title: Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies.
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.
authors.affiliation: Laboratory of Microbiology, Wageningen University, Stippeneng 4, Building 124, 6708 WE Wageningen, the Netherlands.
authors.forename: Sudarshan A
authors.initials: SA
authors.lastname: Shetty
authors.affiliation: Laboratory of Microbiology, Wageningen University, Stippeneng 4, Building 124, 6708 WE Wageningen, the Netherlands.
authors.forename: Floor
authors.initials: F
authors.lastname: Hugenholtz
authors.affiliation: Laboratory of Microbiology, Wageningen University, Stippeneng 4, Building 124, 6708 WE Wageningen, the Netherlands.|VIB Lab for Bioinformatics and (Eco-)systems Biology, KU Leuven, Campus Gasthuisberg, 3000 Leuven, Belgium.|Department of Mathematics and Statistics, University of Turku, 20014 Turku, Finland.
authors.forename: Leo
authors.initials: L
authors.lastname: Lahti
authors.affiliation: Laboratory of Microbiology, Wageningen University, Stippeneng 4, Building 124, 6708 WE Wageningen, the Netherlands.
authors.forename: Hauke
authors.initials: H
authors.lastname: Smidt
authors.affiliation: Laboratory of Microbiology, Wageningen University, Stippeneng 4, Building 124, 6708 WE Wageningen, the Netherlands.|Research Programme Unit Immunobiology, Department of Bacteriology and Immunology, Helsinki University, P.O. Box 21, 00014 Helsinki, Finland.
authors.forename: Willem M
authors.initials: WM
authors.lastname: de Vos
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics; D044822:Biodiversity; D017753:Ecosystem; D000069196:Gastrointestinal Microbiome / Q000502:physiology*; D064349:Genome, Microbial / Q000235:genetics; D006801:Humans; D007422:Intestines / Q000382:microbiology
keywords: alternative stable states; bistability; core microbiota; early warning signals; landscape model; tipping elements