Articles producció científica> Enginyeria Química

Stochastic block models reveal a robust nested pattern in healthy human gut microbiomes

  • Dades identificatives

    Identificador: imarina:9280069
    Autors:
    Cobo-López, SergioGupta, Vinod KSung, JaeyunGuimerà, RogerSales-Pardo, Marta
    Resum:
    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.
  • Altres:

    Autor segons l'article: Cobo-López, Sergio; Gupta, Vinod K; Sung, Jaeyun; Guimerà, Roger; Sales-Pardo, Marta
    Departament: Enginyeria Química
    Autor/s de la URV: Cobo Lopez, Sergio / Guimera Manrique, Roger / Sales Pardo, Marta
    Paraules clau: Stochastic block models Statistical inference Nestedness Human microbiome Ecological networks
    Resum: 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.
    Àrees temàtiques: Social sciences, interdisciplinary Multidisciplinary sciences Multidisciplinary
    Accès a la llicència d'ús: https://creativecommons.org/licenses/by/3.0/es/
    Adreça de correu electrònic de l'autor: sergio.cobo@urv.cat roger.guimera@urv.cat marta.sales@urv.cat
    Identificador de l'autor: 0000-0002-3597-4310 0000-0002-8140-6525
    Data d'alta del registre: 2024-10-19
    Versió de l'article dipositat: info:eu-repo/semantics/publishedVersion
    Enllaç font original: https://academic.oup.com/pnasnexus/article/1/3/pgac055/6590842
    URL Document de llicència: https://repositori.urv.cat/ca/proteccio-de-dades/
    Referència a l'article segons font original: Pnas Nexus. 1 (3): pgac055-
    Referència de l'ítem segons les normes 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
    DOI de l'article: 10.1093/pnasnexus/pgac055
    Entitat: Universitat Rovira i Virgili
    Any de publicació de la revista: 2022
    Tipus de publicació: Journal Publications
  • Paraules clau:

    Multidisciplinary Sciences,Social Sciences, Interdisciplinary
    Stochastic block models
    Statistical inference
    Nestedness
    Human microbiome
    Ecological networks
    Social sciences, interdisciplinary
    Multidisciplinary sciences
    Multidisciplinary
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