Nature Microbiology

Article	Citations
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology	2200
Longitudinal observation and decline of neutralizing antibody responses in the three months following SARS-CoV-2 infection in humans	1039
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic	698
Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets	612
The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets	565
Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies	540
Community-led, integrated, reproducible multi-omics with anvi’o	398
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway	397
Therapeutically administered ribonucleoside analogue MK-4482/EIDD-2801 blocks SARS-CoV-2 transmission in ferrets	314
SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution	311
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome	277
Akkermansia muciniphila secretes a glucagon-like peptide-1-inducing protein that improves glucose homeostasis and ameliorates metabolic disease in mice	270
The SARS-CoV-2 RNA–protein interactome in infected human cells	243
Antibody responses to SARS-CoV-2 vaccines in 45,965 adults from the general population of the United Kingdom	238
Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail	226
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse	217
A standardized archaeal taxonomy for the Genome Taxonomy Database	215
ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity	211
COVID-19-associated fungal infections	207
Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut	204
Quantitative image analysis of microbial communities with BiofilmQ	187
Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems	175
Bacteriophage-resistant Acinetobacter baumannii are resensitized to antimicrobials	174
Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries	171
Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome	169

Effectiveness of COVID-19 vaccines against symptomatic SARS-CoV-2 infection and severe outcomes with variants of concern in Ontario	163
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community	161
Responses to acute infection with SARS-CoV-2 in the lungs of rhesus macaques, baboons and marmosets	157
LY6E impairs coronavirus fusion and confers immune control of viral disease	154
Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice	148
Metallodrug ranitidine bismuth citrate suppresses SARS-CoV-2 replication and relieves virus-associated pneumonia in Syrian hamsters	146
Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity	143
Cellular host factors for SARS-CoV-2 infection	141
Structures of the stator complex that drives rotation of the bacterial flagellum	131
Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes	131
Species- and site-specific genome editing in complex bacterial communities	130
A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome	128
Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes	128
Reduction of microbial diversity in grassland soil is driven by long-term climate warming	120
Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems	118
Towards a deeper understanding of the vaginal microbiota	116
Multi-kingdom microbiota analyses identify bacterial–fungal interactions and biomarkers of colorectal cancer across cohorts	116
Spike-specific circulating T follicular helper cell and cross-neutralizing antibody responses in COVID-19-convalescent individuals	115
Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria	114
Lactate production by Staphylococcus aureus biofilm inhibits HDAC11 to reprogramme the host immune response during persistent infection	113
Mitochondrial dysfunction caused by outer membrane vesicles from Gram-negative bacteria activates intrinsic apoptosis and inflammation	113
Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner	112
Trace gas oxidizers are widespread and active members of soil microbial communities	111
Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients	111
Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness	107
Fungal taxonomy and sequence-based nomenclature	106
Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission	105
Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome	103
Metagenomics-enabled microbial surveillance	101
Systematic evaluation of horizontal gene transfer between eukaryotes and viruses	100
A bottom-up view of antimicrobial resistance transmission in developing countries	99
Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance	98
Genetic circuit design automation for yeast	97
Fetal meconium does not have a detectable microbiota before birth	95
Population genomics confirms acquisition of drug-resistant Aspergillus fumigatus infection by humans from the environment	94
The DarTG toxin-antitoxin system provides phage defence by ADP-ribosylating viral DNA	93
CRISPRi chemical genetics and comparative genomics identify genes mediating drug potency in Mycobacterium tuberculosis	92
Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota	92
Evolution of the human pathogenic lifestyle in fungi	89
Escherichia coli is engineered to grow on CO2 and formic acid	88
Neutralizing antibody activity in convalescent sera from infection in humans with SARS-CoV-2 and variants of concern	88
Microbial metabolites in the marine carbon cycle	88
Harnessing the microbiome to prevent global biodiversity loss	87
Longitudinal analysis of antibody dynamics in COVID-19 convalescents reveals neutralizing responses up to 16 months after infection	84
The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves	84
Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion	82
Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland	81
Mycobiota-induced IgA antibodies regulate fungal commensalism in the gut and are dysregulated in Crohn’s disease	81
Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC	80
Transcriptional and functional insights into the host immune response against the emerging fungal pathogen Candida auris	79

RNA viromes from terrestrial sites across China expand environmental viral diversity	79
The impact of genetic diversity on gene essentiality within the Escherichia coli species	78
Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia	78
Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration	77
Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen	77
A catalogue of 1,167 genomes from the human gut archaeome	75
Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa	74
Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2	74
Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses	72
Phage–host coevolution in natural populations	71
Large freshwater phages with the potential to augment aerobic methane oxidation	71
An orally available Mpro inhibitor is effective against wild-type SARS-CoV-2 and variants including Omicron	69
Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions	69
Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance	67
Molecular structure of the intact bacterial flagellar basal body	67
Wildfire-dependent changes in soil microbiome diversity and function	67
Genome-wide subcellular protein map for the flagellate parasite Trypanosoma brucei	66
Tracking bacterial lineages in complex and dynamic environments with applications for growth control and persistence	66
IFI16 directly senses viral RNA and enhances RIG-I transcription and activation to restrict influenza virus infection	65
Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing	65
Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes	64
Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis	64
Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion	63
Bacteria deplete deoxynucleotides to defend against bacteriophage infection	62
Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women	62
Clinical implications of preterm infant gut microbiome development	61
Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology	61
Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection	61
Mosquito vector competence for dengue is modulated by insect-specific viruses	61
Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean	61
Microbial production and consumption of hydrocarbons in the global ocean	60
Multi-omics analyses of airway host–microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions	60
The science of the host–virus network	60
Bacterial–fungal interactions revealed by genome-wide analysis of bacterial mutant fitness	58
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity	58
Microbiome innovations for a sustainable future	58
A two-track model for the spatiotemporal coordination of bacterial septal cell wall synthesis revealed by single-molecule imaging of FtsW	57
Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda	57
Defending Earth’s terrestrial microbiome	56
Computational identification of a systemic antibiotic for Gram-negative bacteria	56
Immunometabolic crosstalk during bacterial infection	56
Mucoricin is a ricin-like toxin that is critical for the pathogenesis of mucormycosis	55
Transcription in fungal conidia before dormancy produces phenotypically variable conidia that maximize survival in different environments	55
Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution	55
Human microbiome myths and misconceptions	54
Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis	54
A DNA-based vaccine protects against Crimean-Congo haemorrhagic fever virus disease in a Cynomolgus macaque model	54
Monocyte-derived macrophages contain persistent latent HIV reservoirs	54
Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil	54
Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance	54
Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts	54
Spatial integration of transcription and splicing in a dedicated compartment sustains monogenic antigen expression in African trypanosomes	53
Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants	53
An Alveolata secretory machinery adapted to parasite host cell invasion	53
Appressorium-mediated plant infection by Magnaporthe oryzae is regulated by a Pmk1-dependent hierarchical transcriptional network	52
Sec24C is an HIV-1 host dependency factor crucial for virus replication	51
Dissemination of Mycobacterium abscessus via global transmission networks	51
Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria	51
Targeting the trypanosome kinetochore with CLK1 protein kinase inhibitors	50
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics	50
Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean	50
Influenza virus repurposes the antiviral protein IFIT2 to promote translation of viral mRNAs	50
Extracellular SQSTM1 mediates bacterial septic death in mice through insulin receptor signalling	50
Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine	50
Sexually transmitted infections and female reproductive health	50
Cell division in the archaeon Haloferax volcanii relies on two FtsZ proteins with distinct functions in division ring assembly and constriction	49
Single-molecule imaging reveals that Z-ring condensation is essential for cell division in Bacillus subtilis	49
Candida pathogens induce protective mitochondria-associated type I interferon signalling and a damage-driven response in vaginal epithelial cells	49
Characterization of interactions of dietary cholesterol with the murine and human gut microbiome	49
Structure and mechanism of the proton-driven motor that powers type 9 secretion and gliding motility	49
Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams	48
A natural symbiotic bacterium drives mosquito refractoriness to Plasmodium infection via secretion of an antimalarial lipase	48
Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession	48
β-Barrel proteins tether the outer membrane in many Gram-negative bacteria	47
Expanding known viral diversity in the healthy infant gut	47
Structural basis for placental malaria mediated by Plasmodium falciparum VAR2CSA	47
Induction of robust cellular and humoral immunity against SARS-CoV-2 after a third dose of BNT162b2 vaccine in previously unresponsive older adults	47
SeqCode: a nomenclatural code for prokaryotes described from sequence data	47
Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing	47
Discovery of broad-spectrum fungicides that block septin-dependent infection processes of pathogenic fungi	46

Increased small particle aerosol transmission of B.1.1.7 compared with SARS-CoV-2 lineage A in vivo	46
Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults	46
A bacterial pan-genome makes gene essentiality strain-dependent and evolvable	46
Fc-γR-dependent antibody effector functions are required for vaccine-mediated protection against antigen-shifted variants of SARS-CoV-2	46
Crosstalk between γδ T cells and the microbiota	46
Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b2	46
Mating pair stabilization mediates bacterial conjugation species specificity	46
Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut	46
Wolbachia cifB induces cytoplasmic incompatibility in the malaria mosquito vector	46
Escherichia coli Rho GTPase-activating toxin CNF1 mediates NLRP3 inflammasome activation via p21-activated kinases-1/2 during bacteraemia in mice	46
Tecovirimat is effective against human monkeypox virus in vitro at nanomolar concentrations	45
Microbial diversity declines in warmed tropical soil and respiration rise exceed predictions as communities adapt	45
A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings	44
Immune correlates analysis of the ENSEMBLE single Ad26.COV2.S dose vaccine efficacy clinical trial	43
BNT162b2-induced memory T cells respond to the Omicron variant with preserved polyfunctionality	43
Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia	43
Spermine-mediated tight sealing of the Magnaporthe oryzae appressorial pore–rice leaf surface interface	43
Therapeutics for COVID-19	43
Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites	42
LncRNA DINOR is a virulence factor and global regulator of stress responses in Candida auris	41
The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice	41
Haematopoietic cell transplantation outcomes are linked to intestinal mycobiota dynamics and an expansion of Candida parapsilosis complex species	41
Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity	41
Staphylococcus epidermidis clones express Staphylococcus aureus-type wall teichoic acid to shift from a commensal to pathogen lifestyle	40
The microbial gbu gene cluster links cardiovascular disease risk associated with red meat consumption to microbiota l-carnitine catabolism	40
Inhibition of the integrated stress response by viral proteins that block p-eIF2–eIF2B association	39
Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism	38
Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters	38
A cell surface-exposed protein complex with an essential virulence function in Ustilago maydis	38
Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation	38
Dimethyl sulfide mediates microbial predator–prey interactions between zooplankton and algae in the ocean	38
β-Barrels covalently link peptidoglycan and the outer membrane in the α-proteobacterium Brucella abortus	37
Listeria monocytogenes upregulates mitochondrial calcium signalling to inhibit LC3-associated phagocytosis as a survival strategy	37
Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants	37
The cell biology of archaea	37
Detection of respiratory syncytial virus defective genomes in nasal secretions is associated with distinct clinical outcomes	37
Widespread divergent transcription from bacterial and archaeal promoters is a consequence of DNA-sequence symmetry	36
Dinoflagellate symbionts escape vomocytosis by host cell immune suppression	36
Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California	36
Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network	36
Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape	36
Keystone taxa indispensable for microbiome recovery	36
Vertebrate host phylogeny influences gut archaeal diversity	36
Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships	36
Mucin O-glycans suppress quorum-sensing pathways and genetic transformation in Streptococcus mutans	36
Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes	35
Early-life viral infections are associated with disadvantageous immune and microbiota profiles and recurrent respiratory infections	35
Single-molecule imaging of LexA degradation in Escherichia coli elucidates regulatory mechanisms and heterogeneity of the SOS response	35
Bacteriophage genome engineering with CRISPR–Cas13a	35
Microbiota-derived tryptophan catabolites mediate the chemopreventive effects of statins on colorectal cancer	35
Microbiomes of microscopic marine invertebrates do not reveal signatures of phylosymbiosis	35
Regulation of host and virus genes by neuronal miR-138 favours herpes simplex virus 1 latency	35
Epigenetic cell fate in Candida albicans is controlled by transcription factor condensates acting at super-enhancer-like elements	35
Variation and transmission of the human gut microbiota across multiple familial generations	35
SARS-CoV-2 evolution in the Omicron era	34
Coinfection by influenza A virus and respiratory syncytial virus produces hybrid virus particles	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	34
Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon	34
Patient-derived monoclonal antibody neutralizes SARS-CoV-2 Omicron variants and confers full protection in monkeys	34
The Rcs stress response inversely controls surface and CRISPR–Cas adaptive immunity to discriminate plasmids and phages	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
Gut microbial β-glucuronidases regulate host luminal proteases and are depleted in irritable bowel syndrome	33
Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments	33
Collective interactions augment influenza A virus replication in a host-dependent manner	33
Priorities for ocean microbiome research	32
Comparative proteomics identifies Schlafen 5 (SLFN5) as a herpes simplex virus restriction factor that suppresses viral transcription	32
A heat-shock response regulated by the PfAP2-HS transcription factor protects human malaria parasites from febrile temperatures	32
Viral biogeography of the mammalian gut and parenchymal organs	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
PCRCR complex is essential for invasion of human erythrocytes by Plasmodium falciparum	32
Molecular mimicry of NF-κB by vaccinia virus protein enables selective inhibition of antiviral responses	31
Adaptation of the small intestine to microbial enteropathogens in Zambian children with stunting	31
The evolutionary origin of host association in the Rickettsiales	31
Phyllosphere microbiome induces host metabolic defence against rice false-smut disease	31
Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries	31
Dissimilatory sulfate reduction in the archaeon ‘Candidatus Vulcanisaeta moutnovskia’ sheds light on the evolution of sulfur metabolism	30
Interaction dynamics and virus–host range for estuarine actinophages captured by epicPCR	30
Pseudomonas putida mediates bacterial killing, biofilm invasion and biocontrol with a type IVB secretion system	30
An ancient divide in outer membrane tethering systems in bacteria suggests a mechanism for the diderm-to-monoderm transition	30
SARS-CoV-2-specific T-cell epitope repertoire in convalescent and mRNA-vaccinated individuals	30
SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope	30
Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex	30
Pneumococcal within-host diversity during colonization, transmission and treatment	30
Viruses affect picocyanobacterial abundance and biogeography in the North Pacific Ocean	30
Structure of a thylakoid-anchored contractile injection system in multicellular cyanobacteria	29
SARS-CoV-2 restructures host chromatin architecture	29
The shape of pleomorphic virions determines resistance to cell-entry pressure	29
Akkermansia muciniphila protects mice against an emerging tick-borne viral pathogen	29
Reprogramming of host glutamine metabolism during Chlamydia trachomatis infection and its key role in peptidoglycan synthesis	29
A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria	28
Dynamic diel proteome and daytime nitrogenase activity supports buoyancy in the cyanobacterium Trichodesmium	28
SARS-CoV-2 Omicron variant emerged under immune selection	28
Discovery of an orally active benzoxaborole prodrug effective in the treatment of Chagas disease in non-human primates	28