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Stool consistency as a major confounding factor affecting microbiota composition: an ignored variable?
  1. Jack A Gilbert1,2,3,4,5,
  2. John Alverdy3
  1. 1Biosciences Division (BIO), Argonne National Laboratory, Argonne, Illinois, USA
  2. 2Department of Ecology & Evolution, University of Chicago, Chicago, Illinois, USA
  3. 3Department of Surgery, University of Chicago, Chicago, Illinois, USA
  4. 4Institute for Genomic and Systems Biology, University of Chicago, Chicago, Illinois, USA
  5. 5The Marine Biological Laboratory, Woods Hole, Massachusetts, USA
  1. Correspondence to Professor Jack A Gilbert, Biosciences Division (BIO), Argonne National Laboratory, Argonne, IL 60439, USA; gilbertjack{at}uchciago.edu

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In this age of the microbiome, the one request most oft heard is ‘so what is the biomarker for this disease?’ In a world of ‘one-size-fits-all’ solutions, and a one pathogen-one disease framework of investigation, most doctors, clinical healthcare professionals, and healthcare industrialists just want the punchline—what is the bacterium that is causing that disease? The problem with this approach is that it remains a challenge to fully understand whether a given microbiome has any causative influence on a given condition, or whether identified associations have any relevance outside of a given case study. Unlike monomicrobial diseases where Koch's postulates can be applied, the interaction between the microbial ecology of the body, and health and disease is extremely complex, leading to fuzzy concepts of organismal ratios and phylogenetic groups of organisms being associated with a specific condition. In their recent paper, Vandeputte et al1 seek to determine whether gut-transit time has an influence on microbial community profiles in stool, and by what mechanism this occurs, as well as considering whether this influence could have an impact on clinical studies.

Clinicians and microbiome researchers continue to struggle with the delicate balance that exists between elucidating the pathogenesis of a disease and defining the role of a particular organism, or group of organisms in this process. This can be a slippery slope; on the one hand, we want a microbiome-based diagnosis and a discriminative biomarker. …

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