Nature Metabolism, Published online: 21 July 2026; doi:10.1038/s42255-026-01577-xThis Perspective describes the emerging roles of microbiota-derived metabolites in influencing host chromatin and thereby gene regulation and host physiology.

How maternal nutrition influences neonatal immune development and imprinting through breastfeeding remains largely unclear. We report that maternal supplementation with trans-vaccenic acid (TVA), the ...

Mishra et al. show that microbiota-derived short-chain fatty acids (SCFAs) inhibit Candida albicans gastrointestinal colonization through two mechanisms: direct fungal inhibition—via intracellular aci...

Zhou et al. found that Cladosporium tenuissimum alleviates colitis by inhibiting Candida albicans growth through competition for ornithine. C. albicans can escape this suppression by exploiting threon...

Nature Microbiology, Published online: 01 May 2026; doi:10.1038/s41564-026-02333-3This Review summarizes recent advances in bacterial single-cell transcriptomics approaches, while also discussing technological and computational challenges remaining to be met and the need for standardization going forwards.

Colonic stem cells retain a memory of inflammation following disease resolution and there is a mechanistic link between chronic inflammation and malignancy, suggesting potential strategies to mitigate...

Yu et al. demonstrate that Staphylococcus is selectively enriched in metastatic lung tumor lesions. Staphylococcus nepalensis and S. capitis secrete lactate to promote the metastatic potential of tumo...

A short peptide derived from a commensal-fungal-secreted protein promotes repair in models of colon epithelial damage when delivered directly or via probiotic microbes.

While much is known about the identity and regulation of cytokine-producing cells, the cell types that respond to cytokines remain largely uncharacter…

Nature Metabolism, Published online: 07 January 2026; doi:10.1038/s42255-025-01420-9Multi-omics profiling of the mucosal mycobiome in individuals with Crohn’s disease identifies C. sphaerospermum as a protective fungal species that counteracts intestinal inflammation and reinforces the intestinal barrier.

Macrophage-toxic bacteria from patients with ulcerative colitis worsen gut inflammation in mice

Commensal Candida albicans enhances the virulence and dissemination of Salmonella enterica subsp. enterica serovar Typhimurium.

In a recent issue of Immunity, Qiu et al. uncover a pivotal role for commensal fungi in promoting lung fibrosis, showing that their interaction with alveolar macrophages triggers a profibrotic transcr...

Experiments in mouse models show that proper recovery of the intestinal microbiota following depletion, with or without faecal microbiota transplant therapy, is dependent on syntrophic interactions that occur only with specific dietary interventions.

Nature Reviews Gastroenterology & Hepatology, Published online: 22 April 2025; doi:10.1038/s41575-025-01063-xInflammatory bowel disease (IBD) is an immune-mediated disease with substantial burden worldwide. In this Consensus Statement, a global multidisciplinary group of experts identify key priorities and recommendations to raise awareness and advance IBD care and research.

Mucosal-associated invariant T (MAIT) cells are innate-like T cells predominantly located in barrier tissues such as the lung, liver, skin, and colon. These cells recognize metabolites derived from the riboflavin biosynthetic pathway, which can rapidly traverse epithelial barriers and be presented during MAIT cell differentiation in the thymus and maturation in peripheral tissues. Furthermore, microbial metabolites significantly influence MAIT cell functions in various conditions, including cancer. This review summarizes how the microbiota shapes the life trajectory of MAIT cells and their antitumor reactivity. Additionally, we discuss the therapeutic implications of manipulating the microbiota as a ‘bug-drug’ strategy to enhance MAIT cell antitumor immunity, particularly in mucosal cancers, while emphasizing challenges and future directions for integrating microbiota considerations into MAIT cell-based therapies.