A2 Review article in a scientific journal
Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies
List of Authors: Sudarshan A. Shetty, Floor Hugenholtz, Leo Lahti, Hauke Smidt, Willem M. de Vos
Publisher: OXFORD UNIV PRESS
Publication year: 2017
Journal: FEMS Microbiology Reviews
Journal name in source: FEMS MICROBIOLOGY REVIEWS
Journal acronym: FEMS MICROBIOL REV
Volume number: 41
Issue number: 2
ISSN: 0168-6445
eISSN: 1574-6976
Abstract
High individuality, large complexity and limited understanding of the mechanisms underlying human intestinal microbiome function remain the major challenges for designing beneficial modulation strategies. Exemplified by the analysis of intestinal bacteria in a thousand Western adults, we discuss key concepts of the human intestinal microbiome landscape, i.e. the compositional and functional 'core', the presence of community types and the existence of alternative stable states. Genomic investigation of core taxa revealed functional redundancy, which is expected to stabilize the ecosystem, as well as taxa with specialized functions that have the potential to shape the microbiome landscape. The contrast between Prevotella-and Bacteroides-dominated systems has been well described. However, less known is the effect of not so abundant bacteria, for example, Dialister spp. that have been proposed to exhibit distinct bistable dynamics. Studies employing time-series analysis have highlighted the dynamical variation in the microbiome landscape with and without the effect of defined perturbations, such as the use of antibiotics or dietary changes. We incorporate ecosystem-level observations of the human intestinal microbiota and its keystone species to suggest avenues for designing microbiome modulation strategies to improve host health.