This Review summarizes the current knowledge about the cell-intrinsic factors that act against pathogenic bacteria and viruses and the immune evasion strategies that pathogens have to counteract cell-autonomous immunity.

Environmental stress shifts microbial composition towards species with high growth rates, providing community-wide protection.

Lipidomics and proteomics in mice colonized with variable gut microbiota reveal an important role of gut microbes in restricting lipid uptake via triggering Myd88 signalling and the degradation of phosphatidylcholine in bile.

Antiviral candidate GHP-88310 provides therapeutic benefit against measles-like disease and protects against productive direct-contact and airborne viral transmission when used for pre- and post-exposure prophylaxis.

Lactiplantibacillus plantarum-derived fatty-acid metabolite, 10-hydroxystearic acid, interacts directly with PPARα to alter histone crotonylation and the transcriptional landscape which leads to gut barrier functional repair and enhanced viral suppression in non-human primate models when combined with anti-retroviral therapy.

In a small case series, combined phage therapy and faecal microbiota transplantation was safe and led to sustained reductions in recurrence, severity and antibiotic use in women with recurrent urinary tract infections, even without complete eradication of Escherichia coli.

The phage-encoded protein PptA enables its DNA to masquerade as the host and evade cleavage, providing a potential foundation for engineering therapeutic phages that could bypass this widespread defence system.

Lipidomics and proteomics in mice colonized with variable gut microbiota reveal an important role of gut microbes in restricting lipid uptake via triggering Myd88 signalling and the degradation of phosphatidylcholine in bile.

Structural and biochemical follow-up of a serendipitous discovery reveals that Akkermansia muciniphila carbohydrate sulfatases are uniquely adapted to digest colonic mucins in collaboration with other members of gut microbiota.

Antiviral candidate GHP-88310 provides therapeutic benefit against measles-like disease and protects against productive direct-contact and airborne viral transmission when used for pre- and post-exposure prophylaxis.

Nature Microbiology no longer considers presubmission enquiries and instead evaluates all research through full manuscript submissions. This change is intended to improve fairness, rigour and efficiency, ensuring that editorial decisions are based on a complete assessment of the data.

Nature Microbiology asked members of the Global Grants for Gut Health Colloquium about the impact artificial intelligence is having on their microbiome research.

Staffan Svärd reflects on his 30-year relationship with Giardia, which has stayed on his mind in a manner reminiscent of its adhesive trophozoite form.

Effective science communication can help scientists shape impactful research questions, and crucially it can foster curiosity, showcase the importance of research and encourage support and engagement from non-scientists.