TY - JOUR
T1 - Stochastic block models reveal a robust nested pattern in healthy human gut microbiomes
AU - Cobo-López, Sergio
AU - Gupta, Vinod K.
AU - Sung, Jaeyun
AU - Guimerà, Roger
AU - Sales-Pardo, Marta
N1 - Publisher Copyright:
© The Author(s) 2022. Published by Oxford University Press on behalf of the National Academy of Sciences.
PY - 2022/7/1
Y1 - 2022/7/1
N2 - 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.
AB - 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.
KW - ecological networks
KW - human microbiome
KW - nestedness
KW - statistical inference
KW - stochastic block models
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U2 - 10.1093/pnasnexus/pgac055
DO - 10.1093/pnasnexus/pgac055
M3 - Article
AN - SCOPUS:85144438585
SN - 2752-6542
VL - 1
JO - PNAS Nexus
JF - PNAS Nexus
IS - 3
M1 - pgac055
ER -