Author, as appears in the article.: Cobo-López, Sergio; Gupta, Vinod K; Sung, Jaeyun; Guimerà, Roger; Sales-Pardo, Marta
Department: Enginyeria Química
URV's Author/s: Cobo Lopez, Sergio / Guimera Manrique, Roger / Sales Pardo, Marta
Keywords: Stochastic block models Statistical inference Nestedness Human microbiome Ecological networks
Abstract: 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.
Thematic Areas: Social sciences, interdisciplinary Multidisciplinary sciences Multidisciplinary
licence for use: https://creativecommons.org/licenses/by/3.0/es/
Author's mail: sergio.cobo@urv.cat roger.guimera@urv.cat marta.sales@urv.cat
Author identifier: 0000-0002-3597-4310 0000-0002-8140-6525
Record's date: 2024-10-19
Papper version: info:eu-repo/semantics/publishedVersion
Link to the original source: https://academic.oup.com/pnasnexus/article/1/3/pgac055/6590842
Licence document URL: https://repositori.urv.cat/ca/proteccio-de-dades/
Papper original source: Pnas Nexus. 1 (3): pgac055-
APA: Cobo-López, Sergio; Gupta, Vinod K; Sung, Jaeyun; Guimerà, Roger; Sales-Pardo, Marta (2022). Stochastic block models reveal a robust nested pattern in healthy human gut microbiomes. Pnas Nexus, 1(3), pgac055-. DOI: 10.1093/pnasnexus/pgac055
Article's DOI: 10.1093/pnasnexus/pgac055
Entity: Universitat Rovira i Virgili
Journal publication year: 2022
Publication Type: Journal Publications