Nature Microbiology

Nature Microbiology, Published online: 04 May 2026; doi:10.1038/s41564-026-02345-z We reflect on our experiences as principal investigators of two microbiome-focused citizen-science projects, offering opportunities and practical lessons as a guide for researchers considering citizen-science approaches.

Nature Microbiology, Published online: 01 May 2026; doi:10.1038/s41564-026-02346-y The lytic selection and evolution (LySE) system uses a plasmid-encoded, hypermutagenic T7 DNA polymerase and T7 phagemid-encoded target genes to enable controllable, near-continuous directed evolution of large gene clusters.

Nature Microbiology, Published online: 01 May 2026; doi:10.1038/s41564-026-02333-3 This 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.

Nature Microbiology, Published online: 01 May 2026; doi:10.1038/s41564-026-02351-1 Assessment of the metagenome and bile acid profiles of two paediatric sepsis cohorts combined with extensive in vitro, ex vivo and in vivo experiments revealed that a gut microbe, Enterococcus raffinosus, is a primary producer of deoxycholic acid 3-sulfate, which has a protective role against sepsis in mouse models.

Nature Microbiology, Published online: 30 April 2026; doi:10.1038/s41564-026-02342-2 Prioritizing prenatal screening to prevent Chagas disease

Nature Microbiology, Published online: 30 April 2026; doi:10.1038/s41564-026-02315-5 Bioinformatic, structural and functional analyses characterize Streptomyces antiquus insecticidal protein (SAIP) as a diphtheria toxin homologue that is lethal to insect cells and targets the Flower protein as a receptor

Nature Microbiology, Published online: 30 April 2026; doi:10.1038/s41564-026-02337-z Capsular polysaccharides are central to Escherichia coli virulence, but the scarcity of molecular typing has hindered research and development of drug or vaccine candidates. Two studies redefine the diversity, epidemiology and evolutionary dynamics of E. coli capsules by providing tools to integrate modern genomi…

Nature Microbiology, Published online: 27 April 2026; doi:10.1038/s41564-026-02354-y Author Correction: Unbinned contigs expand known diversity in the global microbiome

Nature Microbiology, Published online: 27 April 2026; doi:10.1038/s41564-026-02312-8 A large-scale, comparative cell biology and biochemical screen defines the molecular features controlling antiphage defence systems that encode nuclease effectors and accessory NTPase proteins.

Nature Microbiology, Published online: 24 April 2026; doi:10.1038/s41564-026-02318-2 Cayman 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.

Nature Microbiology, Published online: 24 April 2026; doi:10.1038/s41564-026-02339-x The TRACS algorithm tracks bacteria, viruses and parasites in metagenomic or population sequencing data, detecting microbial transmission even when multiple strains coexist within a host.

Nature Microbiology, Published online: 24 April 2026; doi:10.1038/s41564-026-02344-0 Shotgun metagenomic sequencing is a comprehensive untargeted next-generation sequencing method that enables culture-independent analysis of complex microbial communities. Comparing the results of several metagenome-based analyses at various sequencing depths for known input illustrates which methods and amounts o…

Nature Microbiology, Published online: 24 April 2026; doi:10.1038/s41564-026-02343-1 The oomycete Phytophthora capsici secretes a tailored lipase that targets plant TET8- and TET9-extracellular vesicles to suppress extracellular vesicle-mediated plant defence.

Nature Microbiology, Published online: 24 April 2026; doi:10.1038/s41564-026-02310-w Biotic interactions modulate protein abundance, reducing functional redundancy and increasing productivity in complex bacterial communities.

Nature Microbiology, Published online: 23 April 2026; doi:10.1038/s41564-026-02324-4 Genomic epidemiology of 1,029 Streptococcus pyogenes emm1 and emm12 genome sequences collected between 1993 and 2024 in China reveals dominance of distinct lineages with mobile genetic element-encoded antibiotic resistance and virulence factor genes.

Nature Microbiology, Published online: 23 April 2026; doi:10.1038/s41564-026-02338-y A giant mimivirus encodes its own cap-binding translation initiation complex, revealing an unexpected level of viral autonomy in rewiring host translation towards viral protein production.

Nature Microbiology, Published online: 23 April 2026; doi:10.1038/s41564-026-02323-5 Escherichia 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: 22 April 2026; doi:10.1038/s41564-026-02294-7 Single-cell RNA sequencing is used to study the sexual development of Toxoplasma gondii in cats, generating a transcriptional atlas and showing that the female-specific gene AP2X6 functions as a regulator of oocyst formation.

Nature Microbiology, Published online: 22 April 2026; doi:10.1038/s41564-026-02287-6 Here the authors review current understanding of the mechanistic marine microbial interactions that underpin large-scale ecosystem processes and biogeochemical cycling.

Nature Microbiology, Published online: 21 April 2026; doi:10.1038/s41564-026-02334-2 A comparison of sequencing of complex mock communities performed at multiple depths and analysed using different methods establishes minimum standards that can ensure the accuracy of metagenomic analysis for a particular objective.