Nature Microbiology

(The TQCC of Nature Microbiology is 33. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 500 papers]. The publications cover those that have been published in the past four years, i.e., from 2019-11-01 to 2023-11-01.)
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-24852
Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses2292
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology2023
Longitudinal observation and decline of neutralizing antibody responses in the three months following SARS-CoV-2 infection in humans978
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic648
Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets569
Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies500
The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets480
The continued threat of emerging flaviviruses448
Therapeutically administered ribonucleoside analogue MK-4482/EIDD-2801 blocks SARS-CoV-2 transmission in ferrets291
SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution282
Community-led, integrated, reproducible multi-omics with anvi’o274
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway269
Safety of bacteriophage therapy in severe Staphylococcus aureus infection232
Competition for iron drives phytopathogen control by natural rhizosphere microbiomes217
The SARS-CoV-2 RNA–protein interactome in infected human cells214
Antibody responses to SARS-CoV-2 vaccines in 45,965 adults from the general population of the United Kingdom213
Diversity, ecology and evolution of Archaea213
Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth213
Akkermansia muciniphila secretes a glucagon-like peptide-1-inducing protein that improves glucose homeostasis and ameliorates metabolic disease in mice204
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome201
Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail196
A broad-spectrum antibiotic adjuvant reverses multidrug-resistant Gram-negative pathogens195
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse188
The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks173
ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity171
A standardized archaeal taxonomy for the Genome Taxonomy Database161
Quantitative image analysis of microbial communities with BiofilmQ156
N6-methyladenosine modification enables viral RNA to escape recognition by RNA sensor RIG-I147
Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan145
Responses to acute infection with SARS-CoV-2 in the lungs of rhesus macaques, baboons and marmosets141
Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems137
LY6E impairs coronavirus fusion and confers immune control of viral disease136
Effectiveness of COVID-19 vaccines against symptomatic SARS-CoV-2 infection and severe outcomes with variants of concern in Ontario136
Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut134
Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology134
Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome133
Reactive oxygen species induce antibiotic tolerance during systemic Staphylococcus aureus infection133
SARS-CoV-2 detection in patients with influenza-like illness132
Bacteriophage-resistant Acinetobacter baumannii are resensitized to antimicrobials132
COVID-19-associated fungal infections129
Genome-wide associations of human gut microbiome variation and implications for causal inference analyses129
Metallodrug ranitidine bismuth citrate suppresses SARS-CoV-2 replication and relieves virus-associated pneumonia in Syrian hamsters128
We shouldn’t worry when a virus mutates during disease outbreaks122
Spatial metabolomics of in situ host–microbe interactions at the micrometre scale121
Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries119
Nuclear pore blockade reveals that HIV-1 completes reverse transcription and uncoating in the nucleus119
Control of nitrogen fixation in bacteria that associate with cereals118
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community116
Structures of the stator complex that drives rotation of the bacterial flagellum108
Cellular host factors for SARS-CoV-2 infection107
A jumbo phage that forms a nucleus-like structure evades CRISPR–Cas DNA targeting but is vulnerable to type III RNA-based immunity106
Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice104
Roadmap for naming uncultivated Archaea and Bacteria104
Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance101
Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens98
Species- and site-specific genome editing in complex bacterial communities97
Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes96
Spike-specific circulating T follicular helper cell and cross-neutralizing antibody responses in COVID-19-convalescent individuals95
Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria92
Moving from probiotics to precision probiotics92
Oxysterols provide innate immunity to bacterial infection by mobilizing cell surface accessible cholesterol91
Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems91
Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner91
Developmentally regulated volatiles geosmin and 2-methylisoborneol attract a soil arthropod to Streptomyces bacteria promoting spore dispersal90
Urban informal settlements as hotspots of antimicrobial resistance and the need to curb environmental transmission89
Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation89
The Syntrophy hypothesis for the origin of eukaryotes revisited89
Influenza A variants with reduced susceptibility to baloxavir isolated from Japanese patients are fit and transmit through respiratory droplets88
Mitochondrial dysfunction caused by outer membrane vesicles from Gram-negative bacteria activates intrinsic apoptosis and inflammation88
Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients88
The microbiota programs DNA methylation to control intestinal homeostasis and inflammation88
Fungal taxonomy and sequence-based nomenclature88
Envelope stress responses defend against type six secretion system attacks independently of immunity proteins84
Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing84
Trace gas oxidizers are widespread and active members of soil microbial communities82
Lactate production by Staphylococcus aureus biofilm inhibits HDAC11 to reprogramme the host immune response during persistent infection81
Structural coordination of polymerization and crosslinking by a SEDS–bPBP peptidoglycan synthase complex81
Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes80
Neutralizing antibody activity in convalescent sera from infection in humans with SARS-CoV-2 and variants of concern77
Fetal meconium does not have a detectable microbiota before birth77
Monkeypox virus emergence in wild chimpanzees reveals distinct clinical outcomes and viral diversity76
Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome76
SspABCD–SspE is a phosphorothioation-sensing bacterial defence system with broad anti-phage activities76
A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome76
Dietary l-serine confers a competitive fitness advantage to Enterobacteriaceae in the inflamed gut76
Genetic circuit design automation for yeast76
Multi-kingdom microbiota analyses identify bacterial–fungal interactions and biomarkers of colorectal cancer across cohorts75
Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity74
The intestinal regionalization of acute norovirus infection is regulated by the microbiota via bile acid-mediated priming of type III interferon74
Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland74
Selective sequestration of signalling proteins in a membraneless organelle reinforces the spatial regulation of asymmetry in Caulobacter crescentus73
Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota73
Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness72
Implementation of permeation rules leads to a FabI inhibitor with activity against Gram-negative pathogens72
A MORC-driven transcriptional switch controls Toxoplasma developmental trajectories and sexual commitment71
Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis70
Escherichia coli is engineered to grow on CO2 and formic acid70
Successive blood meals enhance virus dissemination within mosquitoes and increase transmission potential69
Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron69
Combinatorial selection in amoebal hosts drives the evolution of the human pathogen Legionella pneumophila69
Home chemical and microbial transitions across urbanization68
Longitudinal analysis of antibody dynamics in COVID-19 convalescents reveals neutralizing responses up to 16 months after infection68
Systematic evaluation of horizontal gene transfer between eukaryotes and viruses68
Commensal Bacteroidetes protect against Klebsiella pneumoniae colonization and transmission through IL-36 signalling67
Core components of DNA lagging strand synthesis machinery are essential for hepatitis B virus cccDNA formation67
Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission66
Effector-triggered immunity and pathogen sensing in metazoans66
Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing65
Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance64
Bacterial colonization reprograms the neonatal gut metabolome64
Staphylococcus aureus small colony variants impair host immunity by activating host cell glycolysis and inducing necroptosis63
Transcriptional and functional insights into the host immune response against the emerging fungal pathogen Candida auris63
Towards a deeper understanding of the vaginal microbiota63
Antimicrobial resistance in the age of COVID-1962
Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer62
The impact of genetic diversity on gene essentiality within the Escherichia coli species62
General quantitative relations linking cell growth and the cell cycle in Escherichia coli61
Phylogenetic interpretation during outbreaks requires caution60
Mycobiota-induced IgA antibodies regulate fungal commensalism in the gut and are dysregulated in Crohn’s disease59
A bottom-up view of antimicrobial resistance transmission in developing countries59
Symmetry mismatch in the MS-ring of the bacterial flagellar rotor explains the structural coordination of secretion and rotation59
Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia57
Population genomics confirms acquisition of drug-resistant Aspergillus fumigatus infection by humans from the environment57
Klebsiella michiganensis transmission enhances resistance to Enterobacteriaceae gut invasion by nutrition competition57
Microbial metabolites in the marine carbon cycle56
Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology55
Metagenomics-enabled microbial surveillance55
The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves55
CRISPRi chemical genetics and comparative genomics identify genes mediating drug potency in Mycobacterium tuberculosis54
The DarTG toxin-antitoxin system provides phage defence by ADP-ribosylating viral DNA54
Reduction of microbial diversity in grassland soil is driven by long-term climate warming54
Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota53
Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice53
Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda53
Macroecological dynamics of gut microbiota53
Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen53
Large freshwater phages with the potential to augment aerobic methane oxidation52
Long-term stability and Red Queen-like strain dynamics in marine viruses52
Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa52
Molecular structure of the intact bacterial flagellar basal body52
Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria51
Inflammasome-mediated antagonism of type I interferon enhances Rickettsia pathogenesis50
Evolution of the human pathogenic lifestyle in fungi50
Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC50
An orally available Mpro inhibitor is effective against wild-type SARS-CoV-2 and variants including Omicron50
The science of the host–virus network49
Microbial production and consumption of hydrocarbons in the global ocean49
Harnessing the microbiome to prevent global biodiversity loss49
Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease49
A catalogue of 1,167 genomes from the human gut archaeome48
Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-248
Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes48
Tracking bacterial lineages in complex and dynamic environments with applications for growth control and persistence47
Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis46
Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance45
Bacterial–fungal interactions revealed by genome-wide analysis of bacterial mutant fitness45
Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution45
Mucoricin is a ricin-like toxin that is critical for the pathogenesis of mucormycosis45
Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions45
Microbiome innovations for a sustainable future45
IFI16 directly senses viral RNA and enhances RIG-I transcription and activation to restrict influenza virus infection44
Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis44
RNA viromes from terrestrial sites across China expand environmental viral diversity44
Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments44
A nutrient-limited screen unmasks rifabutin hyperactivity for extensively drug-resistant Acinetobacter baumannii43
Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration43
A DNA-based vaccine protects against Crimean-Congo haemorrhagic fever virus disease in a Cynomolgus macaque model43
Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance43
Staphylococcus aureus cell growth and division are regulated by an amidase that trims peptides from uncrosslinked peptidoglycan43
A two-track model for the spatiotemporal coordination of bacterial septal cell wall synthesis revealed by single-molecule imaging of FtsW42
Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion42
Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean42
Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection41
Targeting the trypanosome kinetochore with CLK1 protein kinase inhibitors41
Asymmetric distribution of TLR3 leads to a polarized immune response in human intestinal epithelial cells41
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics41
Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins41
An Alveolata secretory machinery adapted to parasite host cell invasion41
Clinical implications of preterm infant gut microbiome development41
Structural basis for placental malaria mediated by Plasmodium falciparum VAR2CSA41
Regulation underlying hierarchical and simultaneous utilization of carbon substrates by flux sensors in Escherichia coli40
Candida pathogens induce protective mitochondria-associated type I interferon signalling and a damage-driven response in vaginal epithelial cells40
Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis40
Sec24C is an HIV-1 host dependency factor crucial for virus replication40
Spatial integration of transcription and splicing in a dedicated compartment sustains monogenic antigen expression in African trypanosomes40
Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants40
Extracellular SQSTM1 mediates bacterial septic death in mice through insulin receptor signalling40
In vivo structure of the Legionella type II secretion system by electron cryotomography40
Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women40
Gangliosides are essential endosomal receptors for quasi-enveloped and naked hepatitis A virus40
Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing39
β-Barrel proteins tether the outer membrane in many Gram-negative bacteria39
Single-molecule imaging reveals that Z-ring condensation is essential for cell division in Bacillus subtilis39
Structure and mechanism of the proton-driven motor that powers type 9 secretion and gliding motility39
Ornithine capture by a translating ribosome controls bacterial polyamine synthesis38
Transcription in fungal conidia before dormancy produces phenotypically variable conidia that maximize survival in different environments38
Bacteria deplete deoxynucleotides to defend against bacteriophage infection38
Dissemination of Mycobacterium abscessus via global transmission networks38
Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion38
Phage–host coevolution in natural populations37
An exported kinase family mediates species-specific erythrocyte remodelling and virulence in human malaria37
Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams37
Yeasts collectively extend the limits of habitable temperatures by secreting glutathione37
Wildfire-dependent changes in soil microbiome diversity and function37
Spermine-mediated tight sealing of the Magnaporthe oryzae appressorial pore–rice leaf surface interface37
BNT162b2-induced memory T cells respond to the Omicron variant with preserved polyfunctionality36
Herpesviruses induce aggregation and selective autophagy of host signalling proteins NEMO and RIPK1 as an immune-evasion mechanism36
Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil36
Immunometabolic crosstalk during bacterial infection36
Exosome mimicry by a HAVCR1–NPC1 pathway of endosomal fusion mediates hepatitis A virus infection36
Influenza virus repurposes the antiviral protein IFIT2 to promote translation of viral mRNAs36
Unexpected mitochondrial genome diversity revealed by targeted single-cell genomics of heterotrophic flagellated protists35
Induction of robust cellular and humoral immunity against SARS-CoV-2 after a third dose of BNT162b2 vaccine in previously unresponsive older adults35
Increased small particle aerosol transmission of B.1.1.7 compared with SARS-CoV-2 lineage A in vivo35
Inhibition of the integrated stress response by viral proteins that block p-eIF2–eIF2B association35
Crosstalk between γδ T cells and the microbiota35
Designing ecologically optimized pneumococcal vaccines using population genomics34
Appressorium-mediated plant infection by Magnaporthe oryzae is regulated by a Pmk1-dependent hierarchical transcriptional network34
Cell division in the archaeon Haloferax volcanii relies on two FtsZ proteins with distinct functions in division ring assembly and constriction34
Escherichia coli Rho GTPase-activating toxin CNF1 mediates NLRP3 inflammasome activation via p21-activated kinases-1/2 during bacteraemia in mice34
Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis34
A natural symbiotic bacterium drives mosquito refractoriness to Plasmodium infection via secretion of an antimalarial lipase34
Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria33
Select autophagy genes maintain quiescence of tissue-resident macrophages and increase susceptibility to Listeria monocytogenes33
Commensal Escherichia coli are a reservoir for the transfer of XDR plasmids into epidemic fluoroquinolone-resistant Shigella sonnei33
Trypanosoma brucei colonizes the tsetse gut via an immature peritrophic matrix in the proventriculus33
Structure of severe fever with thrombocytopenia syndrome virus L protein elucidates the mechanisms of viral transcription initiation33