ArticlePNAS nexus2022
Stochastic block models reveal a robust nested pattern in healthy human gut microbiomes.
Article in PNAS nexus, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Host traits and environmental factors shape infection heterogeneity in wild rat-protozoa networks.ISME communications · 2026Article
- Bayesian inference captures metabolite-bacteria interactions in a microbial community.ISME communications · 2026Article
- Analysing community-level spending behaviour contributing to high carbon emissions using stochastic block models.Scientific reports · 2025Article
- Reducing redundancy and enhancing accuracy through a phylogenetically-informed microbial community metabolic modeling approach.Bioinformatics (Oxford, England) · 2025Article
- Interplay between children's cognitive profiles and within-school social interactions is nuanced and differs across ages.Communications psychology · 2025Article
- A Generalized Bayesian Stochastic Block Model for Microbiome Community Detection.Statistics in medicine · 2025Article
- Nested patterns of commensals and endosymbionts in microbial communities of mosquito vectors.BMC microbiology · 2024Article
- Integration of metataxonomic data sets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables.Microbiology spectrum · 2024Article
- Ecological network analysis reveals cancer-dependent chaperone-client interaction structure and robustness.Nature communications · 2023Article
- Evaluating the prebiotic effect of oligosaccharides on gut microbiome wellness using in vitro fecal fermentation.NPJ science of food · 2023Article
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Authors and funding
5 authors.
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Abstract
A key question in human gut microbiome research is what are the robust structural patterns underlying its taxonomic composition. Herein, we use whole metagenomic datasets from healthy human guts to show that such robust patterns do exist, albeit not in the conventional enterotype sense. We first introduce the concept of mixed-membership enterotypes using a network inference approach based on stochastic block models. We find that gut microbiomes across a group of people (hosts) display a nested structure, which has been observed in a number of ecological systems. This finding led us to designate distinct ecological roles to both microbes and hosts: generalists and specialists. Specifically, generalist hosts have microbiomes with most microbial species, while specialist hosts only have generalist microbes. Moreover, specialist microbes are only present in generalist hosts. From the nested structure of microbial taxonomies, we show that these ecological roles of microbes are generally conserved across datasets. Our results show that the taxonomic composition of healthy human gut microbiomes is associated with robustly structured combinations of generalist and specialist species.
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