have engendered a microbiomania which determined a terror which will be the opprobrium of the 19th century
Faris December 12 1884 

Now – nevermind that the OCR is not perfect (where is Faris?).  But not only is this fascinating.  But the beginning of the page has another word that seems worthy of resurrecting: microbophobists,  And this pulls up all sorts of fascinating discussions:

And the related search is perhaps more fascinating: microbophobia

So – in the end I did not come up with a totally new word.  But I do now have two words I really want to use more often and which I will use in the following ways:

  • Microbiomania which I define here as the overselling of the impact (beneficial or detrimental or otherwise) of microbiomes without the evidence to support such impact 
  • Microbophobia which I define here as the overwhelming and unreasonable fear of microbes (of any kinds).  This is similar in concept to “germophobia” but gets around the issue some people have with whether “germ” is a term that should be reserved for pathogens and thus that germophobia could be viewed as the fear of pathogens.  

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

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

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

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

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

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

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

The key part of this to me is 

The results provide evidence for a beneficial impact of exercise on gut microbiota diversity

For which they have no support.  They do not in any way show that exercise has ANY affect on the microbiota.  They show it is correlated to the microbiota.

And sadly there is a commentary on the article in the same issue of Gut that makes the same mistake.  Georgina Hold in The gut microbiota, dietary extremes and exercise writes:

The article is the first report that exercise increases gut microbiota richness/diversity and highlights that exercise is another important factor in the complex relationship among the host, host immunity and the microbiota.

No.  They did not show exercise increased gut microbiota diversity.  How can the difference between correlation and causation be missed in these articles?  Are these not even reviewed?  Sure – this is consistent with exercise affecting microbiomes but it is also consistent with rugby players having different diets and other behaviors.  There is a big difference between showing cause and effect and showing correlation.  For not distinguishing between correlation and causation regarding the rugby player microbiomes I am giving all involved here an “Overselling the Microbiome Award“.

Here is a microbiome theory I will leave you with.  I hypothesize that these papers, and all the other ones that oversell the microbiome, themselves cause major changes in the microbiome of many people.  Evidence for this?  Well, none yet.  But I have a correlation.  The correlation is, after reading these papers,  I feel sick to my stomach.  That must be proof right?

UPDATE 6/11/14

Author of the Medscape Medpage today article Kristina Fiore says she will update the article to more accurately reflect the science. See some of the thread below




UPDATE 2: 6/11/14.

The press release from Gut associated with this paper contains many inaccurate statements.

Examples include:

  • Title: Exercise boosts diversity of gut bacteria
  • Text: Exercise boosts the diversity of the bacteria found in the gut, indicates the first study of its kind published online in the journal Gut.
Somewhat surprised that such mistakes would come from the journal itself.

UPDATE 3: 6/12/14.

Kritina Fiore has fixed the Medpage article.  Nice.

UPDATE 4: 6/12/14.

Science Magazine gets the causation vs. correlation issue wrong in their little news piece about this.  Yuck.


UPDATE 5: 6/12.

Alexandra Sifferlin has a good article about this at Time




More accurate coverage by Claire O’Connell in the Irish Times Generally a good article here: Rugby players show good guts


Popular Science messes it up too


Keeping track of some of the Tweets about this on Storfy.

UPDATE 9 6/13/14.

NPR News Falls for the Hype


UPDATE 10: 6/13/14.

Just found another inaccurate claim in the original paper

UPDATE 11: 6/13/14

Oh FFS. Now I have found some articles reporting not only that exercise affects gut microbial diversity but that this is why exercise reduces obesity. See Exercise lowers obesity risk by stimulating diverse gut bacteria in the NVO News, for example.


Quote from the story:

A latest research suggests that exercise actually lowers obesity risk by stimulating diverse gut bacteria

UPDATE 12: 6/13/14

Fox News did better with the science (at least in their headline) than many other News Agencies (and much better than NPR).  They report “Exercise may lead to healthier gut bacteria“.

Just that word “May” makes me happy.  I know.  Low bar.  But I will take what I can get.

UPDATE 13: 6/13/14

Genome Web also is reporting on the story and on the “overselling” that was done.

UPDATE 13: 6/18/14

And now the New York Times joins the fray: Exercise and the ‘Good’ Bugs in Our Gut where Gretchen Reynolds writes:

The findings suggest that, in addition to its other health benefits, frequent exercise may influence our weight and overall health by altering the kinds of organisms that live inside of us.

No – the findings do not suggest that.  The findings are consistent with that theory but they are consistent with many many many other theories.  FFS this is maddening.  And the article ends with a quote from one of the authors:

But even in advance of those findings, he said, it seems likely that any amount of exercise should make your gut more welcoming to the bacteria that you want residing there.

I note – I found out about this article via Twitter


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 |

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:

// Other Tweets of relevance






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?

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.

And in non shocking news of the day – more overselling of the microbiome

Well, just read this story: Possible link between bacteria and breast cancer: study | CTV London News.  Serious overselling of the microbiome going on here.  As far as I can tell, all that was shown in the work discussed here (for which there is no publication or presentation of any kind reported) is that the bacteria found in canecrous breast tissue differs from that in non cancerous tissue.  Interesting perhaps.  But not really that informative as just about every time anyone has ever looked at two samples from patients with different health conditions, the microbiome is different.  Much worse that suggestions about the meaning of the differences they observe, the article then goes on to state:

And since we know that priobiotics can positively affect gut health, might the same beneficial substances influence breast health? Related bacterial research offers tantalizing possibilities. 

“It shows you how closely associated microbes are with our body and our health,” Reid says. “And therefore when you try and modulate them through probiotics chances are you could have an effect that’s beneficial.”

What?  Not only does Dr. Reid say, incorrectly, that “chances are you could have an effect that’s beneficial” simply by trying to use probtiotics to modeulate health.  But the whole ending to the article implies that somehow, magically, probiotics are a good idea for preventing breast cancer.  Uggh.