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

• Published in: FEMS microbiology reviews Vol. 41; no. 2; pp. 182 - 199
• Main Authors: Shetty, Sudarshan A., Hugenholtz, Floor, Lahti, Leo, Smidt, Hauke, de Vos, Willem M.
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01-03-2017
• Subjects: Adults; Alternative stable states; Antibiotics; Bacteria; Bacteria - classification; Bacteria - genetics; Biodiversity; Bistability; Communities; Core microbiota; Early warning signals; Ecosystem; Ecosystems; Gastrointestinal Microbiome - physiology; Genome, Microbial - genetics; Humans; Intestinal microflora; Intestine; Intestines - microbiology; Keystone species; Landscape model; Landscaping; Microbiomes; Microbiota; Microorganisms; Modulation; Redundancy; Review; Taxa; Time series; Tipping elements; landscape model; bistability; core microbiota; alternative stable states; tipping elements; early warning signals
• ISSN: 1574-6976; 0168-6445; 1574-6976
• DOI: 10.1093/femsre/fuw045

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.
A meta-analysis-based review discusses the key features of human intestinal microbiome, i.e. the compositional and functional ‘core’, community types, and the existence of alternative stable states and how these concepts can be used to improve host health.