Nature Microbiology

Article	Citations
Rebound virus in the cerebrospinal fluid reveals a possible HIV-1 reservoir	561
Sickle cell trait enhances malaria transmission	362
Metabolic sensing tips the balance of drug tolerance in fungal meningitis	354
Gene–drug potency screening in M. tuberculosis	268
Author Correction: DART takes aim at community editing	254
Molecular factors shaping whether HCMV infection is productive or latent	245
Horizontal gene transfer explains unusual traits of Armillaria fungi	241
Dietary exclusion of major food groups shapes the gut microbiome and may influence health	239
Microbiome association with coral growth and survival	237
The fast-evolving FIKK kinase family of Plasmodium falciparum can be inhibited by a single compound	200
A dynamic subpopulation of CRISPR–Cas overexpressers allows Streptococcus pyogenes to rapidly respond to phage	200
Explainable artificial intelligence evolves antimicrobial peptides	193
The structure of the complete extracellular bacterial flagellum reveals the mechanism of flagellin incorporation	193
Flipping the magic switch to persistence via GTP depletion	190
Assessing critical thresholds in terrestrial microbiomes	188
Climate extremes disrupt fungal–bacterial interactions	182
Mycobacterium abscessus pathogenesis identified by phenogenomic analyses	171
Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division	169
Host range, transmissibility and antigenicity of a pangolin coronavirus	166
Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan	166
Therapeutic efficacy of monoclonal antibodies and antivirals against SARS-CoV-2 Omicron BA.1 in Syrian hamsters	156
A high-throughput and low-waste viability assay for microbes	155
The Mycobacterium tuberculosis protein O-phosphorylation landscape	152
Cytoplasmic contractile injection systems mediate cell death in Streptomyces	148
OPENPichia: licence-free Komagataella phaffii chassis strains and toolkit for protein expression	148

Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains	148
Appressorium-mediated plant infection by Magnaporthe oryzae is regulated by a Pmk1-dependent hierarchical transcriptional network	147
Recent gene selection and drug resistance underscore clinical adaptation across Candida species	145
Single mutation makes Escherichia coli an insect mutualist	142
The Parkinson’s disease drug entacapone disrupts gut microbiome homeostasis via iron sequestration	139
Mosquitoes provide a transmission route between possums and humans for Buruli ulcer in southeastern Australia	136
Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria	135
Candida albicans extracellular vesicles trigger type I IFN signalling via cGAS and STING	135
Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults	130
Organ-on-chip models for infectious disease research	129
Mechanistic basis for potent neutralization of Sin Nombre hantavirus by a human monoclonal antibody	128
Exceeding expectations out in the cold with Colwellia	126
Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome	126
Blockade of endothelin receptors mitigates SARS-CoV-2-induced osteoarthritis	125
Extracellular vesicles block viral entryways	125
Risk–reward trade-off during carbon starvation generates dichotomy in motility endurance among marine bacteria	124
Kaposi’s sarcoma-associated herpesvirus induces mitochondrial fission to evade host immune responses and promote viral production	124
Call for papers on the clinical microbiome	124
Bacteroides fragilis uses toxins for gut success	124
Prioritizing mentorship	122
SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome	121
Regulators unite to enable plant entry	120
Mineral-eating microorganisms at extinct hydrothermal vents	120
CRISPR-influenced symbiosis	120
Publisher Correction: Breastfeeding promotes bifidobacterial immunomodulatory metabolites	120
Synthesis of lipid-linked precursors of the bacterial cell wall is governed by a feedback control mechanism in Pseudomonas aeruginosa	114
Decoding the impact of nuclear organization on antigenic variation in parasites	113
Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration	109
Coronavirus sampling and surveillance in bats from 1996–2019: a systematic review and meta-analysis	109
Pseudomonas syringae subpopulations cooperate by coordinating flagellar and type III secretion spatiotemporal dynamics to facilitate plant infection	108
Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2	106
Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment	105
Rational attenuation of RNA viruses with zinc finger antiviral protein	104
Expanding known viral diversity in the healthy infant gut	104
Transforming tuberculosis diagnosis	103
Publisher Correction: Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis	102
Streptomyces polyketides mediate bacteria–fungi interactions across soil environments	102
SARS and synapses	101
Switching on cyclic di-GMP heterogeneity in Pseudomonas aeruginosa biofilms	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
Using animation to mediate scientific discourse	98
Discovery of an orally active benzoxaborole prodrug effective in the treatment of Chagas disease in non-human primates	97
The gut–liver axis in HCV infection	97
Cell envelope diversity and evolution across the bacterial tree of life	97
Hunting emerging viruses through participatory community science	97
Mycobacterium tuberculosis as teacher	96
Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study	96
CryoEM reveals that ribosomes in microsporidian spores are locked in a dimeric hibernating state	94
SARS-CoV-2 infection induces pro-fibrotic and pro-thrombotic foam cell formation	94

Characterization of inositol lipid metabolism in gut-associated Bacteroidetes	94
Dietary fibre counters the oncogenic potential of colibactin-producing Escherichia coli in colorectal cancer	91
Increased small particle aerosol transmission of B.1.1.7 compared with SARS-CoV-2 lineage A in vivo	91
Parasite and vector circadian clocks mediate efficient malaria transmission	91
Combining antibiotics to tackle antimicrobial resistance	90
Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes	90
Dynamic diel proteome and daytime nitrogenase activity supports buoyancy in the cyanobacterium Trichodesmium	89
Harnessing the microbiome to prevent global biodiversity loss	89
Therapeutics for COVID-19	89
Clinical implications of preterm infant gut microbiome development	89
An expanded metabolic pathway for androgen production by commensal bacteria	88
Connecting microbiome and menopause for healthy ageing	86
Bacteriophages avoid autoimmunity from cognate immune systems as an intrinsic part of their life cycles	85
Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia	85
From farm to factory to fork	85
Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut	82
A year of microbiology	82
Outbreak dynamics of foodborne pathogen Vibrio parahaemolyticus over a seventeen year period implies hidden reservoirs	82
Species- and site-specific genome editing in complex bacterial communities	82
Escherichia coli integrates chemotaxis and quorum sensing pathways in vivo	81
Reproductive justice must be considered in the scientific community	79
Guiding phage therapy with genomic surveillance	79
Mining the microbiota for antibiotics	78
Bacteria can shed a layer when phages turn up the heat	78
Non-equivalent genomes in polyploid prokaryotes	77
mRNA-encoded Cas13 can be used to treat dengue infections in mice	76
Achilles’ heel of antibiotic resistance	76
A framework for automated scalable designation of viral pathogen lineages from genomic data	76
Siderophores mediate antibiotic resistance	76
TOLLIP inhibits lipid accumulation and the integrated stress response in alveolar macrophages to control Mycobacterium tuberculosis infection	75
A vision for spaceflight microbiology to enable human health and habitat sustainability	75
Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships	74
Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts	74
Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria	74
Safety and immunogenicity of a prefusion non-stabilized spike protein mRNA COVID-19 vaccine: a phase I trial	71
Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters	71
Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes	70
Growth rate is modulated by monitoring cell wall precursors in Bacillus subtilis	69
Environmental stress mediates groundwater microbial community assembly	68
GprC of the nematode-trapping fungus Arthrobotrys flagrans activates mitochondria and reprograms fungal cells for nematode hunting	68
Gut microbial factors predict disease severity in a mouse model of multiple sclerosis	67
Human microbiome myths and misconceptions	67
Metabolic modelling reveals the aging-associated decline of host–microbiome metabolic interactions in mice	66
Bacteria modulate microalgal aging physiology through the induction of extracellular vesicle production to remove harmful metabolites	65
Microbial metabolites in the marine carbon cycle	65
Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine	64
Shining light on the coral photosymbiont family Symbiodiniaceae	64
Amplifying diverse voices in microbiology	64
The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice	64
Parabacteroides distasonis uses dietary inulin to suppress NASH via its metabolite pentadecanoic acid	64
A method to detect origin of transfer sequences for plasmid conjugation	64
The cell biology of archaea	64
CD8+ T cell depletion does not induce an expansion of viral reservoir in HIV model	64
Migrant health matters	64
We must learn from past outbreaks	63
Retracing a tangled tree of archaeal evolution	63
Addressing gaps in author and reviewer gender diversity	63
SARS-CoV-2 Africa dashboard for real-time COVID-19 information	62
Genome-wide protein–DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase	60
Identifying an evolutionary origin for morbilliviruses in bats	59
Metabolites from intact phage-infected Synechococcus chemotactically attract heterotrophic marine bacteria	57
Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial	57
Characterizing extracellular vesicles of human fungal pathogens	56
Dairy cows develop protective immunity against reinfection with bovine H5N1 influenza virus	56
Taurolithocholic acid protects against viral haemorrhagic fever via inhibition of ferroptosis	56
Inactivated whole-virion vaccine BBV152/Covaxin elicits robust cellular immune memory to SARS-CoV-2 and variants of concern	55
Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection	54
Gut bacteria degrade purines via the 2,8-dioxopurine pathway	54
Comprehensive transcription terminator atlas for Bacillus subtilis	54
Staphylococcal virulence factor HlgB targets the endoplasmic-reticulum-resident E3 ubiquitin ligase AMFR to promote pneumonia	54
Phase transition of GvpU regulates gas vesicle clustering in bacteria	54
Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon	54
Molecular organization of the New World arenavirus spike glycoprotein complex	53
Multinational epidemiological analysis of oral human papillomavirus incidence in 3,137 men	53
Preclinical evaluation of the SARS-CoV-2 Mpro inhibitor RAY1216 shows improved pharmacokinetics compared with nirmatrelvir	53
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway	53
AMR, One Health and the environment	52
Sulfated glycosaminoglycans are host epithelial cell targets of the Candida albicans toxin candidalysin	52
The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate	52
Diet switch pre-vaccination improves immune response and metabolic status in formerly obese mice	51

Tecovirimat is effective against human monkeypox virus in vitro at nanomolar concentrations	51
Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen	51
A haem-sequestering plant peptide promotes iron uptake in symbiotic bacteria	51
BacterAI maps microbial metabolism without prior knowledge	51
Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes	50
Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework	50
Rottlerin inhibits La Crosse virus-induced encephalitis in mice and blocks release of replicating virus from the Golgi body in neurons	50
Translating between science and politics as a government adviser	50
Chromosome architecture in an archaeal species naturally lacking structural maintenance of chromosomes proteins	49
Iron-limitation light switch	49
Publisher Correction: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission	49
Microbes and the water nexus	49
Genomics, social media and mobile phone data enable mapping of SARS-CoV-2 lineages to inform health policy in Bangladesh	49
Enterococcus faecalis-derived adenine enhances enterohaemorrhagic Escherichia coli Type 3 Secretion System-dependent virulence	49
Integrons are anti-phage defence libraries in Vibrio parahaemolyticus	48
Exploiting the fitness cost of metallo-β-lactamase expression can overcome antibiotic resistance in bacterial pathogens	48
Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea	48
A high-quality genome compendium of the human gut microbiome of Inner Mongolians	48
Metabolic reprogramming enhances the susceptibility of multidrug- and carbapenem-resistant bacteria to antibiotics	47
Targeting the mosquito prefoldin–chaperonin complex blocks Plasmodium transmission	47
Colonic goblet cell-associated antigen passages mediate physiologic and beneficial translocation of live gut bacteria in preweaning mice	47
Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain	47
Understanding emerging and re-emerging viruses to facilitate pandemic preparedness	47
Remote control designer probiotics	47
The human archaeome in focus	47
The GATE glycoprotein complex enhances human cytomegalovirus entry in endothelial cells	47
Metagenomic characterization of viruses and mobile genetic elements associated with the DPANN archaeal superphylum	46
Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis	46
Sex, gender and infectious disease	45
Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites	45
Cooperative virulence via the collective action of secreted pathogen effectors	45
Dual inhibition of innate immunity and apoptosis by human cytomegalovirus protein UL37x1 enables efficient virus replication	45
Acquired amphotericin B resistance leads to fitness trade-offs that can be mitigated by compensatory evolution in Candida auris	45
Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances	45
Understanding the biology of monkeypox virus to prevent future outbreaks	45
Author Correction: Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host–plant interactions	44
Introducing Microbe Matters	44
The host–parasite–virus triad	44
Talented microbes unlatch peatland carbon	44
Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency	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
Chromosome organization affects genome evolution in Sulfolobus archaea	43
Use microbes to tackle food insecurity	43
CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery	42
The unusual cell wall of the Lyme disease spirochaete Borrelia burgdorferi is shaped by a tick sugar	42
A non-human primate model for human norovirus infection	42
Persistent viral RNA and protein contribute to post-acute pathology	42
Evolution of SARS-CoV-2 in the murine central nervous system drives viral diversification	42
Viral biogeography of the mammalian gut and parenchymal organs	41
Mycobiota and diet-derived fungal xenosiderophores promote Salmonella gastrointestinal colonization	41
scRNA-seq reveals transcriptional plasticity of var gene expression in Plasmodium falciparum for host immune avoidance	41
FungAMR: a comprehensive database for investigating fungal mutations associated with antimicrobial resistance	41
Microbiome alterations in autism spectrum disorder	41
Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever	41
DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms	41
Small organisms with big climate impact	41
Author Correction: Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut	41
Identification of structurally diverse menaquinone-binding antibiotics with in vivo activity against multidrug-resistant pathogens	40
Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses	40
Structural insights into tecovirimat antiviral activity and poxvirus resistance	40
Parkinson’s disease kinase LRRK2 coordinates a cell-intrinsic itaconate-dependent defence pathway against intracellular Salmonella	40
Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda	40
Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation	39
Microplastic research must consider microbes	39
Drug–Fc conjugate CD388 targets influenza virus neuraminidase and is broadly protective in mice	39
Leaf microbiome dysbiosis triggered by T2SS-dependent enzyme secretion from opportunistic Xanthomonas pathogens	39
Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought	39
Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota	39
Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation	39
Intestinal crypt microbiota modulates intestinal stem cell turnover and tumorigenesis via indole acetic acid	39
Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient	38
Knowledge synthesis through scientific visualization	38
Methane-dependent complete denitrification by a single Methylomirabilis bacterium	38
Connecting the dots from viral infection to disease	38
Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information	38
A trove of Asgard archaeal viruses	37
Shigella handcuffs caspases	37
An acidophilic fungus promotes prey digestion in a carnivorous plant	37
Fungal dysbiosis and survival after allo-HCT	37
Toxoplasma protein export and effector function	37
Primal FEAR protects against infection	37
Redefining success	37
A new malaria gene regulator	37
Broadly therapeutic antibody provides cross-serotype protection against enteroviruses via Fc effector functions and by mimicking SCARB2	36
Author Correction: Soil microbiome indicators can predict crop growth response to large-scale inoculation with arbuscular mycorrhizal fungi	36
Streptomyces uses both polar and dispersed cell wall synthesis during exploratory growth	36
Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids	36
Computational discovery of dynobactin antibiotics	36
Deep learning reveals antibiotics in the archaeal proteome	36
Neutralizing antibody activity in convalescent sera from infection in humans with SARS-CoV-2 and variants of concern	36
Autophagy restricts Mycobacterium tuberculosis during acute infection in mice	35
Cytosolic sorting platform complexes shuttle type III secretion system effectors to the injectisome in Yersinia enterocolitica	35
Quantitative principles of microbial metabolism shared across scales	35
Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut	35