Nature Microbiology

Article	Citations
Metabolic sensing tips the balance of drug tolerance in fungal meningitis	626
Rebound virus in the cerebrospinal fluid reveals a possible HIV-1 reservoir	434
Molecular factors shaping whether HCMV infection is productive or latent	377
Flipping the magic switch to persistence via GTP depletion	345
Prodrug florfenicol amine is activated by intrinsic resistance to target Mycobacterium abscessus	310
Salmonella-derived haem inhibits macrophage phagocytosis and promotes infection in mice	242
Mosquitoes provide a transmission route between possums and humans for Buruli ulcer in southeastern Australia	241
Climate extremes disrupt fungal–bacterial interactions	215
Therapeutic efficacy of monoclonal antibodies and antivirals against SARS-CoV-2 Omicron BA.1 in Syrian hamsters	210
The fast-evolving FIKK kinase family of Plasmodium falciparum can be inhibited by a single compound	208
A phosphotransferase system promotes growth of zoonotic Streptococcus species in the brain	203
Explainable artificial intelligence evolves antimicrobial peptides	197
Gut microbial enzymes shape the health benefits of dietary phytonutrients	197
Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division	196
Double recombinant nOPV2 vaccine	191
Mechanistic basis for potent neutralization of Sin Nombre hantavirus by a human monoclonal antibody	190
Rational design of a hospital-specific phage cocktail to treat Enterobacter cloacae complex infections	188
Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria	184
A dynamic subpopulation of CRISPR–Cas overexpressers allows Streptococcus pyogenes to rapidly respond to phage	183
Single mutation makes Escherichia coli an insect mutualist	173
The Mycobacterium tuberculosis protein O-phosphorylation landscape	173
Assessing critical thresholds in terrestrial microbiomes	171
The structure of the complete extracellular bacterial flagellum reveals the mechanism of flagellin incorporation	171
Horizontal gene transfer explains unusual traits of Armillaria fungi	169
Microbiome association with coral growth and survival	164

Sickle cell trait enhances malaria transmission	163
Dietary exclusion of major food groups shapes the gut microbiome and may influence health	159
A high-throughput and low-waste viability assay for microbes	151
Host range, transmissibility and antigenicity of a pangolin coronavirus	150
Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains	149
Organ-on-chip models for infectious disease research	148
Cytoplasmic contractile injection systems mediate cell death in Streptomyces	144
Mycobacterium abscessus pathogenesis identified by phenogenomic analyses	143
Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults	142
Bridging classical and continuous directed evolution	141
The IFIT2–IFIT3 antiviral complex targets short 5’ untranslated regions on viral mRNAs for translation inhibition	139
Wall teichoic acids regulate peptidoglycan synthesis to maintain rod shape in Bacillus subtilis	139
Aspergillus fumigatus dsRNA virus promotes fungal fitness and pathogenicity in the mammalian host	138
Candida albicans extracellular vesicles trigger type I IFN signalling via cGAS and STING	134
Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome	133
The Parkinson’s disease drug entacapone disrupts gut microbiome homeostasis via iron sequestration	131
Recent gene selection and drug resistance underscore clinical adaptation across Candida species	127
OPENPichia: licence-free Komagataella phaffii chassis strains and toolkit for protein expression	126
Structure of a functional archaellum in Bacteria of the Chloroflexota phylum	125
Sulfated bile acid produced by a human gut commensal alleviates paediatric sepsis in mice	124
Mineral-eating microorganisms at extinct hydrothermal vents	123
Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan	123
CRISPR-influenced symbiosis	123
Prioritizing mentorship	122
Call for papers on the clinical microbiome	121
Blockade of endothelin receptors mitigates SARS-CoV-2-induced osteoarthritis	120
Extracellular vesicles block viral entryways	119
Archaeal symbioses all the way down	117
Bacteroides fragilis uses toxins for gut success	116
The complex path towards herpesvirus vaccines	116
Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2	116
Rational attenuation of RNA viruses with zinc finger antiviral protein	115
Structure-guided design of a synthetic bile acid that inhibits Clostridioides difficile TcdB toxin	115
Coronavirus sampling and surveillance in bats from 1996–2019: a systematic review and meta-analysis	113
Decoding the impact of nuclear organization on antigenic variation in parasites	111
Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration	111
Candida auris skin tropism and antifungal resistance are mediated by carbonic anhydrase Nce103	110
Pseudomonas syringae subpopulations cooperate by coordinating flagellar and type III secretion spatiotemporal dynamics to facilitate plant infection	109
Microbial collagenase activity is linked to oral–gut translocation in advanced chronic liver disease	107
Risk–reward trade-off during carbon starvation generates dichotomy in motility endurance among marine bacteria	107
Nuclease–NTPase antiphage defence systems use conserved molecular features to control bacterial immunity	106
Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function	106
Exceeding expectations out in the cold with Colwellia	106
Synthesis of lipid-linked precursors of the bacterial cell wall is governed by a feedback control mechanism in Pseudomonas aeruginosa	104
Skin androgens regulate Staphylococcus aureus pathogenicity via quorum sensing	102
Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment	102
Author Correction: A roadmap for equitable reuse of public microbiome data	99
Initial sites of SIV rebound after antiretroviral treatment cessation in rhesus macaques	99
SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome	98
Transforming tuberculosis diagnosis	98

Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation	98
Expanding known viral diversity in the healthy infant gut	98
Kaposi’s sarcoma-associated herpesvirus induces mitochondrial fission to evade host immune responses and promote viral production	97
Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis	95
Streptomyces polyketides mediate bacteria–fungi interactions across soil environments	94
Placental Streptococcus agalactiae DNA is associated with neonatal unit admission and foetal pro-inflammatory cytokines in term infants	93
The gut–liver axis in HCV infection	92
Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut	91
Characterization of inositol lipid metabolism in gut-associated Bacteroidetes	88
From farm to factory to fork	87
Voices of our past editors	87
Hunting emerging viruses through participatory community science	85
Discovery of an orally active benzoxaborole prodrug effective in the treatment of Chagas disease in non-human primates	84
Bacteriophages avoid autoimmunity from cognate immune systems as an intrinsic part of their life cycles	83
Dietary fibre counters the oncogenic potential of colibactin-producing Escherichia coli in colorectal cancer	83
A microbiologist’s voyage from the lab to The Atlantic	82
CryoEM reveals that ribosomes in microsporidian spores are locked in a dimeric hibernating state	80
Genome-resolved metagenomics reveals microbiome diversity across 48 tick species	79
Cell envelope diversity and evolution across the bacterial tree of life	79
Phages with a broad host range are common across ecosystems	78
Anoxia activates CRISPR–Cas immunity in the mouse intestine	78
Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes	78
Conserved CD4+ T cell staphylococcal and streptococcal epitopes enable broad-acting vaccines in mice	78
Therapeutics for COVID-19	78
A nitrogen-fixing bacterium forms symbioses on land and at sea	77
Interkingdom sensing of fungal tyrosol promotes bacterial antifungal T6SS activity in the murine gut	77
SARS-CoV-2 infection induces pro-fibrotic and pro-thrombotic foam cell formation	76
SARS and synapses	76
An expanded metabolic pathway for androgen production by commensal bacteria	75
Parasite and vector circadian clocks mediate efficient malaria transmission	75
Outbreak dynamics of foodborne pathogen Vibrio parahaemolyticus over a seventeen year period implies hidden reservoirs	75
Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study	74
Mycobacterium tuberculosis as teacher	74
Combining antibiotics to tackle antimicrobial resistance	73
Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants	72
Escherichia coli integrates chemotaxis and quorum sensing pathways in vivo	72
Switching on cyclic di-GMP heterogeneity in Pseudomonas aeruginosa biofilms	72
Harnessing the microbiome to prevent global biodiversity loss	72
Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia	72
Human microbiome myths and misconceptions	71
Bacteria can shed a layer when phages turn up the heat	71
Safety and immunogenicity of a prefusion non-stabilized spike protein mRNA COVID-19 vaccine: a phase I trial	71
Mining the microbiota for antibiotics	71
STREAM-lining guidelines for microbiome research	71
Identified receptors shed light on Epstein–Barr virus infection	71
Epitope-focused discovery of SARS-CoV-2 antibodies that potently neutralize Omicron variants	70
Publisher Correction: Toxoplasma gondii VIP1 mediates parasitophorous vacuole–host endoplasmic reticulum interactions to facilitate parasite development	70
A year of microbiology	70
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism	69
A framework for automated scalable designation of viral pathogen lineages from genomic data	69
Gut microbial factors predict disease severity in a mouse model of multiple sclerosis	69
TOLLIP inhibits lipid accumulation and the integrated stress response in alveolar macrophages to control Mycobacterium tuberculosis infection	69
Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria	68
mRNA-encoded Cas13 can be used to treat dengue infections in mice	68
Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters	68
The cell biology of archaea	68
Siderophores mediate antibiotic resistance	67
The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice	67
Bacteria modulate microalgal aging physiology through the induction of extracellular vesicle production to remove harmful metabolites	67
Guiding phage therapy with genomic surveillance	66
Decreased cytoplasmic crowding via inhibition of ribosome biogenesis can trigger Candida albicans filamentous growth	66
GprC of the nematode-trapping fungus Arthrobotrys flagrans activates mitochondria and reprograms fungal cells for nematode hunting	66
Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts	65
Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine	65
Early-life colonization by aromatic-lactate-producing bifidobacteria lowers the risk of allergic sensitization	65
Parabacteroides distasonis uses dietary inulin to suppress NASH via its metabolite pentadecanoic acid	65
Environmental stress mediates groundwater microbial community assembly	64
Metabolic modelling reveals the aging-associated decline of host–microbiome metabolic interactions in mice	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	63
Gut microbiome-mediated transformation of dietary phytonutrients is associated with health outcomes	63
Migrant health matters	62
Amplifying diverse voices in microbiology	62
A method to detect origin of transfer sequences for plasmid conjugation	62
Shining light on the coral photosymbiont family Symbiodiniaceae	62
Phase transition of GvpU regulates gas vesicle clustering in bacteria	61
We must learn from past outbreaks	61
Retracing a tangled tree of archaeal evolution	60
Identifying an evolutionary origin for morbilliviruses in bats	60
The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate	60

Author Correction: Respiratory immunization using antibiotic-inactivated Bordetella pertussis confers T cell-mediated protection against nasal infection in mice	59
Parasex generates highly recombinant progeny in Candida albicans with increased virulence	59
Addressing gaps in author and reviewer gender diversity	59
Genome-wide protein–DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase	58
Preclinical evaluation of the SARS-CoV-2 Mpro inhibitor RAY1216 shows improved pharmacokinetics compared with nirmatrelvir	58
BacterAI maps microbial metabolism without prior knowledge	57
Dairy cows develop protective immunity against reinfection with bovine H5N1 influenza virus	57
Multinational epidemiological analysis of oral human papillomavirus incidence in 3,137 men	57
Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen	56
Benchmarking shotgun metagenomics	56
Staphylococcal virulence factor HlgB targets the endoplasmic-reticulum-resident E3 ubiquitin ligase AMFR to promote pneumonia	56
Prioritizing prenatal screening to prevent Chagas disease	56
Taurolithocholic acid protects against viral haemorrhagic fever via inhibition of ferroptosis	55
Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection	55
Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes	55
Tecovirimat is effective against human monkeypox virus in vitro at nanomolar concentrations	55
Diet switch pre-vaccination improves immune response and metabolic status in formerly obese mice	55
Gut bacteria degrade purines via the 2,8-dioxopurine pathway	54
Comprehensive transcription terminator atlas for Bacillus subtilis	54
Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial	54
Inactivated whole-virion vaccine BBV152/Covaxin elicits robust cellular immune memory to SARS-CoV-2 and variants of concern	54
SARS-CoV-2 Africa dashboard for real-time COVID-19 information	54
A haem-sequestering plant peptide promotes iron uptake in symbiotic bacteria	54
Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon	53
Characterizing extracellular vesicles of human fungal pathogens	53
AMR, One Health and the environment	53
A phage-encoded anti-CRISPR protein co-opts host enolase to prevent type III CRISPR immunity	53
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway	53
Genomic heterogeneity of NAD(P)H dehydrogenase predisposes Cryptosporidium to clofazimine resistance	53
Sulfated glycosaminoglycans are host epithelial cell targets of the Candida albicans toxin candidalysin	52
Iron-limitation light switch	52
Molecular organization of the New World arenavirus spike glycoprotein complex	52
Metabolites from intact phage-infected Synechococcus chemotactically attract heterotrophic marine bacteria	52
Microbes and the water nexus	51
Translating between science and politics as a government adviser	51
Publisher Correction: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission	50
Remote control designer probiotics	50
Understanding emerging and re-emerging viruses to facilitate pandemic preparedness	50
Metagenomic characterization of viruses and mobile genetic elements associated with the DPANN archaeal superphylum	50
MAP-X reveals distinct protein complex dynamics across Plasmodium falciparum blood stages	49
Exploiting the fitness cost of metallo-β-lactamase expression can overcome antibiotic resistance in bacterial pathogens	49
Chromosome architecture in an archaeal species naturally lacking structural maintenance of chromosomes proteins	49
Enterococcus faecalis-derived adenine enhances enterohaemorrhagic Escherichia coli Type 3 Secretion System-dependent virulence	49
Surface expression of antitoxin on engineered bacteria neutralizes genotoxic colibactin in the gut	49
Nasal Staphylococcus aureus carriage promotes depressive behaviour in mice via sex hormone degradation	49
Targeting the mosquito prefoldin–chaperonin complex blocks Plasmodium transmission	49
Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea	49
Spatial transcriptomics maps host–gut microbiome biogeography at high resolution	48
Acquired amphotericin B resistance leads to fitness trade-offs that can be mitigated by compensatory evolution in Candida auris	48
Dipeptidase 1 is a functional receptor for a porcine coronavirus	48
Colonic goblet cell-associated antigen passages mediate physiologic and beneficial translocation of live gut bacteria in preweaning mice	48
Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain	48
Hunting for new lineages and mechanisms of life	48
The GATE glycoprotein complex enhances human cytomegalovirus entry in endothelial cells	48
Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota	47
Understanding the biology of monkeypox virus to prevent future outbreaks	47
Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances	47
Cooperative virulence via the collective action of secreted pathogen effectors	47
Integrons are anti-phage defence libraries in Vibrio parahaemolyticus	47
Metabolic reprogramming enhances the susceptibility of multidrug- and carbapenem-resistant bacteria to antibiotics	47
A high-quality genome compendium of the human gut microbiome of Inner Mongolians	47
Drug–Fc conjugate CD388 targets influenza virus neuraminidase and is broadly protective in mice	46
Structural insights into tecovirimat antiviral activity and poxvirus resistance	46
Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses	46
The host–parasite–virus triad	46
Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient	46
Methane-dependent complete denitrification by a single Methylomirabilis bacterium	46
Persistent viral RNA and protein contribute to post-acute pathology	46
Introducing Microbe Matters	46
FungAMR: a comprehensive database for investigating fungal mutations associated with antimicrobial resistance	46
Faecalibacterium prausnitzii enzyme reprograms PD-L1 trafficking and sensitizes colorectal cancer to immunotherapy in mice	46
Factors associated with oral HPV infection among a large multinational cohort of men	46
Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information	45
Microbiome alterations in autism spectrum disorder	45
Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation	45
A non-human primate model for human norovirus infection	45
Use microbes to tackle food insecurity	45
Identifying rare and active species that drive carbon turnover in complex microbiotas	45
Author Correction: Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut	44
Talented microbes unlatch peatland carbon	44
scRNA-seq reveals transcriptional plasticity of var gene expression in Plasmodium falciparum for host immune avoidance	44
Author Correction: Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host–plant interactions	44
Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota	44
Intestinal crypt microbiota modulates intestinal stem cell turnover and tumorigenesis via indole acetic acid	44
Microplastic research must consider microbes	43
DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms	43
Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency	43
Mycobiota and diet-derived fungal xenosiderophores promote Salmonella gastrointestinal colonization	43
Moving from hype to hope in diet–microbiome interactions	43
Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda	42
Microbial ethanol production in patients with auto-brewery syndrome	42
Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever	42
Evolution of SARS-CoV-2 in the murine central nervous system drives viral diversification	42
Viral biogeography of the mammalian gut and parenchymal organs	42
CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery	42