The Microbiota of the Human Gastrointestinal Tract: A Molecular View

Kieran M. Tuohy*, Karen P. Scott

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapter

9 Citations (Scopus)


The human gut microbiota represents a complex collection of microorganisms, which contribute considerably to host health. They occupy different ecological niches and habitats within the gastrointestinal tract and vary both in compositional make up and metabolic output at different sites along the gut. In this chapter, we describe the microbial "geography" within the human gastrointestinal tract and discuss available methods for studying the gut microbiota at both taxonomic and metabolic levels. Tremendous advances have been made in culture independent molecular microbiology over the past 20 years giving previously undreamt of insight into the architecture of the gut microbiota. Similarly, advances in "omics" technologies, especially metagenomics and metabolomics, are providing the tools necessary to give, for the first time, a real insight into both the gut microbiota metabolic potential (encoded by the genes of microbiota metagenome) and the metabolic kinetic (comprising the flux of microbially derived metabolites) and how these then interact with host physiology influencing health and disease risk.

Original languageEnglish
Title of host publicationDiet-Microbe Interactions in the Gut
Subtitle of host publicationEffects on Human Health and Disease
PublisherElsevier Inc.
Number of pages15
ISBN (Electronic)9780124079410
ISBN (Print)9780124078253
Publication statusPublished - 2015

Bibliographical note

Kieran M. Tuohy wishes to thank the Autonomous Province of Trento for funding the TrentinoGUT project, an incoming team grant in 2009, under which his contribution to this book has been supported.


  • Colon
  • FISH
  • Gut microbiota
  • Gut models
  • Metabolomics
  • Metabonomics
  • Metagenomics
  • PCR
  • Small intestine
  • Stomach


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