Nature Microbiology

Article	Citations
Metabolic sensing tips the balance of drug tolerance in fungal meningitis	451
Rebound virus in the cerebrospinal fluid reveals a possible HIV-1 reservoir	418
Molecular factors shaping whether HCMV infection is productive or latent	326
Flipping the magic switch to persistence via GTP depletion	265
Prodrug florfenicol amine is activated by intrinsic resistance to target Mycobacterium abscessus	242
Climate extremes disrupt fungal–bacterial interactions	229
A phosphotransferase system promotes growth of zoonotic Streptococcus species in the brain	226
Gut microbial enzymes shape the health benefits of dietary phytonutrients	218
Double recombinant nOPV2 vaccine	211
Horizontal gene transfer explains unusual traits of Armillaria fungi	209
Dietary exclusion of major food groups shapes the gut microbiome and may influence health	207
Sickle cell trait enhances malaria transmission	207
Mycobacterium abscessus pathogenesis identified by phenogenomic analyses	202
Microbiome association with coral growth and survival	195
Sulfated bile acid produced by a human gut commensal alleviates paediatric sepsis in mice	190
A dynamic subpopulation of CRISPR–Cas overexpressers allows Streptococcus pyogenes to rapidly respond to phage	190
Bridging classical and continuous directed evolution	189
Salmonella-derived haem inhibits macrophage phagocytosis and promotes infection in mice	182
Mosquitoes provide a transmission route between possums and humans for Buruli ulcer in southeastern Australia	179
Wall teichoic acids regulate peptidoglycan synthesis to maintain rod shape in Bacillus subtilis	178
Host range, transmissibility and antigenicity of a pangolin coronavirus	165
Single mutation makes Escherichia coli an insect mutualist	161
Explainable artificial intelligence evolves antimicrobial peptides	157
A high-throughput and low-waste viability assay for microbes	154
Cytoplasmic contractile injection systems mediate cell death in Streptomyces	151

Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria	149
Structure of a functional archaellum in Bacteria of the Chloroflexota phylum	149
The IFIT2–IFIT3 antiviral complex targets short 5’ untranslated regions on viral mRNAs for translation inhibition	149
Mechanistic basis for potent neutralization of Sin Nombre hantavirus by a human monoclonal antibody	148
Assessing critical thresholds in terrestrial microbiomes	145
Rational design of a hospital-specific phage cocktail to treat Enterobacter cloacae complex infections	143
The Mycobacterium tuberculosis protein O-phosphorylation landscape	138
Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division	137
Recent gene selection and drug resistance underscore clinical adaptation across Candida species	136
Candida albicans extracellular vesicles trigger type I IFN signalling via cGAS and STING	135
The Parkinson’s disease drug entacapone disrupts gut microbiome homeostasis via iron sequestration	134
Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains	134
The structure of the complete extracellular bacterial flagellum reveals the mechanism of flagellin incorporation	130
The fast-evolving FIKK kinase family of Plasmodium falciparum can be inhibited by a single compound	130
Bacterial cell division protein FtsZ complexes with a phage protein to activate bacterial immunity	129
Aspergillus fumigatus dsRNA virus promotes fungal fitness and pathogenicity in the mammalian host	128
Organ-on-chip models for infectious disease research	128
OPENPichia: licence-free Komagataella phaffii chassis strains and toolkit for protein expression	128
Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan	128
Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults	127
Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome	126
CRISPR-influenced symbiosis	124
Call for papers on the clinical microbiome	123
Prioritizing mentorship	123
Mineral-eating microorganisms at extinct hydrothermal vents	123
Blockade of endothelin receptors mitigates SARS-CoV-2-induced osteoarthritis	122
Archaeal symbioses all the way down	121
The complex path towards herpesvirus vaccines	120
Bacteroides fragilis uses toxins for gut success	119
Coronavirus sampling and surveillance in bats from 1996–2019: a systematic review and meta-analysis	117
Exceeding expectations out in the cold with Colwellia	116
Decoding the impact of nuclear organization on antigenic variation in parasites	114
Author Correction: A roadmap for equitable reuse of public microbiome data	113
Nuclease–NTPase antiphage defence systems use conserved molecular features to control bacterial immunity	112
Kaposi’s sarcoma-associated herpesvirus induces mitochondrial fission to evade host immune responses and promote viral production	110
Extracellular vesicles block viral entryways	109
Synthesis of lipid-linked precursors of the bacterial cell wall is governed by a feedback control mechanism in Pseudomonas aeruginosa	108
Rational attenuation of RNA viruses with zinc finger antiviral protein	107
Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis	107
Streptomyces polyketides mediate bacteria–fungi interactions across soil environments	106
Microbial collagenase activity is linked to oral–gut translocation in advanced chronic liver disease	104
Structure-guided design of a synthetic bile acid that inhibits Clostridioides difficile TcdB toxin	104
Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation	103
Risk–reward trade-off during carbon starvation generates dichotomy in motility endurance among marine bacteria	103
Initial sites of SIV rebound after antiretroviral treatment cessation in rhesus macaques	101
Expanding known viral diversity in the healthy infant gut	101
Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function	99
Pseudomonas syringae subpopulations cooperate by coordinating flagellar and type III secretion spatiotemporal dynamics to facilitate plant infection	98
Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration	97
Skin androgens regulate Staphylococcus aureus pathogenicity via quorum sensing	94

Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment	94
All-trans retinoic acid suppresses systemic inflammation induced by severe fever with thrombocytopenia syndrome virus in mice	93
SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome	92
Transforming tuberculosis diagnosis	92
Candida auris skin tropism and antifungal resistance are mediated by carbonic anhydrase Nce103	90
Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study	89
Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes	87
Discovery of an orally active benzoxaborole prodrug effective in the treatment of Chagas disease in non-human primates	87
Therapeutics for COVID-19	87
Phages with a broad host range are common across ecosystems	86
Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut	86
Interkingdom sensing of fungal tyrosol promotes bacterial antifungal T6SS activity in the murine gut	86
Dietary fibre counters the oncogenic potential of colibactin-producing Escherichia coli in colorectal cancer	85
Parasite and vector circadian clocks mediate efficient malaria transmission	85
A nitrogen-fixing bacterium forms symbioses on land and at sea	85
SARS and synapses	84
Hunting emerging viruses through participatory community science	83
Anoxia activates CRISPR–Cas immunity in the mouse intestine	82
The gut–liver axis in HCV infection	81
Placental Streptococcus agalactiae DNA is associated with neonatal unit admission and foetal pro-inflammatory cytokines in term infants	81
Voices of our past editors	81
Conserved CD4+ T cell staphylococcal and streptococcal epitopes enable broad-acting vaccines in mice	80
A microbiologist’s voyage from the lab to The Atlantic	79
Stuck on you Giardia	79
SARS-CoV-2 infection induces pro-fibrotic and pro-thrombotic foam cell formation	79
From farm to factory to fork	79
Combining antibiotics to tackle antimicrobial resistance	78
Outbreak dynamics of foodborne pathogen Vibrio parahaemolyticus over a seventeen year period implies hidden reservoirs	78
Switching on cyclic di-GMP heterogeneity in Pseudomonas aeruginosa biofilms	78
Genome-resolved metagenomics reveals microbiome diversity across 48 tick species	78
Cell envelope diversity and evolution across the bacterial tree of life	77
CryoEM reveals that ribosomes in microsporidian spores are locked in a dimeric hibernating state	77
An expanded metabolic pathway for androgen production by commensal bacteria	77
Bacteriophages avoid autoimmunity from cognate immune systems as an intrinsic part of their life cycles	76
Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia	76
Mapping in-cell protein contact sites reveals hijacking of paraspeckles during influenza A virus infection	75
Combined phage therapy and faecal microbiota transplantation to treat recurrent urinary tract infection: a case series	75
Mining the microbiota for antibiotics	74
Clarifying objectives to strengthen wastewater-based AMR surveillance	74
Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants	74
Bacteria can shed a layer when phages turn up the heat	74
Mycobacterium tuberculosis as teacher	74
Safety and immunogenicity of a prefusion non-stabilized spike protein mRNA COVID-19 vaccine: a phase I trial	73
STREAM-lining guidelines for microbiome research	73
Publisher Correction: Toxoplasma gondii VIP1 mediates parasitophorous vacuole–host endoplasmic reticulum interactions to facilitate parasite development	72
Identified receptors shed light on Epstein–Barr virus infection	72
Guiding phage therapy with genomic surveillance	70
Siderophores mediate antibiotic resistance	70
A year of microbiology	70
A framework for automated scalable designation of viral pathogen lineages from genomic data	69
TOLLIP inhibits lipid accumulation and the integrated stress response in alveolar macrophages to control Mycobacterium tuberculosis infection	69
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism	69
Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters	69
Decreased cytoplasmic crowding via inhibition of ribosome biogenesis can trigger Candida albicans filamentous growth	69
Early-life colonization by aromatic-lactate-producing bifidobacteria lowers the risk of allergic sensitization	69
Antiviral GHP-88310 blocks contact-mediated and airborne transmission in a ferret model of measles-like disease	68
Epitope-focused discovery of SARS-CoV-2 antibodies that potently neutralize Omicron variants	68
Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria	68
Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts	68
Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine	67
Gut microbiome-mediated transformation of dietary phytonutrients is associated with health outcomes	67
Gut microbial factors predict disease severity in a mouse model of multiple sclerosis	67
GprC of the nematode-trapping fungus Arthrobotrys flagrans activates mitochondria and reprograms fungal cells for nematode hunting	66
The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice	65
Escherichia coli integrates chemotaxis and quorum sensing pathways in vivo	65
Metabolic modelling reveals the aging-associated decline of host–microbiome metabolic interactions in mice	65
Bacteria modulate microalgal aging physiology through the induction of extracellular vesicle production to remove harmful metabolites	65
Human microbiome myths and misconceptions	64
Environmental stress mediates groundwater microbial community assembly	64
Growth rate is modulated by monitoring cell wall precursors in Bacillus subtilis	64
CD8+ T cell depletion does not induce an expansion of viral reservoir in HIV model	64
Parabacteroides distasonis uses dietary inulin to suppress NASH via its metabolite pentadecanoic acid	64
mRNA-encoded Cas13 can be used to treat dengue infections in mice	64
The cell biology of archaea	64
Migrant health matters	63
Retracing a tangled tree of archaeal evolution	63
We must learn from past outbreaks	63
Shining light on the coral photosymbiont family Symbiodiniaceae	63
A phage-encoded anti-CRISPR protein co-opts host enolase to prevent type III CRISPR immunity	63
A method to detect origin of transfer sequences for plasmid conjugation	63

Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial	63
Addressing gaps in author and reviewer gender diversity	62
Identifying an evolutionary origin for morbilliviruses in bats	62
Author Correction: Respiratory immunization using antibiotic-inactivated Bordetella pertussis confers T cell-mediated protection against nasal infection in mice	61
Multinational epidemiological analysis of oral human papillomavirus incidence in 3,137 men	61
Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection	60
Benchmarking shotgun metagenomics	60
Evolved phage cocktails outsmart biofilm defences	60
SARS-CoV-2 Africa dashboard for real-time COVID-19 information	60
Prioritizing prenatal screening to prevent Chagas disease	60
The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate	60
Amplifying diverse voices in microbiology	60
A haem-sequestering plant peptide promotes iron uptake in symbiotic bacteria	59
Parasex generates highly recombinant progeny in Candida albicans with increased virulence	58
Comprehensive transcription terminator atlas for Bacillus subtilis	58
Diet switch pre-vaccination improves immune response and metabolic status in formerly obese mice	57
Molecular organization of the New World arenavirus spike glycoprotein complex	57
Phase transition of GvpU regulates gas vesicle clustering in bacteria	57
Genomic heterogeneity of NAD(P)H dehydrogenase predisposes Cryptosporidium to clofazimine resistance	56
AMR, One Health and the environment	56
Metabolites from intact phage-infected Synechococcus chemotactically attract heterotrophic marine bacteria	56
Tecovirimat is effective against human monkeypox virus in vitro at nanomolar concentrations	56
Gut bacteria degrade purines via the 2,8-dioxopurine pathway	55
Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes	55
Preclinical evaluation of the SARS-CoV-2 Mpro inhibitor RAY1216 shows improved pharmacokinetics compared with nirmatrelvir	54
Staphylococcal virulence factor HlgB targets the endoplasmic-reticulum-resident E3 ubiquitin ligase AMFR to promote pneumonia	54
Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen	54
Taurolithocholic acid protects against viral haemorrhagic fever via inhibition of ferroptosis	54
Characterizing extracellular vesicles of human fungal pathogens	54
Sulfated glycosaminoglycans are host epithelial cell targets of the Candida albicans toxin candidalysin	54
Dairy cows develop protective immunity against reinfection with bovine H5N1 influenza virus	54
Iron-limitation light switch	54
BacterAI maps microbial metabolism without prior knowledge	54
Chromosome architecture in an archaeal species naturally lacking structural maintenance of chromosomes proteins	53
Microbes and the water nexus	53
Understanding emerging and re-emerging viruses to facilitate pandemic preparedness	53
Publisher Correction: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission	53
Translating between science and politics as a government adviser	53
Integrons are anti-phage defence libraries in Vibrio parahaemolyticus	52
Remote control designer probiotics	52
Metagenomic characterization of viruses and mobile genetic elements associated with the DPANN archaeal superphylum	51
Hunting for new lineages and mechanisms of life	51
Communicating microbiology effectively	51
Bacteroides fragilis toxin promotes gall bladder cancer in mice	51
Colonic goblet cell-associated antigen passages mediate physiologic and beneficial translocation of live gut bacteria in preweaning mice	51
MAP-X reveals distinct protein complex dynamics across Plasmodium falciparum blood stages	51
Bacteria–phage coevolution drives variation in bacterial wilt disease incidence via resistance–virulence trade-offs	50
Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain	50
Enterococcus faecalis-derived adenine enhances enterohaemorrhagic Escherichia coli Type 3 Secretion System-dependent virulence	50
Nasal Staphylococcus aureus carriage promotes depressive behaviour in mice via sex hormone degradation	50
Cooperative virulence via the collective action of secreted pathogen effectors	50
Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea	50
Targeting the mosquito prefoldin–chaperonin complex blocks Plasmodium transmission	50
A high-quality genome compendium of the human gut microbiome of Inner Mongolians	49
Exploiting the fitness cost of metallo-β-lactamase expression can overcome antibiotic resistance in bacterial pathogens	49
Dipeptidase 1 is a functional receptor for a porcine coronavirus	49
The GATE glycoprotein complex enhances human cytomegalovirus entry in endothelial cells	49
Surface expression of antitoxin on engineered bacteria neutralizes genotoxic colibactin in the gut	49
Metabolic reprogramming enhances the susceptibility of multidrug- and carbapenem-resistant bacteria to antibiotics	49
Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances	48
Introducing Microbe Matters	48
Author Correction: Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host–plant interactions	48
Understanding the biology of monkeypox virus to prevent future outbreaks	48
Acquired amphotericin B resistance leads to fitness trade-offs that can be mitigated by compensatory evolution in Candida auris	48
The host–parasite–virus triad	48
Spatial transcriptomics maps host–gut microbiome biogeography at high resolution	48
Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota	48
Factors associated with oral HPV infection among a large multinational cohort of men	48
Talented microbes unlatch peatland carbon	47
Persistent viral RNA and protein contribute to post-acute pathology	47
Moving from hype to hope in diet–microbiome interactions	47
Use microbes to tackle food insecurity	47
Microbiome alterations in autism spectrum disorder	47
Identifying rare and active species that drive carbon turnover in complex microbiotas	47
Microplastic research must consider microbes	47
Faecalibacterium prausnitzii enzyme reprograms PD-L1 trafficking and sensitizes colorectal cancer to immunotherapy in mice	46
Small organisms with big climate impact	46
Microbial ethanol production in patients with auto-brewery syndrome	46
Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever	46
Evolution of SARS-CoV-2 in the murine central nervous system drives viral diversification	45
Bacillus subtilis cells can escape biofilms by producing a hydrogel that ejects them	45
scRNA-seq reveals transcriptional plasticity of var gene expression in Plasmodium falciparum for host immune avoidance	45
A non-human primate model for human norovirus infection	45
DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms	45
Viral biogeography of the mammalian gut and parenchymal organs	44
Intestinal crypt microbiota modulates intestinal stem cell turnover and tumorigenesis via indole acetic acid	44
Parkinson’s disease kinase LRRK2 coordinates a cell-intrinsic itaconate-dependent defence pathway against intracellular Salmonella	44
Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota	44
Structure and substrate recognition by the bacterial twin-arginine translocation (Tat) core complex	43
Author Correction: Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut	43
Mycobiota and diet-derived fungal xenosiderophores promote Salmonella gastrointestinal colonization	43
Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency	43
Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought	43
Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda	43
FungAMR: a comprehensive database for investigating fungal mutations associated with antimicrobial resistance	42