Nature Microbiology

Article	Citations
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology	2184
Longitudinal observation and decline of neutralizing antibody responses in the three months following SARS-CoV-2 infection in humans	1031
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic	697
Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets	605
The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets	554
Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies	534
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway	385
Community-led, integrated, reproducible multi-omics with anvi’o	382
Therapeutically administered ribonucleoside analogue MK-4482/EIDD-2801 blocks SARS-CoV-2 transmission in ferrets	313
SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution	309
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome	269
Akkermansia muciniphila secretes a glucagon-like peptide-1-inducing protein that improves glucose homeostasis and ameliorates metabolic disease in mice	260
The SARS-CoV-2 RNA–protein interactome in infected human cells	238
Antibody responses to SARS-CoV-2 vaccines in 45,965 adults from the general population of the United Kingdom	236
Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail	220
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse	213
A standardized archaeal taxonomy for the Genome Taxonomy Database	207
ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity	205
COVID-19-associated fungal infections	202
Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut	198
Quantitative image analysis of microbial communities with BiofilmQ	186
Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems	174
Bacteriophage-resistant Acinetobacter baumannii are resensitized to antimicrobials	167
Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome	167
Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries	166

Effectiveness of COVID-19 vaccines against symptomatic SARS-CoV-2 infection and severe outcomes with variants of concern in Ontario	158
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community	156
Responses to acute infection with SARS-CoV-2 in the lungs of rhesus macaques, baboons and marmosets	154
LY6E impairs coronavirus fusion and confers immune control of viral disease	153
Genome-wide associations of human gut microbiome variation and implications for causal inference analyses	150
Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice	145
Metallodrug ranitidine bismuth citrate suppresses SARS-CoV-2 replication and relieves virus-associated pneumonia in Syrian hamsters	143
Nuclear pore blockade reveals that HIV-1 completes reverse transcription and uncoating in the nucleus	141
Cellular host factors for SARS-CoV-2 infection	139
Structures of the stator complex that drives rotation of the bacterial flagellum	130
Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity	128
Species- and site-specific genome editing in complex bacterial communities	128
A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome	124
Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes	123
Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes	122
Spike-specific circulating T follicular helper cell and cross-neutralizing antibody responses in COVID-19-convalescent individuals	115
Roadmap for naming uncultivated Archaea and Bacteria	114
Reduction of microbial diversity in grassland soil is driven by long-term climate warming	113
Towards a deeper understanding of the vaginal microbiota	112
Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria	111
Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients	111
Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems	111
Multi-kingdom microbiota analyses identify bacterial–fungal interactions and biomarkers of colorectal cancer across cohorts	110
Mitochondrial dysfunction caused by outer membrane vesicles from Gram-negative bacteria activates intrinsic apoptosis and inflammation	110
Trace gas oxidizers are widespread and active members of soil microbial communities	109
Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner	109
Lactate production by Staphylococcus aureus biofilm inhibits HDAC11 to reprogramme the host immune response during persistent infection	109
Fungal taxonomy and sequence-based nomenclature	105
Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness	102
Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission	102
Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome	101
Systematic evaluation of horizontal gene transfer between eukaryotes and viruses	97
Metagenomics-enabled microbial surveillance	95
Genetic circuit design automation for yeast	94
Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance	94
Fetal meconium does not have a detectable microbiota before birth	92
Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota	92
A bottom-up view of antimicrobial resistance transmission in developing countries	92
The DarTG toxin-antitoxin system provides phage defence by ADP-ribosylating viral DNA	89
CRISPRi chemical genetics and comparative genomics identify genes mediating drug potency in Mycobacterium tuberculosis	88
Population genomics confirms acquisition of drug-resistant Aspergillus fumigatus infection by humans from the environment	88
Neutralizing antibody activity in convalescent sera from infection in humans with SARS-CoV-2 and variants of concern	88
Escherichia coli is engineered to grow on CO2 and formic acid	88
Evolution of the human pathogenic lifestyle in fungi	88
Harnessing the microbiome to prevent global biodiversity loss	84
Longitudinal analysis of antibody dynamics in COVID-19 convalescents reveals neutralizing responses up to 16 months after infection	83
The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves	83
Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron	82
Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland	81
Microbial metabolites in the marine carbon cycle	81

Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion	79
Mycobiota-induced IgA antibodies regulate fungal commensalism in the gut and are dysregulated in Crohn’s disease	78
Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC	78
Transcriptional and functional insights into the host immune response against the emerging fungal pathogen Candida auris	76
The impact of genetic diversity on gene essentiality within the Escherichia coli species	76
Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen	76
RNA viromes from terrestrial sites across China expand environmental viral diversity	76
Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia	75
Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration	74
A catalogue of 1,167 genomes from the human gut archaeome	73
Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa	72
Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2	72
Large freshwater phages with the potential to augment aerobic methane oxidation	70
An orally available Mpro inhibitor is effective against wild-type SARS-CoV-2 and variants including Omicron	68
Phage–host coevolution in natural populations	67
Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions	67
Genome-wide subcellular protein map for the flagellate parasite Trypanosoma brucei	65
IFI16 directly senses viral RNA and enhances RIG-I transcription and activation to restrict influenza virus infection	65
Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses	65
Molecular structure of the intact bacterial flagellar basal body	65
Tracking bacterial lineages in complex and dynamic environments with applications for growth control and persistence	64
Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes	63
Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance	62
Bacteria deplete deoxynucleotides to defend against bacteriophage infection	62
Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing	62
Wildfire-dependent changes in soil microbiome diversity and function	61
Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis	60
Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women	60
Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology	60
Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean	60
Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion	60
Microbial production and consumption of hydrocarbons in the global ocean	59
Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection	59
The science of the host–virus network	58
Mosquito vector competence for dengue is modulated by insect-specific viruses	58
Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda	57
Microbiome innovations for a sustainable future	56
Bacterial–fungal interactions revealed by genome-wide analysis of bacterial mutant fitness	56
Defending Earth’s terrestrial microbiome	55
Computational identification of a systemic antibiotic for Gram-negative bacteria	55
Clinical implications of preterm infant gut microbiome development	55
A two-track model for the spatiotemporal coordination of bacterial septal cell wall synthesis revealed by single-molecule imaging of FtsW	55
Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis	54
Multi-omics analyses of airway host–microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions	54
An Alveolata secretory machinery adapted to parasite host cell invasion	53
Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants	53
Transcription in fungal conidia before dormancy produces phenotypically variable conidia that maximize survival in different environments	53
Mucoricin is a ricin-like toxin that is critical for the pathogenesis of mucormycosis	53
Monocyte-derived macrophages contain persistent latent HIV reservoirs	53
Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil	52
Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution	52
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity	52
Immunometabolic crosstalk during bacterial infection	52
A DNA-based vaccine protects against Crimean-Congo haemorrhagic fever virus disease in a Cynomolgus macaque model	52
Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts	52
Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance	52
Spatial integration of transcription and splicing in a dedicated compartment sustains monogenic antigen expression in African trypanosomes	52
Dissemination of Mycobacterium abscessus via global transmission networks	50
Appressorium-mediated plant infection by Magnaporthe oryzae is regulated by a Pmk1-dependent hierarchical transcriptional network	50
Sexually transmitted infections and female reproductive health	49
Cell division in the archaeon Haloferax volcanii relies on two FtsZ proteins with distinct functions in division ring assembly and constriction	49
Candida pathogens induce protective mitochondria-associated type I interferon signalling and a damage-driven response in vaginal epithelial cells	49
Targeting the trypanosome kinetochore with CLK1 protein kinase inhibitors	49
A nutrient-limited screen unmasks rifabutin hyperactivity for extensively drug-resistant Acinetobacter baumannii	49
Single-molecule imaging reveals that Z-ring condensation is essential for cell division in Bacillus subtilis	49
Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean	49
Structure and mechanism of the proton-driven motor that powers type 9 secretion and gliding motility	49
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics	48
Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession	48
Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria	48
Influenza virus repurposes the antiviral protein IFIT2 to promote translation of viral mRNAs	48
Sec24C is an HIV-1 host dependency factor crucial for virus replication	48
Characterization of interactions of dietary cholesterol with the murine and human gut microbiome	48
Structural basis for placental malaria mediated by Plasmodium falciparum VAR2CSA	47
Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing	47
Extracellular SQSTM1 mediates bacterial septic death in mice through insulin receptor signalling	47
A natural symbiotic bacterium drives mosquito refractoriness to Plasmodium infection via secretion of an antimalarial lipase	47
β-Barrel proteins tether the outer membrane in many Gram-negative bacteria	47
Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine	47
Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams	46

SeqCode: a nomenclatural code for prokaryotes described from sequence data	46
Discovery of broad-spectrum fungicides that block septin-dependent infection processes of pathogenic fungi	46
Mating pair stabilization mediates bacterial conjugation species specificity	46
Human microbiome myths and misconceptions	46
Wolbachia cifB induces cytoplasmic incompatibility in the malaria mosquito vector	45
Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b2	45
Tecovirimat is effective against human monkeypox virus in vitro at nanomolar concentrations	45
Crosstalk between γδ T cells and the microbiota	45
Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults	45
Increased small particle aerosol transmission of B.1.1.7 compared with SARS-CoV-2 lineage A in vivo	45
Escherichia coli Rho GTPase-activating toxin CNF1 mediates NLRP3 inflammasome activation via p21-activated kinases-1/2 during bacteraemia in mice	45
Induction of robust cellular and humoral immunity against SARS-CoV-2 after a third dose of BNT162b2 vaccine in previously unresponsive older adults	44
A bacterial pan-genome makes gene essentiality strain-dependent and evolvable	44
Fc-γR-dependent antibody effector functions are required for vaccine-mediated protection against antigen-shifted variants of SARS-CoV-2	44
Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut	43
BNT162b2-induced memory T cells respond to the Omicron variant with preserved polyfunctionality	43
Expanding known viral diversity in the healthy infant gut	43
Spermine-mediated tight sealing of the Magnaporthe oryzae appressorial pore–rice leaf surface interface	43
Microbial diversity declines in warmed tropical soil and respiration rise exceed predictions as communities adapt	43
A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings	42
Immune correlates analysis of the ENSEMBLE single Ad26.COV2.S dose vaccine efficacy clinical trial	41
Therapeutics for COVID-19	41
Inhibition of the integrated stress response by viral proteins that block p-eIF2–eIF2B association	39
LncRNA DINOR is a virulence factor and global regulator of stress responses in Candida auris	39
Staphylococcus epidermidis clones express Staphylococcus aureus-type wall teichoic acid to shift from a commensal to pathogen lifestyle	39
A cell surface-exposed protein complex with an essential virulence function in Ustilago maydis	38
Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia	38
Exosome mimicry by a HAVCR1–NPC1 pathway of endosomal fusion mediates hepatitis A virus infection	38
Haematopoietic cell transplantation outcomes are linked to intestinal mycobiota dynamics and an expansion of Candida parapsilosis complex species	38
The microbial gbu gene cluster links cardiovascular disease risk associated with red meat consumption to microbiota l-carnitine catabolism	38
Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters	37
Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity	37
The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice	37
Dimethyl sulfide mediates microbial predator–prey interactions between zooplankton and algae in the ocean	37
Vertebrate host phylogeny influences gut archaeal diversity	36
Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships	36
Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants	36
Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California	36
Listeria monocytogenes upregulates mitochondrial calcium signalling to inhibit LC3-associated phagocytosis as a survival strategy	36
Dinoflagellate symbionts escape vomocytosis by host cell immune suppression	36
Mucin O-glycans suppress quorum-sensing pathways and genetic transformation in Streptococcus mutans	36
Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network	36
The cell biology of archaea	36
β-Barrels covalently link peptidoglycan and the outer membrane in the α-proteobacterium Brucella abortus	36
Detection of respiratory syncytial virus defective genomes in nasal secretions is associated with distinct clinical outcomes	36
Regulation of host and virus genes by neuronal miR-138 favours herpes simplex virus 1 latency	35
Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation	35
Epigenetic cell fate in Candida albicans is controlled by transcription factor condensates acting at super-enhancer-like elements	35
Single-molecule imaging of LexA degradation in Escherichia coli elucidates regulatory mechanisms and heterogeneity of the SOS response	35
Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites	35
Keystone taxa indispensable for microbiome recovery	35
The Rcs stress response inversely controls surface and CRISPR–Cas adaptive immunity to discriminate plasmids and phages	34
Variation and transmission of the human gut microbiota across multiple familial generations	34
Prophage integration into CRISPR loci enables evasion of antiviral immunity in Streptococcus pyogenes	34
Cell wall synthesis and remodelling dynamics determine division site architecture and cell shape in Escherichia coli	34
Bacteriophage genome engineering with CRISPR–Cas13a	34
Gut-inhabiting Clostridia build human GPCR ligands by conjugating neurotransmitters with diet- and human-derived fatty acids	34
Platform for isolation and characterization of SARS-CoV-2 variants enables rapid characterization of Omicron in Australia	33
Widespread divergent transcription from bacterial and archaeal promoters is a consequence of DNA-sequence symmetry	33
Coinfection by influenza A virus and respiratory syncytial virus produces hybrid virus particles	33
Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape	33
Patient-derived monoclonal antibody neutralizes SARS-CoV-2 Omicron variants and confers full protection in monkeys	33
Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments	33
Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes	33
Collective interactions augment influenza A virus replication in a host-dependent manner	32
Microbiomes of microscopic marine invertebrates do not reveal signatures of phylosymbiosis	32
Spatiotemporal proteomics uncovers cathepsin-dependent macrophage cell death during Salmonella infection	32
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	32
A heat-shock response regulated by the PfAP2-HS transcription factor protects human malaria parasites from febrile temperatures	32
PCRCR complex is essential for invasion of human erythrocytes by Plasmodium falciparum	32
Priorities for ocean microbiome research	31
Adaptation of the small intestine to microbial enteropathogens in Zambian children with stunting	31
Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism	31
Early-life viral infections are associated with disadvantageous immune and microbiota profiles and recurrent respiratory infections	31
Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon	31
Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries	31
Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex	30
Pneumococcal within-host diversity during colonization, transmission and treatment	30
SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope	30
An ancient divide in outer membrane tethering systems in bacteria suggests a mechanism for the diderm-to-monoderm transition	30
The evolutionary origin of host association in the Rickettsiales	30
Viral biogeography of the mammalian gut and parenchymal organs	30
SARS-CoV-2 evolution in the Omicron era	30
Molecular mimicry of NF-κB by vaccinia virus protein enables selective inhibition of antiviral responses	30
Interaction dynamics and virus–host range for estuarine actinophages captured by epicPCR	30
Viruses affect picocyanobacterial abundance and biogeography in the North Pacific Ocean	30
Gut microbial β-glucuronidases regulate host luminal proteases and are depleted in irritable bowel syndrome	29
SARS-CoV-2-specific T-cell epitope repertoire in convalescent and mRNA-vaccinated individuals	29
Pseudomonas putida mediates bacterial killing, biofilm invasion and biocontrol with a type IVB secretion system	29
Phyllosphere microbiome induces host metabolic defence against rice false-smut disease	29
The shape of pleomorphic virions determines resistance to cell-entry pressure	29
Reprogramming of host glutamine metabolism during Chlamydia trachomatis infection and its key role in peptidoglycan synthesis	29
Dissimilatory sulfate reduction in the archaeon ‘Candidatus Vulcanisaeta moutnovskia’ sheds light on the evolution of sulfur metabolism	29
Comparative proteomics identifies Schlafen 5 (SLFN5) as a herpes simplex virus restriction factor that suppresses viral transcription	29
Structure of a thylakoid-anchored contractile injection system in multicellular cyanobacteria	28