Nature Microbiology

Article	Citations
Gene–drug potency screening in M. tuberculosis	570
Sickle cell trait enhances malaria transmission	372
Metabolic sensing tips the balance of drug tolerance in fungal meningitis	360
Author Correction: DART takes aim at community editing	279
Rebound virus in the cerebrospinal fluid reveals a possible HIV-1 reservoir	257
Cytoplasmic contractile injection systems mediate cell death in Streptomyces	252
Molecular factors shaping whether HCMV infection is productive or latent	248
Horizontal gene transfer explains unusual traits of Armillaria fungi	243
Dietary exclusion of major food groups shapes the gut microbiome and may influence health	208
Single mutation makes Escherichia coli an insect mutualist	205
Rational design of a hospital-specific phage cocktail to treat Enterobacter cloacae complex infections	204
Assessing critical thresholds in terrestrial microbiomes	200
The structure of the complete extracellular bacterial flagellum reveals the mechanism of flagellin incorporation	198
Aspergillus fumigatus dsRNA virus promotes fungal fitness and pathogenicity in the mammalian host	194
Structure of a functional archaellum in Bacteria of the Chloroflexota phylum	179
Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains	178
Appressorium-mediated plant infection by Magnaporthe oryzae is regulated by a Pmk1-dependent hierarchical transcriptional network	175
The Mycobacterium tuberculosis protein O-phosphorylation landscape	173
Flipping the magic switch to persistence via GTP depletion	163
Explainable artificial intelligence evolves antimicrobial peptides	160
Therapeutic efficacy of monoclonal antibodies and antivirals against SARS-CoV-2 Omicron BA.1 in Syrian hamsters	157
The Parkinson’s disease drug entacapone disrupts gut microbiome homeostasis via iron sequestration	154
Host range, transmissibility and antigenicity of a pangolin coronavirus	153
Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome	152
Mosquitoes provide a transmission route between possums and humans for Buruli ulcer in southeastern Australia	152

Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan	148
Organ-on-chip models for infectious disease research	147
Climate extremes disrupt fungal–bacterial interactions	147
Recent gene selection and drug resistance underscore clinical adaptation across Candida species	146
Candida albicans extracellular vesicles trigger type I IFN signalling via cGAS and STING	139
Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria	139
A high-throughput and low-waste viability assay for microbes	138
Mechanistic basis for potent neutralization of Sin Nombre hantavirus by a human monoclonal antibody	135
Mycobacterium abscessus pathogenesis identified by phenogenomic analyses	134
Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division	133
A dynamic subpopulation of CRISPR–Cas overexpressers allows Streptococcus pyogenes to rapidly respond to phage	130
Microbiome association with coral growth and survival	129
The fast-evolving FIKK kinase family of Plasmodium falciparum can be inhibited by a single compound	128
Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults	127
Pseudomonas syringae subpopulations cooperate by coordinating flagellar and type III secretion spatiotemporal dynamics to facilitate plant infection	127
OPENPichia: licence-free Komagataella phaffii chassis strains and toolkit for protein expression	127
Exceeding expectations out in the cold with Colwellia	127
Decoding the impact of nuclear organization on antigenic variation in parasites	126
CRISPR-influenced symbiosis	126
Rational attenuation of RNA viruses with zinc finger antiviral protein	126
Regulators unite to enable plant entry	124
Publisher Correction: Breastfeeding promotes bifidobacterial immunomodulatory metabolites	123
Prioritizing mentorship	117
Mineral-eating microorganisms at extinct hydrothermal vents	117
Call for papers on the clinical microbiome	116
Risk–reward trade-off during carbon starvation generates dichotomy in motility endurance among marine bacteria	112
Kaposi’s sarcoma-associated herpesvirus induces mitochondrial fission to evade host immune responses and promote viral production	110
Blockade of endothelin receptors mitigates SARS-CoV-2-induced osteoarthritis	110
Bacteroides fragilis uses toxins for gut success	109
Extracellular vesicles block viral entryways	108
Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2	107
SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome	107
Transforming tuberculosis diagnosis	107
Synthesis of lipid-linked precursors of the bacterial cell wall is governed by a feedback control mechanism in Pseudomonas aeruginosa	107
Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment	106
Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration	104
Expanding known viral diversity in the healthy infant gut	103
Coronavirus sampling and surveillance in bats from 1996–2019: a systematic review and meta-analysis	101
Using animation to mediate scientific discourse	101
Streptomyces polyketides mediate bacteria–fungi interactions across soil environments	101
Switching on cyclic di-GMP heterogeneity in Pseudomonas aeruginosa biofilms	100
SARS and synapses	100
Placental Streptococcus agalactiae DNA is associated with neonatal unit admission and foetal pro-inflammatory cytokines in term infants	98
Publisher Correction: Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis	97
Dietary fibre counters the oncogenic potential of colibactin-producing Escherichia coli in colorectal cancer	97
Publisher Correction: 2021 in review	97
Combining antibiotics to tackle antimicrobial resistance	97
SARS-CoV-2 infection induces pro-fibrotic and pro-thrombotic foam cell formation	97
Parasite and vector circadian clocks mediate efficient malaria transmission	96
Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut	95

CryoEM reveals that ribosomes in microsporidian spores are locked in a dimeric hibernating state	93
From farm to factory to fork	93
The gut–liver axis in HCV infection	92
Hunting emerging viruses through participatory community science	92
Increased small particle aerosol transmission of B.1.1.7 compared with SARS-CoV-2 lineage A in vivo	91
Genome-resolved metagenomics reveals microbiome diversity across 48 tick species	90
Characterization of inositol lipid metabolism in gut-associated Bacteroidetes	89
A nitrogen-fixing bacterium forms symbioses on land and at sea	89
Cell envelope diversity and evolution across the bacterial tree of life	89
Phages with a broad host range are common across ecosystems	88
Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes	88
Outbreak dynamics of foodborne pathogen Vibrio parahaemolyticus over a seventeen year period implies hidden reservoirs	88
Mycobacterium tuberculosis as teacher	87
Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study	86
Dynamic diel proteome and daytime nitrogenase activity supports buoyancy in the cyanobacterium Trichodesmium	84
Clinical implications of preterm infant gut microbiome development	83
Species- and site-specific genome editing in complex bacterial communities	83
Therapeutics for COVID-19	83
Bacteriophages avoid autoimmunity from cognate immune systems as an intrinsic part of their life cycles	82
Connecting microbiome and menopause for healthy ageing	82
Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia	82
An expanded metabolic pathway for androgen production by commensal bacteria	82
Harnessing the microbiome to prevent global biodiversity loss	80
Discovery of an orally active benzoxaborole prodrug effective in the treatment of Chagas disease in non-human primates	80
Escherichia coli integrates chemotaxis and quorum sensing pathways in vivo	78
A year of microbiology	77
TOLLIP inhibits lipid accumulation and the integrated stress response in alveolar macrophages to control Mycobacterium tuberculosis infection	76
Non-equivalent genomes in polyploid prokaryotes	75
Achilles’ heel of antibiotic resistance	75
Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters	75
GprC of the nematode-trapping fungus Arthrobotrys flagrans activates mitochondria and reprograms fungal cells for nematode hunting	74
Growth rate is modulated by monitoring cell wall precursors in Bacillus subtilis	73
Mining the microbiota for antibiotics	73
Guiding phage therapy with genomic surveillance	72
Bacteria can shed a layer when phages turn up the heat	72
Reproductive justice must be considered in the scientific community	71
A framework for automated scalable designation of viral pathogen lineages from genomic data	70
Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes	69
Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria	69
Safety and immunogenicity of a prefusion non-stabilized spike protein mRNA COVID-19 vaccine: a phase I trial	69
mRNA-encoded Cas13 can be used to treat dengue infections in mice	68
Siderophores mediate antibiotic resistance	68
A vision for spaceflight microbiology to enable human health and habitat sustainability	68
Identified receptors shed light on Epstein–Barr virus infection	67
Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships	67
Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine	66
Human microbiome myths and misconceptions	66
Gut microbial factors predict disease severity in a mouse model of multiple sclerosis	66
Bacteria modulate microalgal aging physiology through the induction of extracellular vesicle production to remove harmful metabolites	66
The cell biology of archaea	65
Metabolic modelling reveals the aging-associated decline of host–microbiome metabolic interactions in mice	65
The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice	64
Environmental stress mediates groundwater microbial community assembly	64
Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts	64
Parabacteroides distasonis uses dietary inulin to suppress NASH via its metabolite pentadecanoic acid	63
Microbial metabolites in the marine carbon cycle	61
Shining light on the coral photosymbiont family Symbiodiniaceae	61
CD8+ T cell depletion does not induce an expansion of viral reservoir in HIV model	61
Migrant health matters	60
Amplifying diverse voices in microbiology	60
A method to detect origin of transfer sequences for plasmid conjugation	59
We must learn from past outbreaks	58
A haem-sequestering plant peptide promotes iron uptake in symbiotic bacteria	57
Rottlerin inhibits La Crosse virus-induced encephalitis in mice and blocks release of replicating virus from the Golgi body in neurons	56
AMR, One Health and the environment	56
Tecovirimat is effective against human monkeypox virus in vitro at nanomolar concentrations	56
Comprehensive transcription terminator atlas for Bacillus subtilis	55
Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework	55
Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen	55
Inactivated whole-virion vaccine BBV152/Covaxin elicits robust cellular immune memory to SARS-CoV-2 and variants of concern	55
Metabolites from intact phage-infected Synechococcus chemotactically attract heterotrophic marine bacteria	55
Sulfated glycosaminoglycans are host epithelial cell targets of the Candida albicans toxin candidalysin	55
Identifying an evolutionary origin for morbilliviruses in bats	54
Diet switch pre-vaccination improves immune response and metabolic status in formerly obese mice	54
Retracing a tangled tree of archaeal evolution	54
Phase transition of GvpU regulates gas vesicle clustering in bacteria	54
Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes	54
BacterAI maps microbial metabolism without prior knowledge	53
Addressing gaps in author and reviewer gender diversity	53
Gut bacteria degrade purines via the 2,8-dioxopurine pathway	53

Taurolithocholic acid protects against viral haemorrhagic fever via inhibition of ferroptosis	53
Staphylococcal virulence factor HlgB targets the endoplasmic-reticulum-resident E3 ubiquitin ligase AMFR to promote pneumonia	52
SARS-CoV-2 Africa dashboard for real-time COVID-19 information	52
Preclinical evaluation of the SARS-CoV-2 Mpro inhibitor RAY1216 shows improved pharmacokinetics compared with nirmatrelvir	51
The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate	51
Multinational epidemiological analysis of oral human papillomavirus incidence in 3,137 men	51
Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection	51
Characterizing extracellular vesicles of human fungal pathogens	51
Molecular organization of the New World arenavirus spike glycoprotein complex	50
Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial	50
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway	50
Dairy cows develop protective immunity against reinfection with bovine H5N1 influenza virus	50
Iron-limitation light switch	50
Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon	50
Genome-wide protein–DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase	50
Chromosome architecture in an archaeal species naturally lacking structural maintenance of chromosomes proteins	49
Microbes and the water nexus	49
Enterococcus faecalis-derived adenine enhances enterohaemorrhagic Escherichia coli Type 3 Secretion System-dependent virulence	49
A high-quality genome compendium of the human gut microbiome of Inner Mongolians	49
Translating between science and politics as a government adviser	49
Sex, gender and infectious disease	48
Cooperative virulence via the collective action of secreted pathogen effectors	48
Integrons are anti-phage defence libraries in Vibrio parahaemolyticus	48
The human archaeome in focus	48
Nasal Staphylococcus aureus carriage promotes depressive behaviour in mice via sex hormone degradation	48
Colonic goblet cell-associated antigen passages mediate physiologic and beneficial translocation of live gut bacteria in preweaning mice	48
Exploiting the fitness cost of metallo-β-lactamase expression can overcome antibiotic resistance in bacterial pathogens	48
Metabolic reprogramming enhances the susceptibility of multidrug- and carbapenem-resistant bacteria to antibiotics	47
Targeting the mosquito prefoldin–chaperonin complex blocks Plasmodium transmission	46
Understanding emerging and re-emerging viruses to facilitate pandemic preparedness	46
Remote control designer probiotics	46
Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain	46
Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis	45
Dual inhibition of innate immunity and apoptosis by human cytomegalovirus protein UL37x1 enables efficient virus replication	45
Understanding the biology of monkeypox virus to prevent future outbreaks	45
Metagenomic characterization of viruses and mobile genetic elements associated with the DPANN archaeal superphylum	45
Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota	45
Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances	45
The GATE glycoprotein complex enhances human cytomegalovirus entry in endothelial cells	45
Publisher Correction: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission	45
Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites	44
Acquired amphotericin B resistance leads to fitness trade-offs that can be mitigated by compensatory evolution in Candida auris	44
Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea	43
Author Correction: Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host–plant interactions	43
The host–parasite–virus triad	43
Small organisms with big climate impact	43
Introducing Microbe Matters	43
Moving from hype to hope in diet–microbiome interactions	43
Factors associated with oral HPV infection among a large multinational cohort of men	43
Talented microbes unlatch peatland carbon	43
Microplastic research must consider microbes	42
CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery	42
A non-human primate model for human norovirus infection	42
Parkinson’s disease kinase LRRK2 coordinates a cell-intrinsic itaconate-dependent defence pathway against intracellular Salmonella	42
Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient	42
Multigenerational proteolytic inactivation of restriction upon subtle genomic hypomethylation in Pseudomonas aeruginosa	42
Use microbes to tackle food insecurity	42
The unusual cell wall of the Lyme disease spirochaete Borrelia burgdorferi is shaped by a tick sugar	42
Intestinal crypt microbiota modulates intestinal stem cell turnover and tumorigenesis via indole acetic acid	41
Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota	41
Chromosome organization affects genome evolution in Sulfolobus archaea	41
FungAMR: a comprehensive database for investigating fungal mutations associated with antimicrobial resistance	41
Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency	41
Mycobiota and diet-derived fungal xenosiderophores promote Salmonella gastrointestinal colonization	41
Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever	41
Vientovirus capsid protein mimics autoantigens and contributes to autoimmunity in Sjögren’s disease	41
Identification of structurally diverse menaquinone-binding antibiotics with in vivo activity against multidrug-resistant pathogens	40
Leaf microbiome dysbiosis triggered by T2SS-dependent enzyme secretion from opportunistic Xanthomonas pathogens	40
Microbiome alterations in autism spectrum disorder	40
Author Correction: Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut	40
scRNA-seq reveals transcriptional plasticity of var gene expression in Plasmodium falciparum for host immune avoidance	40
Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought	39
Evolution of SARS-CoV-2 in the murine central nervous system drives viral diversification	39
Persistent viral RNA and protein contribute to post-acute pathology	39
Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses	39
Drug–Fc conjugate CD388 targets influenza virus neuraminidase and is broadly protective in mice	39
Structural insights into tecovirimat antiviral activity and poxvirus resistance	39
Viral biogeography of the mammalian gut and parenchymal organs	39
Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation	38
Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information	38
DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms	38
Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda	38
Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation	38
Methane-dependent complete denitrification by a single Methylomirabilis bacterium	38
An acidophilic fungus promotes prey digestion in a carnivorous plant	37
Shigella handcuffs caspases	37
A trove of Asgard archaeal viruses	37
Primal FEAR protects against infection	37
Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan	37
A new malaria gene regulator	37
Redefining success	37
Connecting the dots from viral infection to disease	37
Sexually transmitted infections and female reproductive health	37
Fungal dysbiosis and survival after allo-HCT	37
Knowledge synthesis through scientific visualization	37