Thursday, May 01, 2014

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?


  1. One of the most compelling reasons (and certainly not the only reason) to study the human microbiome is so that when we do have to use antibiotics, we can make sure that things return to a healthy stable state afterwards.

    tl;dr : antibiotics not actually magic, have consequences which could maybe be mitigated if we were less ignorant.

  2. Other tl;dr: we should only use antibiotics when we really need to, and if we really need to use antibiotics there are more pressing concerns than a potential small effect on body mass down the line.

  3. Thanks for posting this, Jonathan! I've been seeing what seems to be a LOT of hype about this book, and have been hoping that the book itself is not quite so extreme ... I have not yet read the book myself - it's on my list of stuff to read soon.

    The cancer reference is probably relating to Helicobacter pylori. Blaser has been concerned about the increase in of certain cancers (Barrett's esophagus, adenocarcinoma of the esophagus) as H. pylori infections decrease. (E.g., see Blaser, M.J. 2005. An Endangered Species in the Stomach. Sci Am. 292: 38-45.) I have used some of his articles in microbiology classes - had students read arguments for and against the elimination of H. pylori. The consensus of my students, after reviewing evidence, was that his arguments against eliminating H. pylori did not convince them. (This did prompt some really interesting discussions, though!)

  4. Thanks Tanya! I may use that in the courses I teach!

  5. Blaser does talk about some kinds of cancer that are correlated with a loss of H. pylori. But he is always careful to distinguish between causation and correlation.

  6. Perhaps time would be best spent studying, and commenting, how indigenous tribes have been found, and studied, to have twice the diversity in their microbiome that other people do. Shame when so many people, especially children, who suffer from what may most likely be due to long term scientific ignorance/ ego's... others chose to sit and argue against issues that they know little about. As it can be now seen... science and modern medicine are simply BEGINNING to learn about the different types, and roles, of what is now being called "Friendly bacteria" not long ago most bacteria were simply called GERMS


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