Nature Microbiology

Article	Citations
Gene–drug potency screening in M. tuberculosis	622
Metabolic sensing tips the balance of drug tolerance in fungal meningitis	428
Rebound virus in the cerebrospinal fluid reveals a possible HIV-1 reservoir	355
Molecular factors shaping whether HCMV infection is productive or latent	332
Prodrug florfenicol amine is activated by intrinsic resistance to target Mycobacterium abscessus	304
The Parkinson’s disease drug entacapone disrupts gut microbiome homeostasis via iron sequestration	303
Assessing critical thresholds in terrestrial microbiomes	238
Organ-on-chip models for infectious disease research	230
Horizontal gene transfer explains unusual traits of Armillaria fungi	215
Mosquitoes provide a transmission route between possums and humans for Buruli ulcer in southeastern Australia	213
Flipping the magic switch to persistence via GTP depletion	211
Explainable artificial intelligence evolves antimicrobial peptides	207
OPENPichia: licence-free Komagataella phaffii chassis strains and toolkit for protein expression	205
Salmonella-derived haem inhibits macrophage phagocytosis and promotes infection in mice	202
The structure of the complete extracellular bacterial flagellum reveals the mechanism of flagellin incorporation	193
A dynamic subpopulation of CRISPR–Cas overexpressers allows Streptococcus pyogenes to rapidly respond to phage	192
Rational design of a hospital-specific phage cocktail to treat Enterobacter cloacae complex infections	189
Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria	188
Cytoplasmic contractile injection systems mediate cell death in Streptomyces	185
Candida albicans extracellular vesicles trigger type I IFN signalling via cGAS and STING	183
Aspergillus fumigatus dsRNA virus promotes fungal fitness and pathogenicity in the mammalian host	182
Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan	180
Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains	178
The Mycobacterium tuberculosis protein O-phosphorylation landscape	169
Single mutation makes Escherichia coli an insect mutualist	169

Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults	167
The IFIT2–IFIT3 antiviral complex targets short 5’ untranslated regions on viral mRNAs for translation inhibition	166
Host range, transmissibility and antigenicity of a pangolin coronavirus	163
A high-throughput and low-waste viability assay for microbes	162
Gut microbial enzymes shape the health benefits of dietary phytonutrients	159
A phosphotransferase system promotes growth of zoonotic Streptococcus species in the brain	155
Sickle cell trait enhances malaria transmission	155
Mycobacterium abscessus pathogenesis identified by phenogenomic analyses	154
Double recombinant nOPV2 vaccine	149
Recent gene selection and drug resistance underscore clinical adaptation across Candida species	147
Climate extremes disrupt fungal–bacterial interactions	143
Structure of a functional archaellum in Bacteria of the Chloroflexota phylum	142
Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome	139
Therapeutic efficacy of monoclonal antibodies and antivirals against SARS-CoV-2 Omicron BA.1 in Syrian hamsters	139
The fast-evolving FIKK kinase family of Plasmodium falciparum can be inhibited by a single compound	139
Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division	138
Microbiome association with coral growth and survival	137
Mechanistic basis for potent neutralization of Sin Nombre hantavirus by a human monoclonal antibody	134
Dietary exclusion of major food groups shapes the gut microbiome and may influence health	133
Exceeding expectations out in the cold with Colwellia	132
Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment	131
Decoding the impact of nuclear organization on antigenic variation in parasites	130
Kaposi’s sarcoma-associated herpesvirus induces mitochondrial fission to evade host immune responses and promote viral production	124
CRISPR-influenced symbiosis	124
Mineral-eating microorganisms at extinct hydrothermal vents	123
Call for papers on the clinical microbiome	121
Prioritizing mentorship	121
SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome	120
Initial sites of SIV rebound after antiretroviral treatment cessation in rhesus macaques	118
Archaeal symbioses all the way down	117
Extracellular vesicles block viral entryways	117
The complex path towards herpesvirus vaccines	117
Author Correction: A roadmap for equitable reuse of public microbiome data	116
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	115
Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis	113
Expanding known viral diversity in the healthy infant gut	112
Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation	111
Blockade of endothelin receptors mitigates SARS-CoV-2-induced osteoarthritis	111
Streptomyces polyketides mediate bacteria–fungi interactions across soil environments	111
Pseudomonas syringae subpopulations cooperate by coordinating flagellar and type III secretion spatiotemporal dynamics to facilitate plant infection	110
Bacteroides fragilis uses toxins for gut success	107
Risk–reward trade-off during carbon starvation generates dichotomy in motility endurance among marine bacteria	106
Skin androgens regulate Staphylococcus aureus pathogenicity via quorum sensing	106
Candida auris skin tropism and antifungal resistance are mediated by carbonic anhydrase Nce103	105
Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2	103
Nuclease–NTPase antiphage defence systems use conserved molecular features to control bacterial immunity	102
Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function	102
Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration	101
Microbial collagenase activity is linked to oral–gut translocation in advanced chronic liver disease	101

Synthesis of lipid-linked precursors of the bacterial cell wall is governed by a feedback control mechanism in Pseudomonas aeruginosa	100
Rational attenuation of RNA viruses with zinc finger antiviral protein	99
Transforming tuberculosis diagnosis	99
The gut–liver axis in HCV infection	97
Placental Streptococcus agalactiae DNA is associated with neonatal unit admission and foetal pro-inflammatory cytokines in term infants	97
From farm to factory to fork	97
Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut	95
Cell envelope diversity and evolution across the bacterial tree of life	95
Characterization of inositol lipid metabolism in gut-associated Bacteroidetes	94
Bacteriophages avoid autoimmunity from cognate immune systems as an intrinsic part of their life cycles	92
Switching on cyclic di-GMP heterogeneity in Pseudomonas aeruginosa biofilms	91
Voices of our past editors	91
Mycobacterium tuberculosis as teacher	90
Anoxia activates CRISPR–Cas immunity in the mouse intestine	89
Conserved CD4+ T cell staphylococcal and streptococcal epitopes enable broad-acting vaccines in mice	89
SARS-CoV-2 infection induces pro-fibrotic and pro-thrombotic foam cell formation	87
Phages with a broad host range are common across ecosystems	84
Dietary fibre counters the oncogenic potential of colibactin-producing Escherichia coli in colorectal cancer	84
An expanded metabolic pathway for androgen production by commensal bacteria	83
Outbreak dynamics of foodborne pathogen Vibrio parahaemolyticus over a seventeen year period implies hidden reservoirs	81
Parasite and vector circadian clocks mediate efficient malaria transmission	80
Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes	79
Harnessing the microbiome to prevent global biodiversity loss	79
Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study	79
Hunting emerging viruses through participatory community science	79
Genome-resolved metagenomics reveals microbiome diversity across 48 tick species	78
CryoEM reveals that ribosomes in microsporidian spores are locked in a dimeric hibernating state	78
Therapeutics for COVID-19	77
Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia	76
Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants	76
SARS and synapses	75
Interkingdom sensing of fungal tyrosol promotes bacterial antifungal T6SS activity in the murine gut	75
A nitrogen-fixing bacterium forms symbioses on land and at sea	75
Discovery of an orally active benzoxaborole prodrug effective in the treatment of Chagas disease in non-human primates	74
Combining antibiotics to tackle antimicrobial resistance	74
Escherichia coli integrates chemotaxis and quorum sensing pathways in vivo	73
Mining the microbiota for antibiotics	73
Identified receptors shed light on Epstein–Barr virus infection	73
Siderophores mediate antibiotic resistance	72
Bacteria can shed a layer when phages turn up the heat	72
Safety and immunogenicity of a prefusion non-stabilized spike protein mRNA COVID-19 vaccine: a phase I trial	71
STREAM-lining guidelines for microbiome research	71
Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters	71
GprC of the nematode-trapping fungus Arthrobotrys flagrans activates mitochondria and reprograms fungal cells for nematode hunting	70
Growth rate is modulated by monitoring cell wall precursors in Bacillus subtilis	70
Epitope-focused discovery of SARS-CoV-2 antibodies that potently neutralize Omicron variants	69
A year of microbiology	69
Human microbiome myths and misconceptions	69
Early-life colonization by aromatic-lactate-producing bifidobacteria lowers the risk of allergic sensitization	69
Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships	69
Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria	69
Publisher Correction: Toxoplasma gondii VIP1 mediates parasitophorous vacuole–host endoplasmic reticulum interactions to facilitate parasite development	69
Metabolic modelling reveals the aging-associated decline of host–microbiome metabolic interactions in mice	69
TOLLIP inhibits lipid accumulation and the integrated stress response in alveolar macrophages to control Mycobacterium tuberculosis infection	68
mRNA-encoded Cas13 can be used to treat dengue infections in mice	68
A framework for automated scalable designation of viral pathogen lineages from genomic data	68
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism	66
Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes	66
Guiding phage therapy with genomic surveillance	66
Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine	66
The cell biology of archaea	65
Parabacteroides distasonis uses dietary inulin to suppress NASH via its metabolite pentadecanoic acid	65
Gut microbial factors predict disease severity in a mouse model of multiple sclerosis	65
Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts	65
Environmental stress mediates groundwater microbial community assembly	65
Gut microbiome-mediated transformation of dietary phytonutrients is associated with health outcomes	65
The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice	64
Decreased cytoplasmic crowding via inhibition of ribosome biogenesis can trigger Candida albicans filamentous growth	64
Shining light on the coral photosymbiont family Symbiodiniaceae	63
CD8+ T cell depletion does not induce an expansion of viral reservoir in HIV model	63
Amplifying diverse voices in microbiology	63
Bacteria modulate microalgal aging physiology through the induction of extracellular vesicle production to remove harmful metabolites	63
A method to detect origin of transfer sequences for plasmid conjugation	62
Migrant health matters	62
We must learn from past outbreaks	62
Author Correction: Respiratory immunization using antibiotic-inactivated Bordetella pertussis confers T cell-mediated protection against nasal infection in mice	61
Addressing gaps in author and reviewer gender diversity	61
A phage-encoded anti-CRISPR protein co-opts host enolase to prevent type III CRISPR immunity	61
Retracing a tangled tree of archaeal evolution	61
Parasex generates highly recombinant progeny in Candida albicans with increased virulence	61

Identifying an evolutionary origin for morbilliviruses in bats	61
SARS-CoV-2 Africa dashboard for real-time COVID-19 information	60
Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes	60
Metabolites from intact phage-infected Synechococcus chemotactically attract heterotrophic marine bacteria	60
Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection	60
The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate	60
Phase transition of GvpU regulates gas vesicle clustering in bacteria	59
Multinational epidemiological analysis of oral human papillomavirus incidence in 3,137 men	59
Dairy cows develop protective immunity against reinfection with bovine H5N1 influenza virus	59
A haem-sequestering plant peptide promotes iron uptake in symbiotic bacteria	58
Inactivated whole-virion vaccine BBV152/Covaxin elicits robust cellular immune memory to SARS-CoV-2 and variants of concern	58
Sulfated glycosaminoglycans are host epithelial cell targets of the Candida albicans toxin candidalysin	58
Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial	58
Comprehensive transcription terminator atlas for Bacillus subtilis	57
Characterizing extracellular vesicles of human fungal pathogens	57
Tecovirimat is effective against human monkeypox virus in vitro at nanomolar concentrations	56
Gut bacteria degrade purines via the 2,8-dioxopurine pathway	56
AMR, One Health and the environment	55
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway	55
Benchmarking shotgun metagenomics	55
Staphylococcal virulence factor HlgB targets the endoplasmic-reticulum-resident E3 ubiquitin ligase AMFR to promote pneumonia	55
Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon	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
BacterAI maps microbial metabolism without prior knowledge	54
Diet switch pre-vaccination improves immune response and metabolic status in formerly obese mice	54
Molecular organization of the New World arenavirus spike glycoprotein complex	54
Preclinical evaluation of the SARS-CoV-2 Mpro inhibitor RAY1216 shows improved pharmacokinetics compared with nirmatrelvir	53
Microbes and the water nexus	53
Iron-limitation light switch	53
Genome-wide protein–DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase	53
Cooperative virulence via the collective action of secreted pathogen effectors	52
Publisher Correction: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission	52
The GATE glycoprotein complex enhances human cytomegalovirus entry in endothelial cells	52
Remote control designer probiotics	52
Metagenomic characterization of viruses and mobile genetic elements associated with the DPANN archaeal superphylum	52
Translating between science and politics as a government adviser	52
Chromosome architecture in an archaeal species naturally lacking structural maintenance of chromosomes proteins	51
Understanding emerging and re-emerging viruses to facilitate pandemic preparedness	51
Understanding the biology of monkeypox virus to prevent future outbreaks	51
Spatial transcriptomics maps host–gut microbiome biogeography at high resolution	51
Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea	50
Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites	50
Nasal Staphylococcus aureus carriage promotes depressive behaviour in mice via sex hormone degradation	50
Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota	50
MAP-X reveals distinct protein complex dynamics across Plasmodium falciparum blood stages	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	48
Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain	48
Integrons are anti-phage defence libraries in Vibrio parahaemolyticus	48
A high-quality genome compendium of the human gut microbiome of Inner Mongolians	48
Exploiting the fitness cost of metallo-β-lactamase expression can overcome antibiotic resistance in bacterial pathogens	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
Metabolic reprogramming enhances the susceptibility of multidrug- and carbapenem-resistant bacteria to antibiotics	48
Targeting the mosquito prefoldin–chaperonin complex blocks Plasmodium transmission	48
Hunting for new lineages and mechanisms of life	48
Colonic goblet cell-associated antigen passages mediate physiologic and beneficial translocation of live gut bacteria in preweaning mice	48
Dual inhibition of innate immunity and apoptosis by human cytomegalovirus protein UL37x1 enables efficient virus replication	47
Moving from hype to hope in diet–microbiome interactions	47
Introducing Microbe Matters	47
The host–parasite–virus triad	47
Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances	47
A non-human primate model for human norovirus infection	46
Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota	46
Author Correction: Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host–plant interactions	46
Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever	46
Intestinal crypt microbiota modulates intestinal stem cell turnover and tumorigenesis via indole acetic acid	46
Factors associated with oral HPV infection among a large multinational cohort of men	46
Use microbes to tackle food insecurity	46
Multigenerational proteolytic inactivation of restriction upon subtle genomic hypomethylation in Pseudomonas aeruginosa	46
Talented microbes unlatch peatland carbon	46
Small organisms with big climate impact	46
Persistent viral RNA and protein contribute to post-acute pathology	45
Microbiome alterations in autism spectrum disorder	45
Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda	45
Identifying rare and active species that drive carbon turnover in complex microbiotas	45
Microbial ethanol production in patients with auto-brewery syndrome	45
Microplastic research must consider microbes	45
Viral biogeography of the mammalian gut and parenchymal organs	45
CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery	45
Evolution of SARS-CoV-2 in the murine central nervous system drives viral diversification	45
Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient	44
Mycobiota and diet-derived fungal xenosiderophores promote Salmonella gastrointestinal colonization	44
scRNA-seq reveals transcriptional plasticity of var gene expression in Plasmodium falciparum for host immune avoidance	44
Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses	44
Author Correction: Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut	44
Vientovirus capsid protein mimics autoantigens and contributes to autoimmunity in Sjögren’s disease	43
DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms	43
FungAMR: a comprehensive database for investigating fungal mutations associated with antimicrobial resistance	43
Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought	43
Faecalibacterium prausnitzii enzyme reprograms PD-L1 trafficking and sensitizes colorectal cancer to immunotherapy in mice	43
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
Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency	42