Nature Microbiology

Article	Citations
Gene–drug potency screening in M. tuberculosis	582
Sickle cell trait enhances malaria transmission	383
Metabolic sensing tips the balance of drug tolerance in fungal meningitis	288
Author Correction: DART takes aim at community editing	280
Rebound virus in the cerebrospinal fluid reveals a possible HIV-1 reservoir	269
Molecular factors shaping whether HCMV infection is productive or latent	267
Dietary exclusion of major food groups shapes the gut microbiome and may influence health	266
The IFIT2–IFIT3 antiviral complex targets short 5’ untranslated regions on viral mRNAs for translation inhibition	250
Rational design of a hospital-specific phage cocktail to treat Enterobacter cloacae complex infections	221
Prodrug florfenicol amine is activated by intrinsic resistance to target Mycobacterium abscessus	215
Flipping the magic switch to persistence via GTP depletion	214
Microbiome association with coral growth and survival	213
Aspergillus fumigatus dsRNA virus promotes fungal fitness and pathogenicity in the mammalian host	198
Mosquitoes provide a transmission route between possums and humans for Buruli ulcer in southeastern Australia	190
Structure of a functional archaellum in Bacteria of the Chloroflexota phylum	190
Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan	186
Cytoplasmic contractile injection systems mediate cell death in Streptomyces	182
Mechanistic basis for potent neutralization of Sin Nombre hantavirus by a human monoclonal antibody	182
The structure of the complete extracellular bacterial flagellum reveals the mechanism of flagellin incorporation	176
Host range, transmissibility and antigenicity of a pangolin coronavirus	166
Horizontal gene transfer explains unusual traits of Armillaria fungi	164
Single mutation makes Escherichia coli an insect mutualist	164
The Parkinson’s disease drug entacapone disrupts gut microbiome homeostasis via iron sequestration	162
A high-throughput and low-waste viability assay for microbes	161
Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults	161

The Mycobacterium tuberculosis protein O-phosphorylation landscape	160
Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria	159
Organ-on-chip models for infectious disease research	156
Candida albicans extracellular vesicles trigger type I IFN signalling via cGAS and STING	152
A dynamic subpopulation of CRISPR–Cas overexpressers allows Streptococcus pyogenes to rapidly respond to phage	150
Recent gene selection and drug resistance underscore clinical adaptation across Candida species	148
Therapeutic efficacy of monoclonal antibodies and antivirals against SARS-CoV-2 Omicron BA.1 in Syrian hamsters	146
Climate extremes disrupt fungal–bacterial interactions	146
OPENPichia: licence-free Komagataella phaffii chassis strains and toolkit for protein expression	144
The fast-evolving FIKK kinase family of Plasmodium falciparum can be inhibited by a single compound	140
Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division	139
Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome	137
Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains	137
Assessing critical thresholds in terrestrial microbiomes	136
Explainable artificial intelligence evolves antimicrobial peptides	134
Mycobacterium abscessus pathogenesis identified by phenogenomic analyses	133
Exceeding expectations out in the cold with Colwellia	132
CRISPR-influenced symbiosis	130
Mineral-eating microorganisms at extinct hydrothermal vents	130
Prioritizing mentorship	129
Call for papers on the clinical microbiome	126
Rational attenuation of RNA viruses with zinc finger antiviral protein	123
Bacteroides fragilis uses toxins for gut success	122
Synthesis of lipid-linked precursors of the bacterial cell wall is governed by a feedback control mechanism in Pseudomonas aeruginosa	120
Archaeal symbioses all the way down	117
Extracellular vesicles block viral entryways	117
Author Correction: A roadmap for equitable reuse of public microbiome data	117
The complex path towards herpesvirus vaccines	116
Pseudomonas syringae subpopulations cooperate by coordinating flagellar and type III secretion spatiotemporal dynamics to facilitate plant infection	116
Risk–reward trade-off during carbon starvation generates dichotomy in motility endurance among marine bacteria	115
Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment	114
Decoding the impact of nuclear organization on antigenic variation in parasites	114
Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2	113
Streptomyces polyketides mediate bacteria–fungi interactions across soil environments	111
Kaposi’s sarcoma-associated herpesvirus induces mitochondrial fission to evade host immune responses and promote viral production	109
Blockade of endothelin receptors mitigates SARS-CoV-2-induced osteoarthritis	108
Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration	107
Coronavirus sampling and surveillance in bats from 1996–2019: a systematic review and meta-analysis	107
Transforming tuberculosis diagnosis	106
Expanding known viral diversity in the healthy infant gut	106
SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome	105
Structure-guided design of a synthetic bile acid that inhibits Clostridioides difficile TcdB toxin	104
SARS and synapses	102
Switching on cyclic di-GMP heterogeneity in Pseudomonas aeruginosa biofilms	102
Placental Streptococcus agalactiae DNA is associated with neonatal unit admission and foetal pro-inflammatory cytokines in term infants	102
Publisher Correction: Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis	100
Genome-resolved metagenomics reveals microbiome diversity across 48 tick species	100
From farm to factory to fork	100
SARS-CoV-2 infection induces pro-fibrotic and pro-thrombotic foam cell formation	100
Mycobacterium tuberculosis as teacher	100

A nitrogen-fixing bacterium forms symbioses on land and at sea	99
Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants	98
The gut–liver axis in HCV infection	96
Using animation to mediate scientific discourse	96
Hunting emerging viruses through participatory community science	96
Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut	94
CryoEM reveals that ribosomes in microsporidian spores are locked in a dimeric hibernating state	92
Parasite and vector circadian clocks mediate efficient malaria transmission	91
Cell envelope diversity and evolution across the bacterial tree of life	91
Characterization of inositol lipid metabolism in gut-associated Bacteroidetes	91
Species- and site-specific genome editing in complex bacterial communities	90
Connecting microbiome and menopause for healthy ageing	89
An expanded metabolic pathway for androgen production by commensal bacteria	88
Bacteriophages avoid autoimmunity from cognate immune systems as an intrinsic part of their life cycles	88
Increased small particle aerosol transmission of B.1.1.7 compared with SARS-CoV-2 lineage A in vivo	87
Harnessing the microbiome to prevent global biodiversity loss	87
Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes	86
Dietary fibre counters the oncogenic potential of colibactin-producing Escherichia coli in colorectal cancer	83
Combining antibiotics to tackle antimicrobial resistance	81
Outbreak dynamics of foodborne pathogen Vibrio parahaemolyticus over a seventeen year period implies hidden reservoirs	81
Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia	79
Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study	79
Clinical implications of preterm infant gut microbiome development	79
Discovery of an orally active benzoxaborole prodrug effective in the treatment of Chagas disease in non-human primates	78
Phages with a broad host range are common across ecosystems	77
Anoxia activates CRISPR–Cas immunity in the mouse intestine	77
Dynamic diel proteome and daytime nitrogenase activity supports buoyancy in the cyanobacterium Trichodesmium	76
Therapeutics for COVID-19	76
Escherichia coli integrates chemotaxis and quorum sensing pathways in vivo	75
A year of microbiology	75
Bacteria can shed a layer when phages turn up the heat	73
Mining the microbiota for antibiotics	73
Siderophores mediate antibiotic resistance	71
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism	71
Non-equivalent genomes in polyploid prokaryotes	71
Growth rate is modulated by monitoring cell wall precursors in Bacillus subtilis	71
Reproductive justice must be considered in the scientific community	71
Identified receptors shed light on Epstein–Barr virus infection	71
mRNA-encoded Cas13 can be used to treat dengue infections in mice	71
Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters	70
Safety and immunogenicity of a prefusion non-stabilized spike protein mRNA COVID-19 vaccine: a phase I trial	70
Bacteria modulate microalgal aging physiology through the induction of extracellular vesicle production to remove harmful metabolites	70
A vision for spaceflight microbiology to enable human health and habitat sustainability	69
Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts	67
Microbial metabolites in the marine carbon cycle	67
GprC of the nematode-trapping fungus Arthrobotrys flagrans activates mitochondria and reprograms fungal cells for nematode hunting	66
Guiding phage therapy with genomic surveillance	66
A framework for automated scalable designation of viral pathogen lineages from genomic data	65
Metabolic modelling reveals the aging-associated decline of host–microbiome metabolic interactions in mice	64
TOLLIP inhibits lipid accumulation and the integrated stress response in alveolar macrophages to control Mycobacterium tuberculosis infection	64
Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships	63
Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine	63
The cell biology of archaea	61
Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes	61
STREAM-lining guidelines for microbiome research	60
Parabacteroides distasonis uses dietary inulin to suppress NASH via its metabolite pentadecanoic acid	60
Environmental stress mediates groundwater microbial community assembly	60
Human microbiome myths and misconceptions	60
Gut microbial factors predict disease severity in a mouse model of multiple sclerosis	60
The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice	60
Amplifying diverse voices in microbiology	59
Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria	59
Shining light on the coral photosymbiont family Symbiodiniaceae	59
CD8+ T cell depletion does not induce an expansion of viral reservoir in HIV model	59
We must learn from past outbreaks	58
A method to detect origin of transfer sequences for plasmid conjugation	58
Migrant health matters	58
Molecular organization of the New World arenavirus spike glycoprotein complex	58
Genome-wide protein–DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase	57
Sulfated glycosaminoglycans are host epithelial cell targets of the Candida albicans toxin candidalysin	57
Retracing a tangled tree of archaeal evolution	57
Multinational epidemiological analysis of oral human papillomavirus incidence in 3,137 men	56
Addressing gaps in author and reviewer gender diversity	56
Dairy cows develop protective immunity against reinfection with bovine H5N1 influenza virus	56
Identifying an evolutionary origin for morbilliviruses in bats	56
Inactivated whole-virion vaccine BBV152/Covaxin elicits robust cellular immune memory to SARS-CoV-2 and variants of concern	56
SARS-CoV-2 Africa dashboard for real-time COVID-19 information	56
Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes	56
Diet switch pre-vaccination improves immune response and metabolic status in formerly obese mice	56
Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection	55

Gut bacteria degrade purines via the 2,8-dioxopurine pathway	55
Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen	55
A haem-sequestering plant peptide promotes iron uptake in symbiotic bacteria	55
Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework	55
Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial	54
Metabolites from intact phage-infected Synechococcus chemotactically attract heterotrophic marine bacteria	53
Comprehensive transcription terminator atlas for Bacillus subtilis	53
Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon	53
Tecovirimat is effective against human monkeypox virus in vitro at nanomolar concentrations	53
Characterizing extracellular vesicles of human fungal pathogens	53
The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate	51
Phase transition of GvpU regulates gas vesicle clustering in bacteria	51
AMR, One Health and the environment	51
Staphylococcal virulence factor HlgB targets the endoplasmic-reticulum-resident E3 ubiquitin ligase AMFR to promote pneumonia	51
A phage-encoded anti-CRISPR protein co-opts host enolase to prevent type III CRISPR immunity	51
Taurolithocholic acid protects against viral haemorrhagic fever via inhibition of ferroptosis	51
BacterAI maps microbial metabolism without prior knowledge	51
Preclinical evaluation of the SARS-CoV-2 Mpro inhibitor RAY1216 shows improved pharmacokinetics compared with nirmatrelvir	51
Sex, gender and infectious disease	50
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway	50
Translating between science and politics as a government adviser	50
Colonic goblet cell-associated antigen passages mediate physiologic and beneficial translocation of live gut bacteria in preweaning mice	50
Iron-limitation light switch	50
The human archaeome in focus	50
Microbes and the water nexus	50
Dipeptidase 1 is a functional receptor for a porcine coronavirus	49
Understanding emerging and re-emerging viruses to facilitate pandemic preparedness	49
The GATE glycoprotein complex enhances human cytomegalovirus entry in endothelial cells	49
Chromosome architecture in an archaeal species naturally lacking structural maintenance of chromosomes proteins	49
Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis	49
Remote control designer probiotics	48
Integrons are anti-phage defence libraries in Vibrio parahaemolyticus	48
Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites	48
Publisher Correction: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission	48
Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain	48
Targeting the mosquito prefoldin–chaperonin complex blocks Plasmodium transmission	48
Enterococcus faecalis-derived adenine enhances enterohaemorrhagic Escherichia coli Type 3 Secretion System-dependent virulence	48
Nasal Staphylococcus aureus carriage promotes depressive behaviour in mice via sex hormone degradation	48
Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances	47
Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea	47
A high-quality genome compendium of the human gut microbiome of Inner Mongolians	46
Metabolic reprogramming enhances the susceptibility of multidrug- and carbapenem-resistant bacteria to antibiotics	46
Understanding the biology of monkeypox virus to prevent future outbreaks	46
Acquired amphotericin B resistance leads to fitness trade-offs that can be mitigated by compensatory evolution in Candida auris	46
Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota	46
Cooperative virulence via the collective action of secreted pathogen effectors	46
MAP-X reveals distinct protein complex dynamics across Plasmodium falciparum blood stages	45
Moving from hype to hope in diet–microbiome interactions	45
Exploiting the fitness cost of metallo-β-lactamase expression can overcome antibiotic resistance in bacterial pathogens	45
Metagenomic characterization of viruses and mobile genetic elements associated with the DPANN archaeal superphylum	45
Author Correction: Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host–plant interactions	45
Talented microbes unlatch peatland carbon	45
The host–parasite–virus triad	45
Introducing Microbe Matters	45
Dual inhibition of innate immunity and apoptosis by human cytomegalovirus protein UL37x1 enables efficient virus replication	45
Factors associated with oral HPV infection among a large multinational cohort of men	44
Small organisms with big climate impact	44
A non-human primate model for human norovirus infection	44
Viral biogeography of the mammalian gut and parenchymal organs	43
Vientovirus capsid protein mimics autoantigens and contributes to autoimmunity in Sjögren’s disease	43
Use microbes to tackle food insecurity	43
Mycobiota and diet-derived fungal xenosiderophores promote Salmonella gastrointestinal colonization	43
Discovery and artificial intelligence-guided mechanistic elucidation of a narrow-spectrum antibiotic	43
Persistent viral RNA and protein contribute to post-acute pathology	43
Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever	43
Chromosome organization affects genome evolution in Sulfolobus archaea	43
Identifying rare and active species that drive carbon turnover in complex microbiotas	43
Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient	42
DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms	42
Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation	42
CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery	41
Evolution of SARS-CoV-2 in the murine central nervous system drives viral diversification	41
FungAMR: a comprehensive database for investigating fungal mutations associated with antimicrobial resistance	41
Intestinal crypt microbiota modulates intestinal stem cell turnover and tumorigenesis via indole acetic acid	41
Microbiome alterations in autism spectrum disorder	41
scRNA-seq reveals transcriptional plasticity of var gene expression in Plasmodium falciparum for host immune avoidance	41
Drug–Fc conjugate CD388 targets influenza virus neuraminidase and is broadly protective in mice	41
Parkinson’s disease kinase LRRK2 coordinates a cell-intrinsic itaconate-dependent defence pathway against intracellular Salmonella	41
Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses	41
Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency	41
Microplastic research must consider microbes	41
Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda	41
Multigenerational proteolytic inactivation of restriction upon subtle genomic hypomethylation in Pseudomonas aeruginosa	41
Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota	41
Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information	41
Identification of structurally diverse menaquinone-binding antibiotics with in vivo activity against multidrug-resistant pathogens	40
Structural insights into tecovirimat antiviral activity and poxvirus resistance	40
Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation	40
Methane-dependent complete denitrification by a single Methylomirabilis bacterium	40
Author Correction: Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut	40
Leaf microbiome dysbiosis triggered by T2SS-dependent enzyme secretion from opportunistic Xanthomonas pathogens	40
Redefining success	39
Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought	39
Knowledge synthesis through scientific visualization	39
Connecting the dots from viral infection to disease	39