Nature Microbiology

(The median citation count of Nature Microbiology is 8. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-04-01 to 2024-04-01.)
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology2136
Longitudinal observation and decline of neutralizing antibody responses in the three months following SARS-CoV-2 infection in humans1020
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic683
Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets598
The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets530
Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies527
The continued threat of emerging flaviviruses523
Community-led, integrated, reproducible multi-omics with anvi’o356
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway350
Therapeutically administered ribonucleoside analogue MK-4482/EIDD-2801 blocks SARS-CoV-2 transmission in ferrets307
SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution307
Diversity, ecology and evolution of Archaea259
Competition for iron drives phytopathogen control by natural rhizosphere microbiomes256
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome251
Akkermansia muciniphila secretes a glucagon-like peptide-1-inducing protein that improves glucose homeostasis and ameliorates metabolic disease in mice245
A broad-spectrum antibiotic adjuvant reverses multidrug-resistant Gram-negative pathogens236
Antibody responses to SARS-CoV-2 vaccines in 45,965 adults from the general population of the United Kingdom234
The SARS-CoV-2 RNA–protein interactome in infected human cells230
Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail207
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse206
A standardized archaeal taxonomy for the Genome Taxonomy Database192
ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity191
The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks191
COVID-19-associated fungal infections184
Quantitative image analysis of microbial communities with BiofilmQ179
Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut175
Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan164
Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems161
Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome158
Bacteriophage-resistant Acinetobacter baumannii are resensitized to antimicrobials153
Effectiveness of COVID-19 vaccines against symptomatic SARS-CoV-2 infection and severe outcomes with variants of concern in Ontario153
Responses to acute infection with SARS-CoV-2 in the lungs of rhesus macaques, baboons and marmosets152
Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries150
LY6E impairs coronavirus fusion and confers immune control of viral disease149
Genome-wide associations of human gut microbiome variation and implications for causal inference analyses145
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community141
Metallodrug ranitidine bismuth citrate suppresses SARS-CoV-2 replication and relieves virus-associated pneumonia in Syrian hamsters137
SARS-CoV-2 detection in patients with influenza-like illness134
Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice132
Nuclear pore blockade reveals that HIV-1 completes reverse transcription and uncoating in the nucleus132
Cellular host factors for SARS-CoV-2 infection127
Structures of the stator complex that drives rotation of the bacterial flagellum127
Species- and site-specific genome editing in complex bacterial communities123
Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes117
Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity112
Roadmap for naming uncultivated Archaea and Bacteria112
Moving from probiotics to precision probiotics110
A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome109
Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes108
Spike-specific circulating T follicular helper cell and cross-neutralizing antibody responses in COVID-19-convalescent individuals107
Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems106
The Syntrophy hypothesis for the origin of eukaryotes revisited105
Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria105
Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner105
Mitochondrial dysfunction caused by outer membrane vesicles from Gram-negative bacteria activates intrinsic apoptosis and inflammation104
Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing102
Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients102
Fungal taxonomy and sequence-based nomenclature101
Urban informal settlements as hotspots of antimicrobial resistance and the need to curb environmental transmission100
Lactate production by Staphylococcus aureus biofilm inhibits HDAC11 to reprogramme the host immune response during persistent infection99
Trace gas oxidizers are widespread and active members of soil microbial communities99
Multi-kingdom microbiota analyses identify bacterial–fungal interactions and biomarkers of colorectal cancer across cohorts98
Towards a deeper understanding of the vaginal microbiota96
Developmentally regulated volatiles geosmin and 2-methylisoborneol attract a soil arthropod to Streptomyces bacteria promoting spore dispersal95
Oxysterols provide innate immunity to bacterial infection by mobilizing cell surface accessible cholesterol94
Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission93
Reduction of microbial diversity in grassland soil is driven by long-term climate warming92
Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness91
Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome91
Fetal meconium does not have a detectable microbiota before birth90
Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance88
Genetic circuit design automation for yeast88
Systematic evaluation of horizontal gene transfer between eukaryotes and viruses87
SspABCD–SspE is a phosphorothioation-sensing bacterial defence system with broad anti-phage activities85
Neutralizing antibody activity in convalescent sera from infection in humans with SARS-CoV-2 and variants of concern85
Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota84
Monkeypox virus emergence in wild chimpanzees reveals distinct clinical outcomes and viral diversity84
Metagenomics-enabled microbial surveillance83
A bottom-up view of antimicrobial resistance transmission in developing countries81
The DarTG toxin-antitoxin system provides phage defence by ADP-ribosylating viral DNA80
Escherichia coli is engineered to grow on CO2 and formic acid80
Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland80
Population genomics confirms acquisition of drug-resistant Aspergillus fumigatus infection by humans from the environment79
Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron78
Evolution of the human pathogenic lifestyle in fungi78
Longitudinal analysis of antibody dynamics in COVID-19 convalescents reveals neutralizing responses up to 16 months after infection76
Mycobiota-induced IgA antibodies regulate fungal commensalism in the gut and are dysregulated in Crohn’s disease75
Harnessing the microbiome to prevent global biodiversity loss75
The impact of genetic diversity on gene essentiality within the Escherichia coli species74
The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves73
Microbial metabolites in the marine carbon cycle73
Transcriptional and functional insights into the host immune response against the emerging fungal pathogen Candida auris73
A catalogue of 1,167 genomes from the human gut archaeome71
Bacterial colonization reprograms the neonatal gut metabolome69
Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia69
Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion69
Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen68
CRISPRi chemical genetics and comparative genomics identify genes mediating drug potency in Mycobacterium tuberculosis68
RNA viromes from terrestrial sites across China expand environmental viral diversity67
Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-267
Large freshwater phages with the potential to augment aerobic methane oxidation66
Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa66
An orally available Mpro inhibitor is effective against wild-type SARS-CoV-2 and variants including Omicron65
General quantitative relations linking cell growth and the cell cycle in Escherichia coli64
Antimicrobial resistance in the age of COVID-1964
Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC63
Phylogenetic interpretation during outbreaks requires caution63
Symmetry mismatch in the MS-ring of the bacterial flagellar rotor explains the structural coordination of secretion and rotation62
Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration61
Macroecological dynamics of gut microbiota60
IFI16 directly senses viral RNA and enhances RIG-I transcription and activation to restrict influenza virus infection60
Molecular structure of the intact bacterial flagellar basal body60
Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions60
Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology60
Phage–host coevolution in natural populations59
Bacteria deplete deoxynucleotides to defend against bacteriophage infection58
Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean58
The science of the host–virus network58
Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes58
Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance57
Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda57
Microbial production and consumption of hydrocarbons in the global ocean56
Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis56
Tracking bacterial lineages in complex and dynamic environments with applications for growth control and persistence55
Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses55
Wildfire-dependent changes in soil microbiome diversity and function55
Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women54
Microbiome innovations for a sustainable future53
Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection53
Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion53
A two-track model for the spatiotemporal coordination of bacterial septal cell wall synthesis revealed by single-molecule imaging of FtsW52
Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution51
Mosquito vector competence for dengue is modulated by insect-specific viruses51
Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance51
Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing51
Mucoricin is a ricin-like toxin that is critical for the pathogenesis of mucormycosis51
An Alveolata secretory machinery adapted to parasite host cell invasion50
Clinical implications of preterm infant gut microbiome development50
Genome-wide subcellular protein map for the flagellate parasite Trypanosoma brucei50
A DNA-based vaccine protects against Crimean-Congo haemorrhagic fever virus disease in a Cynomolgus macaque model49
Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants49
Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil49
Defending Earth’s terrestrial microbiome48
Candida pathogens induce protective mitochondria-associated type I interferon signalling and a damage-driven response in vaginal epithelial cells48
A nutrient-limited screen unmasks rifabutin hyperactivity for extensively drug-resistant Acinetobacter baumannii48
Bacterial–fungal interactions revealed by genome-wide analysis of bacterial mutant fitness48
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity48
Sec24C is an HIV-1 host dependency factor crucial for virus replication48
Structure and mechanism of the proton-driven motor that powers type 9 secretion and gliding motility48
Monocyte-derived macrophages contain persistent latent HIV reservoirs47
Transcription in fungal conidia before dormancy produces phenotypically variable conidia that maximize survival in different environments47
Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis47
Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis46
Structural basis for placental malaria mediated by Plasmodium falciparum VAR2CSA46
Characterization of interactions of dietary cholesterol with the murine and human gut microbiome46
Dissemination of Mycobacterium abscessus via global transmission networks46
Cell division in the archaeon Haloferax volcanii relies on two FtsZ proteins with distinct functions in division ring assembly and constriction46
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics46
Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria46
β-Barrel proteins tether the outer membrane in many Gram-negative bacteria46
Influenza virus repurposes the antiviral protein IFIT2 to promote translation of viral mRNAs46
Immunometabolic crosstalk during bacterial infection45
Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts45
Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean45
Single-molecule imaging reveals that Z-ring condensation is essential for cell division in Bacillus subtilis45
Targeting the trypanosome kinetochore with CLK1 protein kinase inhibitors45
Spatial integration of transcription and splicing in a dedicated compartment sustains monogenic antigen expression in African trypanosomes45
Crosstalk between γδ T cells and the microbiota45
Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams45
Extracellular SQSTM1 mediates bacterial septic death in mice through insulin receptor signalling44
Computational identification of a systemic antibiotic for Gram-negative bacteria44
A natural symbiotic bacterium drives mosquito refractoriness to Plasmodium infection via secretion of an antimalarial lipase44
Multi-omics analyses of airway host–microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions44
Sexually transmitted infections and female reproductive health43
Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing43
Mating pair stabilization mediates bacterial conjugation species specificity43
An exported kinase family mediates species-specific erythrocyte remodelling and virulence in human malaria43
Appressorium-mediated plant infection by Magnaporthe oryzae is regulated by a Pmk1-dependent hierarchical transcriptional network43
Discovery of broad-spectrum fungicides that block septin-dependent infection processes of pathogenic fungi43
Yeasts collectively extend the limits of habitable temperatures by secreting glutathione43
Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession42
Induction of robust cellular and humoral immunity against SARS-CoV-2 after a third dose of BNT162b2 vaccine in previously unresponsive older adults42
Tecovirimat is effective against human monkeypox virus in vitro at nanomolar concentrations42
Gangliosides are essential endosomal receptors for quasi-enveloped and naked hepatitis A virus42
Wolbachia cifB induces cytoplasmic incompatibility in the malaria mosquito vector42
Escherichia coli Rho GTPase-activating toxin CNF1 mediates NLRP3 inflammasome activation via p21-activated kinases-1/2 during bacteraemia in mice42
Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b241
Increased small particle aerosol transmission of B.1.1.7 compared with SARS-CoV-2 lineage A in vivo41
Microbial diversity declines in warmed tropical soil and respiration rise exceed predictions as communities adapt41
BNT162b2-induced memory T cells respond to the Omicron variant with preserved polyfunctionality41
Spermine-mediated tight sealing of the Magnaporthe oryzae appressorial pore–rice leaf surface interface40
A bacterial pan-genome makes gene essentiality strain-dependent and evolvable39
Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis39
Inhibition of the integrated stress response by viral proteins that block p-eIF2–eIF2B association38
Immune correlates analysis of the ENSEMBLE single Ad26.COV2.S dose vaccine efficacy clinical trial38
Structure of severe fever with thrombocytopenia syndrome virus L protein elucidates the mechanisms of viral transcription initiation38
SeqCode: a nomenclatural code for prokaryotes described from sequence data38
A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings38
Exosome mimicry by a HAVCR1–NPC1 pathway of endosomal fusion mediates hepatitis A virus infection38
Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine37
Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut37
Staphylococcus epidermidis clones express Staphylococcus aureus-type wall teichoic acid to shift from a commensal to pathogen lifestyle37
Dinoflagellate symbionts escape vomocytosis by host cell immune suppression35
Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults35
The microbial gbu gene cluster links cardiovascular disease risk associated with red meat consumption to microbiota l-carnitine catabolism35
β-Barrels covalently link peptidoglycan and the outer membrane in the α-proteobacterium Brucella abortus35
Trypanosoma brucei colonizes the tsetse gut via an immature peritrophic matrix in the proventriculus35
Haematopoietic cell transplantation outcomes are linked to intestinal mycobiota dynamics and an expansion of Candida parapsilosis complex species35
Detection of respiratory syncytial virus defective genomes in nasal secretions is associated with distinct clinical outcomes35
Vertebrate host phylogeny influences gut archaeal diversity34
Fc-γR-dependent antibody effector functions are required for vaccine-mediated protection against antigen-shifted variants of SARS-CoV-234
Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California34
Listeria monocytogenes upregulates mitochondrial calcium signalling to inhibit LC3-associated phagocytosis as a survival strategy34
Mucin O-glycans suppress quorum-sensing pathways and genetic transformation in Streptococcus mutans34
Dimethyl sulfide mediates microbial predator–prey interactions between zooplankton and algae in the ocean34
Keystone taxa indispensable for microbiome recovery34
Epigenetic cell fate in Candida albicans is controlled by transcription factor condensates acting at super-enhancer-like elements33
Regulation of host and virus genes by neuronal miR-138 favours herpes simplex virus 1 latency33
Expanding known viral diversity in the healthy infant gut33
Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites33
Prophage integration into CRISPR loci enables evasion of antiviral immunity in Streptococcus pyogenes33
Lysogenic host–virus interactions in SAR11 marine bacteria33
LncRNA DINOR is a virulence factor and global regulator of stress responses in Candida auris33
Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network32
A cell surface-exposed protein complex with an essential virulence function in Ustilago maydis32
Patient-derived monoclonal antibody neutralizes SARS-CoV-2 Omicron variants and confers full protection in monkeys32
The Rcs stress response inversely controls surface and CRISPR–Cas adaptive immunity to discriminate plasmids and phages32
Gut-inhabiting Clostridia build human GPCR ligands by conjugating neurotransmitters with diet- and human-derived fatty acids32
Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes32
Cell wall synthesis and remodelling dynamics determine division site architecture and cell shape in Escherichia coli32
A heat-shock response regulated by the PfAP2-HS transcription factor protects human malaria parasites from febrile temperatures31
The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice31
Variation and transmission of the human gut microbiota across multiple familial generations31
Human microbiome myths and misconceptions31
DNA methylation enzymes and PRC1 restrict B-cell Epstein–Barr virus oncoprotein expression31
Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation31
Platform for isolation and characterization of SARS-CoV-2 variants enables rapid characterization of Omicron in Australia31
Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters31
Therapeutics for COVID-1931
Single-molecule imaging of LexA degradation in Escherichia coli elucidates regulatory mechanisms and heterogeneity of the SOS response31
Coinfection by influenza A virus and respiratory syncytial virus produces hybrid virus particles30
Collective interactions augment influenza A virus replication in a host-dependent manner30
The evolutionary origin of host association in the Rickettsiales30
Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape30
Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships30
Identification of Tse8 as a Type VI secretion system toxin from Pseudomonas aeruginosa that targets the bacterial transamidosome to inhibit protein synthesis in prey cells30
Bacteriophage genome engineering with CRISPR–Cas13a30
Adaptation of the small intestine to microbial enteropathogens in Zambian children with stunting30
Spatiotemporal proteomics uncovers cathepsin-dependent macrophage cell death during Salmonella infection30
Interaction dynamics and virus–host range for estuarine actinophages captured by epicPCR29