Nature Microbiology

Article	Citations
Gene–drug potency screening in M. tuberculosis	577
Sickle cell trait enhances malaria transmission	373
Metabolic sensing tips the balance of drug tolerance in fungal meningitis	282
Author Correction: DART takes aim at community editing	270
Molecular factors shaping whether HCMV infection is productive or latent	260
Rebound virus in the cerebrospinal fluid reveals a possible HIV-1 reservoir	260
Horizontal gene transfer explains unusual traits of Armillaria fungi	254
Dietary exclusion of major food groups shapes the gut microbiome and may influence health	224
Structure of a functional archaellum in Bacteria of the Chloroflexota phylum	214
Cytoplasmic contractile injection systems mediate cell death in Streptomyces	211
The structure of the complete extracellular bacterial flagellum reveals the mechanism of flagellin incorporation	210
The Mycobacterium tuberculosis protein O-phosphorylation landscape	202
Candida albicans extracellular vesicles trigger type I IFN signalling via cGAS and STING	197
Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division	186
Recent gene selection and drug resistance underscore clinical adaptation across Candida species	182
Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome	178
Aspergillus fumigatus dsRNA virus promotes fungal fitness and pathogenicity in the mammalian host	177
Flipping the magic switch to persistence via GTP depletion	173
Explainable artificial intelligence evolves antimicrobial peptides	168
The Parkinson’s disease drug entacapone disrupts gut microbiome homeostasis via iron sequestration	160
Microbiome association with coral growth and survival	158
Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan	157
The fast-evolving FIKK kinase family of Plasmodium falciparum can be inhibited by a single compound	157
Climate extremes disrupt fungal–bacterial interactions	155
Assessing critical thresholds in terrestrial microbiomes	154

Mechanistic basis for potent neutralization of Sin Nombre hantavirus by a human monoclonal antibody	153
Mosquitoes provide a transmission route between possums and humans for Buruli ulcer in southeastern Australia	152
OPENPichia: licence-free Komagataella phaffii chassis strains and toolkit for protein expression	148
A high-throughput and low-waste viability assay for microbes	145
Host range, transmissibility and antigenicity of a pangolin coronavirus	144
Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria	142
Organ-on-chip models for infectious disease research	142
A dynamic subpopulation of CRISPR–Cas overexpressers allows Streptococcus pyogenes to rapidly respond to phage	140
Single mutation makes Escherichia coli an insect mutualist	135
Rational design of a hospital-specific phage cocktail to treat Enterobacter cloacae complex infections	134
Mycobacterium abscessus pathogenesis identified by phenogenomic analyses	134
The IFIT2–IFIT3 antiviral complex targets short 5’ untranslated regions on viral mRNAs for translation inhibition	134
Prodrug florfenicol amine is activated by intrinsic resistance to target Mycobacterium abscessus	133
Therapeutic efficacy of monoclonal antibodies and antivirals against SARS-CoV-2 Omicron BA.1 in Syrian hamsters	131
Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains	130
Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults	130
Pseudomonas syringae subpopulations cooperate by coordinating flagellar and type III secretion spatiotemporal dynamics to facilitate plant infection	129
Exceeding expectations out in the cold with Colwellia	129
Publisher Correction: Breastfeeding promotes bifidobacterial immunomodulatory metabolites	127
Mineral-eating microorganisms at extinct hydrothermal vents	127
CRISPR-influenced symbiosis	127
Prioritizing mentorship	122
Call for papers on the clinical microbiome	119
Blockade of endothelin receptors mitigates SARS-CoV-2-induced osteoarthritis	118
Bacteroides fragilis uses toxins for gut success	118
Extracellular vesicles block viral entryways	114
Synthesis of lipid-linked precursors of the bacterial cell wall is governed by a feedback control mechanism in Pseudomonas aeruginosa	113
Kaposi’s sarcoma-associated herpesvirus induces mitochondrial fission to evade host immune responses and promote viral production	112
Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment	112
Risk–reward trade-off during carbon starvation generates dichotomy in motility endurance among marine bacteria	112
SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome	112
Rational attenuation of RNA viruses with zinc finger antiviral protein	111
Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration	110
Decoding the impact of nuclear organization on antigenic variation in parasites	109
Transforming tuberculosis diagnosis	106
Archaeal symbioses all the way down	105
The complex path towards herpesvirus vaccines	105
Streptomyces polyketides mediate bacteria–fungi interactions across soil environments	104
Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2	103
Switching on cyclic di-GMP heterogeneity in Pseudomonas aeruginosa biofilms	102
Expanding known viral diversity in the healthy infant gut	102
Coronavirus sampling and surveillance in bats from 1996–2019: a systematic review and meta-analysis	102
SARS and synapses	101
Placental Streptococcus agalactiae DNA is associated with neonatal unit admission and foetal pro-inflammatory cytokines in term infants	100
Publisher Correction: 2021 in review	99
Publisher Correction: Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis	99
CryoEM reveals that ribosomes in microsporidian spores are locked in a dimeric hibernating state	98
From farm to factory to fork	98
SARS-CoV-2 infection induces pro-fibrotic and pro-thrombotic foam cell formation	97
Mycobacterium tuberculosis as teacher	97

A nitrogen-fixing bacterium forms symbioses on land and at sea	96
Genome-resolved metagenomics reveals microbiome diversity across 48 tick species	96
The gut–liver axis in HCV infection	94
Connecting microbiome and menopause for healthy ageing	94
Hunting emerging viruses through participatory community science	94
Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study	93
Therapeutics for COVID-19	92
Using animation to mediate scientific discourse	91
Phages with a broad host range are common across ecosystems	91
Parasite and vector circadian clocks mediate efficient malaria transmission	91
Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes	90
An expanded metabolic pathway for androgen production by commensal bacteria	89
Anoxia activates CRISPR–Cas immunity in the mouse intestine	89
Combining antibiotics to tackle antimicrobial resistance	88
Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia	88
Cell envelope diversity and evolution across the bacterial tree of life	86
Characterization of inositol lipid metabolism in gut-associated Bacteroidetes	85
Dynamic diel proteome and daytime nitrogenase activity supports buoyancy in the cyanobacterium Trichodesmium	85
Bacteriophages avoid autoimmunity from cognate immune systems as an intrinsic part of their life cycles	84
Discovery of an orally active benzoxaborole prodrug effective in the treatment of Chagas disease in non-human primates	83
Clinical implications of preterm infant gut microbiome development	83
Species- and site-specific genome editing in complex bacterial communities	82
Harnessing the microbiome to prevent global biodiversity loss	81
Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants	79
Increased small particle aerosol transmission of B.1.1.7 compared with SARS-CoV-2 lineage A in vivo	78
Outbreak dynamics of foodborne pathogen Vibrio parahaemolyticus over a seventeen year period implies hidden reservoirs	77
Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut	77
Escherichia coli integrates chemotaxis and quorum sensing pathways in vivo	76
Dietary fibre counters the oncogenic potential of colibactin-producing Escherichia coli in colorectal cancer	76
A year of microbiology	75
TOLLIP inhibits lipid accumulation and the integrated stress response in alveolar macrophages to control Mycobacterium tuberculosis infection	75
GprC of the nematode-trapping fungus Arthrobotrys flagrans activates mitochondria and reprograms fungal cells for nematode hunting	74
Mining the microbiota for antibiotics	74
Guiding phage therapy with genomic surveillance	73
Bacteria can shed a layer when phages turn up the heat	72
Reproductive justice must be considered in the scientific community	71
Safety and immunogenicity of a prefusion non-stabilized spike protein mRNA COVID-19 vaccine: a phase I trial	70
Non-equivalent genomes in polyploid prokaryotes	70
Metabolic modelling reveals the aging-associated decline of host–microbiome metabolic interactions in mice	70
mRNA-encoded Cas13 can be used to treat dengue infections in mice	70
A vision for spaceflight microbiology to enable human health and habitat sustainability	70
Siderophores mediate antibiotic resistance	70
Bacteria modulate microalgal aging physiology through the induction of extracellular vesicle production to remove harmful metabolites	69
Growth rate is modulated by monitoring cell wall precursors in Bacillus subtilis	69
Human microbiome myths and misconceptions	69
A framework for automated scalable designation of viral pathogen lineages from genomic data	69
Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria	68
Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships	68
Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine	67
Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters	66
The cell biology of archaea	66
Microbial metabolites in the marine carbon cycle	65
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism	65
Identified receptors shed light on Epstein–Barr virus infection	65
Gut microbial factors predict disease severity in a mouse model of multiple sclerosis	64
Environmental stress mediates groundwater microbial community assembly	63
Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts	62
Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes	62
The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice	60
Parabacteroides distasonis uses dietary inulin to suppress NASH via its metabolite pentadecanoic acid	59
Migrant health matters	58
CD8+ T cell depletion does not induce an expansion of viral reservoir in HIV model	58
Amplifying diverse voices in microbiology	58
Shining light on the coral photosymbiont family Symbiodiniaceae	58
A method to detect origin of transfer sequences for plasmid conjugation	57
Diet switch pre-vaccination improves immune response and metabolic status in formerly obese mice	57
We must learn from past outbreaks	57
Molecular organization of the New World arenavirus spike glycoprotein complex	57
Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes	57
Phase transition of GvpU regulates gas vesicle clustering in bacteria	56
Metabolites from intact phage-infected Synechococcus chemotactically attract heterotrophic marine bacteria	56
Characterizing extracellular vesicles of human fungal pathogens	56
Identifying an evolutionary origin for morbilliviruses in bats	56
Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection	56
Staphylococcal virulence factor HlgB targets the endoplasmic-reticulum-resident E3 ubiquitin ligase AMFR to promote pneumonia	56
Retracing a tangled tree of archaeal evolution	56
BacterAI maps microbial metabolism without prior knowledge	56
Comprehensive transcription terminator atlas for Bacillus subtilis	55
The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate	55
Addressing gaps in author and reviewer gender diversity	54

Multinational epidemiological analysis of oral human papillomavirus incidence in 3,137 men	54
Preclinical evaluation of the SARS-CoV-2 Mpro inhibitor RAY1216 shows improved pharmacokinetics compared with nirmatrelvir	54
SARS-CoV-2 Africa dashboard for real-time COVID-19 information	54
A haem-sequestering plant peptide promotes iron uptake in symbiotic bacteria	53
Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen	53
Gut bacteria degrade purines via the 2,8-dioxopurine pathway	53
Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial	53
Sulfated glycosaminoglycans are host epithelial cell targets of the Candida albicans toxin candidalysin	52
Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon	52
Inactivated whole-virion vaccine BBV152/Covaxin elicits robust cellular immune memory to SARS-CoV-2 and variants of concern	52
Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework	52
Dairy cows develop protective immunity against reinfection with bovine H5N1 influenza virus	52
AMR, One Health and the environment	51
Tecovirimat is effective against human monkeypox virus in vitro at nanomolar concentrations	51
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway	51
Genome-wide protein–DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase	50
Iron-limitation light switch	50
Translating between science and politics as a government adviser	50
Taurolithocholic acid protects against viral haemorrhagic fever via inhibition of ferroptosis	50
Microbes and the water nexus	50
Sex, gender and infectious disease	49
The human archaeome in focus	49
Colonic goblet cell-associated antigen passages mediate physiologic and beneficial translocation of live gut bacteria in preweaning mice	49
The GATE glycoprotein complex enhances human cytomegalovirus entry in endothelial cells	48
Understanding emerging and re-emerging viruses to facilitate pandemic preparedness	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
Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota	48
Targeting the mosquito prefoldin–chaperonin complex blocks Plasmodium transmission	48
Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis	48
Chromosome architecture in an archaeal species naturally lacking structural maintenance of chromosomes proteins	48
Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain	48
Publisher Correction: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission	47
Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances	47
Remote control designer probiotics	47
Nasal Staphylococcus aureus carriage promotes depressive behaviour in mice via sex hormone degradation	47
Enterococcus faecalis-derived adenine enhances enterohaemorrhagic Escherichia coli Type 3 Secretion System-dependent virulence	46
Metagenomic characterization of viruses and mobile genetic elements associated with the DPANN archaeal superphylum	46
Understanding the biology of monkeypox virus to prevent future outbreaks	46
Exploiting the fitness cost of metallo-β-lactamase expression can overcome antibiotic resistance in bacterial pathogens	46
Metabolic reprogramming enhances the susceptibility of multidrug- and carbapenem-resistant bacteria to antibiotics	46
Cooperative virulence via the collective action of secreted pathogen effectors	46
Dual inhibition of innate immunity and apoptosis by human cytomegalovirus protein UL37x1 enables efficient virus replication	46
Introducing Microbe Matters	45
Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea	45
Integrons are anti-phage defence libraries in Vibrio parahaemolyticus	45
A high-quality genome compendium of the human gut microbiome of Inner Mongolians	45
Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites	45
Moving from hype to hope in diet–microbiome interactions	44
Small organisms with big climate impact	44
The host–parasite–virus triad	44
Author Correction: Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host–plant interactions	44
Talented microbes unlatch peatland carbon	44
Persistent viral RNA and protein contribute to post-acute pathology	43
Parkinson’s disease kinase LRRK2 coordinates a cell-intrinsic itaconate-dependent defence pathway against intracellular Salmonella	43
Use microbes to tackle food insecurity	43
Factors associated with oral HPV infection among a large multinational cohort of men	43
Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota	43
A non-human primate model for human norovirus infection	43
Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever	43
Identifying rare and active species that drive carbon turnover in complex microbiotas	42
Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient	42
Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information	41
Microplastic research must consider microbes	41
Discovery and artificial intelligence-guided mechanistic elucidation of a narrow-spectrum antibiotic	41
Author Correction: Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut	41
Methane-dependent complete denitrification by a single Methylomirabilis bacterium	41
Identification of structurally diverse menaquinone-binding antibiotics with in vivo activity against multidrug-resistant pathogens	41
Leaf microbiome dysbiosis triggered by T2SS-dependent enzyme secretion from opportunistic Xanthomonas pathogens	41
Viral biogeography of the mammalian gut and parenchymal organs	41
Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation	41
Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda	41
Mycobiota and diet-derived fungal xenosiderophores promote Salmonella gastrointestinal colonization	41
Structural insights into tecovirimat antiviral activity and poxvirus resistance	41
Microbiome alterations in autism spectrum disorder	40
Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation	40
scRNA-seq reveals transcriptional plasticity of var gene expression in Plasmodium falciparum for host immune avoidance	40
Intestinal crypt microbiota modulates intestinal stem cell turnover and tumorigenesis via indole acetic acid	40
Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought	40
The unusual cell wall of the Lyme disease spirochaete Borrelia burgdorferi is shaped by a tick sugar	40
Vientovirus capsid protein mimics autoantigens and contributes to autoimmunity in Sjögren’s disease	40
Multigenerational proteolytic inactivation of restriction upon subtle genomic hypomethylation in Pseudomonas aeruginosa	40
Drug–Fc conjugate CD388 targets influenza virus neuraminidase and is broadly protective in mice	40
Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses	40
FungAMR: a comprehensive database for investigating fungal mutations associated with antimicrobial resistance	39
DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms	39
Redefining success	39
Chromosome organization affects genome evolution in Sulfolobus archaea	39
Connecting the dots from viral infection to disease	39
Evolution of SARS-CoV-2 in the murine central nervous system drives viral diversification	39
CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery	39
Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency	39
Knowledge synthesis through scientific visualization	39
Broadly therapeutic antibody provides cross-serotype protection against enteroviruses via Fc effector functions and by mimicking SCARB2	38
Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags	38