Everything is everywhere but Escherichia coli adapts to different niches

TL;DR

This study explores how Escherichia coli adapts to different environments and hosts, challenging the idea that bacteria are spread everywhere equally.

Contribution

The study uses pangenome-wide association studies to identify genomic signatures of niche adaptation in Escherichia coli.

Findings

Escherichia coli shows genomic adaptations linked to specific host species and environments.

Agriculture significantly impacts the evolution of Escherichia coli and antimicrobial resistance.

The research links genomics with host ecology to inform One Health approaches.

Abstract

Pathogens that are harmless in one environment can cause a serious disease in another. Among host-associated bacteria, transition between hosts can have serious consequences for animal and human health. However, much remains unknown about how adaptation shapes bacterial distribution in the wild. Here, investigating the ecological genomics of Escherichia coli from diverse hosts and environments, we address the idea that bacteria disperse freely, and challenge the “everything is everywhere” paradigm. Using comparative genomics and parallelised high throughout pangenome-wide association studies (900 experiments) we investigate lineage distribution and identify adaptive genomic signatures associated with host species, physiology and ecology. Our findings provide insights into bacterial niche adaptation, emphasize the impact of agriculture on microbial evolution, and inform One Health frameworks by linking genomics, host ecology, and the emergence of antimicrobial resistance.

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