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Nature Microbiology, Published online: 30 September 2026; doi:10.1038/s41564-026-02498-xHybridization of wild and cultivated rice plants improves nitrogen use efficiency through microbiome re-domestication.

Nature Microbiology, Published online: 30 September 2026; doi:10.1038/s41564-026-02477-2Whole-organism malaria vaccine efficacy relies on host cell traversal by Plasmodium parasites, which promotes protective liver-resident CD8 T cell responses independently of intrahepatic parasite development.

Nature Microbiology, Published online: 30 September 2026; doi:10.1038/s41564-026-02460-xPlasmodium sporozoites trigger innate immune activation through cell traversal-induced membrane damage. This wounding response, sensed via γδ T cells, is required for protective CD8+ T cell priming and underlies the immunogenicity of sporozoites.

Nature Microbiology, Published online: 30 September 2026; doi:10.1038/s41564-026-02468-3This study extends the Pango lineage nomenclature system beyond SARS-CoV-2, introducing a dynamic framework for tracking and communicating viral diversity, demonstrated through its application to CHIKV.

Nature Microbiology, Published online: 29 September 2026; doi:10.1038/s41564-026-02510-4Despite major advances in HIV therapies and access to care, an HIV vaccine or cure strategy has yet to be realized. To achieve these goals, more support for collaborative research is needed.

Nature Microbiology, Published online: 29 September 2026; doi:10.1038/s41564-026-02482-5This platform identifies phages capable of infecting specific bacterial strains using genome sequences alone and could enable rational phage-therapy design and precision microbiome engineering.

Nature Microbiology, Published online: 29 September 2026; doi:10.1038/s41564-026-02476-3TRIM32-mediated SUMOylation of LAMP2A triggers classical chaperone-mediated autophagy, which viruses hijack to drive tumour growth. Peptide blockers of this modification show antitumour activity in mice model, identifying LAMP2A as a viable target.

Nature Microbiology, Published online: 28 September 2026; doi:10.1038/s41564-026-02491-4Two independent studies identified host species-specific aminopeptidase N as the entry receptor for hedgehog merbecoviruses, revealing convergent receptor use with alphacoronaviruses, but through a distinct binding site. Defining barriers to receptor use across species could help predict future host jumps and emerging transmission risks at the wildlife–veterinary–human interface.

Nature Microbiology, Published online: 28 September 2026; doi:10.1038/s41564-026-02467-4Prophylactic bnAb VRC01 selected for escape mutations in 31% of HIV breakthrough infections, but these mutations were rare in circulating viruses suggesting a fitness cost. More potent bnAbs such as N6 and 1-18 largely retained activity against escape variants.

Nature Microbiology, Published online: 25 September 2026; doi:10.1038/s41564-026-02486-1Phage Tn-seq uses Tn5 transposon mutagenesis with anti-CRISPR-based selection and deep sequencing as a method to generate unbiased, genome-wide mutations across diverse phages

Nature Microbiology, Published online: 25 September 2026; doi:10.1038/s41564-026-02455-8HIDEN-SEQ (hidden Acr-enabled transposon-insertion sequencing) is a transposon-insertion sequencing method for phages that systematically links their genes to selectable phenotypes.

Nature Microbiology, Published online: 24 September 2026; doi:10.1038/s41564-026-02469-2Pseudomonas aeruginosa drives harmful immune responses in cystic fibrosis by reprogramming protective Th17 cells into pathogenic populations that damage lung tissue and sustain chronic inflammation.

In this Perspective, Levin and Wang give a brief history of bacterial growth rate and discuss how it is connected to nutrient availability and macromolecule synthesis, with a focus on (p)ppGpp as a ce...

Researchers are racing to culture a menagerie of exotic organisms and finding lots of surprises along the way.

Nature Microbiology, Published online: 17 September 2026; doi:10.1038/s41564-026-02473-6This study describes the complex transcriptional regulatory mechanism enabling fine-tuned and rapid regulation of Plasmodium falciparum investment in transmission under changing blood conditions.

Nature Microbiology, Published online: 17 September 2026; doi:10.1038/s41564-026-02483-4Genomic and functional analyses reveal sequential gene loss events affecting dinB and fljB in monophasic Salmonella Typhimurium ST34 conferring a competitive advantage during gut infection and potentially contributing to emergence of this lineage.

Nature Microbiology, Published online: 17 September 2026; doi:10.1038/s41564-026-02471-8In vivo silencing of genes in E. coli strains using CRISPRi reveals specific genetic factors and metabolic adaptations that influence colonization in the mouse gut under variable physiological conditions.

Nature Microbiology, Published online: 17 September 2026; doi:10.1038/s41564-026-02493-2Functional versatility plays a key role in shaping root microbiota.

Nature Microbiology, Published online: 17 September 2026; doi:10.1038/s41564-026-02449-6In this Perspective, Levin and Wang give a brief history of bacterial growth rate and discuss how it is connected to nutrient availability and macromolecule synthesis, with a focus on (p)ppGpp as a central hub regulating resource allocation and, indirectly, growth rate at the single-cell level.

Nature Microbiology, Published online: 16 September 2026; doi:10.1038/s41564-026-02478-1Hedgehog merbecoviruses are shown to use aminopeptidase N as a functional receptor through a distinct binding mode, revealing convergent receptor usage among merbecoviruses.

Nature Microbiology, Published online: 16 September 2026; doi:10.1038/s41564-026-02447-8Hedgehog merbecoviruses utilize hedgehog aminopeptidase N, but not the human orthologue, as their entry receptor. Structural resolution of the glycoprotein–receptor interface reveals the molecular interactions underlying this species-specific barrier.

Nature Microbiology, Published online: 16 September 2026; doi:10.1038/s41564-026-02484-3An engineered non-pathogenic bacterium produces lytic phages and is protective in mouse models of Salmonella infection.

Nature Microbiology, Published online: 15 September 2026; doi:10.1038/s41564-026-02479-0Environmental temperature can be accurately inferred from the DNA composition of microbial communities across marine and soil ecosystems, using machine learning and based on tetranucleotide frequencies. GC content shows an opposing trend to temperature in these environments, associated with differences in nutrient availability.

Nature Microbiology, Published online: 15 September 2026; doi:10.1038/s41564-026-02485-2Structures of Candida albicans class II chitin synthase reveal mechanisms of oligosaccharide translocation and inhibition. The translocation channel is a class II-specific druggable site, and its inhibitor synergizes with a class I inhibitor.

Nature Microbiology, Published online: 15 September 2026; doi:10.1038/s41564-026-02490-5An enrichment culture from hot spring sediments in China suggests that Ca. M. sphaerolipidus uses a suite of metabolic pathways to convert long-chain fatty acids such as oleic acid to methane, a process they term liparotrophy.

Nature Microbiology, Published online: 15 September 2026; doi:10.1038/s41564-026-02475-4The Rad6B–Tex1 ubiquitination complex drives malaria parasite sexual commitment by monoubiquitinating histone H2B, and thereby enabling gametocyte formation and mosquito transmission.

Nature Microbiology, Published online: 14 September 2026; doi:10.1038/s41564-026-02495-0To successfully translate microbiome knowledge into practical interventions for farmers, research must be designed with agriculture in mind and shift from retrospective observation to predictive actions.

Nature Microbiology, Published online: 14 September 2026; doi:10.1038/s41564-026-02488-zAir pollution increases the risk of invasive pneumococcal disease and bacterial lineage changes the timing of that risk, making pathogen genomic diversity an effect modifier.

Nature Microbiology, Published online: 14 September 2026; doi:10.1038/s41564-026-02458-5Air quality and climate factors alter the risk of invasive pneumococcal diseases such as meningitis. Importantly, the lineage and serotype (population structure) of circulating bacteria can alter how quickly disease risk rises in the weeks following exposure.

Air quality and climate factors alter the risk of invasive pneumococcal diseases such as meningitis. Importantly, the lineage and serotype (population structure) of circulating bacteria can alter how ...

By studying over 59,000 cases of invasive disease caused by Streptococcus pneumoniae, experts have found that the subtype of bacteria influences the impact of environmental factors, such as air pollution, on disease risk.

Nature Microbiology, Published online: 09 September 2026; doi:10.1038/s41564-026-02503-3Author Correction: Longitudinal plasma metabolomics reveals a role for taurine in asymptomatic malaria and seasonal persistence

Strengthening Cambridge's leadership in bacteriology research Bacterial infection and antimicrobial resistance remain among the most pressing global health challenges of our time. At Cambridge, the De...

Integron insertion sites engineered into counterselection markers allow large-scale and high-throughput capture of integron-encoded genes from genetically tractable bacteria or DNA samples.

Nature Microbiology, Published online: 03 September 2026; doi:10.1038/s41564-026-02466-5Researchers identify interleukin-17A+ γδ T cells as key immune defenders against non-tuberculous mycobacteria infections, demonstrating their ability to protect hosts when IFNγ immunity is impaired.

Nature Microbiology, Published online: 03 September 2026; doi:10.1038/s41564-026-02464-7Inhibition of the pro-survival protein BCL-2 at the initiation of antiretroviral therapy in macaques reduced persistent viral reservoirs in both blood and lymph nodes during SIV infection.

Nature Microbiology, Published online: 03 September 2026; doi:10.1038/s41564-026-02474-5Integron insertion sites engineered into counterselection markers allow large-scale and high-throughput capture of integron-encoded genes from genetically tractable bacteria or DNA samples.

Nature Microbiology, Published online: 02 September 2026; doi:10.1038/s41564-026-02463-8Reply to ‘Grounding microbial conservation in ecological principles’

Nature Microbiology, Published online: 01 September 2026; doi:10.1038/s41564-026-02489-yPlatforms for community-led but globally connected knowledge and resource sharing can move us towards more equitable and more effective research and solutions for infectious diseases.

Nature Microbiology, Published online: 01 September 2026; doi:10.1038/s41564-026-02472-7MetaCAT is a computational framework to assess host–microbiome interaction via a combination of high-accuracy and efficient microbial genome reconstruction and metagenome-wide association studies with the host physiology using metagenomics data.

Nature Microbiology, Published online: 31 August 2026; doi:10.1038/s41564-026-02461-wThe journey of Mycobacterium tuberculosis between hosts in aerosol droplets has often been viewed as a passive phase in its life cycle. Recent evidence shows that the inevitable desiccation associated with aerosol transmission triggers a program that imperfectly repairs DNA damage, generating genetic diversity and increased recovery of antibiotic-resistant mutants.