Nature Reviews Genetics, Published online: 03 November 2025; doi:10.1038/s41576-025-00909-zMicrobial genomics can improve our understanding of antimicrobial resistance dynamics across ecosystems. In this Comment, Kathryn Holt emphasizes the interconnectedness of human, animal and environmental health and calls for greater integration of microbial genomic data through robust analytical frameworks to unravel the complexity of antimicrobial resistance dynamics.

Nature Reviews Gastroenterology & Hepatology, Published online: 03 November 2025; doi:10.1038/s41575-025-01140-1The gut microbiome presents in a multi-kingdom form and tunes host health in various ways. Studies published in 2025 have further pushed this frontier by unveiling the enigmatic roles of the gut fungi and bacteria in cross-organ regulations of host homeostasis through metabolite and immune cell-mediated pathways.

This Perspective discusses virus-encoded auxiliary metabolic genes and provides a framework for the biological interpretation of these genes.

Bacterial resistance to chlorine disinfectant reduces its effectiveness in killing pathogenic bacteria and poses a severe threat to environmental and health safety. The interaction between bacteria and phages is the most frequent biological activity in Earth's biosphere, but little is known about wh …

An analysis of prescription medications shows that several non-antibiotic drugs, such as the heart medication digoxin, can reduce the immune response to pathogens and increase the risk of gastrointest...

A rapid expansion of new discoveries and knowledge lays the foundation for a new era in medicine

Nature - Geographic and age variations in mutational processes in colorectal cancer

Not all viruses associated with humans cause disease. Non-pathogenic human-infecting viruses are predicted as important for immune system induction and preparation. Phages that infect bacteria are the most abundant predators of the human microbial ecosystem, promoting and maintaining bacterial diver …

The gut microbiota is implicated in adverse effects associated with low-calorie sweeteners. Yet, the direct impact of sweeteners on gut bacteria remains largely uncharacterized. Here we report interac...

In this Review, Ahmad et al. examine how antibiotics influence bacterial metabolism and how metabolism, in turn, affects drug efficacy and the emergence and evolution of antimicrobial resistance. They...

Bacteriophages (phages) play a critical role in microbial ecology and evolution. Their interactions with bacteria are influenced by a complex network of chemical signals derived from a wide range of sources including both endogenous bacterial metabolites and exogenous environmental compounds. In thi …

Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) can be applied to complex microbial communities to reveal spatial co-localization of microbes at the micron scale.

Scientific Reports - Modulating the human gut microbiome and health markers through kombucha consumption: a controlled clinical study

Bacteroides vulgatus, a gut bacterium, promotes GLP-1 secretion through its metabolite, pantothenate, inhibiting sugar preference in mice.