Progress in Our Understanding of the Gut Microbiome: Implications for the Clinician

Curr Gastroenterol Rep. 2016 Sep;18(9):49. doi: 10.1007/s11894-016-0524-y.


The investigation of the role of the microbial communities of our gastrointestinal tract (microbiota) has accelerated dramatically in recent years thanks to rapid developments in the technologies that allow us to fully enumerate and evaluate the full complement of bacterial species and strains that normally inhabit the gut. Laboratory studies in a range of inventive animal models continue to provide insights into the role of the microbiota in health and to generate plausible hypotheses relating to its potential involvement in the pathogenesis of human disease. Studies of the composition of human gut microbiota continue to accumulate but their interpretation needs to be tempered by an appreciation of the limitations of single-point-in-time studies of fecal samples from small study populations. Nevertheless, clinically important examples of a central role for microbiota-host interactions in disease pathogenesis have emerged and many more have been postulated but await confirmation in appropriately powered and conducted studies.

Keywords: Antibiotic-associated diarrhea; Bacteria; Clostridium difficile; Colorectal cancer; Inflammatory bowel disease; Irritable bowel syndrome; Liver disease; Microbiome; Microbiota.

Publication types

  • Review

MeSH terms

  • Anti-Bacterial Agents / adverse effects
  • Colorectal Neoplasms / microbiology
  • Diarrhea / chemically induced
  • Diarrhea / microbiology
  • Gastrointestinal Diseases / microbiology*
  • Gastrointestinal Microbiome*
  • Gastrointestinal Tract / microbiology
  • Humans
  • Inflammatory Bowel Diseases / microbiology
  • Irritable Bowel Syndrome / microbiology
  • Liver Diseases / microbiology
  • Metabolic Syndrome / microbiology
  • Terminology as Topic


  • Anti-Bacterial Agents