Gut microbiome testing: Do current methods paint the full picture?


A pair of articles published in Cell from the laboratories of Eran Segal and Eran Elinav at the Weizmann Institute of Science caused a stir when media cited these papers in reports suggesting that probiotics were found to be ineffective.  The media certainly over-simplified these studies with respect to probiotic health benefits, but these studies reported other findings relevant to consumers interested in gut microbiome testing.

Fascination in the gut microbiome spans the spectrum of society, from those simply curious to know what they are flushing down the toilet to elite athletes and others seeking applications for personalized medicine.  Direct-to-consumer gut microbiome tests typically provide a sample kit, involving at-home stool collection, which is returned by post to the company and analyzed via genetic sequencing.  Reports are generated to provide an overview of the microbial ecosystem and to make general recommendations about diet and/or activity level.  Efforts like the American Gut Project have been instrumental in building awareness and interest in gut microbiome testing, and the ease of stool sampling (despite the ‘ick’ factor) makes sampling straightforward.

But are current stool sampling methods giving you a good picture of the bacteria that actually inhabit your intestines?  The article Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics is Associated with Unique Host and Microbiome Features by Niv Zmora and colleagues suggests not.  They found that microbes associated with the mucosa, a thin layer produced by the body that separates the contents of the gut from the surrounding tissue, are poorly representing in typical stool samples.  However, treatment with Pico-Salax, a diarrhea-causing bowel cleanser typically used prior to colonoscopies, did produce stool samples in which mucosa-associated bacteria were detectable, leading the authors to use this protocol for subsequent microbiome studies.

While bowel cleansing agents may help paint a better picture of the gut microbiome, there is a risk that such protocols could adversely affect the ecosystem they are trying to measure.  Research from Justin Sonnenburg’s laboratory at Stanford University demonstrated that transient diarrhea produced by the common laxative polyethylene glycol led to significant and, in some cases, permanent changes to the gut microbiome.  Zmora and colleagues did not compare the microbial ecosystem before and after Pico-Salax treatment, but it is certainly possible that the effort to capture a better portrait ended up changing the subject of the picture.

The gut microbiome is an emerging frontier in medical science, with advancements in technology and interpretation continuously updating our understanding of the relationship between the gut microbial ecosystem and the host in which it resides.  Debates over probiotic supplementation, colonization, and the best way to study the gut microbiome are certain to continue for the foreseeable future.