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 biology mouse experiments
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 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 biology mouse experiments
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 biology
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 CRISPR Genomics Microbiology Evolution
