Nature Microbiology

Article	Citations
Rebound virus in the cerebrospinal fluid reveals a possible HIV-1 reservoir	552
Sickle cell trait enhances malaria transmission	353
Metabolic sensing tips the balance of drug tolerance in fungal meningitis	349
Author Correction: MX2-mediated innate immunity against HIV-1 is regulated by serine phosphorylation	346
Gene–drug potency screening in M. tuberculosis	259
Author Correction: DART takes aim at community editing	254
Molecular factors shaping whether HCMV infection is productive or latent	238
Horizontal gene transfer explains unusual traits of Armillaria fungi	234
Dietary exclusion of major food groups shapes the gut microbiome and may influence health	227
Mechanistic basis for potent neutralization of Sin Nombre hantavirus by a human monoclonal antibody	226
A dynamic subpopulation of CRISPR–Cas overexpressers allows Streptococcus pyogenes to rapidly respond to phage	196
A high-throughput and low-waste viability assay for microbes	191
Cytoplasmic contractile injection systems mediate cell death in Streptomyces	191
The structure of the complete extracellular bacterial flagellum reveals the mechanism of flagellin incorporation	189
Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria	183
Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains	178
Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults	168
Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division	163
Mycobacterium abscessus pathogenesis identified by phenogenomic analyses	162
Candida albicans extracellular vesicles trigger type I IFN signalling via cGAS and STING	161
Recent gene selection and drug resistance underscore clinical adaptation across Candida species	161
Host range, transmissibility and antigenicity of a pangolin coronavirus	155
Climate extremes disrupt fungal–bacterial interactions	150
Microbiome association with coral growth and survival	147
The fast-evolving FIKK kinase family of Plasmodium falciparum can be inhibited by a single compound	146

Explainable artificial intelligence evolves antimicrobial peptides	144
Assessing critical thresholds in terrestrial microbiomes	144
Flipping the magic switch to persistence via GTP depletion	144
OPENPichia: licence-free Komagataella phaffii chassis strains and toolkit for protein expression	140
Organ-on-chip models for infectious disease research	138
The Mycobacterium tuberculosis protein O-phosphorylation landscape	137
Therapeutic efficacy of monoclonal antibodies and antivirals against SARS-CoV-2 Omicron BA.1 in Syrian hamsters	133
The Parkinson’s disease drug entacapone disrupts gut microbiome homeostasis via iron sequestration	133
Single mutation makes Escherichia coli an insect mutualist	132
Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan	129
Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome	126
Appressorium-mediated plant infection by Magnaporthe oryzae is regulated by a Pmk1-dependent hierarchical transcriptional network	125
Mosquitoes provide a transmission route between possums and humans for Buruli ulcer in southeastern Australia	123
Exceeding expectations out in the cold with Colwellia	122
Blockade of endothelin receptors mitigates SARS-CoV-2-induced osteoarthritis	121
Extracellular vesicles block viral entryways	120
CRISPR-influenced symbiosis	119
Risk–reward trade-off during carbon starvation generates dichotomy in motility endurance among marine bacteria	118
Call for papers on the clinical microbiome	118
Bacteroides fragilis uses toxins for gut success	118
Prioritizing mentorship	117
Kaposi’s sarcoma-associated herpesvirus induces mitochondrial fission to evade host immune responses and promote viral production	117
Publisher Correction: Fungal biology: Fungal spores are future-proofed	117
Regulators unite to enable plant entry	115
Publisher Correction: Breastfeeding promotes bifidobacterial immunomodulatory metabolites	114
Mineral-eating microorganisms at extinct hydrothermal vents	114
Synthesis of lipid-linked precursors of the bacterial cell wall is governed by a feedback control mechanism in Pseudomonas aeruginosa	113
SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome	108
Coronavirus sampling and surveillance in bats from 1996–2019: a systematic review and meta-analysis	106
Rational attenuation of RNA viruses with zinc finger antiviral protein	106
Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment	105
Pseudomonas syringae subpopulations cooperate by coordinating flagellar and type III secretion spatiotemporal dynamics to facilitate plant infection	104
Decoding the impact of nuclear organization on antigenic variation in parasites	104
Identification of Tse8 as a Type VI secretion system toxin from Pseudomonas aeruginosa that targets the bacterial transamidosome to inhibit protein synthesis in prey cells	102
Expanding known viral diversity in the healthy infant gut	102
Transforming tuberculosis diagnosis	102
Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration	102
Streptomyces polyketides mediate bacteria–fungi interactions across soil environments	101
Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2	98
Publisher Correction: Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis	97
Placental Streptococcus agalactiae DNA is associated with neonatal unit admission and foetal pro-inflammatory cytokines in term infants	96
SARS and synapses	96
Switching on cyclic di-GMP heterogeneity in Pseudomonas aeruginosa biofilms	96
Using animation to mediate scientific discourse	95
Publisher Correction: 2021 in review	95
Dynamic diel proteome and daytime nitrogenase activity supports buoyancy in the cyanobacterium Trichodesmium	94
Bacteriophages avoid autoimmunity from cognate immune systems as an intrinsic part of their life cycles	94
Dietary fibre counters the oncogenic potential of colibactin-producing Escherichia coli in colorectal cancer	93
Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia	93
CryoEM reveals that ribosomes in microsporidian spores are locked in a dimeric hibernating state	93

Therapeutics for COVID-19	92
The gut–liver axis in HCV infection	90
An expanded metabolic pathway for androgen production by commensal bacteria	89
Hunting emerging viruses through participatory community science	89
Parasite and vector circadian clocks mediate efficient malaria transmission	88
Connecting microbiome and menopause for healthy ageing	88
Increased small particle aerosol transmission of B.1.1.7 compared with SARS-CoV-2 lineage A in vivo	88
Discovery of an orally active benzoxaborole prodrug effective in the treatment of Chagas disease in non-human primates	87
Cell envelope diversity and evolution across the bacterial tree of life	87
Characterization of inositol lipid metabolism in gut-associated Bacteroidetes	86
Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut	85
Mycobacterium tuberculosis as teacher	85
Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study	85
Combining antibiotics to tackle antimicrobial resistance	85
Harnessing the microbiome to prevent global biodiversity loss	84
Outbreak dynamics of foodborne pathogen Vibrio parahaemolyticus over a seventeen year period implies hidden reservoirs	83
Clinical implications of preterm infant gut microbiome development	82
From farm to factory to fork	81
Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes	78
Species- and site-specific genome editing in complex bacterial communities	77
A year of microbiology	77
Guiding phage therapy with genomic surveillance	76
Escherichia coli integrates chemotaxis and quorum sensing pathways in vivo	76
A vision for spaceflight microbiology to enable human health and habitat sustainability	75
Mining the microbiota for antibiotics	75
Reproductive justice must be considered in the scientific community	75
Bacteria can shed a layer when phages turn up the heat	74
Siderophores mediate antibiotic resistance	74
Achilles’ heel of antibiotic resistance	72
Safety and immunogenicity of a prefusion non-stabilized spike protein mRNA COVID-19 vaccine: a phase I trial	72
Metabolic modelling reveals the aging-associated decline of host–microbiome metabolic interactions in mice	72
Growth rate is modulated by monitoring cell wall precursors in Bacillus subtilis	72
Non-equivalent genomes in polyploid prokaryotes	71
Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships	71
Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria	70
The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice	70
Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts	68
Gut microbial factors predict disease severity in a mouse model of multiple sclerosis	67
Bacteria modulate microalgal aging physiology through the induction of extracellular vesicle production to remove harmful metabolites	67
mRNA-encoded Cas13 can be used to treat dengue infections in mice	67
A framework for automated scalable designation of viral pathogen lineages from genomic data	66
GprC of the nematode-trapping fungus Arthrobotrys flagrans activates mitochondria and reprograms fungal cells for nematode hunting	65
Human microbiome myths and misconceptions	65
Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters	65
Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine	65
The cell biology of archaea	64
Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes	64
Microbial metabolites in the marine carbon cycle	63
Shining light on the coral photosymbiont family Symbiodiniaceae	63
TOLLIP inhibits lipid accumulation and the integrated stress response in alveolar macrophages to control Mycobacterium tuberculosis infection	63
CD8+ T cell depletion does not induce an expansion of viral reservoir in HIV model	63
Environmental stress mediates groundwater microbial community assembly	63
Parabacteroides distasonis uses dietary inulin to suppress NASH via its metabolite pentadecanoic acid	63
Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon	62
Metabolites from intact phage-infected Synechococcus chemotactically attract heterotrophic marine bacteria	62
Rottlerin inhibits La Crosse virus-induced encephalitis in mice and blocks release of replicating virus from the Golgi body in neurons	62
A method to detect origin of transfer sequences for plasmid conjugation	62
Tecovirimat is effective against human monkeypox virus in vitro at nanomolar concentrations	61
Characterizing extracellular vesicles of human fungal pathogens	60
Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen	60
Comprehensive transcription terminator atlas for Bacillus subtilis	60
A haem-sequestering plant peptide promotes iron uptake in symbiotic bacteria	57
Amplifying diverse voices in microbiology	56
Migrant health matters	56
Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection	55
Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial	55
We must learn from past outbreaks	55
Multinational epidemiological analysis of oral human papillomavirus incidence in 3,137 men	54
SARS-CoV-2 Africa dashboard for real-time COVID-19 information	54
Diet switch pre-vaccination improves immune response and metabolic status in formerly obese mice	53
Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework	53
Genome-wide protein–DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase	53
Identifying an evolutionary origin for morbilliviruses in bats	53
Addressing gaps in author and reviewer gender diversity	52
Retracing a tangled tree of archaeal evolution	52
Inactivated whole-virion vaccine BBV152/Covaxin elicits robust cellular immune memory to SARS-CoV-2 and variants of concern	52
Sulfated glycosaminoglycans are host epithelial cell targets of the Candida albicans toxin candidalysin	51
Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes	51
BacterAI maps microbial metabolism without prior knowledge	51
AMR, One Health and the environment	51

Dairy cows develop protective immunity against reinfection with bovine H5N1 influenza virus	50
Staphylococcal virulence factor HlgB targets the endoplasmic-reticulum-resident E3 ubiquitin ligase AMFR to promote pneumonia	50
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway	50
Taurolithocholic acid protects against viral haemorrhagic fever via inhibition of ferroptosis	50
Phase transition of GvpU regulates gas vesicle clustering in bacteria	50
Preclinical evaluation of the SARS-CoV-2 Mpro inhibitor RAY1216 shows improved pharmacokinetics compared with nirmatrelvir	50
Translating between science and politics as a government adviser	49
The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate	49
Microbes and the water nexus	49
Exploiting the fitness cost of metallo-β-lactamase expression can overcome antibiotic resistance in bacterial pathogens	48
Iron-limitation light switch	48
Genomics, social media and mobile phone data enable mapping of SARS-CoV-2 lineages to inform health policy in Bangladesh	48
Chromosome architecture in an archaeal species naturally lacking structural maintenance of chromosomes proteins	47
Colonic goblet cell-associated antigen passages mediate physiologic and beneficial translocation of live gut bacteria in preweaning mice	47
Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea	47
Enterococcus faecalis-derived adenine enhances enterohaemorrhagic Escherichia coli Type 3 Secretion System-dependent virulence	47
Targeting the mosquito prefoldin–chaperonin complex blocks Plasmodium transmission	46
The human archaeome in focus	46
Publisher Correction: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission	46
Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain	46
Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances	45
Sex, gender and infectious disease	45
Understanding emerging and re-emerging viruses to facilitate pandemic preparedness	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
Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites	45
Dual inhibition of innate immunity and apoptosis by human cytomegalovirus protein UL37x1 enables efficient virus replication	45
Cooperative virulence via the collective action of secreted pathogen effectors	45
The GATE glycoprotein complex enhances human cytomegalovirus entry in endothelial cells	45
Integrons are anti-phage defence libraries in Vibrio parahaemolyticus	45
Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis	44
Remote control designer probiotics	44
A high-quality genome compendium of the human gut microbiome of Inner Mongolians	44
Acquired amphotericin B resistance leads to fitness trade-offs that can be mitigated by compensatory evolution in Candida auris	44
Moving from hype to hope in diet–microbiome interactions	43
The host–parasite–virus triad	43
Author Correction: Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host–plant interactions	43
Talented microbes unlatch peatland carbon	43
Introducing Microbe Matters	43
Factors associated with oral HPV infection among a large multinational cohort of men	42
CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery	42
Small organisms with big climate impact	42
Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda	42
Microplastic research must consider microbes	41
Drug–Fc conjugate CD388 targets influenza virus neuraminidase and is broadly protective in mice	41
Microbiome alterations in autism spectrum disorder	41
Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses	41
Persistent viral RNA and protein contribute to post-acute pathology	41
Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information	41
Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever	41
Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota	41
DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms	40
scRNA-seq reveals transcriptional plasticity of var gene expression in Plasmodium falciparum for host immune avoidance	40
Identification of structurally diverse menaquinone-binding antibiotics with in vivo activity against multidrug-resistant pathogens	40
Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient	40
Mycobiota and diet-derived fungal xenosiderophores promote Salmonella gastrointestinal colonization	39
Use microbes to tackle food insecurity	39
Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency	39
Evolution of SARS-CoV-2 in the murine central nervous system drives viral diversification	39
Structural insights into tecovirimat antiviral activity and poxvirus resistance	39
A non-human primate model for human norovirus infection	39
The unusual cell wall of the Lyme disease spirochaete Borrelia burgdorferi is shaped by a tick sugar	39
Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought	39
Chromosome organization affects genome evolution in Sulfolobus archaea	38
Intestinal crypt microbiota modulates intestinal stem cell turnover and tumorigenesis via indole acetic acid	38
Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation	38
Viral biogeography of the mammalian gut and parenchymal organs	38
Parkinson’s disease kinase LRRK2 coordinates a cell-intrinsic itaconate-dependent defence pathway against intracellular Salmonella	38
Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation	38
Author Correction: Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut	38
Methane-dependent complete denitrification by a single Methylomirabilis bacterium	37
Leaf microbiome dysbiosis triggered by T2SS-dependent enzyme secretion from opportunistic Xanthomonas pathogens	37
Connecting the dots from viral infection to disease	37
Knowledge synthesis through scientific visualization	37
An acidophilic fungus promotes prey digestion in a carnivorous plant	36
A new malaria gene regulator	36
Primal FEAR protects against infection	36
Toxoplasma protein export and effector function	36
Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut	36
Fungal dysbiosis and survival after allo-HCT	36
Redefining success	36
Broadly therapeutic antibody provides cross-serotype protection against enteroviruses via Fc effector functions and by mimicking SCARB2	36
Shigella handcuffs caspases	36
A trove of Asgard archaeal viruses	36
Computational discovery of dynobactin antibiotics	35
Neutralizing antibody activity in convalescent sera from infection in humans with SARS-CoV-2 and variants of concern	35
Microbial oxidation of short-chain gaseous alkanes	35
Author Correction: Soil microbiome indicators can predict crop growth response to large-scale inoculation with arbuscular mycorrhizal fungi	35
Phosphatidylserine-exposing extracellular vesicles in body fluids are an innate defence against apoptotic mimicry viral pathogens	35
Cytosolic sorting platform complexes shuttle type III secretion system effectors to the injectisome in Yersinia enterocolitica	35
The collapse of cooperation during range expansion of Pseudomonas aeruginosa	35
Quantitative principles of microbial metabolism shared across scales	34
Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids	34
Enterobactin inhibits microbiota-dependent activation of AhR to promote bacterial sepsis in mice	34
Gut epithelial electrical cues drive differential localization of enterobacteria	34