Nature Reviews Gastroenterology & Hepatology, Published online: 14 September 2026; doi:10.1038/s41575-026-01258-wMany compounds not classified as antibiotics can exert antimicrobial activity, with drug–microbiome–host interactions having profound effects on the human microbiome and human health. This Review explores how non-antibiotic compounds exert these antimicrobial effects, highlighting which compounds can influence the microbiome, the underlying mechanisms, and implications for translation and clinical practice.

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Beyond the commonly considered factor of diet, small-molecule drugs have been identified as effectors of microbiota composition. Recently, two studies (Grießhammer et al. and Kumar et al.) reported that non-antibiotics, like antibiotics, could disrupt gut microbial homeostasis, reducing colonization resistance and facilitating pathogen invasion. These findings hold profound implications for our understanding of drug–host–microbiome interactions.

Metalog is a repository of manually annotated metadata (or contextual data) for metagenomic sequencing data from across the globe.

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Non-antibiotic drugs from a wide range of therapeutic classes can alter the ability of gut commensals to resist invasion by enteropathogens, a previously underappreciated side effect of such drugs.

Some human-targeted drugs can alter gut microbes, creating a favorable environment for pathogens like Salmonella to thrive.

Nature - Non-antibiotic drugs from a wide range of therapeutic classes can alter the ability of gut commensals to resist invasion by enteropathogens, a previously underappreciated side effect of...

Nature Communications - Acute systemic immune activation may affect gut-luminal colonisation dynamics. Here, the authors show that LPS exposure in mice elevates gut-luminal oxygen species levels,...

The human gut microbiome, a community of microbes that plays a crucial role in our wellbeing, is highly adaptable but also vulnerable to drug treatments. This vulnerability can have serious consequenc...

Nature - Some non-antibiotic drugs have been associated with changes in gut microbiome composition, but the extent of this phenomenon is unknown. Athanasios Typas and colleagues screened more than...

Non-antibiotic drugs can alter the composition of the gut microbiome, with largely undefined implications for human health. Here we compared the susceptibility of commensal and pathogenic bacteria to ...

Background Lifestyle plays an important role in shaping the gut microbiome. However, its contributions to the oral microbiome remain less clear, due to the confounding effects of geography and methodo...

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The gut microbiota is diverse across various taxonomic levels. At the intra-species level, it comprises multiple strains, some of which may be host-specific. However, our understanding of fine-grained...