Nature Microbiology

Article	Citations
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2	4852
Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses	2292
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology	2023
Longitudinal observation and decline of neutralizing antibody responses in the three months following SARS-CoV-2 infection in humans	978
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic	648
Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets	569
Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies	500
The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets	480
The continued threat of emerging flaviviruses	448
Therapeutically administered ribonucleoside analogue MK-4482/EIDD-2801 blocks SARS-CoV-2 transmission in ferrets	291
SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution	282
Community-led, integrated, reproducible multi-omics with anvi’o	274
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway	269
Safety of bacteriophage therapy in severe Staphylococcus aureus infection	232
Competition for iron drives phytopathogen control by natural rhizosphere microbiomes	217
The SARS-CoV-2 RNA–protein interactome in infected human cells	214
Antibody responses to SARS-CoV-2 vaccines in 45,965 adults from the general population of the United Kingdom	213
Diversity, ecology and evolution of Archaea	213
Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth	213
Akkermansia muciniphila secretes a glucagon-like peptide-1-inducing protein that improves glucose homeostasis and ameliorates metabolic disease in mice	204
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome	201
Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail	196
A broad-spectrum antibiotic adjuvant reverses multidrug-resistant Gram-negative pathogens	195
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse	188
The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks	173

ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity	171
A standardized archaeal taxonomy for the Genome Taxonomy Database	161
Quantitative image analysis of microbial communities with BiofilmQ	156
N6-methyladenosine modification enables viral RNA to escape recognition by RNA sensor RIG-I	147
Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan	145
Responses to acute infection with SARS-CoV-2 in the lungs of rhesus macaques, baboons and marmosets	141
Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems	137
LY6E impairs coronavirus fusion and confers immune control of viral disease	136
Effectiveness of COVID-19 vaccines against symptomatic SARS-CoV-2 infection and severe outcomes with variants of concern in Ontario	136
Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut	134
Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology	134
Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome	133
Reactive oxygen species induce antibiotic tolerance during systemic Staphylococcus aureus infection	133
SARS-CoV-2 detection in patients with influenza-like illness	132
Bacteriophage-resistant Acinetobacter baumannii are resensitized to antimicrobials	132
COVID-19-associated fungal infections	129
Genome-wide associations of human gut microbiome variation and implications for causal inference analyses	129
Metallodrug ranitidine bismuth citrate suppresses SARS-CoV-2 replication and relieves virus-associated pneumonia in Syrian hamsters	128
We shouldn’t worry when a virus mutates during disease outbreaks	122
Spatial metabolomics of in situ host–microbe interactions at the micrometre scale	121
Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries	119
Nuclear pore blockade reveals that HIV-1 completes reverse transcription and uncoating in the nucleus	119
Control of nitrogen fixation in bacteria that associate with cereals	118
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community	116
Structures of the stator complex that drives rotation of the bacterial flagellum	108
Cellular host factors for SARS-CoV-2 infection	107
A jumbo phage that forms a nucleus-like structure evades CRISPR–Cas DNA targeting but is vulnerable to type III RNA-based immunity	106
Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice	104
Roadmap for naming uncultivated Archaea and Bacteria	104
Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance	101
Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens	98
Species- and site-specific genome editing in complex bacterial communities	97
Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes	96
Spike-specific circulating T follicular helper cell and cross-neutralizing antibody responses in COVID-19-convalescent individuals	95
Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria	92
Moving from probiotics to precision probiotics	92
Oxysterols provide innate immunity to bacterial infection by mobilizing cell surface accessible cholesterol	91
Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems	91
Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner	91
Developmentally regulated volatiles geosmin and 2-methylisoborneol attract a soil arthropod to Streptomyces bacteria promoting spore dispersal	90
Urban informal settlements as hotspots of antimicrobial resistance and the need to curb environmental transmission	89
Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation	89
The Syntrophy hypothesis for the origin of eukaryotes revisited	89
Influenza A variants with reduced susceptibility to baloxavir isolated from Japanese patients are fit and transmit through respiratory droplets	88
Mitochondrial dysfunction caused by outer membrane vesicles from Gram-negative bacteria activates intrinsic apoptosis and inflammation	88
Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients	88
The microbiota programs DNA methylation to control intestinal homeostasis and inflammation	88
Fungal taxonomy and sequence-based nomenclature	88
Envelope stress responses defend against type six secretion system attacks independently of immunity proteins	84
Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing	84

Trace gas oxidizers are widespread and active members of soil microbial communities	82
Lactate production by Staphylococcus aureus biofilm inhibits HDAC11 to reprogramme the host immune response during persistent infection	81
Structural coordination of polymerization and crosslinking by a SEDS–bPBP peptidoglycan synthase complex	81
Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes	80
Neutralizing antibody activity in convalescent sera from infection in humans with SARS-CoV-2 and variants of concern	77
Fetal meconium does not have a detectable microbiota before birth	77
Monkeypox virus emergence in wild chimpanzees reveals distinct clinical outcomes and viral diversity	76
Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome	76
SspABCD–SspE is a phosphorothioation-sensing bacterial defence system with broad anti-phage activities	76
A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome	76
Dietary l-serine confers a competitive fitness advantage to Enterobacteriaceae in the inflamed gut	76
Genetic circuit design automation for yeast	76
Multi-kingdom microbiota analyses identify bacterial–fungal interactions and biomarkers of colorectal cancer across cohorts	75
Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity	74
The intestinal regionalization of acute norovirus infection is regulated by the microbiota via bile acid-mediated priming of type III interferon	74
Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland	74
Selective sequestration of signalling proteins in a membraneless organelle reinforces the spatial regulation of asymmetry in Caulobacter crescentus	73
Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota	73
Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness	72
Implementation of permeation rules leads to a FabI inhibitor with activity against Gram-negative pathogens	72
A MORC-driven transcriptional switch controls Toxoplasma developmental trajectories and sexual commitment	71
Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis	70
Escherichia coli is engineered to grow on CO2 and formic acid	70
Successive blood meals enhance virus dissemination within mosquitoes and increase transmission potential	69
Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron	69
Combinatorial selection in amoebal hosts drives the evolution of the human pathogen Legionella pneumophila	69
Home chemical and microbial transitions across urbanization	68
Longitudinal analysis of antibody dynamics in COVID-19 convalescents reveals neutralizing responses up to 16 months after infection	68
Systematic evaluation of horizontal gene transfer between eukaryotes and viruses	68
Commensal Bacteroidetes protect against Klebsiella pneumoniae colonization and transmission through IL-36 signalling	67
Core components of DNA lagging strand synthesis machinery are essential for hepatitis B virus cccDNA formation	67
Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission	66
Effector-triggered immunity and pathogen sensing in metazoans	66
Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing	65
Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance	64
Bacterial colonization reprograms the neonatal gut metabolome	64
Staphylococcus aureus small colony variants impair host immunity by activating host cell glycolysis and inducing necroptosis	63
Transcriptional and functional insights into the host immune response against the emerging fungal pathogen Candida auris	63
Towards a deeper understanding of the vaginal microbiota	63
Antimicrobial resistance in the age of COVID-19	62
Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer	62
The impact of genetic diversity on gene essentiality within the Escherichia coli species	62
General quantitative relations linking cell growth and the cell cycle in Escherichia coli	61
Phylogenetic interpretation during outbreaks requires caution	60
Mycobiota-induced IgA antibodies regulate fungal commensalism in the gut and are dysregulated in Crohn’s disease	59
A bottom-up view of antimicrobial resistance transmission in developing countries	59
Symmetry mismatch in the MS-ring of the bacterial flagellar rotor explains the structural coordination of secretion and rotation	59
Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia	57
Population genomics confirms acquisition of drug-resistant Aspergillus fumigatus infection by humans from the environment	57
Klebsiella michiganensis transmission enhances resistance to Enterobacteriaceae gut invasion by nutrition competition	57
Microbial metabolites in the marine carbon cycle	56
Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology	55
Metagenomics-enabled microbial surveillance	55
The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves	55
CRISPRi chemical genetics and comparative genomics identify genes mediating drug potency in Mycobacterium tuberculosis	54
The DarTG toxin-antitoxin system provides phage defence by ADP-ribosylating viral DNA	54
Reduction of microbial diversity in grassland soil is driven by long-term climate warming	54
Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota	53
Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice	53
Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda	53
Macroecological dynamics of gut microbiota	53
Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen	53
Large freshwater phages with the potential to augment aerobic methane oxidation	52
Long-term stability and Red Queen-like strain dynamics in marine viruses	52
Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa	52
Molecular structure of the intact bacterial flagellar basal body	52
Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria	51
Inflammasome-mediated antagonism of type I interferon enhances Rickettsia pathogenesis	50
Evolution of the human pathogenic lifestyle in fungi	50
Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC	50
An orally available Mpro inhibitor is effective against wild-type SARS-CoV-2 and variants including Omicron	50
The science of the host–virus network	49
Microbial production and consumption of hydrocarbons in the global ocean	49
Harnessing the microbiome to prevent global biodiversity loss	49
Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease	49
A catalogue of 1,167 genomes from the human gut archaeome	48
Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2	48
Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes	48
Tracking bacterial lineages in complex and dynamic environments with applications for growth control and persistence	47
Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis	46

Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance	45
Bacterial–fungal interactions revealed by genome-wide analysis of bacterial mutant fitness	45
Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution	45
Mucoricin is a ricin-like toxin that is critical for the pathogenesis of mucormycosis	45
Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions	45
Microbiome innovations for a sustainable future	45
IFI16 directly senses viral RNA and enhances RIG-I transcription and activation to restrict influenza virus infection	44
Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis	44
RNA viromes from terrestrial sites across China expand environmental viral diversity	44
Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments	44
A nutrient-limited screen unmasks rifabutin hyperactivity for extensively drug-resistant Acinetobacter baumannii	43
Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration	43
A DNA-based vaccine protects against Crimean-Congo haemorrhagic fever virus disease in a Cynomolgus macaque model	43
Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance	43
Staphylococcus aureus cell growth and division are regulated by an amidase that trims peptides from uncrosslinked peptidoglycan	43
A two-track model for the spatiotemporal coordination of bacterial septal cell wall synthesis revealed by single-molecule imaging of FtsW	42
Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion	42
Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean	42
Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection	41
Targeting the trypanosome kinetochore with CLK1 protein kinase inhibitors	41
Asymmetric distribution of TLR3 leads to a polarized immune response in human intestinal epithelial cells	41
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics	41
Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins	41
An Alveolata secretory machinery adapted to parasite host cell invasion	41
Clinical implications of preterm infant gut microbiome development	41
Structural basis for placental malaria mediated by Plasmodium falciparum VAR2CSA	41
Regulation underlying hierarchical and simultaneous utilization of carbon substrates by flux sensors in Escherichia coli	40
Candida pathogens induce protective mitochondria-associated type I interferon signalling and a damage-driven response in vaginal epithelial cells	40
Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis	40
Sec24C is an HIV-1 host dependency factor crucial for virus replication	40
Spatial integration of transcription and splicing in a dedicated compartment sustains monogenic antigen expression in African trypanosomes	40
Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants	40
Extracellular SQSTM1 mediates bacterial septic death in mice through insulin receptor signalling	40
In vivo structure of the Legionella type II secretion system by electron cryotomography	40
Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women	40
Gangliosides are essential endosomal receptors for quasi-enveloped and naked hepatitis A virus	40
Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing	39
β-Barrel proteins tether the outer membrane in many Gram-negative bacteria	39
Single-molecule imaging reveals that Z-ring condensation is essential for cell division in Bacillus subtilis	39
Structure and mechanism of the proton-driven motor that powers type 9 secretion and gliding motility	39
Ornithine capture by a translating ribosome controls bacterial polyamine synthesis	38
Transcription in fungal conidia before dormancy produces phenotypically variable conidia that maximize survival in different environments	38
Bacteria deplete deoxynucleotides to defend against bacteriophage infection	38
Dissemination of Mycobacterium abscessus via global transmission networks	38
Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion	38
Phage–host coevolution in natural populations	37
An exported kinase family mediates species-specific erythrocyte remodelling and virulence in human malaria	37
Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams	37
Yeasts collectively extend the limits of habitable temperatures by secreting glutathione	37
Wildfire-dependent changes in soil microbiome diversity and function	37
Spermine-mediated tight sealing of the Magnaporthe oryzae appressorial pore–rice leaf surface interface	37
BNT162b2-induced memory T cells respond to the Omicron variant with preserved polyfunctionality	36
Herpesviruses induce aggregation and selective autophagy of host signalling proteins NEMO and RIPK1 as an immune-evasion mechanism	36
Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil	36
Immunometabolic crosstalk during bacterial infection	36
Exosome mimicry by a HAVCR1–NPC1 pathway of endosomal fusion mediates hepatitis A virus infection	36
Influenza virus repurposes the antiviral protein IFIT2 to promote translation of viral mRNAs	36
Unexpected mitochondrial genome diversity revealed by targeted single-cell genomics of heterotrophic flagellated protists	35
Induction of robust cellular and humoral immunity against SARS-CoV-2 after a third dose of BNT162b2 vaccine in previously unresponsive older adults	35
Increased small particle aerosol transmission of B.1.1.7 compared with SARS-CoV-2 lineage A in vivo	35
Inhibition of the integrated stress response by viral proteins that block p-eIF2–eIF2B association	35
Crosstalk between γδ T cells and the microbiota	35
Designing ecologically optimized pneumococcal vaccines using population genomics	34
Appressorium-mediated plant infection by Magnaporthe oryzae is regulated by a Pmk1-dependent hierarchical transcriptional network	34
Cell division in the archaeon Haloferax volcanii relies on two FtsZ proteins with distinct functions in division ring assembly and constriction	34
Escherichia coli Rho GTPase-activating toxin CNF1 mediates NLRP3 inflammasome activation via p21-activated kinases-1/2 during bacteraemia in mice	34
Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis	34
A natural symbiotic bacterium drives mosquito refractoriness to Plasmodium infection via secretion of an antimalarial lipase	34
Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria	33
Select autophagy genes maintain quiescence of tissue-resident macrophages and increase susceptibility to Listeria monocytogenes	33
Commensal Escherichia coli are a reservoir for the transfer of XDR plasmids into epidemic fluoroquinolone-resistant Shigella sonnei	33
Trypanosoma brucei colonizes the tsetse gut via an immature peritrophic matrix in the proventriculus	33
Structure of severe fever with thrombocytopenia syndrome virus L protein elucidates the mechanisms of viral transcription initiation	33