Nature Microbiology

Article	Citations
The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets	585
Community-led, integrated, reproducible multi-omics with anvi’o	455
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway	433
SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution	320
Therapeutically administered ribonucleoside analogue MK-4482/EIDD-2801 blocks SARS-CoV-2 transmission in ferrets	319
Akkermansia muciniphila secretes a glucagon-like peptide-1-inducing protein that improves glucose homeostasis and ameliorates metabolic disease in mice	301
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome	301
The SARS-CoV-2 RNA–protein interactome in infected human cells	249
Antibody responses to SARS-CoV-2 vaccines in 45,965 adults from the general population of the United Kingdom	247
COVID-19-associated fungal infections	238
Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail	233
A standardized archaeal taxonomy for the Genome Taxonomy Database	233
Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut	230
ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity	222
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse	221
Quantitative image analysis of microbial communities with BiofilmQ	198
Bacteriophage-resistant Acinetobacter baumannii are resensitized to antimicrobials	192
Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries	191
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community	173
Effectiveness of COVID-19 vaccines against symptomatic SARS-CoV-2 infection and severe outcomes with variants of concern in Ontario	166
Responses to acute infection with SARS-CoV-2 in the lungs of rhesus macaques, baboons and marmosets	161
Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity	161
Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice	160
Cellular host factors for SARS-CoV-2 infection	157
Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes	147

Reduction of microbial diversity in grassland soil is driven by long-term climate warming	147
A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome	146
Species- and site-specific genome editing in complex bacterial communities	144
Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes	139
Towards a deeper understanding of the vaginal microbiota	138
Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems	125
Multi-kingdom microbiota analyses identify bacterial–fungal interactions and biomarkers of colorectal cancer across cohorts	122
Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner	120
Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients	120
Spike-specific circulating T follicular helper cell and cross-neutralizing antibody responses in COVID-19-convalescent individuals	118
Trace gas oxidizers are widespread and active members of soil microbial communities	117
Metagenomics-enabled microbial surveillance	117
Fungal taxonomy and sequence-based nomenclature	116
Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission	116
Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness	116
Systematic evaluation of horizontal gene transfer between eukaryotes and viruses	113
Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome	110
Population genomics confirms acquisition of drug-resistant Aspergillus fumigatus infection by humans from the environment	109
A bottom-up view of antimicrobial resistance transmission in developing countries	109
Evolution of the human pathogenic lifestyle in fungi	108
Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance	107
The DarTG toxin-antitoxin system provides phage defence by ADP-ribosylating viral DNA	105
Microbial metabolites in the marine carbon cycle	105
CRISPRi chemical genetics and comparative genomics identify genes mediating drug potency in Mycobacterium tuberculosis	105
Fetal meconium does not have a detectable microbiota before birth	103
Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota	100
Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC	98
Harnessing the microbiome to prevent global biodiversity loss	97
Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion	96
RNA viromes from terrestrial sites across China expand environmental viral diversity	93
The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves	93
Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses	92
Neutralizing antibody activity in convalescent sera from infection in humans with SARS-CoV-2 and variants of concern	91
Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia	90
Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration	88
A catalogue of 1,167 genomes from the human gut archaeome	87
Mycobiota-induced IgA antibodies regulate fungal commensalism in the gut and are dysregulated in Crohn’s disease	87
The impact of genetic diversity on gene essentiality within the Escherichia coli species	86
Longitudinal analysis of antibody dynamics in COVID-19 convalescents reveals neutralizing responses up to 16 months after infection	86
Wildfire-dependent changes in soil microbiome diversity and function	85
Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen	84
Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2	83
Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions	82
Human microbiome myths and misconceptions	77
Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa	77
Phage–host coevolution in natural populations	77
Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland	76
Molecular structure of the intact bacterial flagellar basal body	75
Genome-wide subcellular protein map for the flagellate parasite Trypanosoma brucei	74
Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis	74

An orally available Mpro inhibitor is effective against wild-type SARS-CoV-2 and variants including Omicron	73
Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing	72
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity	71
Tracking bacterial lineages in complex and dynamic environments with applications for growth control and persistence	71
Monocyte-derived macrophages contain persistent latent HIV reservoirs	71
Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance	71
Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes	71
Multi-omics analyses of airway host–microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions	70
Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants	70
Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women	70
Clinical implications of preterm infant gut microbiome development	69
Immunometabolic crosstalk during bacterial infection	68
Microbial production and consumption of hydrocarbons in the global ocean	68
Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis	68
Mosquito vector competence for dengue is modulated by insect-specific viruses	67
Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection	67
Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion	67
IFI16 directly senses viral RNA and enhances RIG-I transcription and activation to restrict influenza virus infection	67
Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean	67
Sexually transmitted infections and female reproductive health	66
Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine	66
Appressorium-mediated plant infection by Magnaporthe oryzae is regulated by a Pmk1-dependent hierarchical transcriptional network	66
Bacteria deplete deoxynucleotides to defend against bacteriophage infection	66
The science of the host–virus network	65
Defending Earth’s terrestrial microbiome	64
Bacterial–fungal interactions revealed by genome-wide analysis of bacterial mutant fitness	64
Computational identification of a systemic antibiotic for Gram-negative bacteria	64
Microbiome innovations for a sustainable future	63
A bacterial pan-genome makes gene essentiality strain-dependent and evolvable	62
Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology	62
A two-track model for the spatiotemporal coordination of bacterial septal cell wall synthesis revealed by single-molecule imaging of FtsW	60
Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil	60
Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda	60
Transcription in fungal conidia before dormancy produces phenotypically variable conidia that maximize survival in different environments	60
Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts	59
Fc-γR-dependent antibody effector functions are required for vaccine-mediated protection against antigen-shifted variants of SARS-CoV-2	59
Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut	58
Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria	57
A DNA-based vaccine protects against Crimean-Congo haemorrhagic fever virus disease in a Cynomolgus macaque model	57
Expanding known viral diversity in the healthy infant gut	57
Mucoricin is a ricin-like toxin that is critical for the pathogenesis of mucormycosis	57
Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution	57
Therapeutics for COVID-19	57
Single-molecule imaging reveals that Z-ring condensation is essential for cell division in Bacillus subtilis	57
Sec24C is an HIV-1 host dependency factor crucial for virus replication	56
Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean	56
Characterization of interactions of dietary cholesterol with the murine and human gut microbiome	56
Mating pair stabilization mediates bacterial conjugation species specificity	55
An Alveolata secretory machinery adapted to parasite host cell invasion	55
Dissemination of Mycobacterium abscessus via global transmission networks	55
Spatial integration of transcription and splicing in a dedicated compartment sustains monogenic antigen expression in African trypanosomes	55
Structure and mechanism of the proton-driven motor that powers type 9 secretion and gliding motility	55
Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing	55
The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice	54
Microbial diversity declines in warmed tropical soil and respiration rise exceed predictions as communities adapt	54
Candida pathogens induce protective mitochondria-associated type I interferon signalling and a damage-driven response in vaginal epithelial cells	54
Wolbachia cifB induces cytoplasmic incompatibility in the malaria mosquito vector	54
Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession	53
A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings	53
Induction of robust cellular and humoral immunity against SARS-CoV-2 after a third dose of BNT162b2 vaccine in previously unresponsive older adults	53
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics	53
Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults	52
Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia	52
SeqCode: a nomenclatural code for prokaryotes described from sequence data	52
A natural symbiotic bacterium drives mosquito refractoriness to Plasmodium infection via secretion of an antimalarial lipase	52
Soil microbiome indicators can predict crop growth response to large-scale inoculation with arbuscular mycorrhizal fungi	51
Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites	50
Structural basis for placental malaria mediated by Plasmodium falciparum VAR2CSA	50
Escherichia coli Rho GTPase-activating toxin CNF1 mediates NLRP3 inflammasome activation via p21-activated kinases-1/2 during bacteraemia in mice	50
Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity	50
Cell division in the archaeon Haloferax volcanii relies on two FtsZ proteins with distinct functions in division ring assembly and constriction	50
Tecovirimat is effective against human monkeypox virus in vitro at nanomolar concentrations	50
Immune correlates analysis of the ENSEMBLE single Ad26.COV2.S dose vaccine efficacy clinical trial	50
β-Barrel proteins tether the outer membrane in many Gram-negative bacteria	49
The microbial gbu gene cluster links cardiovascular disease risk associated with red meat consumption to microbiota l-carnitine catabolism	49
Crosstalk between γδ T cells and the microbiota	49
LncRNA DINOR is a virulence factor and global regulator of stress responses in Candida auris	48
Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams	48
Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b2	48
Microbiota-derived tryptophan catabolites mediate the chemopreventive effects of statins on colorectal cancer	47

Increased small particle aerosol transmission of B.1.1.7 compared with SARS-CoV-2 lineage A in vivo	47
SARS-CoV-2 evolution in the Omicron era	46
Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism	45
A cell surface-exposed protein complex with an essential virulence function in Ustilago maydis	45
BNT162b2-induced memory T cells respond to the Omicron variant with preserved polyfunctionality	45
The cell biology of archaea	44
Haematopoietic cell transplantation outcomes are linked to intestinal mycobiota dynamics and an expansion of Candida parapsilosis complex species	43
Bacteriophage genome engineering with CRISPR–Cas13a	43
Cell wall synthesis and remodelling dynamics determine division site architecture and cell shape in Escherichia coli	43
Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters	43
Staphylococcus epidermidis clones express Staphylococcus aureus-type wall teichoic acid to shift from a commensal to pathogen lifestyle	42
Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation	42
Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape	42
Coinfection by influenza A virus and respiratory syncytial virus produces hybrid virus particles	42
Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes	42
Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants	41
Dimethyl sulfide mediates microbial predator–prey interactions between zooplankton and algae in the ocean	41
Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon	41
PCRCR complex is essential for invasion of human erythrocytes by Plasmodium falciparum	40
Regulation of host and virus genes by neuronal miR-138 favours herpes simplex virus 1 latency	40
Early-life viral infections are associated with disadvantageous immune and microbiota profiles and recurrent respiratory infections	40
Detection of respiratory syncytial virus defective genomes in nasal secretions is associated with distinct clinical outcomes	39
Phyllosphere microbiome induces host metabolic defence against rice false-smut disease	39
Metabolic exchanges are ubiquitous in natural microbial communities	39
No evidence for a common blood microbiome based on a population study of 9,770 healthy humans	39
Dinoflagellate symbionts escape vomocytosis by host cell immune suppression	39
Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network	39
Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships	39
An ancient divide in outer membrane tethering systems in bacteria suggests a mechanism for the diderm-to-monoderm transition	38
Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries	38
β-Barrels covalently link peptidoglycan and the outer membrane in the α-proteobacterium Brucella abortus	38
Transforming tuberculosis diagnosis	38
Gut microbial β-glucuronidases regulate host luminal proteases and are depleted in irritable bowel syndrome	38
Mucin O-glycans suppress quorum-sensing pathways and genetic transformation in Streptococcus mutans	38
Listeria monocytogenes upregulates mitochondrial calcium signalling to inhibit LC3-associated phagocytosis as a survival strategy	37
Gut-inhabiting Clostridia build human GPCR ligands by conjugating neurotransmitters with diet- and human-derived fatty acids	37
Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California	37
Vertebrate host phylogeny influences gut archaeal diversity	37
Widespread divergent transcription from bacterial and archaeal promoters is a consequence of DNA-sequence symmetry	37
Microbiomes of microscopic marine invertebrates do not reveal signatures of phylosymbiosis	37
Single-molecule imaging of LexA degradation in Escherichia coli elucidates regulatory mechanisms and heterogeneity of the SOS response	37
Adaptation of the small intestine to microbial enteropathogens in Zambian children with stunting	37
Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats	37
Probe-based bacterial single-cell RNA sequencing predicts toxin regulation	37
Variation and transmission of the human gut microbiota across multiple familial generations	36
The Rcs stress response inversely controls surface and CRISPR–Cas adaptive immunity to discriminate plasmids and phages	36
Platform for isolation and characterization of SARS-CoV-2 variants enables rapid characterization of Omicron in Australia	36
SARS-CoV-2 restructures host chromatin architecture	35
A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria	35
Viral biogeography of the mammalian gut and parenchymal organs	35
Prophage integration into CRISPR loci enables evasion of antiviral immunity in Streptococcus pyogenes	35
Discovery of an orally active benzoxaborole prodrug effective in the treatment of Chagas disease in non-human primates	35
Priorities for ocean microbiome research	35
Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota	35
Interaction dynamics and virus–host range for estuarine actinophages captured by epicPCR	35
Gene gain facilitated endosymbiotic evolution of Chlamydiae	34
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	34
SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope	34
Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments	34
Pneumococcal within-host diversity during colonization, transmission and treatment	34
Comparative proteomics identifies Schlafen 5 (SLFN5) as a herpes simplex virus restriction factor that suppresses viral transcription	34
Akkermansia muciniphila protects mice against an emerging tick-borne viral pathogen	34
A heat-shock response regulated by the PfAP2-HS transcription factor protects human malaria parasites from febrile temperatures	34
Patient-derived monoclonal antibody neutralizes SARS-CoV-2 Omicron variants and confers full protection in monkeys	34
Molecular mimicry of NF-κB by vaccinia virus protein enables selective inhibition of antiviral responses	33
Genome content predicts the carbon catabolic preferences of heterotrophic bacteria	33
Dormant phages communicate via arbitrium to control exit from lysogeny	33
Chloroquine resistance evolution in Plasmodium falciparum is mediated by the putative amino acid transporter AAT1	33
Parabacteroides distasonis uses dietary inulin to suppress NASH via its metabolite pentadecanoic acid	33
The evolutionary origin of host association in the Rickettsiales	33
A genetic system for Akkermansia muciniphila reveals a role for mucin foraging in gut colonization and host sterol biosynthesis gene expression	33
Lignin deconstruction by anaerobic fungi	33
A citizen-science-enabled catalogue of the vaginal microbiome and associated factors	33
The shape of pleomorphic virions determines resistance to cell-entry pressure	32
Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan	32
Viruses affect picocyanobacterial abundance and biogeography in the North Pacific Ocean	32
Trafficked Malayan pangolins contain viral pathogens of humans	32
A slicing mechanism facilitates host entry by plant-pathogenic Phytophthora	32
Autophagy restricts Mycobacterium tuberculosis during acute infection in mice	32
Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial	32
SARS-CoV-2 Omicron variant emerged under immune selection	32
Pseudomonas putida mediates bacterial killing, biofilm invasion and biocontrol with a type IVB secretion system	32
Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes	31
Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria	31
Inactivated whole-virion vaccine BBV152/Covaxin elicits robust cellular immune memory to SARS-CoV-2 and variants of concern	31
Cryo-EM structure of the bacterial divisome core complex and antibiotic target FtsWIQBL	31
Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex	31
SARS-CoV-2-specific T-cell epitope repertoire in convalescent and mRNA-vaccinated individuals	31
Single mutation makes Escherichia coli an insect mutualist	31
Screening the Toxoplasma kinome with high-throughput tagging identifies a regulator of invasion and egress	31
A haem-sequestering plant peptide promotes iron uptake in symbiotic bacteria	30
Outbreak dynamics of foodborne pathogen Vibrio parahaemolyticus over a seventeen year period implies hidden reservoirs	30
Evasion of cGAS and TRIM5 defines pandemic HIV	30
Metavirome of 31 tick species provides a compendium of 1,801 RNA virus genomes	30
Chikungunya virus assembly and budding visualized in situ using cryogenic electron tomography	29