N Nature Microbiology · Dec 05, 2025 Interkingdom sensing of fungal tyrosol promotes bacterial antifungal T6SS activity in the murine gut Type VI secretion systems (T6SSs) are molecular machines used by bacteria to release effectors that target either host cells, competing bacteria or fungi. Regulatory mechanisms underlying antifungal T6SS activity remain unexplored. Here we show, using mouse infection with wild-type and T6SS mutant bacteria, that T6SS activity of the enteropathogen,Yersinia pseudotuberculosis(Yptb), reduces fungal prevalence in the gut microbiota and has direct activity onCandida albicans. Screening of bacterial effector mutant strains, and structural and biochemical analyses identify TfeC as an antifungal chitinase T6SS effector that can killC. albicans. In vivo experiments confirm that TfeC expression promotesYptbcolonization and reducesC. albicansabundance. We also show thatYptbsenses the fungal quorum-sensing molecule, tyrosol, through the two-component system, EnvZ–OmpR, and responds by activating T6SS4. Our findings suggest thatYptbmodulates its antifungal activities by detecting changes in fungal population density cues, revealing a mechanism of fungal–bacterial interkingdom communication mediated by fungal quorum-sensing molecules. Bacteriology Microbial ecology biology mouse experiments
N Nature Microbiology · Dec 05, 2025 Influenza A(H5N8) vaccine induces humoral and cell-mediated immunity against highly pathogenic avian influenza clade 2.3.4.4b A(H5N1) viruses in at-risk individuals Finland faced an outbreak of highly pathogenic clade 2.3.4.4b A(H5N1) avian influenza in 2023, which spread from wild birds to fur farms. Vaccinations of at-risk individuals began in June 2024 using the MF59-adjuvanted inactivated A(H5N8) vaccine (Seqirus; A/Astrakhan/3212/2020, clade 2.3.4.4b). Here, in an observational study, we assessed vaccine-induced immune responses in occupational at-risk individuals participating in the phase IV trial, including virus-specific antibody (n= 39 individuals) and T-cell (n= 18 individuals) responses. Vaccination elicited functional antibodies against the vaccine virus and two heterologous clade 2.3.4.4b strains associated with outbreaks on Finnish fur farms and dairy cattle in the United States. Among previously unvaccinated individuals, seroprotection rates against the vaccine virus were 83% (95% CI 70–97%) by microneutralization assay (titre ≥20) and 97% (90–100%) by haemagglutination inhibition assay (titre ≥40). In those previously vaccinated against avian influenza, a single dose induced seroprotection. A(H5N8)-specific memory CD4+T-cell responses were detectable, with ~5-fold increase in IFNγ secretion after two doses. These results demonstrate that the vaccine probably provides cross-protection against circulating H5 clade 2.3.4.4b viruses. EU Clinical Trial Number 2023-509178-44-00. Influenza virus Vaccines biology mouse experiments
N Nature Microbiology · Dec 04, 2025 A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models Understanding the human gut microbiome requires comprehensive genomic catalogues, yet many lack geographic diversity and contain medium-quality metagenome-assembled genomes (MAGs) missing up to 50% of genomic regions, potentially distorting functional insights. Here we describe an enhanced Human Reference Gut Microbiome (HRGM2) resource, a catalogue of near-complete MAGs (≥90% completeness, ≤5% contamination) and isolate genomes. HRGM2 comprises 155,211 non-redundant near-complete genomes from 4,824 prokaryotic species across 41 countries, representing a 66% increase in genome count and a 50% boost in species diversity compared to the Unified Human Gastrointestinal Genome catalogue. It enabled improved DNA-based species profiling, resolution of strain heterogeneity and survey of the human gut resistome. The exclusive use of these genomes improved metabolic capacity assessment, enabling high-confidence, automated genome-scale metabolic models of the entire microbiota and revealing disease-associated microbial metabolic interactions. This resource will facilitate reliable functional insights into gut microbiomes. Metagenomics Microbiome biology
N Nature Microbiology · Dec 04, 2025 Phage resistance mutations in a marine bacterium impact biogeochemically relevant cellular processes Phage–bacteria interactions shape ecology and biogeochemistry across biomes. Resistance, arising from their evolutionary arms race, is well documented for receptor mutations, but other resistance mechanisms and their ecological implications remain unexplored. Here we isolated, sequenced and characterized 13 phage-resistant mutants of marineCellulophaga baltica(Flavobacteriia). Mechanistically, mutations in surface proteins provided broad and complete extracellular resistance against multiple phages through decreased adsorption. Intracellular mutations affecting serine, glycine and threonine metabolism produced narrower resistance against a single phage, permitting viral DNA replication, and, in one mutant, were shown to be lipid mediated. Putative ecosystem impacts inferred from in vitro experiments include: (1) altered carbon utilization for all mutants, but especially by surface ones, (2) increased metabolite secretion for one modelled intracellular mutant (including experimentally verified acetate) and (3) increased ‘stickiness’ for all mutants, with surface mutants also sedimenting faster. Our findings highlight new resistance mechanisms and suggest that the phage–host arms race could result in ecosystem-level biogeochemical impacts in marine microorganisms. Bacteriophages Microbial ecology Phage biology Water microbiology biology
N Nature Microbiology · Dec 03, 2025 Transcription co-inhibition alters drug resistance evolution and enhancesMycobacterium tuberculosisclearance from granulomas Mycobacterium tuberculosis(Mtb), the causative agent of tuberculosis, remains the deadliest human pathogen. Treatment is hampered by drug resistance and the persistence of slow-growing or non-replicating populations. Rifampicin, a cornerstone of first-line therapy, inhibits transcription during promoter escape, but resistance mutations undermine efficacy and drive resistance spread. We revisited the transcription cycle as an antibacterial target by characterizing AAP-SO2, an RNA polymerase inhibitor with whole-cell activity against Mtb. AAP-SO2slows the nucleotide addition cycle, disrupting elongation and termination. Rifampicin-resistant mutations impose fitness costs by perturbing the balance of these steps, creating exploitable weaknesses. Inhibition of transcription with AAP-SO2reduced the evolution of rifampicin resistance and was especially effective against the most common resistant mutant. Combination treatment with rifampicin and AAP-SO2synergistically killed non-replicating Mtb in an ex vivo rabbit granuloma model. These findings show that exploiting functional vulnerabilities of the transcription cycle can counter rifampicin resistance and improve clearance of recalcitrant Mtb populations. Antibiotics Cryoelectron microscopy Pathogens Transcription biology
N Nature Microbiology · Dec 03, 2025 Gut microbiome-mediated transformation of dietary phytonutrients is associated with health outcomes Food, especially plant-based diet, has complex chemical diversity. However, large-scale phytonutrient-metabolizing activities of gut bacteria are largely unknown. Here we integrated and systematically analysed multiple databases containing information on enzymatic reactions and food health benefits, and 3,068 global public human microbiomes. Transformation of 775 phytonutrients from edible plants was associated with enzymes encoded by diverse gut microbes. In vitro assays validated the biotransformation activity of gut species, for example,Eubacterium ramulus. The biotransformation of phytonutrients demonstrated high interpersonal and geographical variability. Machine learning models based on 2,486 public case–control microbiomes, using the abundances of enzymes associated with modification of phytonutrients present in health-associated foods, discriminated the health status of individuals in multiple disease contexts, suggesting altered biotransformation potential in disease. We validated the association of microbiome-encoded enzymes with the anti-inflammatory activity of common edible plants by combining metagenomics and metatranscriptomics analysis in specific-pathogen-free and germ-free mice. These findings have implications for designing precise, personalized diets to guide an individual towards a healthy state. Microbial communities Computational biology and bioinformatics biology mouse experiments
N Nature Microbiology · Nov 28, 2025 Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes Mirusviruses infect unicellular eukaryotes and are related to tailed bacteriophages and herpesviruses. Here we expand the known diversity of mirusviruses by screening diverse metagenomic assemblies and characterizing 1,202 non-redundant environmental genomes.Mirusviricotacomprises a highly diversified phylum of large and giant eukaryotic viruses that rivals the evolutionary scope and functional complexity of nucleocytoviruses. Critically, majorMirusviricotalineages lack essential genes encoding components of the replication and transcription machineries and, concomitantly, encompass numerous spliceosomal introns that are enriched in virion morphogenesis genes. These features point to multiple transitions from cytoplasmic to nuclear reproduction during mirusvirus evolution. Many mirusvirus introns encode diverse homing endonucleases, suggestive of a previously undescribed mechanism promoting the horizontal mobility of spliceosomal introns. Available metatranscriptomes reveal long-range trans-splicing in a virion morphogenesis gene. Collectively, our data strongly suggest that nuclei of unicellular eukaryotes across marine and freshwater ecosystems worldwide are a major niche for replication of intron-rich mirusviruses. Evolutionary theory Metagenomics Microbial ecology Water microbiology biology
N Nature Microbiology · Nov 28, 2025 MAP-X reveals distinct protein complex dynamics acrossPlasmodium falciparumblood stages The malaria parasitePlasmodium falciparumundergoes a complex intraerythrocytic developmental cycle (IDC) that relies on a dynamic network of protein–protein interactions. These are usually mapped ex vivo, limiting our understanding of their dynamics and composition in natural environments. Here we introduce the meltome-assisted profiling of protein complexes (MAP-X) that maps the complexome through thermal proteome profiling in intact cells. We applied MAP-X across seven timepoints in theP. falciparumIDC. MAP-X predicted more than 20,000 interactions, resolving conserved protein complexes, reproducing previously identified interactions and finding previously unreported associations. We found that malaria protein complexes undergo distinct dynamic alterations, and we predicted their moonlighting subunits that dissociate from their native complex to assume different biological functions. Altogether, our findings provide a resource for uncoveringPlasmodiumbiology and show that MAP-X can characterize protein complexes in intact cells to reveal cellular physiology at a proteome-wide level. Parasite biology Proteome informatics biology
N Nature Microbiology · Nov 27, 2025 Historical and current spatiotemporal patterns of wild and vaccine-derived poliovirus spread Outbreaks of vaccine-derived poliovirus type 2 (cVDPV2) have become a major threat to polio eradication. However, variations in spatiotemporal spread have not been quantified. Here we analysed cVDPV2 cases and wild poliovirus type 1 sequences to uncover spatiotemporal patterns and drivers of poliovirus spread. Between 1 May 2016 and 29 September 2023, 3,120 cVDPV2 poliomyelitis cases were reported across 75 outbreaks in 39 countries. Outbreaks had a median observed circulation of 202 (range 0–1,905) days and a median maximum distance of 231 (range 0–4,442) km. Wavefront velocity analysis of large outbreaks revealed a median velocity of spread of 2.3 (5th–95th percentile 0.7–9.2) km per day. International borders were associated with a slower velocity of spread (P< 0.001), in periods with high estimated population immunity. Phylogeographic analysis of 1,572 global wild poliovirus 1 sequences revealed that historic spread resembles recent cVDPV2 patterns and that international spread is largely sustained by unidirectional movement between neighbouring countries. Our findings offer insights for enhancing the geographical scope of vaccination response in the final phases of poliovirus eradication. Phylogenetics Population dynamics Viral infection biology
N Nature Microbiology · Nov 26, 2025 Industrial and agricultural chemicals exhibit antimicrobial activity against human gut bacteria in vitro Industrial and agricultural chemicals such as pesticides are often considered to have restricted biological activity. Yet, there are concerns regarding their broader toxicity range and impact on human gut microbiota. Here we report a systematic in vitro screening to assess the impact of 1,076 pollutants, spanning diverse chemistries and indicated applications, on 22 prevalent gut bacteria. Our investigation uncovered 588 inhibitory interactions involving 168 chemicals, the majority of which were not previously reported to have antibacterial properties. Fungicides and industrial chemicals showed the largest impact, with around 30% exhibiting anti-gut-bacterial properties. We demonstrate that the scale of our dataset enables a machine learning approach for predicting the antibacterial activity of pesticides. Mechanistically, chemical–genetic screens using transposon mutant libraries ofParabacteroides merdaeandBacteroides thetaiotaomicronimplicated genes involved in conserved efflux pathways, including theacrRlocus, as mediators of pollutant resistance. We also found that loss-of-function mutations in genes coding for metabolic enzymes were selected under pollutant exposure, including those for branched short-chain fatty acid biosynthesis under tetrabromobisphenol A, a flame retardant. Taken together, our results suggest that the antibacterial activity of chemical pollutants should be considered in future studies on the microbiome and the emergence of antimicrobial resistance, as well as in toxicological assessments. Chemical biology Microbial genetics Microbiology biology
N Nature Microbiology · Nov 25, 2025 Toxoplasma effector TgROP1 establishes membrane contact sites with the endoplasmic reticulum during infection Membrane contact sites (MCS) are essential for organelle communication in eukaryotic cells. Pathogens also establish MCS with host organelles, but the mechanisms underlying these interactions and their role in infection remain poorly understood. Here, using a fluorescence sensor and CRISPR-based loss-of-function screening, together with imaging and proteomics, we identify the parasite effector mediating MCS between host endoplasmic reticulum (ER) and the vacuole containing the intracellular parasiteToxoplasma gondii. TgROP1 acts as a tether and mimics a canonical FFAT motif to bind the host ER proteins VAPA and VAPB. The loss of VAPA/B abolished host ER–ToxoplasmaMCS and decreased pathogen growth. These findings indicate that targeting of host MCS tethers is a strategy exploited by pathogens during infection, which could inform future treatment design. Cellular microbiology Endoplasmic reticulum Mitochondria Parasite host response biology
N Nature Microbiology · Nov 24, 2025 Metabolic control of porin permeability influences antibiotic resistance inEscherichia coli Porins mediate the passage of hydrophilic nutrients and antibiotics across the outer membrane but might contribute to proton leak from the periplasm, suggesting that their conductance could be regulated. Here we show, using single-cell imaging, that porin permeability inEscherichia coliis controlled by changes in periplasmic H+and K+concentration. Conductance through porins increases with low periplasmic H+caused by starvation, promoting nutrient uptake, and decreases with periplasmic acidification during growth in lipid media, limiting proton loss. High metabolic activity during growth in glucose media, however, activates the inner membrane voltage-gated potassium channel, Kch, increasing periplasmic potassium and enhancing porin permeability to dissipate reactive oxygen species. This metabolic control of porin permeability explains the observed increase in ciprofloxacin resistance of bacteria catabolizing lipids and clarifies the impact of mutations in central metabolism genes on drug resistance, identifying Kch as a therapeutic target to improve bacterial killing by antibiotics. Antibiotics Bacteriology biology
N Nature Microbiology · Nov 24, 2025 Nanozymes modulate probiotic tryptophan metabolism to preventSalmonellainfection in mammalian models Probiotics are promising alternatives to antibiotics for the treatment of intestinal infections, but the effects of probiotics alone are often insufficient. Here we uncovered synergism between antibacterial iron–sulfur nanozymes (nFeS) and tryptophan derivatives that protects mice and pigs against bacterial gut infections. nFeS selectively inhibited potential intestinal pathogens while sparing commensalLactobacillus vaginalis, whose presence enhanced the protective activity of nFeS againstSalmonella entericasubsp.entericaserovar Typhimurium in vivo. Metabolomics and mutational analysis revealed thatL. vaginalissynthesized 2-indolecarboxylic acid from a tryptophan derivative, indole-3-carboxaldehyde, a reaction that was catalysed by nFeS. The cytoplasmic pH ofL. vaginalis(pH 7.5) allowed 2-indolecarboxylic acid to chelate free ferrous ions released by nFeS, thereby protecting it from antibacterial effects, whereas pathogens such asS. Typhimurium with a lower cytoplasmic pH were susceptible (pH 6.5). Pretreatment of pigs and mice withL. vaginalisand nFeS protected them againstSalmonellainfection. Our findings provide a foundation for improving probiotic bacteria-based therapies against intestinal infections. Antimicrobials Biocatalysis Nanoscale materials biology mouse experiments
N Nature Microbiology · Nov 21, 2025 Models and co-culture experiments assess four mechanisms of phytoplankton–bacteria interactions Phytoplankton growth and death depend on interactions with heterotrophic bacteria, yet the underlying mechanisms remain mostly unclear. Here we ask whether mathematical models explicitly representing four putative mechanisms of interaction (overflow metabolism, mixotrophy, exoenzymes and reactive oxygen species detoxification) can recapitulate diverse dynamics observed in laboratory co-cultures between the cyanobacteriumProchlorococcusand eight heterotrophic bacteria. Two distinct modes of interaction emerge from our models: (1) organic carbon and nitrogen recycling through exoenzymes or an overflow metabolism, in which the high biomass of both organisms leads to more productivity and recalcitrant organic matter, and (2) reactive oxygen species detoxification, in which a small number of ‘exploited’ heterotrophs are sufficient to supportProchlorococcussurvival. Recycling is probably the main process in laboratory co-cultures. Models do not reproduce total inhibition ofProchlorococcus, suggesting that additional mechanisms such as allelopathy may be involved. The models highlight cell death and biomass recycling as unconstrained, key processes that could enhance our understanding of how interactions impact ecologically and biogeochemically important processes. Marine microbiology Microbial ecology biology
N Nature Microbiology · Nov 21, 2025 Eosinophils enhance granuloma-mediated control of persistentSalmonellainfection in mice Salmonella entericacan persist asymptomatically within tissues for extended periods. This is achieved through intricate host–pathogen interactions in immune cell aggregates called granulomas, whereinSalmonellaestablish favourable cellular niches to exploit while the host limits its expansion and tissue dissemination. Here, using a mouse model of persistentSalmonellainfection, we identify a host-protective role for eosinophils in the control ofSalmonellaTyphimurium (STm) infection within the mesenteric lymph nodes, the main lymphoid tissue ofSTm persistence. Combining spatial transcriptomics and experimental manipulations, we found that monocytes and macrophages responding toSTm infection recruited eosinophils in a C-C motif chemokine ligand 11 (CCL11)-dependent manner and enhanced their activation. The protein major basic protein, primarily expressed by eosinophils, was associated with altered macrophage polarization and bacterial control. Thus, eosinophils play a vital role in restrainingSalmonellaexploitation of granuloma macrophages at a key site of bacterial persistence. Bacterial host response Bacterial infection biology mouse experiments
N Nature Microbiology · Nov 18, 2025 Structure-guided design of a synthetic bile acid that inhibitsClostridioides difficileTcdB toxin Intestinal bile acids are a family of host and microbiota metabolites that can directly inhibit toxin B (TcdB), the primary virulence factor ofClostridioides difficilethat causes infectious diarrhoea and colitis. However, the mechanism underlying the inhibition is unclear. Here we used cryogenic electron microscopy and determined the structure of TcdB bound to inhibitory bile acids cholic acid (methyl ester) and taurochenodeoxycholic acid at 2.9 Å and 3.3 Å resolution, respectively. These structures revealed that bile acids lock the C-terminal CROP domain of TcdB in a conformation that allosterically masks the two receptor-binding sites and prevents target cell recognition. Guided by the structure, we synthesized gut-restricted bile acid derivatives, designed to evade the bile acid reuptake transporters within the gut. One of the derivatives, sBA-2, was retained within the gut upon oral dosing and protected mice from toxin-inducedC. difficiledisease pathology. Our study uncovers the structural basis of inhibition of TcdB by bile acids and its analogues, paving the way for the development of orally deliverable therapeutics againstC. difficile. Drug discovery and development Pathogens
N Nature Microbiology · Nov 11, 2025 A phage-encoded anti-CRISPR protein co-opts host enolase to prevent type III CRISPR immunity CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) systems provide powerful adaptive immunity against phage infection. In response, phages use anti-CRISPR (Acr) proteins to evade CRISPR immunity. The few type III Acrs identified so far show conditional effectiveness in countering type III immunity or rely on unknown or poorly understood inhibitory mechanisms. Here we report the discovery of AcrIIIA2, a type III-A Acr encoded byStreptococcus thermophilusphages. Biochemical and structural analyses reveal that phage AcrIIIA2 co-opts host enolase, a highly abundant glycolysis enzyme, to form a ternary complex with theS. thermophilustype III-A (Csm) CRISPR ribonucleoprotein complex, obstructing its immune responses. The enolase-chaperoned AcrIIIA2 blocks the initial step of phage RNA binding, thereby preventing downstream type III anti-phage immune responses. Enolase participates in the anti-immune response by serving as an essential structural scaffold, stabilizing Acr–CRISPR interactions. These findings uncover a new anti-defence strategy that exploits a well-conserved host factor to block CRISPR immunity. Bacteriophages Phage biology
N Nature Microbiology · Nov 10, 2025 Respiratory immunization using antibiotic-inactivatedBordetella pertussisconfers T cell-mediated protection against nasal infection in mice The Gram-negative bacteriumBordetella pertussiscauses whooping cough (pertussis), a severe respiratory disease, especially in young children, which is resurgent despite high vaccine coverage. The current acellular pertussis vaccine prevents severe disease but does not prevent nasal infection withB. pertussis. This parenterally delivered vaccine induces potent circulating antibody responses but limited respiratory tissue-resident memory T cells and IgA responses. Here we developed a vaccine approach based on respiratory delivery of antibiotic-inactivatedB. pertussis(AIBP). Ciprofloxacin-treatedB. pertussispotently activated antigen-presenting cells to drive T cell responses. AIBP immunization via aerosol or intranasal administration conferred a high level of protection against lung and nasal infection. The AIBP vaccine inducedB. pertussis-specific interleukin (IL)-17-producing CD4 tissue-resident memory T cells that recruited neutrophils to the respiratory tract. Protection was abrogated by depletion of CD4 T cells or neutralization of IL-17 in mice. Unlike a parenterally delivered whole-cell pertussis vaccine, which induced high levels of serum IL-1β, IL-6, tumour necrosis factor and C-reactive protein, aerosol immunization with the AIBP vaccine did not promote systemic pro-inflammatory responses. We present preclinical evidence of a safe and effective respiratory-delivered vaccine platform for inducing T cell-mediated sterilizing immunity against a respiratory pathogen. Bacterial infection Cell vaccines
N Nature Microbiology · Nov 07, 2025 Strain displacement in microbiomes via ecological competition Microorganisms commonly live in diverse communities where changes in composition can be critical for health, industry and the environment. Yet, what enables one strain to competitively replace another in these complex conditions remains poorly understood. Here we develop a mathematical model to determine general principles of strain displacement. Our modelling reveals that weak resource competition enables successful invasion while strong interference competition, for example, via antimicrobial production, enables successful displacement. We verify these predictions using in vitro assays with genetically engineeredEscherichia coli. We then apply our principles to displace multidrug-resistant clinical isolates using strains that are equipped with a potent bacteriocin. Finally, we perform experiments with diverse human gut symbionts, which reveal that displacement relies on low resource competition not only between competing strains but also with the broader community, that is, limited nutrient blocking. These general rules for ecological success in microbial communities could be applied for targeted displacement of bacteria. Microbial ecology Microbiome
N Nature Microbiology · Nov 06, 2025 An updated evolutionary classification of CRISPR–Cas systems including rare variants The known diversity of CRISPR–Cas systems continues to expand. To encompass new discoveries, here we present an updated evolutionary classification of CRISPR–Cas systems. The updated CRISPR–Cas classification includes 2 classes, 7 types and 46 subtypes, compared with the 6 types and 33 subtypes in our previous survey 5 years ago. In addition, a classification of the cyclic oligoadenylate-dependent signalling pathway in type III systems is presented. We also discuss recently characterized alternative CRISPR–Cas functionalities, notably, type IV variants that cleave the target DNA and type V variants that inhibit the target replication without cleavage. Analysis of the abundance of CRISPR–Cas variants in genomes and metagenomes shows that the previously defined systems are relatively common, whereas the more recently characterized variants are comparatively rare. These low abundance variants comprise the long tail of the CRISPR–Cas distribution in prokaryotes and their viruses, and remain to be characterized experimentally. Genome informatics Microbial genetics
N Nature Microbiology · Nov 05, 2025 Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes Viruses and other extracellular genetic elements play essential roles in marine communities. However, methods to capture their full diversity remain limited by the constraints of bulk sequencing assemblers or pre-sorting throughput. Here we introduce environmental micro-compartment genomics (EMCG), which vastly improves the throughput and efficiency of single-particle genomic sequencing obtained from nanolitre volumes by compartmentalizing particles of a sample into picolitre-sized, semi-permeable capsules for in-capsule DNA amplification and barcoding. From 300 nanolitres of seawater, EMCG obtained genomic sequences of 2,037 particles. The microbiome composition agreed with other methods, and the virus-like assembly lengths indicated that most were near complete. Many viral assemblies belonged to theNaomiviridae, lacked metagenomic representation and aligned to outlier contigs of abundant, putative host lineages, suggesting their use of non-canonical DNA and overlooked ecological importance. This approach provides opportunities for high-throughput, quantitative and cost-effective genome analyses of individual cells and extracellular particles across complex microbiomes. Biodiversity Genomic analysis Microbial ecology Mobile elements Virology
N Nature Microbiology · Nov 04, 2025 Structural and mechanistic insights into herpesvirus helicase–primase and its therapeutic inhibitors The herpes simplex virus (HSV) helicase–primase (HP) complex is a promising anti-herpes therapeutic target. However, progress in developing highly effective small-molecule HP inhibitors (HPIs) for the treatment of genital herpes has been hindered by the lack of structural information on the HP complex and the incomplete understanding of the mechanism of action of HPIs. Here we present the cryogenic electron microscopy structure of the HSV-1 HP apo-complex (3.8 Å), along with structures bound to pritelivir (3.2 Å) and amenamevir (3.2 Å)—two clinically active, chemically distinct HPIs. The potency of both inhibitors against HSV variants bearing mutations within the HPI binding pocket supports the high-resolution mapping of key molecular interactions while revealing residues that govern their antiviral spectrum against alphaherpesviruses. Our results provide important insight into the unique architecture of the HP complex and the mechanism of inhibition of HPIs, paving the way for the development of next-generation antivirals to treat herpesvirus infections. Cryoelectron microscopy Herpes virus Structure-based drug design
N Nature Microbiology · Oct 31, 2025 Lysine-specific histone demethylase complex restricts Epstein–Barr virus lytic reactivation Epstein–Barr virus (EBV) infects >95% of adults and contributes to several human cancers. EBV can remain latent where viral lytic genes are silenced, precluding the use of antiviral agents such as ganciclovir. Little is known about the host factors involved in EBV latency. Here we performed a human genome-wide CRISPR–Cas9 screen in Burkitt lymphoma B cells, which identified lysine-specific histone demethylase 1 (LSD1) and its corepressors REST corepressor 1 (CoREST) and zinc finger protein 217 (ZNF217) as critical for EBV latency. Gene knockout or LSD1 inhibition triggered EBV reactivation, and the latter sensitized cells to ganciclovir cytotoxicity, including in murine tumour xenografts. Mechanistically, ZNF217 recruits LSD1 and CoREST to form a complex that binds a specific DNA motif associated with regions implicated in EBV reactivation. It removes histone 3 lysine 4 (H3K4) methylation marks and restricts host DNA looping. Alternatively, the H3K4 lysine methyltransferase 2D supports EBV lytic reactivation. Our results highlight H3K4 methylation as a major EBV lytic switch regulator and therapeutic target. Herpes virus Infection
N Nature Microbiology · Oct 31, 2025 Taxonomic expansion and reorganization ofFlaviviridae Flaviviridaeis a family of non-segmented positive-sense RNA viruses that includes major pathogens such as hepatitis C virus, dengue viruses and yellow fever virus. Recent large-scale metagenomic surveys have identified many RNA viruses related to members of this family, such as orthoflaviviruses and pestiviruses. These viruses diverge by having different genome lengths and configurations, and host range. Here we performed an analysis of RNA-directed RNA polymerase (RdRP) hallmark gene sequences of flaviviruses and ‘flavi-like’ viruses. We uncovered four divergent clades and multiple lineages that are congruent with phylogenies of their helicase genes, protein profile hidden Markov model profiles, and evolutionary relationships based on predicted RdRP protein structures. These results support their classification into three families (Flaviviridae,PestiviridaeandHepaciviridae) and 12 genera in the established orderAmarillovirales, with groupings correlating with genome properties and host range. This taxonomy provides a framework for future evolutionary studies on this important viral family. Taxonomy Systems virology
N Nature Microbiology · Oct 31, 2025 Prefusion structure, evasion and neutralization of HSV-1 glycoprotein B Glycoprotein B (gB) refolds between prefusion and postfusion conformations to facilitate herpesvirus entry into host cells. However, the isolation of prefusion-specific neutralizing antibodies, effective against other viral entry machines, has been challenging. Here we describe stabilization of the prefusion gB ectodomain from herpes simplex virus 1 (HSV-1), determine ectodomain structures at 2.9- to 4.1-Å resolution using cryogenic electron microscopy (cryo-EM) and isolate a prefusion-specific gB-neutralizing antibody termed WS.HSV-1.24. Murine immunization with gB stabilized in the prefusion conformation induced high titres of antibodies binding to both prefusion and postfusion gB, but—most notably—without measurable serum neutralization. Accessibility analysis revealed iso-surface exposure, with accessible surfaces on prefusion HSV-1 gB also exposed on postfusion gB. Structural analysis suggested substantial plasticity, with regions that refolded between pre- and postfusion conformations relegated to domain interfaces with limited accessibility; indeed, WS.HSV-1.24 recognized a domain-interface refolding region to facilitate neutralization. We propose that prefusion HSV-1 gB evades neutralization by most antibodies through an iso-surface display that is coupled to structural plasticity. Cryo-EM structures of the stabilized prefusion conformation of the glycoprotein B ectodomain—the HSV-1 entry machine—identify a prefusion-specific neutralizing antibody and reveal how prefusion glycoprotein B may evade antibody-mediated neutralization. Antibodies Cryoelectron microscopy Herpes virus Vaccines Viral immune evasion
N Nature Microbiology · Oct 31, 2025 Genetic population structure ofHaemophilus influenzaeat local and global scales Haemophilus influenzaeis an opportunistic bacterial pathogen that causes both non-invasive and invasive disease in humans. Although theH. influenzaetype b vaccine can reduce invasive disease, it is not effective against non-b serotypes or unencapsulated non-typeableH. influenzae(NTHi). The genetic population structure ofH. influenzae, especially NTHi, which is typically prevalent in lower- and middle-income countries, is unclear. Here we whole-genome sequenced 4,474 isolates ofH. influenzaefrom an unvaccinated paediatric carriage and pneumonia cohort from the Maela camp for displaced persons in northwestern Thailand. Despite noH. influenzaetype b immunization, serotype b was uncommon, whereas 92.4% of the isolates were NTHi. Most multidrug-resistant lineages were NTHi, and there were no lineages enriched among disease samples. Incorporating 5,976 published genomes revealed a highly admixed population structure, low core genome nucleotide diversity and evidence of pervasive negative selection. Our findings expand our understanding of this major pathogen in lower- and middle-income countries and at a global scale. Bacterial evolution Bacterial genetics
N Nature Microbiology · Oct 31, 2025 Structures of the sheathed flagellum reveal mechanisms of assembly and rotation inVibrio cholerae Motility promotes the complex life cycle and infectious capabilities ofVibrio choleraeand is driven by rotation of a single polar flagellum. The flagellar filament comprises four flagellin proteins (FlaA–D) and is covered by a membranous sheath continuous with the outer membrane. Here we combine in situ cryo-electron microscopy single-particle analysis, fluorescence microscopy and molecular genetics to determine 2.92–3.43 Å structures of the sheathed flagellar filament from intact bacteria. Our data reveal the spatial arrangement of FlaA–D, showing that FlaA localizes at the cell pole and functions as a template for filament assembly involving multiple flagellins. Unlike unsheathed flagellar filaments, the sheathed filament fromV. choleraepossesses a highly conserved core but a smooth, hydrophilic surface adjacent to the membranous sheath. A tiny conformational change at the single flagellin level results in a supercoiled filament and curved membranous sheath, supporting a model wherein the filament rotates separately from the sheath, enabling the distinct motility ofV. cholerae. Bacterial structural biology Cryoelectron microscopy
N Nature Microbiology · Oct 30, 2025 Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants Drought alters the soil microbiota by selecting for functional traits that preserve fitness in dry conditions. Legacy effects or ecological memory refers to how past stress exposure influences microbiota responses to future environmental challenges. How precipitation legacy effects impact soil microorganisms and plants is unclear, especially in the context of subsequent drought. Here we characterized the metagenomes of six prairie soils spanning a precipitation gradient in Kansas, United States. A microbial precipitation legacy, which persisted over a 5-month-long experimental drought, mitigated the negative physiological effects of acute drought for a native wild grass species, but not for the domesticated crop species maize. RNA sequencing of roots revealed that soil microbiota with a low precipitation legacy altered expression of plant genes that mediate transpiration and intrinsic water-use efficiency during drought. Our results show how historical exposure to water stress alters soil microbiota, with consequences for future drought responses of some plant species. Ecophysiology Microbial ecology Microbiome Plant symbiosis Soil microbiology
N Nature Microbiology · Oct 30, 2025 HKU25 clade MERS-related coronaviruses use ACE2 as a functional receptor Dipeptidyl peptidase-4 (DPP4) is an established receptor for Middle East respiratory syndrome-related coronaviruses (MERSr-CoVs), while recent studies have identified angiotensin-converting enzyme 2 (ACE2) usage in multiple merbecovirus clades. Yet, receptor usage of many genetically diverse bat MERSr-CoVs remains unclear. Here we show that broadly distributed HKU25 clade merbecoviruses use ACE2, rather than DPP4, as their receptor. Cryo-electron microscopy revealed that HsItaly2011 and VsCoV-a7 strains engage ACE2 similarly to HKU5 but with remodelled interfaces and distinct orthologue selectivity, suggesting a shared evolutionary origin of ACE2 recognition. EjCoV-3, a close relative of the DPP4-using BtCoV422, showed broad multi-species ACE2 tropism and preadaptation to human ACE2. Several ACE2 glycans and residues within or near the binding interface were identified as determinants of orthologue selectivity. These viruses remain sensitive to several broadly neutralizing antibodies and entry inhibitors, indicating potential countermeasures for future outbreaks. These findings highlight the versatility of ACE2 as a functional receptor for diverse coronaviruses. Virus–host interactions Virus structures
N Nature Microbiology · Oct 30, 2025 Human immunodeficiency virus and antiretroviral therapies exert distinct influences across diverse gut microbiomes Human immunodeficiency virus (HIV) infection alters gut microbiota composition and function, but the impact of geography and antiretroviral therapy remains unclear. Here we determined gut microbiome alterations linked to HIV infection and antiretroviral treatment in 327 individuals with HIV and 260 control participants in cohorts from Uganda, Botswana and the USA via faecal metagenomics. We found that while HIV-associated taxonomic differences were mostly site specific, changes in microbial functional pathways were broadly consistent across the cohorts and exacerbated in individuals with acquired immunodeficiency syndrome. Microbiome perturbations associated with antiretroviral medications were also geography dependent. In Botswana and Uganda, use of the non-nucleoside reverse transcriptase inhibitor efavirenz was linked to depletion ofPrevotella, disruption of interspecies metabolic networks, exacerbation of systemic inflammation and atherosclerosis. Efavirenz-associatedPrevotelladepletion may occur through cross-inhibition of prokaryotic reverse transcriptases involved in antiphage defences, as shown by computational and in vitro experiments. These observations could inform future geography-specific and microbiome-guided therapy. HIV infections Metagenomics Transcriptomics
N Nature Microbiology · Oct 30, 2025 Prodrug florfenicol amine is activated by intrinsic resistance to targetMycobacterium abscessus Non-tuberculous mycobacteria are emerging pathogens with high intrinsic drug resistance. Among these,Mycobacterium abscessusis particularly refractory owing to its extensive array of resistance mechanisms. Here we introduce florfenicol amine (FF-NH2), a major metabolite of the antibiotic florfenicol, which acts as a prodrug with narrow-spectrum activity againstM.abscessus−chelonaecomplex species. FF-NH2leverages intrinsicM.abscessusresistance conferred by the transcription factor WhiB7. It avoids WhiB7-dependent resistance mediated by theO-acetyltransferase Cat and is activated by the WhiB7-dependentN-acetyltransferase Eis2 in a prodrug fashion to generate the active translational inhibitor FF acetyl (FF-ac). FF-NH2induces Eis2 expression through WhiB7, creating a feed-forward bioactivation loop, which increases FF-ac accumulation and antimicrobial action. FF-NH2displays antiresistance properties, can synergize with other antibiotics and mitigates toxicity linked to mammalian mitochondrial ribosome inhibition. Importantly, FF-NH2demonstrated efficacy in a murine model ofM.abscessusinfection. These findings suggest intrinsic resistance can be exploited to develop safer and more effective treatments for this pathogen. Antimicrobial resistance Mechanism of action
N Nature Microbiology · Oct 29, 2025 Anoxia activates CRISPR–Cas immunity in the mouse intestine The natural context in which CRISPR–Cas systems are active in Enterobacteriaceae has remained enigmatic. Here we find that theCitrobacter rodentiumtype I-E CRISPR–Cas system is activated by the oxygen-responsive transcriptional regulator Fnr in the anoxic environment of the mouse intestine. Since Fnr-dependent regulation is predicted in ~41% of Enterobacteriaceaecas3orthologues, we propose that anoxic regulation of CRISPR–Cas immunity is an adaptation that protects Enterobacteriaceae against threats from foreign DNA within the intestinal microbiome. Bacterial genetics Infection Microbial ecology Molecular biology Pathogens
N Nature Microbiology · Oct 24, 2025 Bacterial TIR-based immune systems sense phage capsids to initiate defense Thoeris systems use proteins with Toll/interleukin-1 receptor domains to protect prokaryotes from phage infection through the synthesis of a cyclic adenosine diphosphate ribose signalling molecule, which activates an effector that depletes the host of the essential metabolite NAD+to limit viral propagation. How infection is recognized during Thoeris immunity is not known. Here we investigate the staphylococcal Thoeris defense system, ThsA–B1–B2, and found that, upon infection, the major capsid proteins ofSiphoviridaephages from serogroup B, but not A, form a complex with ThsB1 and ThsB2 to activate Thoeris defense. Thoeris cyclases fromStreptococcusalso recognize major capsid proteins. Our results suggest that the accumulation of capsid mutations that enable avoidance of Thoeris recognition may be an important evolutionary force behind the structural diversity of prokaryotic viruses. More broadly, given that some mammalian immune pathways contain Toll/interleukin-1 receptor domains that recognize viral structures, our findings highlight a conserved mechanism of innate antiviral immunity. Bacteria Bacteriophages
N Nature Microbiology · Oct 24, 2025 EngineeredMetarhiziumfungi produce longifolene to attract and kill mosquitoes Chemical insecticides have been the primary method of mosquito control, but in recent years, mosquitoes have become resistant to these compounds.Metarhiziumfungi are emerging as promising alternatives and can kill mosquitoes with a small number of spores. It was previously shown that caterpillars affected by fungal infections can attract mosquitoes. However, the mechanisms and potential applications of this attraction are lacking. Here we show thatMetarhizium-colonized insect cadavers release the volatile longifolene to attract and infect healthy insects, facilitating spore dispersal. We identified the responsible odorant receptors inDrosophila melanogasterandAedes albopictus. The virulent mosquito pathogenMetarhizium pingshaensewas engineered to express pine longifolene synthase to produce a large amount of longifolene on media. The transgenic spores effectively attracted and killed male and femaleA. albopictus,Anopheles sinensisandCulex pipiens. Attraction of wild-caught mosquitoes was not impacted by human presence, but mosquito-attracting flowering plants competed with transgenicM. pingshaensefor attractiveness, although mortality remained over 90%. This study uncovered an active spore dispersal mechanism in broad-host-range entomopathogenicMetarhizium, enhancing mosquito control efficacy. Biotechnology Fungi
N Nature Microbiology · Oct 23, 2025 A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people Disruption of hydrogen (H2) cycling in the gut is linked to gastrointestinal disorders, infections and cancers. However, the mechanisms and microorganisms controlling H2production in the gut remain unresolved. Here we show that gut H2production is primarily driven by the microbial group B [FeFe]-hydrogenase. Metagenomics and metatranscriptomics of stool and tissue biopsy samples show that hydrogenase-encoding genes are widely present and transcribed in gut bacteria. Assessment of 19 taxonomically diverse gut isolates revealed that the group B [FeFe]-hydrogenases produce large amounts of H2gas and support fermentative growth of Bacteroidetes and Firmicutes. Further biochemical and spectroscopic characterization of purified enzymes show that they are catalytically active, bind a di-iron active site and reoxidize ferredoxin derived from the pyruvate:ferredoxin oxidoreductase reaction. Group B hydrogenase-encoding genes are significantly depleted in favour of other fermentative hydrogenases in patients with Crohn’s disease. Finally, metabolically flexible respiratory bacteria may be the dominant hydrogenotrophs in the gut, rather than acetogens, methanogens and sulfate reducers. These results uncover the enzymes and microorganisms controlling H2cycling in the healthy human gut. Gastroenterology Microbial ecology
N Nature Microbiology · Oct 22, 2025 Long-read metagenomics for strain tracking after faecal microbiota transplant Accurate tracking of bacterial strains that stably engraft in faecal microbiota transplant (FMT) recipients is critical for understanding the determinants of strain engraftment, evaluating correlations with clinical outcomes and guiding the development of therapeutic consortia. While short-read sequencing has advanced FMT research, it faces challenges in strain-level de novo metagenomic assembly. Here we describe LongTrack, a method that uses long-read metagenomic assemblies for FMT strain tracking. LongTrack shows higher precision and specificity than short-read approaches, especially when multiple strains co-exist in the same sample. We uncovered 648 engrafted strains across six FMT cases involving patients with recurrentClostridioides difficileinfection and inflammatory bowel disease. Furthermore, long reads enabled assessment of the genomic and epigenomic stability of engrafted strains at the 5-year follow-up timepoint, revealing structural variations that may be associated with strain adaptation in a new host environment. Our findings support the use of long-read metagenomics to track microbial strains and their adaptations. Metagenomics Microbiome
N Nature Microbiology · Oct 21, 2025 Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism Syntrophic microbial consortia can contribute substantially to the activity of anoxic ecosystems but are often too rare to allow the study of their in situ physiologies using traditional molecular methods. Here we combined bioorthogonal non-canonical amino acid tagging (BONCAT), stable isotope probing and metaproteomics to improve the recovery of proteins from active members and track isotope incorporation in an anaerobic digestion community. Click-chemistry-enabled cell sorting and direct protein pull-down coupled to metaproteomics improved recovery of isotopically labelled proteins during anaerobic acetate oxidation. BONCAT-enabled protein profiles revealed elevated activity and labelling of a rare and so-far uncharacterized syntrophic bacterium belonging to the family Natronincolaceae that expressed a previously hypothesized oxidative glycine pathway for syntrophic acetate oxidation. Stable-isotope-probing-informed metabolic modelling predicted that this organism accounted for a majority of acetate flux, suggesting that the oxidative glycine pathway is an important route for anaerobic carbon transformation and is probably central to community metabolism in natural and engineered ecosystems. An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community. Applied microbiology Metagenomics Microbial ecology Microbiome Water microbiology
N Nature Microbiology · Oct 17, 2025 Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions Nested symbioses, including hyperparasitism in which parasites exploit other parasites within a host, are common in nature. However, such nested interactions remain poorly studied in archaea. Here we characterize this phenomenon in ultra-small archaea of the candidate phylum Nanohaloarchaeota, members of the DPANN superphylum (named after its first representative phyla: Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota) that form obligate interactions with halophilic archaea of the class Halobacteria. We reconstructed the viromes from geothermally influenced salt lakes in the Danakil Depression, Ethiopia, and find that nanohaloarchaea and haloarchaea are both associated with head-tailed, tailless icosahedral, pleomorphic and spindle-shaped viruses, representing 16 different families. These viruses exhibit convergent adaptation to hypersaline environments, encode diverse auxiliary metabolic genes and exchange genes horizontally with each other. We further characterize plasmid-derived satellites that independently evolved to parasitize spindle-shaped viruses of haloarchaea and nanohaloarchaea, revealing another layer of nested symbiosis. Collectively, our findings highlight the complexity of virus–host and virus–virus interactions in hypersaline environments. Metagenomics Phage biology
N Nature Microbiology · Oct 15, 2025 The IFIT2–IFIT3 antiviral complex targets short 5’ untranslated regions on viral mRNAs for translation inhibition Recognition of foreign RNA is critical for the innate immune response to viruses. Interferon (IFN)-induced proteins with tetratricopeptide repeats (IFIT) 2 and 3 are highly upregulated following viral infection, but mechanistic insight into their antiviral role is lacking. Here we demonstrate that short 5’ untranslated regions (UTRs), a characteristic of many viral mRNAs, can serve as a molecular pattern for innate immune recognition via IFIT2 and IFIT3. Structure determination of the IFIT2–IFIT3 complex at 3.2 Å using cryo-EM reveals a domain-swapped heterodimer that is required for recognition of the viral mRNA 5’ end, translation inhibition and antiviral activity. Critically, viral or host 5’ UTR lengths less than 50 nucleotides are necessary and sufficient to enable translation inhibition by the IFIT2–IFIT3 complex. Accordingly, diverse viruses whose mRNAs contain short 5’ UTRs, such as vesicular stomatitis virus and parainfluenza virus 3, are sensitive to IFIT2–IFIT3-mediated antiviral activity. Our work thus reveals a pattern of antiviral nucleic acid immune recognition that takes advantage of the inherent constraints on viral genome size. Innate immunity Interferons Viral host response Viral infection Virus–host interactions
N Nature Microbiology · Oct 14, 2025 Cross-neutralizing and potent human monoclonal antibodies against historical and emerging H5Nx influenza viruses Highly pathogenic avian influenza H5Nx viruses are an emerging threat for global health, especially clade 2.3.4.4b H5N1 virus which causes panzootic infections. Here we describe the isolation and characterization of broadly cross-neutralizing monoclonal antibodies (mAbs) against diverse H5Nx viruses from individuals who received a monovalent H5N1 vaccine 15 years ago. By screening over 500 mAbs, we identified 5 mAbs that neutralized the majority of H5 clades including 2.3.4.4b and target three distinct conserved epitopes within the HA globular head. Cryo-electron microscopy structures of these mAbs in complex with HA, deep mutational scanning and neutralization escape studies define the sites of vulnerability of H5 HA. These mAbs mediated stronger prophylactic protection against clade 2.3.4.4b H5N1 infection in mice than the best-in-class mAb targeting the HA stem. Our study identified several highly potent broadly neutralizing H5 mAbs from humans that either alone or in combination provide a pragmatic pandemic preparedness option against the threat of panzootic H5N1 influenza. Antibodies Influenza virus
N Nature Microbiology · Oct 10, 2025 Dipeptidase 1 is a functional receptor for a porcine coronavirus Coronaviruses of the subgenusEmbecovirusinclude several important pathogens, such as the human seasonal coronaviruses HKU1 and OC43, bovine coronavirus and porcine haemagglutinating encephalomyelitis virus (PHEV). While sialic acid is thought to be required for embecovirus entry, protein receptors remain unknown for most of these viruses. Here we show that PHEV does not require sialic acid for entry and instead uses dipeptidase 1 (DPEP1) as a receptor. Cryo-electron microscopy at 3.4–4.4 Å resolution revealed that, unlike other embecoviruses, PHEV displays both open and closed conformations of its spike trimer at steady state. The spike receptor-binding domain (RBD) exhibits extremely high sequence variability across embecoviruses, and we found that DPEP1 usage is specific to PHEV. In contrast, the X-ray structure of the RBD–DPEP1 complex at 2.25 Å showed that the structural elements involved in receptor binding are conserved, highlighting the remarkable versatility of this structural organization in adopting novel receptor specificities. Cryoelectron microscopy Viral evolution Virus–host interactions Virus structures X-ray crystallography
N Nature Microbiology · Oct 10, 2025 Human gut bacteria produce structurally related monoglycolipids with contrasting immune functions Gut symbiontBacteroides fragiliscan produce α-galactosylceramides (BfaGCs), sphingolipids with immunomodulatory functions that regulate colonic natural killer T (NKT) cells. However, their synthesis pathway and whether other human gut bacteria can produce them are unclear. Here, using genetic and metabolomic approaches, we mapped the sphingolipid biosynthesis pathway ofB. fragilisand determined that α-galactosyltransferase (agcT) is essential and sufficient for colonic NKT cell regulation in mice. The distribution ofagcTis restricted to only a few species among Bacteroidales. However, structural homologues of AgcT, such as BgsB, are widely distributed in gut microbiota and produce α-glycosyldiacylglycerols (aGDGs), particularly inEnterococcus. Analysis of infant gut metagenomes revealed thatB. fragilispredominantly accounts foragcTabundance regardless of the cohort, butbgsB-encoding bacteria were taxonomically diverse and showed dynamic changes with host age. In addition, aGDGs frombgsB-encoding species act as antagonistic ligands for BfaGC-mediated NKT cell activation in vitro and in vivo. Our findings highlight the distinct natures of immunoactive glycolipid-producing symbionts and their relevance in the human gut microbiome, particularly in early life. Bacterial genetics Innate immune cells Lipidomics Microbiome
N Nature Microbiology · Oct 10, 2025 Toxoplasma gondiiVIP1 mediates parasitophorous vacuole–host endoplasmic reticulum interactions to facilitate parasite development Membrane contact sites (MCS) are areas of close apposition between organelles without membrane fusion, allowing for exchange of biomolecules. The endoplasmic reticulum (ER) forms many MCS via two proteins, vesicle-associated membrane protein-associated proteins A and B (VAPA and VAPB). The obligate intracellular parasiteToxoplasma gondiiresides within mammalian cells in a parasitophorous vacuole (PV), which closely contacts the host ER at distances compatible with MCS. However, the proteins mediating this interaction remain largely unknown. Here, using molecular and microscopy approaches, we show that VAPA and VAPB localize at the PV membrane and, with motile sperm domain-containing protein 2 (MOSPD2), mediate ER–PV interactions. Cells deficient in VAPA, VAPB and MOSPD2 do not recruit host ER at the PV, and parasites show growth defects. We identify a parasite protein that localizes at the PV membrane, called TgVIP1, which harbours an FFAT-like motif that binds VAPA and VAPB. These findings lay the basis for understanding how and whyToxoplasmaexploits ER–PV interactions and may uncover new drug targets. Endoplasmic reticulum Parasite biology Transport carrier
N Nature Microbiology · Oct 10, 2025 Mycobacterium tuberculosis-derived linoleic acid increases regulatory T cell function to promote bacterial survival within macrophages Regulatory T (Treg) cells expand duringMycobacterium tuberculosis(Mtb) infection and suppress T cell-mediated control. Whether Mtb actively contributes to this process is unclear. Here, using a genome-wide mutant library, we show that the expression of Mtb Rv1272c, an ATP-binding cassette transporter, increased under hypoxic conditions and promotes Mtb survival in vivo by increasing lecithin import, followed by the production and release of linoleic acid. Linoleic acid released by infected macrophages promoted surface trafficking of the immune checkpoint molecule cytotoxic T lymphocyte antigen 4 (CTLA-4) in Tregcells via the Ca²⁺ transporter ATP2a3. This in turn inhibited macrophage reactive oxygen species production and promoted Mtb survival inside macrophages. Rv1272c-induced linoleic acid further promoted Mtb immune evasion by increasing CTLA-4 surface trafficking on Tregcells in vivo. Mechanistically, linoleic acid interacts with ATP2a3 in Tregcells and promotes mitochondria-associated endoplasmic reticulum (ER) membrane formation. This facilitates ER-to-mitochondria Ca2+transfer and depletion of Ca2+in the ER, and triggers store-operated calcium entry, thus elevating cytosolic Ca2+levels to increase Ca2+-dependent CTLA-4 surface trafficking in Tregcells. These findings reveal that Mtb can use a metabolite to manipulate host responses and promote its intracellular survival. Cellular microbiology Immune evasion
N Nature Microbiology · Oct 10, 2025 A host-directed adjuvant sensitizes intracellular bacterial persisters to antibiotics Intracellular bacterial reservoirs contribute to antibiotic treatment failure by fostering metabolically dormant persister cells that are highly tolerant to killing. However, strategies to effectively target intracellular persister cells remain limited. Here we developed a high-throughput screen to identify compounds that modulate the metabolic activity of intracellularStaphylococcus aureus. The identified compound, KL1, increases intracellular bacterial metabolic activity and sensitizes persister populations ofS. aureusto antibiotics, without causing cytotoxicity or bacterial outgrowth. KL1 also exhibits adjuvant activity against intramacrophageSalmonella entericaTyphimurium andMycobacterium tuberculosis, as well as in murine infection models ofS. aureusandS. Typhimurium infection. Transcriptomic analysis and further mechanistic studies reveal that KL1 modulates host immune response genes and suppresses the production of reactive species in host macrophages, alleviating a key inducer of antibiotic tolerance. Our findings highlight the potential to target intracellular persisters by stimulating their metabolism. There are two major problems in the field of antimicrobial chemotherapy–antibiotic resistance and antibiotic tolerance. Antibiotic tolerance has been frequently connected with poor treatment outcomes in the clinic. Unlike antibiotic resistance, which permits bacterial growth in the presence of drugs, antibiotic tolerance allows bacteria to withstand multiple antibiotics for prolonged periods. The extended survival of tolerant bacteria further predisposes them to evolve antibiotic resistance over time, underscoring the critical need to address antibiotic tolerance. Host interactions have been shown to induce persister formation in numerous pathogens, with the production of reactive oxygen and nitrogen species heavily implicated in the collapse of bacterial metabolic activity and entry into an antibiotic-tolerant state. Yet, tools to study or target this process remain limited. Here we developed a high-throughput screen to identify compounds that modulate intracellularS. aureusmetabolism, leading to the discovery of KL1, a host-directed compound that sensitizes persisters to antibiotic killing. Antibiotics Bacterial host response High-throughput screening
N Nature Microbiology · Oct 03, 2025 A generative artificial intelligence approach for the discovery of antimicrobial peptides against multidrug-resistant bacteria The discovery of novel antimicrobial peptides (AMPs) against clinical superbugs is urgently needed to address the ongoing antibiotic resistance crisis. AMPs are promising candidates due to their broad-spectrum activity, rapid bactericidal mechanisms and reduced likelihood of inducing resistance compared with conventional antibiotics. Here, a pre-trained protein large language model (LLM), ProteoGPT, was established and further developed into multiple specialized subLLMs to assemble a sequential pipeline. This pipeline enables rapid screening across hundreds of millions of peptide sequences, ensuring potent antimicrobial activity and minimizing cytotoxic risks. Through transfer learning, we endowed the LLMs with different domain-specific knowledge to achieve high-throughput mining and generation of AMPs within a unified methodological framework. Notably, both mined and generated AMPs exhibited reduced susceptibility to resistance development in ICU-derived carbapenem-resistantAcinetobacter baumannii(CRAB) and methicillin-resistantStaphylococcus aureus(MRSA) in vitro. The AMPs also showed comparable or superior therapeutic efficacy in in vivo thigh infection mouse models compared with clinical antibiotics, without causing organ damage and disrupting gut microbiota. The mechanisms of action of these AMPs involve disruption of the cytoplasmic membrane and membrane depolarization. Overall, this study presents a generative artificial intelligence approach for the discovery of novel antimicrobials against multidrug-resistant bacteria, enabling efficient and extensive exploration of AMP space. Antibiotics Antimicrobial resistance Data mining High-throughput screening
N Nature Microbiology · Oct 03, 2025 Discovery and artificial intelligence-guided mechanistic elucidation of a narrow-spectrum antibiotic Current clinical antibiotics are largely broad-spectrum agents that can alter the gut microbiome and promote colonization by Enterobacteriaceae, which are often drug resistant. This includes adherent-invasiveEscherichia coli(AIEC), particularly in patients with inflammatory bowel disease, in which dysbiosis creates a niche for this pathogen to colonize. There is an urgent and unmet need for novel narrow-spectrum and microbiome-sparing antibiotics. Here we screened 10,747 bioactive small molecules for antibacterial activity against AIEC and discovered enterololin, an antibacterial compound with targeted activity against Enterobacteriaceae species. Enterololin could overcome intrinsic and acquired resistance mechanisms in clinical isolates when combined with a subinhibitory concentration of SPR741, a polymyxin B analogue used here to increase outer membrane permeability in Gram-negative bacteria. Molecular substructure- and deep learning-guided mechanism-of-action investigations revealed that enterololin perturbs lipoprotein trafficking through a mechanism involving the LolCDE complex, laboratory-evolved resistant mutants predominantly mapped tololCandlolE, with an in vitro frequency of resistance of ~10−8to 10−7. Enterololin showed low mammalian cytotoxicity (HEK293 half-maximal inhibitory concentration ~100 µg ml−1) and suppressed AIEC infection in mouse models when administered in combination with SPR741, while largely preserving the overall microbiome composition. This study highlights the utility of deep learning methods for predicting molecular interactions and identifies a promising Enterobacteriaceae-specific antibacterial candidate for further development. High-throughput screening Target validation
N Nature Microbiology · Oct 03, 2025 Superinfection promotes replication and diversification of defective HIV-1 proviruses in people with non-suppressible viraemia During replication of some RNA viruses, defective particles can spontaneously arise and interfere with wild-type (WT) virus replication. However, these defective interfering particles (DIPs) have not been reported in people with HIV-1 (PWH). Here we find DIPs in PWH who have a rare, polyclonal form of non-suppressible viraemia (NSV). We characterized the source of NSV in two PWH who never reached undetectable viral load despite adherence to antiretroviral therapy (ART). Remarkably, in each participant, we found a diverse set of defective viral genomes sharing the same fatal deletions. This paradoxical accumulation of mutations by viruses with fatal defects was driven by superinfection with intact viruses, resulting in mobilization of defective genomes and accumulation of additional mutations during untreated infection. These defective proviruses interfere with WT virus replication, conditionally replicate and, in one case, have anR0> 1, enabling in vivo spread. Despite this, clinical outcomes showed no beneficial effect of these DIPs. These findings demonstrate that fatally defective proviruses, traditionally considered evolutionary dead ends, can replicate and diversify upon superinfection without preventing disease progression. Viral evolution Viral reservoirs
N Nature Microbiology · Oct 01, 2025 Structure of a distinct β-barrel assembly machinery complex in the Bacteroidota The Gram-negative β-barrel assembly machinery (BAM) complex catalyses the folding and membrane insertion of newly synthesized β-barrel outer membrane proteins. The BAM is structurally conserved, but most studies have focused on Gammaproteobacteria. Here, using single-particle cryogenic electron microscopy, quantitative proteomics and functional assays, we show that the BAM complex is distinct within the Bacteroidota. Cryogenic electron microscopy structures of BAM complexes from the human gut symbiontBacteroides thetaiotaomicron(3.3 Å) and the human oral pathogenPorphyromonas gingivalis(3.2 Å) show similar, seven-component complexes of ~325 kDa. The complexes are mostly extracellular and comprise canonical BamA and BamD; an integral, essential outer membrane protein, BamG, that associates with BamA; and four surface-exposed lipoproteins: BamH–K. Absent from the BAM in Pseudomonadota, BamG–K form a large, extracellular dome that may confer additional functionality to enable the folding and assembly of β-barrel–surface-exposed lipoprotein complexes that are a hallmark of the Bacteroidota. Our findings develop our understanding of fundamental biological processes in an important bacterial phylum. Bacterial structural biology Cryoelectron microscopy
N Nature Microbiology · Sep 29, 2025 Polymyxin B lethality requires energy-dependent outer membrane disruption Polymyxin antibiotics target lipopolysaccharides (LPSs) in both membranes of the bacterial cell envelope, leading to bacterial killing through a poorly defined mechanism. Here we demonstrate that metabolic activity is essential for the lethality of clinically relevant doses of polymyxin B (PmB) and leverage this insight to determine its mode of action. PmB killed exponential-phaseEscherichia colibut did not eliminate stationary-phase cells unless a carbon source was available. Antibiotic lethality correlated with surface protrusions visible by atomic force microscopy and LPS loss from the outer membrane via processes that required LPS synthesis and transport but that were blocked by the MCR-1 polymyxin resistance determinant. While energy-dependent outer-membrane disruption was not directly lethal, it facilitated PmB access to the inner membrane, which the antibiotic permeabilized in an energy-independent manner, leading to cell death. This work reveals how metabolic inactivity confers tolerance of an important, membrane-targeting antibiotic. Antibiotics Antimicrobial resistance Bacterial physiology
N Nature Microbiology · Sep 26, 2025 Epstein–Barr virus exploits desmocollin 2 as the principal epithelial cell entry receptor Epstein–Barr virus (EBV) infects B and epithelial cells, causing various lymphomas and epithelial malignancies. Although cell-free infection of epithelial cells is inefficient, direct B–epithelial cell contact infection is highly efficient and probably the dominant route. To identify mechanisms of contact-mediated infection, we implemented a genome-wide CRISPR screen and uncovered desmocollin 2 (DSC2) as an EBV epithelial receptor and DSC3 as a co-factor for infection.DSC2andDSC3double knockout significantly inhibited both cell-free and cell–cell contact EBV infection of normal oral keratinocytes, while their overexpression permitted infection in receptor-negative cells. Antibodies to DSC2 blocked infection across normal oral keratinocytes, primary oral keratinocytes, and head and neck epithelial organoids. Combining DSC2 and DSC3 antibodies efficiently blocked cell–cell contact infection. Mechanistically, DSC2 interacted with the EBV gH/gL glycoprotein and facilitated epithelial fusion. Notably, EphA2 overexpression failed to restore infection inDSC2/3-deficient cells, indicating its dependence on DSC2/3. Our findings establish DSC2 as a principal EBV entry receptor and target for vaccine and therapeutic development. Microbiology Virology
N Nature Microbiology · Sep 26, 2025 HIV infection reprogrammes CD4+ T cells for quiescence and entry into proviral latency Human immunodeficiency virus (HIV) persists in infected individuals despite effective antiretroviral therapy due to the rapid establishment of latent reservoirs, mainly composed of quiescent memory CD4+ T cells. The mechanisms governing latent reservoir formation remain poorly understood. Here, using single-cell RNA-seq and functional studies in human primary CD4+ T cell models, we show that HIV infection with reporter constructs and laboratory and patient-derived strains triggers transcriptomic remodelling, activating the p53 pathway and a quiescence programme mediated by Krüppel-like factor 2 (KLF2), a key quiescence regulator. Loss- and gain-of-function studies, including unbiased shRNA screens and confirmatory studies in CD4+ T cells from HIV+ donors, demonstrate that HIV infection drives KLF2 and p53 signalling, which downregulate MYC and proliferation pathways, resulting in proviral transcriptional silencing. This enhances latent reservoir formation in T cells, ensuring viral persistence. These findings present a mechanism for forming the latent HIV reservoir and broaden the repertoire of strategies through which viruses control host cells to their advantage. Viral reservoirs Virus–host interactions
N Nature Microbiology · Sep 25, 2025 Dynamic expression of candidalysin facilitates oral colonization ofCandida albicansin mice Candida albicansis a common fungal member of the human microbiota but can also cause infections via expression of virulence factors associated with the yeast-to-hyphae transition. The evolutionary selection pressure to retain these pathogenic traits for a commensal microorganism remains unclear. Here we show that filamentation and hyphae-associated factors, including the toxin candidalysin, are crucial for colonization of the oral cavity, a major reservoir ofC. albicans. Low-virulent strains ofC. albicansexpressed the candidalysin-encoding geneECE1transiently upon exposure to keratinocytes in vitro. In mice,ECE1mutants were defective at accessing terminally differentiated oral epithelial layers where the fungus is protected from IL-17-mediated immune defence. Tight regulation ofECE1expression prevented detrimental effects of candidalysin on the host. Our results suggest that hyphae-associated factors such as candidalysin govern not only pathogenicity, but also mucosal colonization through direct host interactions enablingC. albicansto create and maintain its niche in the oral mucosa. Fungal immune evasion Fungal pathogenesis
N Nature Microbiology · Sep 24, 2025 Rational design of a hospital-specific phage cocktail to treatEnterobacter cloacaecomplex infections The Alfred Hospital in Melbourne, Australia, has reported an ongoing outbreak of infections caused by multidrug-resistantEnterobacter cloacaecomplex (ECC). Phage therapy is a promising strategy to treat antimicrobial-resistant infections. Utilizing the hospital’s isolate collection, built over the past decade, we established an initial 3-phage cocktail with 54% ECC coverage. We then iteratively improved this product by enhancing phage killing efficiency using phage adaptation and expanded host range through targeted phage isolation against low-coverage ECC isolates. This optimization yielded Entelli-02, containing five well-characterized virulent phages that target clinical ECC isolates via distinct bacterial cell surface receptors. Entelli-02 exhibits 88% host coverage against The Alfred Hospital’s ECC isolate collection (n= 206), confirmed by plaque formation and reduced bacterial load in septicaemic mice by >99%. We produced this cocktail as a therapeutic-grade product, ready for clinical use. Entelli-02 represents a hospital-specific phage cocktail with frontline efficacy and on-demand availability. Antibiotics Bacteriophages
N Nature Microbiology · Sep 23, 2025 Genome-resolved metagenomics reveals microbiome diversity across 48 tick species Ticks are arthropod vectors capable of transmitting a wide spectrum of pathogens affecting humans and animals. However, we have relatively limited information of their genomic characteristics and the diversity of associated microbiomes. Here we used long- and short-read sequencing on 1,479 samples from 48 tick species across eight genera from China to determine their genome and associated pathogens and microbiome. Through de novo assembly, we reconstructed 7,783 bacterial genomes representing 1,373 bacterial species, of which, 712 genomes represented 32 potentially pathogenic species. Computational analysis found nutritional endosymbionts to be prevalent and highly specific to tick genera. The microbiome genome-wide association study revealed host genetic variants linked to pathogen diversity, abundance and key biological pathways essential to tick biology, including blood-feeding and pathogen invasion. These findings provide a resource for studying the host–microbe interactions within ticks, paving the way for strategies to control tick populations and tick-borne diseases. Bacterial genetics Metagenomics Pathogens
N Nature Microbiology · Sep 22, 2025 NasalStaphylococcus aureuscarriage promotes depressive behaviour in mice via sex hormone degradation The human microbiome has a pronounced impact on human physiology and behaviour. Despite its unique anatomical connection to the brain, the role of the nasal microbiome in neurological diseases is understudied. Here, using human data and experiments in mice, we show that nasalStaphylococcus aureusis linked to depression. Nasal microbiome analyses revealed a positive correlation between depression scores andS. aureusabundance among patients with depression and healthy controls. Metabolomics of the nasal cavity showed decreased sex hormones, estradiol and testosterone in patients with depression versus controls. Nasal microbiota transplants from patients reproduced depression-like behaviour in mice with differential abundance ofS. aureus. Further homology and mutational analysis uncovered anS. aureussex hormone-degrading enzyme, 17b-hydroxysteroid dehydrogenase (Hsd12), which degraded testosterone and estradiol in mice, leading to lower levels of dopamine and serotonin in the murine brain. These findings reveal a nasal commensal that influences depressive behaviour and provides insights into the nose–brain axis. Microbiome Neurological disorders
N Nature Microbiology · Sep 22, 2025 Oxaloacetate sensing promotes innate immune antiviral defence against influenza virus infection Metabolic pathways determine cellular fate and function; however, the exact roles of metabolites in host defence against influenza virus remain undefined. Here we employed pharmacological inhibition and metabolomics analysis to show that the metabolic pathways of oxaloacetate (OAA) are integrated with antiviral responses to influenza virus. Cytosolic malate dehydrogenase 1 senses intracellular OAA to undergo dimerization and functions as a scaffold to recruit the transcription factor ETS2 for phosphorylation by the kinase TAOK1 at serine 313. The phosphorylated ETS2 translocates into the nucleus and supports optimal expression of TBK1, an indispensable activator of type I interferon responses. OAA supplementation provides a broad-spectrum antiviral ability, and OAA deficiency caused byAclygenetic ablation decreases antiviral immunity and renders mice more susceptible to lethal H1N1 virus infection. Our results uncover a signalling pathway through cellular OAA sensing that links metabolism and innate immunity to coordinate defence against viral challenge. Infection Influenza virus
N Nature Microbiology · Sep 19, 2025 Phages with a broad host range are common across ecosystems Phages are diverse and abundant within microbial communities, where they play major roles in their evolution and adaptation. Phage replication, and multiplication, is generally thought to be restricted within a single or narrow host range. Here we use published and newly generated proximity-ligation-based metagenomic Hi-C (metaHiC) data from various environments to explore virus–host interactions. We reconstructed 4,975 microbial and 6,572 phage genomes of medium quality or higher. MetaHiC yielded a contact network between genomes and enabled assignment of approximately half of phage genomes to their hosts, revealing that a substantial proportion of these phages interact with multiple species in environments as diverse as the oceanic water column or the human gut. This observation challenges the traditional view of a narrow host spectrum of phages by unveiling that multihost associations are common across ecosystems, with implications for how they might impact ecology and evolution and phage therapy approaches. Environmental microbiology Software Virology
N Nature Microbiology · Sep 19, 2025 A dominant subgroup of marine Bathyarchaeia assimilates organic and inorganic carbon into unconventional membrane lipids Bathyarchaeia, an abundant and ecologically versatile archaea found commonly in marine sediments, has a key role in the global carbon cycle. However, its lipid biomarkers and carbon assimilation mechanisms are poorly understood. Here, using a highly enriched Bathyarchaeia culture (>95% archaea) obtained from estuarine sediment of the East China Sea, we show thatBaizosediminiarchaeum(formerly subgroup Bathy-8), the most abundant and widespread Bathyarchaeia group on Earth, synthesizes butanetriol dialkyl glycerol tetraethers (BDGTs) as its dominant membrane lipids. BDGTs are unusual archaeal tetraether lipids characterized by a butanetriol backbone instead of the typical glycerol, challenging fundamental assumptions in archaeal lipid biochemistry. Although BDGTs have been previously identified in the methanogenMethanomassiliicoccus luminyensis, we now provide direct evidence that Bathyarchaeia also synthesizes BDGTs, definitively establishing this globally abundant group as a natural BDGT producer. Stable isotope probing with13C-bicarbonate shows thatBaizosediminiarchaeumassimilates carbon into BDGTs from both inorganic carbon and lignin. These unique carbon assimilation strategies suggest the biogeochemical importance ofBaizosediminarchaeumin marine carbon cycling and organic matter decomposition. Biogeochemistry
N Nature Microbiology · Sep 17, 2025 Structure of a functional archaellum in Bacteria of the Chloroflexota phylum Motility in Archaea is driven by the archaellum, a rotary ATP-driven machinery unrelated to the bacterial flagellum. To date, archaella have been described exclusively in archaea; however, recent work reported archaellum genes in bacterial strains of the SAR202 clade (Chloroflexota). Here, using MacSyFinder, we show that bona fide archaellum gene clusters are widespread in several members of the Chloroflexota. Analysis of archaellum-encoding loci and Alphafold3-predicted structures show similarity to the archaellum machinery. Using cryo electron microscopy single-particle analysis, we solved the structure of the bacterial archaellum fromLitorilinea aerophilato 2.7 Å. We also show the expression and assembly of this machinery in bacteria and its function in swimming motility. Finally, a phylogenomic analysis revealed two horizontal gene transfer events from euryarchaeal members to Chloroflexota. In summary, our study shows that a functional and assembled archaellum machinery can be exchanged between the two prokaryotic domains. Microbiology Molecular biology
N Nature Microbiology · Sep 11, 2025 Phenazines contribute to microbiome dynamics by targeting topoisomerase IV Phenazines are highly prevalent, natural bioactive substances secreted by microbes. However, their mode of action and potential involvement in shaping microbiomes remain elusive. Here we performed a comprehensive analysis of over 1.35 million bacterial genomes to identify phenazine-producing bacteria distributed across 193 species in 34 families. Analysis of rhizosphere microbiome and public rhizosphere metagenomic datasets revealed that phenazines could shape the microbial community by inhibiting Gram-positive bacteria, which was verified by pairwise interaction assays using Phenazine-1-carboxamide (PCN)-producing Pseudomonas chlororaphis. PCN induced DNA damage in Bacillus subtilis, a model Gram-positive target, where it directly bound to the bacterial topoisomerase IV, inhibiting its decatenation activity and leading to cell death. A two-species consortium of phenazine-producing Pseudomonas and resistant B. subtilis exhibited superior synergistic activity in preventing Fusarium crown rot in wheat plants. This work advances our understanding of a prevalent microbial interaction and its potential for biocontrol. Computational analysis and pairwise assays reveal that bacterial topoisomerase IV is a target of microbially produced phenazines, which informs synthetic-community design to treat fungal crop infection. Antimicrobial resistance Microbial ecology Soil microbiology
N Nature Microbiology · Sep 09, 2025 Learning ecosystem-scale dynamics from microbiome data with MDSINE2 Although dynamical systems models are a powerful tool for analysing microbial ecosystems, challenges in learning these models from complex microbiome datasets and interpreting their outputs limit use. We introduce the Microbial Dynamical Systems Inference Engine 2 (MDSINE2), a Bayesian method that learns compact and interpretable ecosystems-scale dynamical systems models from microbiome timeseries data. Microbial dynamics are modelled as stochastic processes driven by interaction modules, or groups of microbes with similar interaction structure and responses to perturbations, and additionally, noise characteristics of data are modelled. Our open-source software package provides multiple tools for interpreting learned models, including phylogeny/taxonomy of modules, and stability, interaction topology and keystoneness. To benchmark MDSINE2, we generated microbiome timeseries data from two murine cohorts that received faecal transplants from human donors and were then subjected to dietary and antibiotic perturbations. MDSINE2 outperforms state-of-the-art methods and identifies interaction modules that provide insights into ecosystems-scale interactions in the gut microbiome. Bayesian inference Dynamical systems Ecological networks Machine learning
N Nature Microbiology · Sep 08, 2025 Vientovirus capsid protein mimics autoantigens and contributes to autoimmunity in Sjögren’s disease Viral infections are implicated in the pathogenesis of autoimmune diseases, including Sjögren’s disease (SjD), but the mechanisms linking viral antigens to disease development remain poorly understood. To address this, we conducted shotgun metagenomic sequencing of saliva samples from 35 patients with SjD and 25 healthy controls. The salivary virome of the patients with SjD, particularly those with high disease activity, had an expansion ofSiphoviridaebacteriophages and increased eukaryotic viral sequences, including Vientovirus. This virus was associated with lacrimal gland dysfunction and elevated anti-SSA/Ro52 autoantibody levels. Alignment analysis and cross-blocking assay identified molecular mimicry between the Vientovirus capsid protein and the autoantigen SSA/Ro52. Mice immunized with a Vientovirus capsid peptide developed anti-SSA/Ro52 antibodies and showed immunological features resembling those of patients with SjD. These findings highlight distinct virome profiles in SjD and provide mechanistic evidence supporting the role of Vientovirus in triggering autoimmunity through molecular mimicry. Autoimmune diseases Risk factors
N Nature Microbiology · Sep 08, 2025 Multigenerational proteolytic inactivation of restriction upon subtle genomic hypomethylation inPseudomonas aeruginosa Restriction-modification (R-M) systems protect against phage infection by detecting and degrading invading foreign DNA. However, like many prokaryotic anti-phage defences, R-M systems pose a major risk of autoimmunity, exacerbated by the presence of hundreds to thousands of potential cleavage sites in the bacterial genome.Pseudomonas aeruginosastrains experience the temporary inactivation of restriction endonucleases following growth at high temperatures, but the reason and mechanisms for this phenomenon are unknown. Here we report thatP. aeruginosatype I restriction endonuclease is degraded and the methyltransferase is partially degraded, by two Lon-like proteases when replicating at >41 °C. This post-translational regulation prevents self-DNA targeting, which is a risk due to stable genomic hypomethylation, as demonstrated by single-molecule, real-time sequencing and TadA-assistedN6-methyladenosine sequencing. When cells grown at >41 °C are returned to 37 °C, full genomic methylation does not fully recover for up to 60 bacterial generations, and thus restriction activity remains off for the duration. Our findings demonstrate that type I R-M is tightly regulated post-translationally with a long memory effect that ensures genomic stability and mitigates autotoxicity. Bacteriophages Microbial genetics
N Nature Microbiology · Sep 08, 2025 Future ocean warming may cause large reductions inProchlorococcusbiomass and productivity The cyanobacteriumProchlorococcusis Earth’s most abundant photosynthetic organism and crucial to oceanic ecosystems. However, its sensitivity to a changing climate remains unclear. Here we analysed decade-long field measurements using continuous-flow cytometry from our SeaFlow instrument, collecting per-cell chlorophyll fluorescence and size data for ~800 billion phytoplankton cells across the tropical and subtropical Pacific Ocean to quantify the temperature dependence of cell division.Prochlorococcusdivision rates appear primarily determined by temperature, increasing exponentially to 28 °C, then sharply declining. Regional surface water temperatures may exceed this range by the end of the century under both moderate and high warming scenarios. Under these future conditions, our global ocean ecosystem model suggests a possible 17–51% reduction inProchlorococcusproduction in tropical oceans. Even with the inclusion of hypothetical warm-adapted strains, models show significant production declines in the warmest regions, suggesting that thermal adaptation may not prevent negative impacts. These results highlight the potential vulnerability ofProchlorococcus-dependent marine ecosystems to future warming. Climate-change ecology Ecology
N Nature Microbiology · Sep 05, 2025 Single-cell analysis of genetically minimizedSalmonellareveals effector gene cooperation in vivo Bacterial pathogens such asSalmonellaTyphimurium (S.Tm) can deliver large repertoires of effector proteins directly into host cells. Due to the genetic and functional redundancies found in these systems, it has been difficult to determine how individual effector proteins cooperate with one another to elicit pathogenic phenotypes in vivo. To overcome this challenge, targeted genome minimization has been used to identify small effector protein networks sufficient forS.Tm colonization of complex tissues. Here we used mass cytometry to generate a comprehensive map of minimal effector network functions at single-cell resolution. This approach revealed the temporal progression ofS.Tm transmission and uncovered a CD62L+monocyte population as a major bottleneck to cell-to-cell dissemination in the spleen. We further show how cooperation between two effector gene networks acquired during distinct episodes of bacterial evolution has shaped the cellular and tissue tropism of non-typhoidalSalmonellaspecies. Bacterial infection Pathogens
N Nature Microbiology · Sep 05, 2025 Pseudomonas aeruginosasenses exopolysaccharide trails using type IV pili and adhesins during biofilm formation During early stages of biofilm formation,Pseudomonas aeruginosa(Pa) PAO1 can sense exopolysaccharide (EPS) trails of Psl deposited on a surface by previous Pa cells to detect trajectories of other cells and to orchestrate motility. This sensory signal is transduced into cyclic diGMP second messengers, but no known Psl receptors and adhesins participate in signal transduction. Here, using bacteria-secreted Psl trails, glycopolymer-patterned surfaces, longitudinal cell tracking, second messenger dual reporters and genetic mutations targeting EPS binding and surface twitching, we find that Pa is capable of sensing EPS directly through mutually constitutive interactions between type IV pili (T4P)-powered twitching and specific adhesin–EPS bonds. This unanticipated mechanochemical surveillance of the Pa environment, where T4P pull against cell-body localized adhesins interacting with EPS trails, such as mannose-binding CdrA, generates a hybrid, transitional planktonic-to-biofilm population with elevated cyclic diGMP and elevated cyclic AMP, as well as increased motility capable of following EPS trails. These results show a generalizable mechanism of surface chemosensing through mechanosensitive appendages. Bacteriology Biofilms Cellular motility Glycobiology
N Nature Microbiology · Sep 05, 2025 ABradyrhizobiumisolate from a marine diatom induces nitrogen-fixing nodules in a terrestrial legume Biological nitrogen fixation converts atmospheric nitrogen into ammonia, essential to the global nitrogen cycle. While cyanobacterial diazotrophs are well characterized, recent studies have revealed a broad distribution of non-cyanobacterial diazotrophs (NCDs) in marine environments, although their study is limited by poor cultivability. Here we report a previously uncharacterizedBradyrhizobiumisolated from the marine diatomPhaeodactylum tricornutum. Phylogenomic analysis places the strain within photosyntheticBradyrhizobium, suggesting evolutionary adaptations to marine and terrestrial niches. Average nucleotide identity supports its classification as a previously undescribed species. Remarkably, inoculation experiments showed that the isolate induced nitrogen-fixing nodules in theAeschynomene indicalegume, pointing to symbiotic capabilities across ecological boundaries. Pangenome analysis and metabolic predictions indicate that this isolate shares more features with terrestrial photosyntheticBradyrhizobiumthan with marine NCDs. Overall, these findings suggest that symbiotic interactions could evolve across different ecological niches, and raise questions about the evolution of nitrogen fixation and microbe–host interactions. Marine microbiology Water microbiology
N Nature Microbiology · Sep 04, 2025 Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marineBacteroidota Microbial rhodopsins are photoreceptor proteins widely distributed in marine microorganisms that harness light energy and support marine ecosystems. While retinal is typically the sole chromophore in microbial rhodopsins, some proteorhodopsins, which are proton-pumping rhodopsins abundant in the ocean, use carotenoid antennae to transfer light energy to retinal. However, the mechanism by which carotenoids enhance rhodopsin functions remains unclear. Here, using the marineBacteroidotaisolateNonlabens marinusS1-08T, we reconstituted complexes of rhodopsins with the carotenoid myxol and detected energy transfer to retinal in both proteorhodopsin and chloride ion-pumping rhodopsin. Carotenoid binding facilitated light harvesting and accelerated the photocycle, thereby improving the light utilization efficiency of proteorhodopsin. Cryogenic electron microscopy structural analysis further revealed the molecular architecture of the carotenoid–rhodopsin complexes. The ability to bind carotenoids is conserved in rhodopsins of the marine-dominant phylumBacteroidota, which are widely transcribed in the photic zone. These findings reveal how carotenoids enhance rhodopsin functions in marineBacteroidota. Ion transport Microbial ecology
N Nature Microbiology · Aug 22, 2025 SARS-CoV-2 infection induces pro-fibrotic and pro-thrombotic foam cell formation COVID-19 and long COVID are characterized by a dysregulated immune response. However, the role of macrophages during viral infection is poorly defined. Here we demonstrate that SARS-CoV-2 infection results in increased macrophage numbers and extensive formation of enlarged lipid-laden macrophages or foam cells using humanized mice, rhesus macaques and post-mortem human lung tissue. Notably, infection by other coronaviruses tested, SARS-CoV-1, MERS-CoV and two bat coronaviruses (SHC014-CoV or WIV1-CoV), did not result in macrophage proliferation or foam cell formation. Foam cells in SARS-CoV-2-infected human lung tissue display a pro-fibrotic and pro-thrombotic phenotype as they are enriched for genes associated with platelet activation and aggregation, as well as extracellular matrix organization and collagen synthesis. After viral clearance, macrophage numbers remain elevated, and lung fibrosis and thrombi persist. Importantly, we show that pre-exposure prophylaxis or early treatment with a SARS-CoV-2 antiviral, EIDD-2801, prevents increases in macrophage cell numbers and foam cell formation, and reduces fibrosis markers. These observations highlight the contribution of macrophages to lung inflammation and tissue injury leading to the pulmonary fibrosis observed in COVID-19 patients. SARS-CoV-2 Viral infection
N Nature Microbiology · Aug 21, 2025 Ume6 protein complexes connect morphogenesis, adherence and hypoxic genes to shapeCandida albicansbiofilm architecture Biofilms of the fungal pathogenCandida albicanscan form on implanted medical devices and contribute to fungal virulence and are recalcitrant to antifungal therapy. The transcription factor Ume6 directs hyphal cell elongation and thus promotes biofilm formation inC. albicans. However, how exactly this key biofilm and virulence regulator functions has remained unclear. Here RNA sequencing and chromatin immunoprecipitation with sequencing data show that Ume6 binds to and activates multiple biofilm-relevant genes. Ume6-associated sequence motifs correspond to binding sites for biofilm master regulators Efg1 and Ndt80, and hypoxic response regulator Upc2. Co-immunoprecipitation assays show the existence of Ume6–Efg1, Ume6–Ndt80 and Ume6–Upc2 protein complexes. Promoter binding of Ume6 is partially dependent upon Efg1, Ndt80 or Upc2, as is Ume6 target gene activation, thus indicating that the protein complexes function to drive Ume6–target gene interaction. Ume6 therefore acts as a bridge that connects the hyphal morphogenesis and adherence genes that shape biofilm architecture and the hypoxic response genes required for growth in the low-oxygen biofilm environment. These findings are vital for our understanding of the pathobiology ofC. albicansand could open the way to new treatment options. Biofilms Fungi
N Nature Microbiology · Aug 20, 2025 Aquarius helicase facilitates HIV-1 integration into R-loop enriched genomic regions HIV-1 integration into host chromosomes, essential for viral replication, is catalysed by viral integrase (IN). IN recurrently targets intronic regions of transcriptionally active genes, but a detailed understanding of this process is still unclear. Here, using ex vivo activated human primary CD4+T cells, we find that genomic RNA:DNA hybrids (R-loops) preferentially map to intronic regions of active genes that are typical HIV-1 integration sites. IN binds R-loops and their resolution enhances viral integration in vitro. We identify Aquarius (AQR), the splicing RNA helicase of the pentameric intron binding complex (IBC), which associates with IN and show that its RNA:DNA helicase activity promotes integration into hybrid substrates in vitro. Knockout ofAQRin primary CD4+T cells impaired overall integration efficiency, while sequencing of remaining integrations mapped them to intergenic and R-loop distal regions. These findings may have important implications for HIV-1 latency and reactivation and may thus identify novel therapeutic targets. Nuclear organization Retrovirus
N Nature Microbiology · Aug 19, 2025 Aggresomes protect mRNA under stress inEscherichia coli Membraneless droplets formed through liquid–liquid phase separation of ribonucleoprotein particles contribute to mRNA storage in eukaryotic cells. How such aggresomes contribute to mRNA dynamics under stress and their functional role are less understood in bacteria. Here we used multiple approaches including live-cell imaging, polymer physics modelling and transcriptomics to show that prolonged stress leading to ATP depletion inEscherichia coliresults in increased aggresome formation, compaction and selective mRNA enrichment within these aggresomes. Longer transcripts accumulate more in aggresomes than in the cytosol. Mass spectrometry and mutagenesis studies showed that mRNA ribonucleases are excluded from aggresomes due to electrostatic repulsion arising from their negative surface charges. Experiments with fluorescent reporters and disruption of aggresome formation showed that mRNA storage within aggresomes promoted rapid translation reactivation and is associated with reduced lag phases during growth after stress removal. Our findings suggest that mRNA storage within aggresomes confers an advantage for bacterial survival and recovery from stress. Bacterial development Molecular biophysics
N Nature Microbiology · Aug 18, 2025 A defined microbial community reproduces attributes of fine flavour chocolate fermentation Cocoa (Theobroma cacaoL.) bean fermentation is a spontaneous process involving interactions between abiotic and biotic factors that contribute to the final flavours of chocolate. Understanding these underlying interactions could enable desired flavour profiles to be reproduced under controlled conditions. Here, using bean fermentation samples from Colombian farms, we established that pH, temperature and microbiota composition, including both bacteria and fungi, influence key flavour attributes of premium chocolate. Genome-resolved metagenomics revealed that metabolic traits necessary for the development of the flavour profile of chocolate are redundantly present in the fermentation microbial community. Using a defined and metabolically competent microbial consortium, the feasibility of replicating fine flavour attributes of chocolate under controlled conditions was confirmed via omics, metabolic networks and a trained tasting panel. Our results provide the basis for the design of fermentation starters to robustly reproduce fine chocolate characteristics. Applied microbiology Microbiome
N Nature Microbiology · Aug 15, 2025 Ecophysiology and global dispersal of the freshwater SAR11-IIIb genusFontibacterium The SAR11-IIIb genusFontibacteriumwithin the order‘Ca. Pelagibacterales’ is recognized for its ubiquitous presence in freshwater environments. However, cultivation limitations have hampered deeper ecophysiological understanding of this genus, with most data limited to lakes in the Northern Hemisphere. Here we present seven isolates representing two previously undescribed species, along with 93 high-quality metagenome-assembled genomes (MAGs) derived from a global survey across five continents. Phylogenomic analysis revealed 16 species forming nine distinct biogeographic clusters, indicating speciation patterns linked to water temperature and latitude. We observed endemic species restricted to African lakes, and quasi-endemic species confined to the Northern or Southern Hemisphere, which co-exist alongside cosmopolitan species. Metabolic profiling and growth experiments uncovered species- and strain-specific adaptations for nutrient uptake, along with unique pathways for sulfur metabolism. These findings provide a global-scale genomic and ecological overview for this underexplored lineage of freshwater SAR11. Bacterial genomics Biogeography Freshwater ecology Microbial ecology Water microbiology
