Nature Microbiology

Article	Citations
A rhesus macaque model of human norovirus infection	637
Data availability is the golden rule in research	503
Horizontal gene transfer explains unusual traits of Armillaria fungi	373
Author Correction: Aspergillus cvjetkovicii protects against phytopathogens through interspecies chemical signalling in the phyllosphere	362
Rethinking concepts of virulence with Neisseria gonorrhoeae	335
Microplastic research must consider microbes	308
CryoEM structures reveal how the bacterial flagellum rotates and switches direction	297
Therapeutic efficacy of monoclonal antibodies and antivirals against SARS-CoV-2 Omicron BA.1 in Syrian hamsters	283
Rebound virus in the cerebrospinal fluid reveals a possible HIV-1 reservoir	261
Organ-on-chip models for infectious disease research	250
Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda	241
Cryo-EM structure of the bacterial divisome core complex and antibiotic target FtsWIQBL	214
Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation	206
Stage-specific transcription activator ESB1 regulates monoallelic antigen expression in Trypanosoma brucei	203
Mycobacterium abscessus pathogenesis identified by phenogenomic analyses	195
Explainable artificial intelligence evolves antimicrobial peptides	191
Streptomyces secretes a siderophore that sensitizes competitor bacteria to phage infection	179
KorB switching from DNA-sliding clamp to repressor mediates long-range gene silencing in a multi-drug resistance plasmid	177
A divergent bacterium lives in association with bacterivorous protists in the ocean	172
Introducing Microbe Matters	167
Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome	153
Akkermansia muciniphila exacerbates food allergy in fibre-deprived mice	149
Virulence of banana wilt-causing fungal pathogen Fusarium oxysporum tropical race 4 is mediated by nitric oxide biosynthesis and accessory genes	147
Towards a unifying system for the naming of cultured and uncultured prokaryotes	145
Characterization of interactions of dietary cholesterol with the murine and human gut microbiome	145

When specialized clones go global	142
Psychosocial stress and the gut microbiota	141
Factors associated with oral HPV infection among a large multinational cohort of men	139
Microbiome alterations in autism spectrum disorder	136
Small organisms with big climate impact	136
Molecular factors shaping whether HCMV infection is productive or latent	136
Author Correction: Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut	135
Use microbes to tackle food insecurity	132
Parkinson’s disease kinase LRRK2 coordinates a cell-intrinsic itaconate-dependent defence pathway against intracellular Salmonella	132
Dietary exclusion of major food groups shapes the gut microbiome and may influence health	130
Mechanistic basis for potent neutralization of Sin Nombre hantavirus by a human monoclonal antibody	126
Fine-tuning fungal effector secretion	125
Microsporidian spores contain hibernating dimeric ribosomes	124
Assessing critical thresholds in terrestrial microbiomes	121
Sickle cell trait enhances malaria transmission	120
Bacteroides fragilis toxin expression enables lamina propria niche acquisition in the developing mouse gut	116
Author Correction: Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host–plant interactions	116
Symbiosis for rhizobia is not an easy ride	115
Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division	112
Autophagy promotes efficient T cell responses to restrict high-dose Mycobacterium tuberculosis infection in mice	109
DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms	108
Crimean–Congo haemorrhagic fever virus uses LDLR to bind and enter host cells	108
Recent gene selection and drug resistance underscore clinical adaptation across Candida species	107
Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments	106
Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever	106
Talented microbes unlatch peatland carbon	105
SARS-CoV-2-related bat viruses evade human intrinsic immunity but lack efficient transmission capacity	105
Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient	103
Staphylococcus aureus adapts to exploit collagen-derived proline during chronic infection	102
Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought	102
The Parkinson’s disease drug entacapone disrupts gut microbiome homeostasis via iron sequestration	98
Engineering Toxoplasma gondii secretion systems for intracellular delivery of multiple large therapeutic proteins to neurons	98
The host–parasite–virus triad	98
Persistent viral RNA and protein contribute to post-acute pathology	96
Evolution of SARS-CoV-2 in the murine central nervous system drives viral diversification	96
A non-human primate model for human norovirus infection	95
Systematic mapping of antibiotic cross-resistance and collateral sensitivity with chemical genetics	93
Metabolic sensing tips the balance of drug tolerance in fungal meningitis	93
Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria	92
A widespread phage-encoded kinase enables evasion of multiple host antiphage defence systems	89
Expanding the arsenal of bacterial spearguns	89
Linking DNA replication to the Z ring	89
Chromosome organization affects genome evolution in Sulfolobus archaea	88
Growth temperature and chromatinization in archaea	88
A talent network of Black microbiologists	87
Angiopoietin-like 4 protects against endothelial dysfunction during bacterial sepsis	87
Effectiveness of COVID-19 vaccines against symptomatic SARS-CoV-2 infection and severe outcomes with variants of concern in Ontario	87
Uropathogenic Escherichia coli subverts mitochondrial metabolism to enable intracellular bacterial pathogenesis in urinary tract infection	87
Author Correction: Differential neutralizing antibody responses elicited by CoronaVac and BNT162b2 against SARS-CoV-2 Lambda in Chile	86
Bacterial divisome protein FtsA forms curved antiparallel double filaments when binding to FtsN	86

Gene–drug potency screening in M. tuberculosis	86
Spacer prioritization in CRISPR–Cas9 immunity is enabled by the leader RNA	86
Mycobiota and diet-derived fungal xenosiderophores promote Salmonella gastrointestinal colonization	85
Multitasking to prevent viral haemorrhagic fevers	84
CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery	84
The potential of genomics for infectious disease forecasting	84
PCRCR complex is essential for invasion of human erythrocytes by Plasmodium falciparum	82
Mechanosensitive extrusion of Enterovirus A71-infected cells from colonic organoids	81
Soluble lectin LePin mediates alga recognition to initiate coral–algal endosymbiosis	81
Restriction endonuclease cleavage of phage DNA enables resuscitation from Cas13-induced bacterial dormancy	81
An expanded transcriptome atlas for Bacteroides thetaiotaomicron reveals a small RNA that modulates tetracycline sensitivity	80
Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan	80
Microbes in a sea of sinking particles	79
Biology and applications of co-produced, synergistic antimicrobials from environmental bacteria	79
Characterizing cytomegalovirus infection one cell at a time	79
Managing the mycobiota with IgA	79
Author Correction: MX2-mediated innate immunity against HIV-1 is regulated by serine phosphorylation	78
Dormant phages communicate via arbitrium to control exit from lysogeny	76
Author Correction: DART takes aim at community editing	75
Publisher Correction: Adaptation of the small intestine to microbial enteropathogens in Zambian children with stunting	75
Microbiome assembly in The Gambia	74
Scientist or artist? Why not be both?	74
Viruses affect picocyanobacterial abundance and biogeography in the North Pacific Ocean	73
Maternal antibody level, sex and birth route drive individual measles immunity differences	72
Drug–Fc conjugate CD388 targets influenza virus neuraminidase and is broadly protective in mice	71
Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses	71
Viral biogeography of the mammalian gut and parenchymal organs	70
Structural insights into tecovirimat antiviral activity and poxvirus resistance	70
Single-molecule imaging of LexA degradation in Escherichia coli elucidates regulatory mechanisms and heterogeneity of the SOS response	69
Mosquitoes provide a transmission route between possums and humans for Buruli ulcer in southeastern Australia	69
SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution	69
A dynamic subpopulation of CRISPR–Cas overexpressers allows Streptococcus pyogenes to rapidly respond to phage	69
The Mycobacterium tuberculosis protein O-phosphorylation landscape	68
Patient-derived monoclonal antibody neutralizes SARS-CoV-2 Omicron variants and confers full protection in monkeys	68
Assimilatory sulfate reduction in the marine methanogen Methanothermococcus thermolithotrophicus	67
Microbiology must be represented at climate change talks	66
The meaning of oral bacteria in faeces	65
Understanding pathogen emergence through the lens of Candida auris	65
Biotin-dependent cell envelope remodelling is required for Mycobacterium abscessus survival in lung infection	64
Fungal taxonomy and sequence-based nomenclature	64
Appressorium-mediated plant infection by Magnaporthe oryzae is regulated by a Pmk1-dependent hierarchical transcriptional network	63
Capsid adaptation defines pandemic HIV	62
Microbial metabolite harmaline protects against virus-induced systemic inflammation	62
Above- and belowground fungal biodiversity of Populus trees on a continental scale	61
Leaf microbiome dysbiosis triggered by T2SS-dependent enzyme secretion from opportunistic Xanthomonas pathogens	61
Gut–liver translocation of pathogen Klebsiella pneumoniae promotes hepatocellular carcinoma in mice	61
Fetal meconium does not have a detectable microbiota before birth	60
Cell wall synthesis and remodelling dynamics determine division site architecture and cell shape in Escherichia coli	59
Fungal spores are future-proofed	59
Targeted accurate RNA consensus sequencing (tARC-seq) reveals mechanisms of replication error affecting SARS-CoV-2 divergence	59
Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota	59
Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency	58
Challenges and opportunities in sharing microbiome data and analyses	58
Loving mucus with Akkermansia muciniphila	58
Pseudomonas putida mediates bacterial killing, biofilm invasion and biocontrol with a type IVB secretion system	58
Moving from hype to hope in diet–microbiome interactions	57
Microbiome ownership for Indigenous peoples	57
Differential rates of Mycobacterium tuberculosis transmission associate with host–pathogen sympatry	57
Spatially resolved protein map of intact human cytomegalovirus virions	55
Analysing the fitness cost of antibiotic resistance to identify targets for combination antimicrobials	55
Tracking bacterial lineages in complex and dynamic environments with applications for growth control and persistence	55
Population genomics confirms acquisition of drug-resistant Aspergillus fumigatus infection by humans from the environment	54
Pseudomonas aeruginosa breaches respiratory epithelia through goblet cell invasion in a microtissue model	54
ERK pathway reactivation prevents anthrax toxin lethality in mice	54
Candida albicans extracellular vesicles trigger type I IFN signalling via cGAS and STING	54
A genome catalogue of lake bacterial diversity and its drivers at continental scale	53
OPENPichia: licence-free Komagataella phaffii chassis strains and toolkit for protein expression	53
The unusual cell wall of the Lyme disease spirochaete Borrelia burgdorferi is shaped by a tick sugar	53
Cytoplasmic contractile injection systems mediate cell death in Streptomyces	53
Climate extremes disrupt fungal–bacterial interactions	52
A splitCas9 phenotypic screen in Toxoplasma gondii identifies proteins involved in host cell egress and invasion	52
Host range, transmissibility and antigenicity of a pangolin coronavirus	52
Intestinal crypt microbiota modulates intestinal stem cell turnover and tumorigenesis via indole acetic acid	51
Revitalizing antibiotic discovery and development through in vitro modelling of in-patient conditions	51
Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota	51
Multi-kingdom microbiota analyses identify bacterial–fungal interactions and biomarkers of colorectal cancer across cohorts	50
Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b2	50
Metabolic rearrangement enables adaptation of microbial growth rate to temperature shifts	49
Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts	49
Obligate biotroph downy mildew consistently induces near-identical protective microbiomes in Arabidopsis thaliana	48

Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains	48
Host defence peptide plectasin targets bacterial cell wall precursor lipid II by a calcium-sensitive supramolecular mechanism	48
Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information	48
Single mutation makes Escherichia coli an insect mutualist	48
Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium	48
Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California	47
Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes	47
Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation	47
Identification of structurally diverse menaquinone-binding antibiotics with in vivo activity against multidrug-resistant pathogens	46
Methane-dependent complete denitrification by a single Methylomirabilis bacterium	46
A foldon-free prefusion F trimer vaccine for respiratory syncytial virus to reduce off-target immune responses	46
A high-throughput and low-waste viability assay for microbes	46
Induction of robust cellular and humoral immunity against SARS-CoV-2 after a third dose of BNT162b2 vaccine in previously unresponsive older adults	46
Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults	45
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome	45
Immune imprinting and next-generation coronavirus vaccines	45
Akkermansia muciniphila secretes a glucagon-like peptide-1-inducing protein that improves glucose homeostasis and ameliorates metabolic disease in mice	45
CRISPRi-ART enables functional genomics of diverse bacteriophages using RNA-binding dCas13d	45
Decoding the impact of nuclear organization on antigenic variation in parasites	44
Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing	44
Bacterial amylases enable glycogen degradation by the vaginal microbiome	44
Better training for non-academic careers	44
Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection	44
Streptomyces polyketides mediate bacteria–fungi interactions across soil environments	44
SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope	44
A genetic switch controls Pseudomonas aeruginosa surface colonization	44
Bacterial adhesion strategies and countermeasures in urinary tract infection	44
Blockade of endothelin receptors mitigates SARS-CoV-2-induced osteoarthritis	43
A soybean cyst nematode suppresses microbial plant symbionts using a lipochitooligosaccharide-hydrolysing enzyme	43
The collapse of cooperation during range expansion of Pseudomonas aeruginosa	43
CRISPR meets caspase	43
Author Correction: Peptidoglycan synthesis drives a single population of septal cell wall synthases during division in Bacillus subtilis	42
Deep mining reveals the diversity of endogenous viral elements in vertebrate genomes	42
Author Correction: Commensal production of a broad-spectrum and short-lived antimicrobial peptide polyene eliminates nasal Staphylococcus aureus	42
An acidophilic fungus promotes prey digestion in a carnivorous plant	42
Primal FEAR protects against infection	42
Immune imprinting in early life shapes cross-reactivity to influenza B virus haemagglutinin	42
Dietary zinc deficiency promotes Acinetobacter baumannii lung infection via IL-13 in mice	41
Post-acute sequelae of SARS-CoV-2 cardiovascular symptoms are associated with trace-level cytokines that affect cardiomyocyte function	41
Parasitic bacteria control foam formation	41
Epigenetic modifications influence urinary tract infection outcome	40
CRISPR-influenced symbiosis	40
Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut	40
Author Correction: A positive feedback loop controls Toxoplasma chronic differentiation	40
A predicted CRISPR-mediated symbiosis between uncultivated archaea	40
Advocating a watch-and-prepare approach with avian influenza	40
Understanding antimicrobial resistance to manage cholera	39
Synthesis of lipid-linked precursors of the bacterial cell wall is governed by a feedback control mechanism in Pseudomonas aeruginosa	39
Turning the tide against antimicrobial resistance in Africa	39
Bacteroides fragilis uses toxins for gut success	39
Author Correction: Soil microbiome indicators can predict crop growth response to large-scale inoculation with arbuscular mycorrhizal fungi	39
Toxoplasma protein export and effector function	39
Mineral-eating microorganisms at extinct hydrothermal vents	38
Designed secretion deters microbiome depletion	38
Author Correction: Autophagy restricts Mycobacterium tuberculosis during acute infection in mice	38
Pleiotropic prebiotic for liver disease	38
Fast track to mutualism	37
Author Correction: Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes	37
Microbial regulation of cholesterol homeostasis	37
Uncontrolled transposition following RNAi loss causes hypermutation and antifungal drug resistance in clinical isolates of Cryptococcus neoformans	37
Computational discovery of dynobactin antibiotics	36
Chikungunya virus assembly and budding visualized in situ using cryogenic electron tomography	36
Combining pathogen and host metagenomics for a better sepsis diagnostic	36
Mixotrophy in depth	35
Histones direct site-specific CRISPR spacer acquisition in model archaeon	35
Stepwise assembly and release of Tc toxins from Yersinia entomophaga	35
Tracking outbreak dynamics using within-host variation	35
Bluetongue virus capsid protein VP5 perforates membranes at low endosomal pH during viral entry	35
The gut microbiome in anorexia nervosa	35
Differential carbon utilization enables co-existence of recently speciated Campylobacteraceae in the cow rumen epithelial microbiome	35
Comparative effectiveness of third doses of mRNA-based COVID-19 vaccines in US veterans	35
Building a career during a revolution in biology	35
Author Correction: Select autophagy genes maintain quiescence of tissue-resident macrophages and increase susceptibility to Listeria monocytogenes	34
Gut microorganism enzymes unlock universal blood	34
Keeping division on track	34
Author Correction: Rhinoviruses usurp STING for replication	34
Phage proteins target and co-opt host ribosomes immediately upon infection	34
Publisher Correction: Mosquitoes provide a transmission route between possums and humans for Buruli ulcer in southeastern Australia	34
Filamentous viruses prevail under pressure	34
Phosphatidylserine-exposing extracellular vesicles in body fluids are an innate defence against apoptotic mimicry viral pathogens	34
Establishing microbiome causality to tackle malnutrition	34
A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants	33
Host cell glycosylation selects for infection with CCR5- versus CXCR4-tropic HIV-1	33
Prioritizing mentorship	33
Multiple sclerosis patient-derived spontaneous B cells have distinct EBV and host gene expression profiles in active disease	33
Design and regulation of engineered bacteria for environmental release	33
Plant roots temporarily leak iron to promote colonization by beneficial rhizobacterium	33
Connecting the dots from viral infection to disease	33
Plant killers make the cut	32
Diadenosine tetraphosphate regulates biosynthesis of GTP in Bacillus subtilis	32
Klebsiella oxytoca inhibits Salmonella infection through multiple microbiota-context-dependent mechanisms	32
Broadly therapeutic antibody provides cross-serotype protection against enteroviruses via Fc effector functions and by mimicking SCARB2	32
A trove of Asgard archaeal viruses	32
Author Correction: Age-specific nasal epithelial responses to SARS-CoV-2 infection	32
Tackling non-typhoidal Salmonella with humility	32