Detection of stable community structures within gut microbiota co-occurrence networks from different human populations

Abstract

Microbes in the gut microbiome form sub-communities based on shared niche specialisations and specific interactions between individual taxa. The inter-microbial relationships that define these communities can be inferred from the co-occurrence of taxa across multiple samples. Here, we present an approach to identify comparable communities within different gut microbiota co-occurrence networks, and demonstrate its use by comparing the gut microbiota community structures of three geographically diverse populations. We combine gut microbiota profiles from 2,764 British, 1,023 Dutch, and 639 Israeli individuals, derive co-occurrence networks between their operational taxonomic units, and detect comparable communities within them. Comparing populations we find that community structure is significantly more similar between datasets than expected by chance. Mapping communities across the datasets, we also show that communities can have similar associations to host phenotypes in different populations. This study shows that the community structure within the gut microbiota is stable across populations, and describes a novel approach that facilitates comparative community-centric microbiome analyses.

Syntrophy via Interspecies H 2 Transfer between Christensenella and Methanobrevibacter Underlies Their Global Cooccurrence in the Human Gut

“…O besity was the first human disease phenotype to be associated with an altered microbial ecology of the gut (1,2). The link between the relative abundance in the gut of the bacterial family Christensenellaceae and a low host body mass index (BMI) now stands as one of the most robust associations described between the human gut microbiome and host BMI (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15). Compared to other families of bacteria that comprise the human gut microbiome, the family Christensenellaceae was described relatively recently, when the type strain, Christensenella minuta, was reported in 2012 (16).…”

A comprehensive co-expression network analysis inVibrio cholerae

“…Major motivations for this work include the successful implementation of bacterial-focus, microarray-based co-expression networks and the lack of clear functional knowledge for a large portion of V. cholerae genes. Besides more simple guilt-by-association studies (22, 23), co-expression networks have helped to elucidate relationships in diverse microbial communities (47–50) and enable comparisons across strains and species (51–53). These works as well as the relative dearth of knowledge about the V. cholerae genome (roughly two third of genes are annotated compared to around 86% percent of all E. coli genes (54)) and the growing abundance of V. cholerae focused NGS data served as the impetus for this research.…”

Fire in the Forest: Adverse Effects of Antibiotics on the Healthy Human Gut Microbiome

“…24 Furthermore, another study identified the gut microbiome of urban and rural Russian populations. 25 Based on the findings of these studies, the diet, genetic differences, mode of delivery, lifestyle, medical treatment, and immune status of the host have been suggested as factors affecting the community structure of the gut microbiome. [21][22][23][24][25] In contrast, the stable community structure of gut microbiota was detected in different human populations in a very recent study.…”

“…25 Based on the findings of these studies, the diet, genetic differences, mode of delivery, lifestyle, medical treatment, and immune status of the host have been suggested as factors affecting the community structure of the gut microbiome. [21][22][23][24][25] In contrast, the stable community structure of gut microbiota was detected in different human populations in a very recent study. 26 Furthermore, the presence of a certain degree of functional redundancy is suggested with similar protein or metabolic profiles of gut microbiome, irrespective of their compositional variations.…”