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Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations
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Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations
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Journal Article
Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations
2025
Overview
Gut bacteria from the Enterobacteriaceae family are a major cause of opportunistic infections worldwide. Given their prevalence among healthy human gut microbiomes, interspecies interactions may play a role in modulating infection resistance. Here we uncover global ecological patterns linked to Enterobacteriaceae colonization and abundance by leveraging a large-scale dataset of 12,238 public human gut metagenomes spanning 45 countries. Machine learning analyses identified a robust gut microbiome signature associated with Enterobacteriaceae colonization status, consistent across health states and geographic locations. We classified 172 gut microbial species as co-colonizers and 135 as co-excluders, revealing a genus-wide signal of colonization resistance within
Faecalibacterium
and strain-specific co-colonization patterns of the underexplored
Faecalimonas phoceensis
. Co-exclusion is linked to functions involved in short-chain fatty acid production, iron metabolism and quorum sensing, while co-colonization is linked to greater functional diversity and metabolic resemblance to Enterobacteriaceae. Our work underscores the critical role of the intestinal environment in the colonization success of gut-associated opportunistic pathogens with implications for developing non-antibiotic therapeutic strategies.
Assessing more than 12,000 metagenomic samples from across the world using computational approaches, the authors determined interactions between species that co-colonize or co-exclude Enterobacteriaceae in terms of functional pathways and metabolites in healthy human gut microbiomes.
Publisher
Nature Publishing Group UK,Nature Publishing Group
Subject
/ Analysis
/ Biomedical and Life Sciences
/ E coli
/ Enterobacteriaceae - classification
/ Enterobacteriaceae - genetics
/ Enterobacteriaceae - isolation & purification
/ Enterobacteriaceae - physiology
/ Enterobacteriaceae Infections - microbiology
/ Gastrointestinal Microbiome - genetics
/ Humans
/ Virology
