Nature Microbiology

Article	Citations
Rebound virus in the cerebrospinal fluid reveals a possible HIV-1 reservoir	519
Assessing critical thresholds in terrestrial microbiomes	385
Recent gene selection and drug resistance underscore clinical adaptation across Candida species	338
The Parkinson’s disease drug entacapone disrupts gut microbiome homeostasis via iron sequestration	316
Sickle cell trait enhances malaria transmission	310
Metabolic sensing tips the balance of drug tolerance in fungal meningitis	295
Author Correction: MX2-mediated innate immunity against HIV-1 is regulated by serine phosphorylation	263
Gene–drug potency screening in M. tuberculosis	252
Author Correction: DART takes aim at community editing	244
Molecular factors shaping whether HCMV infection is productive or latent	224
Climate extremes disrupt fungal–bacterial interactions	213
Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome	210
Dietary exclusion of major food groups shapes the gut microbiome and may influence health	202
Explainable artificial intelligence evolves antimicrobial peptides	199
Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division	186
Horizontal gene transfer explains unusual traits of Armillaria fungi	178
Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains	176
OPENPichia: licence-free Komagataella phaffii chassis strains and toolkit for protein expression	174
Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan	164
A dynamic subpopulation of CRISPR–Cas overexpressers allows Streptococcus pyogenes to rapidly respond to phage	158
Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults	151
Host range, transmissibility and antigenicity of a pangolin coronavirus	149
Mechanistic basis for potent neutralization of Sin Nombre hantavirus by a human monoclonal antibody	149
Cytoplasmic contractile injection systems mediate cell death in Streptomyces	148
The Mycobacterium tuberculosis protein O-phosphorylation landscape	140

Therapeutic efficacy of monoclonal antibodies and antivirals against SARS-CoV-2 Omicron BA.1 in Syrian hamsters	139
Mycobacterium abscessus pathogenesis identified by phenogenomic analyses	139
Single mutation makes Escherichia coli an insect mutualist	138
Mosquitoes provide a transmission route between possums and humans for Buruli ulcer in southeastern Australia	138
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome	136
Appressorium-mediated plant infection by Magnaporthe oryzae is regulated by a Pmk1-dependent hierarchical transcriptional network	135
Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria	134
Candida albicans extracellular vesicles trigger type I IFN signalling via cGAS and STING	133
Tracking bacterial lineages in complex and dynamic environments with applications for growth control and persistence	132
Organ-on-chip models for infectious disease research	129
A high-throughput and low-waste viability assay for microbes	127
Exceeding expectations out in the cold with Colwellia	124
Prioritizing mentorship	122
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	120
Blockade of endothelin receptors mitigates SARS-CoV-2-induced osteoarthritis	117
Pseudomonas syringae subpopulations cooperate by coordinating flagellar and type III secretion spatiotemporal dynamics to facilitate plant infection	114
Extracellular vesicles block viral entryways	114
CRISPR-influenced symbiosis	113
Rational attenuation of RNA viruses with zinc finger antiviral protein	111
Publisher Correction: Fungal biology: Fungal spores are future-proofed	111
Synthesis of lipid-linked precursors of the bacterial cell wall is governed by a feedback control mechanism in Pseudomonas aeruginosa	110
Regulators unite to enable plant entry	110
Mineral-eating microorganisms at extinct hydrothermal vents	109
Publisher Correction: Breastfeeding promotes bifidobacterial immunomodulatory metabolites	109
Coronavirus sampling and surveillance in bats from 1996–2019: a systematic review and meta-analysis	106
Decoding the impact of nuclear organization on antigenic variation in parasites	106
Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2	106
Streptomyces polyketides mediate bacteria–fungi interactions across soil environments	105
Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration	103
SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome	103
Transforming tuberculosis diagnosis	101
Expanding known viral diversity in the healthy infant gut	100
Bacteroides fragilis uses toxins for gut success	100
Publisher Correction: Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis	99
Switching on cyclic di-GMP heterogeneity in Pseudomonas aeruginosa biofilms	98
CryoEM reveals that ribosomes in microsporidian spores are locked in a dimeric hibernating state	98
Mycobacterium tuberculosis as teacher	97
SARS and synapses	95
Publisher Correction: 2021 in review	93
Placental Streptococcus agalactiae DNA is associated with neonatal unit admission and foetal pro-inflammatory cytokines in term infants	93
Combining antibiotics to tackle antimicrobial resistance	93
Bacteriophages avoid autoimmunity from cognate immune systems as an intrinsic part of their life cycles	91
Using animation to mediate scientific discourse	91
Cell envelope diversity and evolution across the bacterial tree of life	91
Discovery of an orally active benzoxaborole prodrug effective in the treatment of Chagas disease in non-human primates	90
Parasite and vector circadian clocks mediate efficient malaria transmission	90
Dietary fibre counters the oncogenic potential of colibactin-producing Escherichia coli in colorectal cancer	89
Dynamic diel proteome and daytime nitrogenase activity supports buoyancy in the cyanobacterium Trichodesmium	89
Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study	89
Species- and site-specific genome editing in complex bacterial communities	88

Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes	88
An expanded metabolic pathway for androgen production by commensal bacteria	87
Clinical implications of preterm infant gut microbiome development	85
Characterization of inositol lipid metabolism in gut-associated Bacteroidetes	85
Hunting emerging viruses through participatory community science	84
The gut–liver axis in HCV infection	84
Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut	84
Connecting microbiome and menopause for healthy ageing	83
Therapeutics for COVID-19	82
Increased small particle aerosol transmission of B.1.1.7 compared with SARS-CoV-2 lineage A in vivo	82
Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia	82
Outbreak dynamics of foodborne pathogen Vibrio parahaemolyticus over a seventeen year period implies hidden reservoirs	80
Harnessing the microbiome to prevent global biodiversity loss	80
A standardized archaeal taxonomy for the Genome Taxonomy Database	79
A year of microbiology	78
Escherichia coli integrates chemotaxis and quorum sensing pathways in vivo	78
Guiding phage therapy with genomic surveillance	77
TOLLIP inhibits lipid accumulation and the integrated stress response in alveolar macrophages to control Mycobacterium tuberculosis infection	77
A vision for spaceflight microbiology to enable human health and habitat sustainability	76
Reproductive justice must be considered in the scientific community	75
Mining the microbiota for antibiotics	74
Safety and immunogenicity of a prefusion non-stabilized spike protein mRNA COVID-19 vaccine: a phase I trial	74
Bacteria can shed a layer when phages turn up the heat	73
Non-equivalent genomes in polyploid prokaryotes	73
Metabolic modelling reveals the aging-associated decline of host–microbiome metabolic interactions in mice	73
Gut microbial factors predict disease severity in a mouse model of multiple sclerosis	72
Achilles’ heel of antibiotic resistance	72
A framework for automated scalable designation of viral pathogen lineages from genomic data	72
Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes	71
Growth rate is modulated by monitoring cell wall precursors in Bacillus subtilis	70
The cell biology of archaea	70
Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships	70
Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria	69
Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters	69
Human microbiome myths and misconceptions	67
GprC of the nematode-trapping fungus Arthrobotrys flagrans activates mitochondria and reprograms fungal cells for nematode hunting	66
Siderophores mediate antibiotic resistance	66
Microbial metabolites in the marine carbon cycle	66
Bacteria modulate microalgal aging physiology through the induction of extracellular vesicle production to remove harmful metabolites	66
The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice	66
mRNA-encoded Cas13 can be used to treat dengue infections in mice	65
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	64
Environmental stress mediates groundwater microbial community assembly	62
Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine	62
Diet switch pre-vaccination improves immune response and metabolic status in formerly obese mice	61
CD8+ T cell depletion does not induce an expansion of viral reservoir in HIV model	61
Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection	61
Shining light on the coral photosymbiont family Symbiodiniaceae	60
Multinational epidemiological analysis of oral human papillomavirus incidence in 3,137 men	59
Comprehensive transcription terminator atlas for Bacillus subtilis	59
A method to detect origin of transfer sequences for plasmid conjugation	59
Amplifying diverse voices in microbiology	58
Migrant health matters	58
We must learn from past outbreaks	57
Genome-wide protein–DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase	57
Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial	57
The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate	56
Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon	56
Phase transition of GvpU regulates gas vesicle clustering in bacteria	56
BacterAI maps microbial metabolism without prior knowledge	56
Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework	56
Metabolites from intact phage-infected Synechococcus chemotactically attract heterotrophic marine bacteria	56
SARS-CoV-2 Africa dashboard for real-time COVID-19 information	55
Tecovirimat is effective against human monkeypox virus in vitro at nanomolar concentrations	55
Characterizing extracellular vesicles of human fungal pathogens	55
Dairy cows develop protective immunity against reinfection with bovine H5N1 influenza virus	55
Inactivated whole-virion vaccine BBV152/Covaxin elicits robust cellular immune memory to SARS-CoV-2 and variants of concern	54
Sulfated glycosaminoglycans are host epithelial cell targets of the Candida albicans toxin candidalysin	54
Taurolithocholic acid protects against viral haemorrhagic fever via inhibition of ferroptosis	53
Preclinical evaluation of the SARS-CoV-2 Mpro inhibitor RAY1216 shows improved pharmacokinetics compared with nirmatrelvir	53
Staphylococcal virulence factor HlgB targets the endoplasmic-reticulum-resident E3 ubiquitin ligase AMFR to promote pneumonia	52
Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen	51
Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes	51
Rottlerin inhibits La Crosse virus-induced encephalitis in mice and blocks release of replicating virus from the Golgi body in neurons	51
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway	51
A haem-sequestering plant peptide promotes iron uptake in symbiotic bacteria	50
Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner	50
AMR, One Health and the environment	50
Metagenomic characterization of viruses and mobile genetic elements associated with the DPANN archaeal superphylum	50

Publisher Correction: Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments	49
The human archaeome in focus	49
Translating between science and politics as a government adviser	49
Colonic goblet cell-associated antigen passages mediate physiologic and beneficial translocation of live gut bacteria in preweaning mice	48
Chromosome architecture in an archaeal species naturally lacking structural maintenance of chromosomes proteins	48
Microbes and the water nexus	48
Exploiting the fitness cost of metallo-β-lactamase expression can overcome antibiotic resistance in bacterial pathogens	48
Enterococcus faecalis-derived adenine enhances enterohaemorrhagic Escherichia coli Type 3 Secretion System-dependent virulence	48
Iron-limitation light switch	48
Publisher Correction: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission	48
Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments	47
Targeting the mosquito prefoldin–chaperonin complex blocks Plasmodium transmission	47
Integrons are anti-phage defence libraries in Vibrio parahaemolyticus	47
Cooperative virulence via the collective action of secreted pathogen effectors	47
Acquired amphotericin B resistance leads to fitness trade-offs that can be mitigated by compensatory evolution in Candida auris	47
Understanding emerging and re-emerging viruses to facilitate pandemic preparedness	46
Sex, gender and infectious disease	46
A high-quality genome compendium of the human gut microbiome of Inner Mongolians	46
Dual inhibition of innate immunity and apoptosis by human cytomegalovirus protein UL37x1 enables efficient virus replication	45
Genomics, social media and mobile phone data enable mapping of SARS-CoV-2 lineages to inform health policy in Bangladesh	45
Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites	45
Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis	45
Understanding the biology of monkeypox virus to prevent future outbreaks	45
CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery	44
Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient	44
Evolution of SARS-CoV-2 in the murine central nervous system drives viral diversification	44
Introducing Microbe Matters	44
Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever	44
Talented microbes unlatch peatland carbon	43
Persistent viral RNA and protein contribute to post-acute pathology	43
The host–parasite–virus triad	43
Moving from hype to hope in diet–microbiome interactions	42
Microplastic research must consider microbes	42
Intestinal crypt microbiota modulates intestinal stem cell turnover and tumorigenesis via indole acetic acid	42
Microbiome alterations in autism spectrum disorder	42
Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation	42
Author Correction: Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host–plant interactions	42
Small organisms with big climate impact	42
Structural insights into tecovirimat antiviral activity and poxvirus resistance	42
Factors associated with oral HPV infection among a large multinational cohort of men	41
Use microbes to tackle food insecurity	41
Mycobiota and diet-derived fungal xenosiderophores promote Salmonella gastrointestinal colonization	40
Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency	40
Drug–Fc conjugate CD388 targets influenza virus neuraminidase and is broadly protective in mice	40
A non-human primate model for human norovirus infection	40
Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation	40
Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota	40
Identification of structurally diverse menaquinone-binding antibiotics with in vivo activity against multidrug-resistant pathogens	39
Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda	39
Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought	39
Chromosome organization affects genome evolution in Sulfolobus archaea	39
Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information	38
Parkinson’s disease kinase LRRK2 coordinates a cell-intrinsic itaconate-dependent defence pathway against intracellular Salmonella	38
DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms	38
Leaf microbiome dysbiosis triggered by T2SS-dependent enzyme secretion from opportunistic Xanthomonas pathogens	38
Viral biogeography of the mammalian gut and parenchymal organs	38
An acidophilic fungus promotes prey digestion in a carnivorous plant	37
The unusual cell wall of the Lyme disease spirochaete Borrelia burgdorferi is shaped by a tick sugar	37
Author Correction: Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut	37
Explainable deep learning and virtual evolution identifies antimicrobial peptides with activity against multidrug-resistant human pathogens	37
Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses	37
Author Correction: Soil microbiome indicators can predict crop growth response to large-scale inoculation with arbuscular mycorrhizal fungi	37
Connecting the dots from viral infection to disease	37
Methane-dependent complete denitrification by a single Methylomirabilis bacterium	37
Redefining success	36
Primal FEAR protects against infection	36
Knowledge synthesis through scientific visualization	36
Computational discovery of dynobactin antibiotics	35
Toxoplasma protein export and effector function	35
Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut	35
Fungal dysbiosis and survival after allo-HCT	35
Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids	35
Enterobactin inhibits microbiota-dependent activation of AhR to promote bacterial sepsis in mice	35
Shigella handcuffs caspases	35
A trove of Asgard archaeal viruses	35
Host cell glycosylation selects for infection with CCR5- versus CXCR4-tropic HIV-1	35
Plant killers make the cut	35
A new malaria gene regulator	35
The collapse of cooperation during range expansion of Pseudomonas aeruginosa	34
Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut	34
Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags	34
Pathogenomic analyses of Shigella isolates inform factors limiting shigellosis prevention and control across LMICs	34
Cytosolic sorting platform complexes shuttle type III secretion system effectors to the injectisome in Yersinia enterocolitica	34
Phosphatidylserine-exposing extracellular vesicles in body fluids are an innate defence against apoptotic mimicry viral pathogens	34
Quantitative principles of microbial metabolism shared across scales	34
Microbial oxidation of short-chain gaseous alkanes	34
Broadly therapeutic antibody provides cross-serotype protection against enteroviruses via Fc effector functions and by mimicking SCARB2	34
Bifidobacteria metabolize lactulose to optimize gut metabolites and prevent systemic infection in patients with liver disease	33
Reduction of microbial diversity in grassland soil is driven by long-term climate warming	33
Neutralizing antibody activity in convalescent sera from infection in humans with SARS-CoV-2 and variants of concern	33
Gut epithelial electrical cues drive differential localization of enterobacteria	33
Crosstalk between γδ T cells and the microbiota	33
Sexually transmitted infections and female reproductive health	33
Comparative effectiveness of third doses of mRNA-based COVID-19 vaccines in US veterans	33
An orally available Mpro inhibitor is effective against wild-type SARS-CoV-2 and variants including Omicron	33