Stability of the human gut microbiota

121022_r22702_p233The work of Dr. Gordon and colleagues has generated a lot of excitementabout the gut microbiome and its impact on health and disease, and their recent work is no different. After a first read, this substantial Science paper (see link in Mendeley) seems to actually be both a method and a study wrapped into one convenient package. We’ll dive into the nitty gritty of both the methods and the findings, this Thursday at 3 pm at the Phoenix, to determine:

  • How the LEA-Seq method works and how it stacks up to current sequencing protocols
  • How direct sequencing of 16S rRNA genes compares to whole genome sequencing of cultured bacterial isolates for displaying stability of the gut microbiota over time
  • What data filtering is recommended, for as they say: “…without filtering the microbiota appears much more diverse and much less stable.”
  • What fraction of the microbiota is persistent within an individual over time and after a perturbation like dieting
  • Which members of the microbiota are shared among family members

Abstract: A low-error 16S ribosomal RNA amplicon sequencing method, in combination with whole-genome sequencing of >500 cultured isolates, was used to characterize bacterial strain composition in the fecal microbiota of 37 U.S. adults sampled for up to 5 years. Microbiota stability followed a power-law function, which when extrapolated suggests that most strains in an individual are residents for decades. Shared strains were recovered from family members but not from unrelated individuals. Sampling of individuals who consumed a monotonous liquid diet for up to 32 weeks indicated that changes in strain composition were better predicted by changes in weight than by differences in sampling interval. This combination of stability and responsiveness to physiologic change confirms the potential of the gut microbiota as a diagnostic tool and therapeutic target.

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About Jennifer Stearns

Farncombe Family Chair in Microbial Ecology and Bioinformatics and Assistant Professor at McMaster University
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4 Responses to Stability of the human gut microbiota

  1. WvSchaik says:

    I have been quite critical of this study on twitter as the author’s definition of ‘same strain’ appears to be ‘same 16S’ which is definitely not enough to claim that two strains are identical.

    • Jen Stearns says:

      Good point. I’ll bring this up at tomorrow’s discussion. Did you hashtag your comments on twitter so that I can find them? No worries if not, I’ll post our comments after the discussion and you can see if we hit any of the same points.

  2. wvschaik says:

    I didn’t use an hashtag but Ed Yong covered some of the points of which me and others were critical here: http://phenomena.nationalgeographic.com/2013/07/05/as-constant-as-a-colon/

  3. Jen Stearns says:

    Thanks to Matt Workentine who found this handy add-on for tracking a paper of interest. Here’s what people said about this paper on twitter, Facebook etc… http://www.altmetric.com/details.php?citation_id=1604579&src=bookmarklet

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