Measles vaccination rates fell during the COVID-19 pandemic and have yet to recover, fuelling large and disruptive outbreaks globally. Now, a substantial outbreak in the Americas threatens elimination status in the region. The US response, marked by mixed messaging and a retreat from global health leadership and partnerships, further jeopardizes progress that took decades to achieve.

This Genome Watch article discusses the dominance of uncultivated microorganisms in natural ecosystems and how the consequent genome-driven insights could guide the rational design of synthetic microbial communities.

This study explored the inheritance of bacterial metabolic activity at the single-cell level.

This Genome Watch highlights the advantages and limitations of k-mer approaches versus standard alignment-based methods for analysing metagenomic data, assisting microbial species identification, microbial abundance estimation and their application in pathogen genomic epidemiology.

In this study, Su et al. engineered a Vibrio natriegens strain for the remediation of multiple organic pollutants.

This study reports that that a gut fungus produces a secondary metabolite that protects against metabolic disease in mice.

Despite the global burden of HIV-1, the majority of sequence data and research remain disproportionately focused on subtype B, primarily circulating in the global north. Sub-Saharan Africa, the epicentre of HIV-1 genetic diversity and prevalence, requires increased representation in sequencing efforts and regionally led research to inform effective interventions.

In this study, Ryan et al. underscore the role of a balanced gut microbiota in infant immunity and responses to vaccination.

Mitigating climate change requires innovative solutions, and microorganisms, combined with artificial intelligence, can help. This Comment explores artificial intelligence strategies aimed at supporting and improving the development of microbial technologies for climate change action.

In this study, Mills et al. identify bacteriocin T8 as a key factor conferring a competitive advantage to successful vancomycin-resistant Enterococcus faecium lineages in hospital settings.

In this study, Munneke et al. demonstrate that Clostridioides difficile scavenges the modified pyrimidine nucleobase 4-thiouracil to promote its pathogenesis in the vertebrate gut.

This study reports the identification of a ribosome-targeting lasso peptide that acts on a new ribosomal binding site.

This study shows that mechanical pressure induces multicellular development in Haloferax volcanii.

This Genome Watch article highlights recent findings of cellular-like genes in giant viruses and how these viruses acquire and repurpose host cellular machinery.

This Genome Watch discusses advancements in our understanding of interpersonal transmission dynamics of the human gut microbiota and their implications for host health and therapeutic outcomes.

Correction to: Nature Reviews Microbiology https://doi.org/10.1038/s41579-025-01163-0, published online 10 March 2025.

In this study, Proctor et al. demonstrate that the skin of residents in nursing homes serves as a reservoir for Candida auris, ESKAPE pathogens and their antimicrobial resistance genes.

In this study, Thakur et al. demonstrate the interconnected role of diet, host genetics and oncogenic microorganisms in colon carcinogenesis.

This study reports the biosynthesis and characterization of poly(ester amide)s in Escherichia coli.

This Genome Watch highlights how genomic lineage resolution is revolutionizing precision diagnostics by providing insights into pathogen evolution, transmission dynamics and the emergence of antimicrobial resistance.

This study shows that fungal plant pathogens use hydrolase effectors to induce phosphate starvation signalling in host plants and suppress immune responses to promote disease.

This study reports two different mechanisms that enable bacterial surface colonization under high flow conditions.

This study describes the bacterial type IV Thoeris defence system, which contains both a Toll/interleukin-1 receptor (TIR) domain protein and a caspase-like protease.

This Genome Watch article highlights how genomics and different experimental approaches reveal how intracellular bacteria control key processes of their hosts.

In this study, Mears et al. show that SARS-CoV-2 can evolve not only through protein changes but also through functional RNA adaptations to increase fitness and immune evasion.

In this study, Li et al. perform a randomized controlled feeding trial to test the effects of a microbiome restoration strategy on gut microbiome features, host physiology and health.

This Genome Watch discusses strategies to detect small open reading frames and study microproteins encoded in microbiomes to understand their diversity and functions across microorganisms.

This Comment highlights the challenges and rewards of researchers working in resource-limited settings, specifically Thailand, and provides potential solutions to help Thai researchers overcome these difficulties.

This study reports that bacteria protect plants against filamentous fungal infections via intercellular contacts between the bacterial cells and the conidia of the fungi.

In two recent studies, Smith, Su, Wallach et al. engineered a safer version of Bacille Calmette–Guerin with strong protection against Mycobacterium tuberculosis, while Wang, Su, Wallach, Wagner et al. developed an engineered M. tuberculosis strain as a candidate for human challenge studies.

In this study, Cross, Woolsey, Prasad et al. report obeldesivir as a promising post-exposure prophylaxis for filoviruses.

This study shows that metabolites from both an infecting pathogen and the gut microbiota of the host are major determinants of survival from bacterial sepsis in mice.

In this Journal Club, Flora Vincent revisits a paper that summarized the ecological roles of microorganisms in the ocean ecosystem and that greatly impacted the field of marine microbiology.

In a recent study, Lin et al. uncovered that a single substitution in the bovine influenza H5N1 haemagglutinin protein switches the specificity to human receptors.

A recent study found that soil microbial communities show consistent and predictable responses to extreme climatic events.

Correction to: Nature Reviews Microbiology https://doi.org/10.1038/s41579-024-01107-0, published online 23 October 2024

A recent study shows that the commensal bacterium Lactiplantibacillus plantarum recognizes the foregut of the fruit fly as its physical niche via sugar-binding adhesins.

In this study, Castells-Nobau et al. show that bacteriophages present in the gut microbiome contribute to the regulation of food addiction.