Nature Microbiology

Article	Citations
Gene–drug potency screening in M. tuberculosis	590
Sickle cell trait enhances malaria transmission	387
Metabolic sensing tips the balance of drug tolerance in fungal meningitis	295
Author Correction: DART takes aim at community editing	290
Rebound virus in the cerebrospinal fluid reveals a possible HIV-1 reservoir	278
Molecular factors shaping whether HCMV infection is productive or latent	276
Dietary exclusion of major food groups shapes the gut microbiome and may influence health	274
Prodrug florfenicol amine is activated by intrinsic resistance to target Mycobacterium abscessus	271
The fast-evolving FIKK kinase family of Plasmodium falciparum can be inhibited by a single compound	222
Flipping the magic switch to persistence via GTP depletion	222
Microbiome association with coral growth and survival	220
Structure of a functional archaellum in Bacteria of the Chloroflexota phylum	200
Cytoplasmic contractile injection systems mediate cell death in Streptomyces	199
The IFIT2–IFIT3 antiviral complex targets short 5’ untranslated regions on viral mRNAs for translation inhibition	196
Single mutation makes Escherichia coli an insect mutualist	196
Mechanistic basis for potent neutralization of Sin Nombre hantavirus by a human monoclonal antibody	188
Aspergillus fumigatus dsRNA virus promotes fungal fitness and pathogenicity in the mammalian host	185
Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan	179
The Mycobacterium tuberculosis protein O-phosphorylation landscape	179
Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome	172
Assessing critical thresholds in terrestrial microbiomes	168
Explainable artificial intelligence evolves antimicrobial peptides	168
Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults	166
Climate extremes disrupt fungal–bacterial interactions	164
Therapeutic efficacy of monoclonal antibodies and antivirals against SARS-CoV-2 Omicron BA.1 in Syrian hamsters	162

Mycobacterium abscessus pathogenesis identified by phenogenomic analyses	162
Rational design of a hospital-specific phage cocktail to treat Enterobacter cloacae complex infections	158
The Parkinson’s disease drug entacapone disrupts gut microbiome homeostasis via iron sequestration	157
Horizontal gene transfer explains unusual traits of Armillaria fungi	155
A dynamic subpopulation of CRISPR–Cas overexpressers allows Streptococcus pyogenes to rapidly respond to phage	154
Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division	149
Recent gene selection and drug resistance underscore clinical adaptation across Candida species	148
OPENPichia: licence-free Komagataella phaffii chassis strains and toolkit for protein expression	148
Candida albicans extracellular vesicles trigger type I IFN signalling via cGAS and STING	144
Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains	144
Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria	143
The structure of the complete extracellular bacterial flagellum reveals the mechanism of flagellin incorporation	139
A high-throughput and low-waste viability assay for microbes	138
Host range, transmissibility and antigenicity of a pangolin coronavirus	137
Organ-on-chip models for infectious disease research	133
Mosquitoes provide a transmission route between possums and humans for Buruli ulcer in southeastern Australia	130
Exceeding expectations out in the cold with Colwellia	129
Pseudomonas syringae subpopulations cooperate by coordinating flagellar and type III secretion spatiotemporal dynamics to facilitate plant infection	126
Structure-guided design of a synthetic bile acid that inhibits Clostridioides difficile TcdB toxin	125
SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome	124
Risk–reward trade-off during carbon starvation generates dichotomy in motility endurance among marine bacteria	123
Transforming tuberculosis diagnosis	123
Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2	122
Candida auris skin tropism and antifungal resistance are mediated by carbonic anhydrase Nce103	119
Microbial collagenase activity is linked to oral–gut translocation in advanced chronic liver disease	118
Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration	118
Mineral-eating microorganisms at extinct hydrothermal vents	117
CRISPR-influenced symbiosis	117
Prioritizing mentorship	116
Archaeal symbioses all the way down	115
Extracellular vesicles block viral entryways	115
Call for papers on the clinical microbiome	115
Author Correction: A roadmap for equitable reuse of public microbiome data	112
The complex path towards herpesvirus vaccines	112
Bacteroides fragilis uses toxins for gut success	110
Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment	109
Decoding the impact of nuclear organization on antigenic variation in parasites	108
Coronavirus sampling and surveillance in bats from 1996–2019: a systematic review and meta-analysis	108
Kaposi’s sarcoma-associated herpesvirus induces mitochondrial fission to evade host immune responses and promote viral production	107
Blockade of endothelin receptors mitigates SARS-CoV-2-induced osteoarthritis	106
Synthesis of lipid-linked precursors of the bacterial cell wall is governed by a feedback control mechanism in Pseudomonas aeruginosa	105
Streptomyces polyketides mediate bacteria–fungi interactions across soil environments	103
Rational attenuation of RNA viruses with zinc finger antiviral protein	103
Switching on cyclic di-GMP heterogeneity in Pseudomonas aeruginosa biofilms	102
Expanding known viral diversity in the healthy infant gut	102
SARS and synapses	101
Placental Streptococcus agalactiae DNA is associated with neonatal unit admission and foetal pro-inflammatory cytokines in term infants	99
From farm to factory to fork	98
Publisher Correction: Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis	98
A nitrogen-fixing bacterium forms symbioses on land and at sea	97

Genome-resolved metagenomics reveals microbiome diversity across 48 tick species	97
Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants	96
Interkingdom sensing of fungal tyrosol promotes bacterial antifungal T6SS activity in the murine gut	96
Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study	96
The gut–liver axis in HCV infection	95
Hunting emerging viruses through participatory community science	94
Discovery of an orally active benzoxaborole prodrug effective in the treatment of Chagas disease in non-human primates	91
Parasite and vector circadian clocks mediate efficient malaria transmission	91
CryoEM reveals that ribosomes in microsporidian spores are locked in a dimeric hibernating state	89
Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut	89
Cell envelope diversity and evolution across the bacterial tree of life	89
An expanded metabolic pathway for androgen production by commensal bacteria	86
Characterization of inositol lipid metabolism in gut-associated Bacteroidetes	86
Mycobacterium tuberculosis as teacher	86
Combining antibiotics to tackle antimicrobial resistance	85
Therapeutics for COVID-19	84
Dietary fibre counters the oncogenic potential of colibactin-producing Escherichia coli in colorectal cancer	83
Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes	81
Increased small particle aerosol transmission of B.1.1.7 compared with SARS-CoV-2 lineage A in vivo	80
Connecting microbiome and menopause for healthy ageing	80
Harnessing the microbiome to prevent global biodiversity loss	80
SARS-CoV-2 infection induces pro-fibrotic and pro-thrombotic foam cell formation	79
Bacteriophages avoid autoimmunity from cognate immune systems as an intrinsic part of their life cycles	77
Dynamic diel proteome and daytime nitrogenase activity supports buoyancy in the cyanobacterium Trichodesmium	77
Anoxia activates CRISPR–Cas immunity in the mouse intestine	77
Outbreak dynamics of foodborne pathogen Vibrio parahaemolyticus over a seventeen year period implies hidden reservoirs	74
Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia	74
Phages with a broad host range are common across ecosystems	73
Escherichia coli integrates chemotaxis and quorum sensing pathways in vivo	73
Bacteria can shed a layer when phages turn up the heat	72
A year of microbiology	72
Reproductive justice must be considered in the scientific community	72
Mining the microbiota for antibiotics	72
A framework for automated scalable designation of viral pathogen lineages from genomic data	71
Guiding phage therapy with genomic surveillance	71
Identified receptors shed light on Epstein–Barr virus infection	71
STREAM-lining guidelines for microbiome research	71
Gut microbiome-mediated transformation of dietary phytonutrients is associated with health outcomes	71
Siderophores mediate antibiotic resistance	71
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism	69
Safety and immunogenicity of a prefusion non-stabilized spike protein mRNA COVID-19 vaccine: a phase I trial	68
Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes	67
mRNA-encoded Cas13 can be used to treat dengue infections in mice	66
Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria	66
Publisher Correction: Toxoplasma gondii VIP1 mediates parasitophorous vacuole–host endoplasmic reticulum interactions to facilitate parasite development	65
The cell biology of archaea	65
Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters	65
GprC of the nematode-trapping fungus Arthrobotrys flagrans activates mitochondria and reprograms fungal cells for nematode hunting	64
The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice	64
Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine	63
Growth rate is modulated by monitoring cell wall precursors in Bacillus subtilis	63
Human microbiome myths and misconceptions	62
Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships	62
Microbial metabolites in the marine carbon cycle	61
Metabolic modelling reveals the aging-associated decline of host–microbiome metabolic interactions in mice	61
TOLLIP inhibits lipid accumulation and the integrated stress response in alveolar macrophages to control Mycobacterium tuberculosis infection	61
Decreased cytoplasmic crowding via inhibition of ribosome biogenesis can trigger Candida albicans filamentous growth	60
Parabacteroides distasonis uses dietary inulin to suppress NASH via its metabolite pentadecanoic acid	60
Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts	60
Gut microbial factors predict disease severity in a mouse model of multiple sclerosis	60
Migrant health matters	59
CD8+ T cell depletion does not induce an expansion of viral reservoir in HIV model	59
Amplifying diverse voices in microbiology	59
Bacteria modulate microalgal aging physiology through the induction of extracellular vesicle production to remove harmful metabolites	59
Shining light on the coral photosymbiont family Symbiodiniaceae	59
Environmental stress mediates groundwater microbial community assembly	59
A method to detect origin of transfer sequences for plasmid conjugation	58
We must learn from past outbreaks	58
Molecular organization of the New World arenavirus spike glycoprotein complex	58
Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes	57
Identifying an evolutionary origin for morbilliviruses in bats	57
Preclinical evaluation of the SARS-CoV-2 Mpro inhibitor RAY1216 shows improved pharmacokinetics compared with nirmatrelvir	57
Retracing a tangled tree of archaeal evolution	57
Multinational epidemiological analysis of oral human papillomavirus incidence in 3,137 men	56
SARS-CoV-2 Africa dashboard for real-time COVID-19 information	56
Staphylococcal virulence factor HlgB targets the endoplasmic-reticulum-resident E3 ubiquitin ligase AMFR to promote pneumonia	56
Dairy cows develop protective immunity against reinfection with bovine H5N1 influenza virus	56
Addressing gaps in author and reviewer gender diversity	56
Author Correction: Respiratory immunization using antibiotic-inactivated Bordetella pertussis confers T cell-mediated protection against nasal infection in mice	56
Genome-wide protein–DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase	56

Metabolites from intact phage-infected Synechococcus chemotactically attract heterotrophic marine bacteria	55
Gut bacteria degrade purines via the 2,8-dioxopurine pathway	55
Diet switch pre-vaccination improves immune response and metabolic status in formerly obese mice	55
Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection	54
The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate	54
Tecovirimat is effective against human monkeypox virus in vitro at nanomolar concentrations	54
Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon	53
Sulfated glycosaminoglycans are host epithelial cell targets of the Candida albicans toxin candidalysin	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
Comprehensive transcription terminator atlas for Bacillus subtilis	53
Characterizing extracellular vesicles of human fungal pathogens	53
Phase transition of GvpU regulates gas vesicle clustering in bacteria	53
Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen	52
Inactivated whole-virion vaccine BBV152/Covaxin elicits robust cellular immune memory to SARS-CoV-2 and variants of concern	52
BacterAI maps microbial metabolism without prior knowledge	52
A haem-sequestering plant peptide promotes iron uptake in symbiotic bacteria	52
Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial	52
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway	51
Microbes and the water nexus	51
Iron-limitation light switch	51
Taurolithocholic acid protects against viral haemorrhagic fever via inhibition of ferroptosis	51
Dipeptidase 1 is a functional receptor for a porcine coronavirus	50
Colonic goblet cell-associated antigen passages mediate physiologic and beneficial translocation of live gut bacteria in preweaning mice	50
Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis	50
Translating between science and politics as a government adviser	50
Targeting the mosquito prefoldin–chaperonin complex blocks Plasmodium transmission	50
Publisher Correction: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission	49
Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea	49
Nasal Staphylococcus aureus carriage promotes depressive behaviour in mice via sex hormone degradation	49
Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain	49
Metagenomic characterization of viruses and mobile genetic elements associated with the DPANN archaeal superphylum	49
Enterococcus faecalis-derived adenine enhances enterohaemorrhagic Escherichia coli Type 3 Secretion System-dependent virulence	49
Remote control designer probiotics	49
MAP-X reveals distinct protein complex dynamics across Plasmodium falciparum blood stages	49
Chromosome architecture in an archaeal species naturally lacking structural maintenance of chromosomes proteins	48
Exploiting the fitness cost of metallo-β-lactamase expression can overcome antibiotic resistance in bacterial pathogens	48
Sex, gender and infectious disease	48
Surface expression of antitoxin on engineered bacteria neutralizes genotoxic colibactin in the gut	48
Understanding emerging and re-emerging viruses to facilitate pandemic preparedness	48
Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota	48
The GATE glycoprotein complex enhances human cytomegalovirus entry in endothelial cells	47
Integrons are anti-phage defence libraries in Vibrio parahaemolyticus	47
A high-quality genome compendium of the human gut microbiome of Inner Mongolians	47
Understanding the biology of monkeypox virus to prevent future outbreaks	47
Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites	47
Dual inhibition of innate immunity and apoptosis by human cytomegalovirus protein UL37x1 enables efficient virus replication	46
Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances	46
Introducing Microbe Matters	46
Cooperative virulence via the collective action of secreted pathogen effectors	46
Acquired amphotericin B resistance leads to fitness trade-offs that can be mitigated by compensatory evolution in Candida auris	46
Metabolic reprogramming enhances the susceptibility of multidrug- and carbapenem-resistant bacteria to antibiotics	46
The host–parasite–virus triad	45
Moving from hype to hope in diet–microbiome interactions	45
Author Correction: Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host–plant interactions	44
Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever	44
Factors associated with oral HPV infection among a large multinational cohort of men	44
Persistent viral RNA and protein contribute to post-acute pathology	44
Small organisms with big climate impact	44
Chromosome organization affects genome evolution in Sulfolobus archaea	44
Microbiome alterations in autism spectrum disorder	43
Discovery and artificial intelligence-guided mechanistic elucidation of a narrow-spectrum antibiotic	43
Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda	43
Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota	43
Identifying rare and active species that drive carbon turnover in complex microbiotas	43
Viral biogeography of the mammalian gut and parenchymal organs	43
CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery	43
Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency	43
Use microbes to tackle food insecurity	43
scRNA-seq reveals transcriptional plasticity of var gene expression in Plasmodium falciparum for host immune avoidance	42
Author Correction: Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut	42
Talented microbes unlatch peatland carbon	42
Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation	42
Drug–Fc conjugate CD388 targets influenza virus neuraminidase and is broadly protective in mice	42
Evolution of SARS-CoV-2 in the murine central nervous system drives viral diversification	42
Microplastic research must consider microbes	42
Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation	41
Structural insights into tecovirimat antiviral activity and poxvirus resistance	41
FungAMR: a comprehensive database for investigating fungal mutations associated with antimicrobial resistance	41
Leaf microbiome dysbiosis triggered by T2SS-dependent enzyme secretion from opportunistic Xanthomonas pathogens	41
Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient	41
Intestinal crypt microbiota modulates intestinal stem cell turnover and tumorigenesis via indole acetic acid	41
Vientovirus capsid protein mimics autoantigens and contributes to autoimmunity in Sjögren’s disease	41
A non-human primate model for human norovirus infection	41
Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses	40
DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms	40
Parkinson’s disease kinase LRRK2 coordinates a cell-intrinsic itaconate-dependent defence pathway against intracellular Salmonella	40
Mycobiota and diet-derived fungal xenosiderophores promote Salmonella gastrointestinal colonization	40
Methane-dependent complete denitrification by a single Methylomirabilis bacterium	40
Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought	39
Knowledge synthesis through scientific visualization	39
Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information	39
Connecting the dots from viral infection to disease	39
Multigenerational proteolytic inactivation of restriction upon subtle genomic hypomethylation in Pseudomonas aeruginosa	39
Redefining success	39