Amino acid auxotrophy, the loss of biosynthetic potential for an amino acid, is a highly prevalent feature of microbial life, yet the evolutionary processes driving its distribution in nature remain u...

In a process known as phenotypic heterogeneity or phenotypic variation, bacteria can produce distinct phenotypes within an isogenic population in response to shifting environmental conditions. Noise i...

The T7 bacteriophage deactivates bacterial defence systems through T7K phosphorylation of nearly all host and phage proteins during infection.

Dietary fibers are a primary energy source for gut bacteria and shape the composition and function of the microbiome. Now, an active learning approach integrating explainable machine learning, Bayesia...

Nature Microbiology, Published online: 23 July 2026; doi:10.1038/s41564-026-02414-3Antibiotic resistance gene acquisition by Pseudomonas aeruginosa and Achromobacter from transiently infecting bacteria drives rapid and extreme resistance to tobramycin during chronic lung infection within patients.

Nature Microbiology, Published online: 21 July 2026; doi:10.1038/s41564-026-02425-0Vasodilation is inhibited by Klebsiella pneumonia through a multipronged approach involving type VI secretion system activity and the VgrG4 effector, plus capsule, to limit eNOS-dependent and endothelial hyperpolarization routes to vasodilation.

Nature Microbiology, Published online: 06 July 2026; doi:10.1038/s41564-026-02415-2Transposon-associated amplifications are dominated by a previously underappreciated architecture, where the transposon is found only between, not flanking, the amplicons. These amplifications facilitate the evolution of bacteria and their adaptation to antibiotics.

Fecal microbiome transplantation restores disrupted microbial ecosystems and is established for recurrent Clostridioides difficile infection, with expanding investigation across diverse diseases. This...

Fink et al. outline a precision-medicine strategy for patient-specific anti-infective therapy based on predicting antimicrobial susceptibility and pathogen vulnerabilities to improve existing treatmen...

Taxonomically and functionally distinct communities assemble on cellulose and its monomer, glucose. Although single carbon sources were provided, high and comparable diversity was maintained in both ...

Abstract. Environmental stress leads to changes in community composition by altering competitive hierarchies and pushing taxa towards extinction. Parasites

Nature Microbiology, Published online: 16 June 2026; doi:10.1038/s41564-026-02394-4In mouse models, small intestine microbiota of children suffering from environmental enteric dysfunction is transmitted maternally and recapitulates growth defects by modulation of inflammatory pathways

A randomized, single-blind, parallel-group, phase 1b clinical trial compared fecal microbiota transplant or a 15-strain live biotherapeutic product (MTC01) derived from the same donor and found similar efficacy and engraftment between treatments.

A randomized, single-blind, parallel-group, phase 1b clinical trial compared fecal microbiota transplant or a 15-strain live biotherapeutic product (MTC01) derived from the same donor and found simila...

A rapid, inexpensive, and easy to implement experimental protocol enables the construction of combinatorially complete sets of microbial consortia.

Ni et al. show that epigenetic phase variation (ePV)—gene expression changes mediated by bacterial DNA methylation—is prevalent in the human gut microbiome and associated with fluctuating environments...

The pangenome is the total genetic repertoire of a group of organisms. It is a property of populations, maintained by evolutionary processes.

Genome-wide selective sweeps commonly occur in the human gut microbiome and can spread across the world within decades to produce epidemic-like population structures.

The purpose of these awards is to provide support for students entering U.S.-based Ph.D. programs with a plan to perform research in ecology and evolution. While we will consider all projects in ecolo...

Engineered Lactobacillus plantarum strains metabolize ammonia and reshape amino acid balance in hepatic encephalopathy. In two mouse models, treatment lowers blood and brain ammonia, improves anxiety-like behavior, and preserves gut microbiota diversity, while the engineered strains are cleared after dosing stops.

Nature Microbiology, Published online: 23 April 2026; doi:10.1038/s41564-026-02323-5Escherichia coli ABC transporter-dependent capsule gene analysis alongside the development and application of the kTYPr in silico capsule typing tool uncovers E. coli capsule diversity across environments.

Nature Microbiology, Published online: 24 April 2026; doi:10.1038/s41564-026-02318-2Cayman enables computational analysis of carbohydrate-active enzymes (CAZymes) in microbial community data. It revealed novel mucus-foraging gut microorganisms and differences in gut microbial CAZyme repertoires associated with lifestyle and disease.

Turquoise killifish are naturally short-lived vertebrates that serve as a model system for aging. The authors show that killifish exhibit age-related transformation in the immune system, which rapidly...

Chronic kidney disease (CKD) is linked to an elevated fecal abundance of Enterobacteriaceae, but the ecological drivers of this shift and its impact on disease progression remain unclear. The uremic t...

In this phase 1 randomized trial of women with bacterial vaginosis in South Africa and the United States, Potloane et al. show that a multi-strain vaginal Lactobacillus crispatus live biotherapeutic a...

Nature Microbiology, Published online: 23 March 2026; doi:10.1038/s41564-026-02274-xDrought conditions in soil systems lead to elevated concentrations of natural antibiotics, as well as the enrichment of antibiotic-resistant microorganisms, highlighting a link between climate and the spread of antimicrobial resistance.

Nature Microbiology, Published online: 27 February 2026; doi:10.1038/s41564-026-02261-2Testosterone produced by skin cells enhances Staphylococcus aureus pathogenicity by activating quorum sensing, and a stereoisomer of testosterone that blocks this interaction inhibits bacterial cytotoxicity towards human cells.