Studying the Microbiota and Microbial Ecology of the Gastrointestinal Tract in the Omics Era: Tools for Stools
Kieran M. Tuohy, Francesca Fava and Nicola Segata
from: Probiotics and Prebiotics: Current Research and Future Trends (Edited by: Koen Venema and Ana Paula do Carmo). Caister Academic Press, U.K. (2015) Pages: 235-244.
The human gut microbiota is now recognised as an important contributor to host health and disease, with diet:microbe interactions playing critical roles in immune function, energy balance and even brain development and cognitive function. Importantly, these advances in the fields of physiology and nutrition have come at a time when methodologies for studying microbial communities are providing a comprehensive tool-kit of unparalleled resolution and breadth of coverage, allowing for the first time efficacious measurement of important ecological parameters within the gut microbiome. Over the past thirty years a diverse tool kit has been developed, including molecular methods both for targeted microbial quantitation and semi-quantitative but high resolution/broad spectrum methods capable of identifying theoretically all microorganisms within an ecosystem. These methods too allow us to measure both the metabolic potential and metabolic kinetic of the gut microbiota allowing researchers to shed new light on what was until very recently the black hole of microbiota ecological function within the gut. This chapter describes a collection of molecular genetic and metabolomic approaches used to study the human gut microbiota read more ...