Sunday, November 03, 2013

Short post- a bad taste in my mouth for overselling the microbiome

Well, this just leaves a bad taste in my mouth: Oral Bacteria Create a ‘Fingerprint’ in Your Mouth.  Basically, the researchers compared microbial diversity in the oral microbiome of people and they looked at how correlated the microbiome was with ethnicity.  And they published a PLOS One paper and wrote a press release about it.  And there are many lines in the PR and some in the paper I take issue with.  These include:

  • PR: "The most important point of this paper is discovering that ethnicity-specific oral microbial communities may predispose individuals to future disease”.
    • Uggh.  I cannot find anything anywhere that indicates anything about predisposition to disease
  • PR: “Nature appears to win over nurture in shaping these communities,” Kumar noted, because African Americans and whites had distinct microbial signatures despite sharing environmental exposures to nutrition and lifestyle over several generations.
    • Double uggh.  So - different ethnic groups have different microbes.  And since some of the ethnic groups have similar environmental exposures to each other (actually, they do not even test this - they simply assume this) yet do not have similar micro biomes, therefore the cause of the differences in the microbiomes must be genetic differences between the ethnic groups.
  • Paper: "Our data demonstrates that ethnicity exerts a selection pressure on the oral microbiome, and that this selection pressure is genetic rather than environmental, since the two ethnicities that shared a common food, nutritional and lifestyle heritage (Caucasians and African Americans) demonstrated significant microbial divergence." 
    • Triple uggh.  This should not have been allowed in the paper.  Their work in no way demonstrates any genetic component to the differences in the microbiome.  

This is certainly a case of overselling the microbiome.  But it is also a case of just bad science in relation to the "nature vs. nurture" issues.


  1. I'm interested in whether you intend to post this on the original PLOS ONE paper as a comment too. When PLOS first appeared, I believed that commenting was going to be the route to post-publication peer review. Sadly, that's clearly not the case.

  2. This comment has been removed by the author.

  3. I agree with Alan Cann that you should post a comment on the original article. I frequently look at the comments section on PLoS ONE as well, and I'm surprised at the general lack of commenting. I guess people prefer to blog instead, but then useful commentary is basically lost in cyberspace.

    1. Hah - you two don't know me very well - for most blog posts about papers I have been posting to the journal site a comment. AND now I am planning to start to do it with Pubmed Commons

    2. Comment posted at article site ... article not up in Pubmed yet so no comment there

    3. Great, thanks for posting. I don't have access to the pubmed comments, so it's PLOS or nothing for me.


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