Intestinal microbiome landscaping : insight in community assemblage and implications for microbial modulation strategies

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Shetty , S A , Hugenholtz , F , Lahti , L , Smidt , H & de Vos , W M 2017 , ' Intestinal microbiome landscaping : insight in community assemblage and implications for microbial modulation strategies ' , FEMS Microbiology Reviews , vol. 41 , no. 2 , pp. 182-199 . https://doi.org/10.1093/femsre/fuw045

Title: Intestinal microbiome landscaping : insight in community assemblage and implications for microbial modulation strategies
Author: Shetty, Sudarshan A.; Hugenholtz, Floor; Lahti, Leo; Smidt, Hauke; de Vos, Willem M.
Contributor: University of Helsinki, Medicum
Date: 2017-03
Language: eng
Number of pages: 18
Belongs to series: FEMS Microbiology Reviews
ISSN: 0168-6445
URI: http://hdl.handle.net/10138/178243
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.
Subject: alternative stable states
bistability
core microbiota
early warning signals
landscape model
tipping elements
HUMAN GUT MICROBIOME
INFLAMMATORY-BOWEL-DISEASE
PHYLOGENETIC MICROARRAY
FECAL MICROBIOTA
AKKERMANSIA-MUCINIPHILA
GASTROINTESTINAL-TRACT
ULCERATIVE-COLITIS
IN-VITRO
BACTERIA
DIVERSITY
1183 Plant biology, microbiology, virology
3111 Biomedicine
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