Nature Microbiology

(The TQCC of Nature Microbiology is 29. 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 2020-05-01 to 2024-05-01.)
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology2158
Longitudinal observation and decline of neutralizing antibody responses in the three months following SARS-CoV-2 infection in humans1022
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic690
Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets599
The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets536
The continued threat of emerging flaviviruses535
Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies531
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway365
Community-led, integrated, reproducible multi-omics with anvi’o363
Therapeutically administered ribonucleoside analogue MK-4482/EIDD-2801 blocks SARS-CoV-2 transmission in ferrets309
SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution308
Diversity, ecology and evolution of Archaea267
Competition for iron drives phytopathogen control by natural rhizosphere microbiomes264
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome261
Akkermansia muciniphila secretes a glucagon-like peptide-1-inducing protein that improves glucose homeostasis and ameliorates metabolic disease in mice253
A broad-spectrum antibiotic adjuvant reverses multidrug-resistant Gram-negative pathogens242
Antibody responses to SARS-CoV-2 vaccines in 45,965 adults from the general population of the United Kingdom235
The SARS-CoV-2 RNA–protein interactome in infected human cells232
Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail214
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse208
ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity195
A standardized archaeal taxonomy for the Genome Taxonomy Database195
COVID-19-associated fungal infections193
Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut183
Quantitative image analysis of microbial communities with BiofilmQ181
Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems169
Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan167
Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome162
Bacteriophage-resistant Acinetobacter baumannii are resensitized to antimicrobials157
Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries156
Effectiveness of COVID-19 vaccines against symptomatic SARS-CoV-2 infection and severe outcomes with variants of concern in Ontario156
Responses to acute infection with SARS-CoV-2 in the lungs of rhesus macaques, baboons and marmosets154
LY6E impairs coronavirus fusion and confers immune control of viral disease150
Genome-wide associations of human gut microbiome variation and implications for causal inference analyses147
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community147
Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice139
Metallodrug ranitidine bismuth citrate suppresses SARS-CoV-2 replication and relieves virus-associated pneumonia in Syrian hamsters139
Nuclear pore blockade reveals that HIV-1 completes reverse transcription and uncoating in the nucleus136
Cellular host factors for SARS-CoV-2 infection133
Structures of the stator complex that drives rotation of the bacterial flagellum129
Species- and site-specific genome editing in complex bacterial communities124
Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes120
Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity118
Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes115
Roadmap for naming uncultivated Archaea and Bacteria114
A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome113
Moving from probiotics to precision probiotics113
Spike-specific circulating T follicular helper cell and cross-neutralizing antibody responses in COVID-19-convalescent individuals110
Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems108
Mitochondrial dysfunction caused by outer membrane vesicles from Gram-negative bacteria activates intrinsic apoptosis and inflammation108
Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients107
Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner107
Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria105
Trace gas oxidizers are widespread and active members of soil microbial communities104
Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing103
Urban informal settlements as hotspots of antimicrobial resistance and the need to curb environmental transmission103
Multi-kingdom microbiota analyses identify bacterial–fungal interactions and biomarkers of colorectal cancer across cohorts102
Lactate production by Staphylococcus aureus biofilm inhibits HDAC11 to reprogramme the host immune response during persistent infection102
Fungal taxonomy and sequence-based nomenclature102
Towards a deeper understanding of the vaginal microbiota101
Reduction of microbial diversity in grassland soil is driven by long-term climate warming100
Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness98
Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission97
Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome95
Systematic evaluation of horizontal gene transfer between eukaryotes and viruses91
Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance90
Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota90
Fetal meconium does not have a detectable microbiota before birth90
Genetic circuit design automation for yeast90
Metagenomics-enabled microbial surveillance89
Neutralizing antibody activity in convalescent sera from infection in humans with SARS-CoV-2 and variants of concern86
Population genomics confirms acquisition of drug-resistant Aspergillus fumigatus infection by humans from the environment85
A bottom-up view of antimicrobial resistance transmission in developing countries85
Evolution of the human pathogenic lifestyle in fungi84
Escherichia coli is engineered to grow on CO2 and formic acid82
The DarTG toxin-antitoxin system provides phage defence by ADP-ribosylating viral DNA82
Harnessing the microbiome to prevent global biodiversity loss81
The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves81
Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron80
Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland80
Longitudinal analysis of antibody dynamics in COVID-19 convalescents reveals neutralizing responses up to 16 months after infection78
Mycobiota-induced IgA antibodies regulate fungal commensalism in the gut and are dysregulated in Crohn’s disease76
CRISPRi chemical genetics and comparative genomics identify genes mediating drug potency in Mycobacterium tuberculosis75
The impact of genetic diversity on gene essentiality within the Escherichia coli species75
Transcriptional and functional insights into the host immune response against the emerging fungal pathogen Candida auris75
Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion74
Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen73
Microbial metabolites in the marine carbon cycle73
A catalogue of 1,167 genomes from the human gut archaeome73
Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia72
RNA viromes from terrestrial sites across China expand environmental viral diversity70
Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC70
Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-268
Large freshwater phages with the potential to augment aerobic methane oxidation68
An orally available Mpro inhibitor is effective against wild-type SARS-CoV-2 and variants including Omicron67
Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa67
General quantitative relations linking cell growth and the cell cycle in Escherichia coli64
Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration64
IFI16 directly senses viral RNA and enhances RIG-I transcription and activation to restrict influenza virus infection64
Antimicrobial resistance in the age of COVID-1964
Phylogenetic interpretation during outbreaks requires caution63
Molecular structure of the intact bacterial flagellar basal body62
Phage–host coevolution in natural populations62
Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions61
Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes61
Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology60
Bacteria deplete deoxynucleotides to defend against bacteriophage infection59
Tracking bacterial lineages in complex and dynamic environments with applications for growth control and persistence59
The science of the host–virus network58
Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance58
Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses58
Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women58
Microbial production and consumption of hydrocarbons in the global ocean57
Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda57
Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean57
Wildfire-dependent changes in soil microbiome diversity and function57
Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis57
Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion55
Genome-wide subcellular protein map for the flagellate parasite Trypanosoma brucei55
Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection55
Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing55
Microbiome innovations for a sustainable future54
Mucoricin is a ricin-like toxin that is critical for the pathogenesis of mucormycosis53
Mosquito vector competence for dengue is modulated by insect-specific viruses53
A two-track model for the spatiotemporal coordination of bacterial septal cell wall synthesis revealed by single-molecule imaging of FtsW52
Clinical implications of preterm infant gut microbiome development52
Bacterial–fungal interactions revealed by genome-wide analysis of bacterial mutant fitness51
Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance51
Multi-omics analyses of airway host–microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions51
Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants51
Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution51
Immunometabolic crosstalk during bacterial infection50
Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil50
A DNA-based vaccine protects against Crimean-Congo haemorrhagic fever virus disease in a Cynomolgus macaque model50
An Alveolata secretory machinery adapted to parasite host cell invasion50
Monocyte-derived macrophages contain persistent latent HIV reservoirs50
Structure and mechanism of the proton-driven motor that powers type 9 secretion and gliding motility49
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity49
Candida pathogens induce protective mitochondria-associated type I interferon signalling and a damage-driven response in vaginal epithelial cells49
Defending Earth’s terrestrial microbiome49
Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis49
Computational identification of a systemic antibiotic for Gram-negative bacteria48
Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria48
A nutrient-limited screen unmasks rifabutin hyperactivity for extensively drug-resistant Acinetobacter baumannii48
Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts48
Sec24C is an HIV-1 host dependency factor crucial for virus replication48
Transcription in fungal conidia before dormancy produces phenotypically variable conidia that maximize survival in different environments48
Dissemination of Mycobacterium abscessus via global transmission networks48
Cell division in the archaeon Haloferax volcanii relies on two FtsZ proteins with distinct functions in division ring assembly and constriction48
Structural basis for placental malaria mediated by Plasmodium falciparum VAR2CSA47
Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing47
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics47
Characterization of interactions of dietary cholesterol with the murine and human gut microbiome47
Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis47
Influenza virus repurposes the antiviral protein IFIT2 to promote translation of viral mRNAs47
Extracellular SQSTM1 mediates bacterial septic death in mice through insulin receptor signalling46
Spatial integration of transcription and splicing in a dedicated compartment sustains monogenic antigen expression in African trypanosomes46
β-Barrel proteins tether the outer membrane in many Gram-negative bacteria46
Sexually transmitted infections and female reproductive health46
A natural symbiotic bacterium drives mosquito refractoriness to Plasmodium infection via secretion of an antimalarial lipase46
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
Crosstalk between γδ T cells and the microbiota45
Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams45
Appressorium-mediated plant infection by Magnaporthe oryzae is regulated by a Pmk1-dependent hierarchical transcriptional network45
Wolbachia cifB induces cytoplasmic incompatibility in the malaria mosquito vector44
Discovery of broad-spectrum fungicides that block septin-dependent infection processes of pathogenic fungi44
Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean44
Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession43
Neutralizing antibody activity against 21 SARS-CoV-2 variants in older adults vaccinated with BNT162b243
Escherichia coli Rho GTPase-activating toxin CNF1 mediates NLRP3 inflammasome activation via p21-activated kinases-1/2 during bacteraemia in mice43
Mating pair stabilization mediates bacterial conjugation species specificity43
Induction of robust cellular and humoral immunity against SARS-CoV-2 after a third dose of BNT162b2 vaccine in previously unresponsive older adults43
Microbial diversity declines in warmed tropical soil and respiration rise exceed predictions as communities adapt42
Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut42
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
SeqCode: a nomenclatural code for prokaryotes described from sequence data42
BNT162b2-induced memory T cells respond to the Omicron variant with preserved polyfunctionality42
Spermine-mediated tight sealing of the Magnaporthe oryzae appressorial pore–rice leaf surface interface41
Increased small particle aerosol transmission of B.1.1.7 compared with SARS-CoV-2 lineage A in vivo41
A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings40
Expanding known viral diversity in the healthy infant gut40
Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine40
A bacterial pan-genome makes gene essentiality strain-dependent and evolvable40
Fc-γR-dependent antibody effector functions are required for vaccine-mediated protection against antigen-shifted variants of SARS-CoV-240
Human microbiome myths and misconceptions39
Inhibition of the integrated stress response by viral proteins that block p-eIF2–eIF2B association38
Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults38
Exosome mimicry by a HAVCR1–NPC1 pathway of endosomal fusion mediates hepatitis A virus infection38
Staphylococcus epidermidis clones express Staphylococcus aureus-type wall teichoic acid to shift from a commensal to pathogen lifestyle38
Immune correlates analysis of the ENSEMBLE single Ad26.COV2.S dose vaccine efficacy clinical trial38
The microbial gbu gene cluster links cardiovascular disease risk associated with red meat consumption to microbiota l-carnitine catabolism37
Haematopoietic cell transplantation outcomes are linked to intestinal mycobiota dynamics and an expansion of Candida parapsilosis complex species36
Dimethyl sulfide mediates microbial predator–prey interactions between zooplankton and algae in the ocean36
Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters35
β-Barrels covalently link peptidoglycan and the outer membrane in the α-proteobacterium Brucella abortus35
Detection of respiratory syncytial virus defective genomes in nasal secretions is associated with distinct clinical outcomes35
Vertebrate host phylogeny influences gut archaeal diversity35
Therapeutics for COVID-1935
Mucin O-glycans suppress quorum-sensing pathways and genetic transformation in Streptococcus mutans35
Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California35
LncRNA DINOR is a virulence factor and global regulator of stress responses in Candida auris35
Dinoflagellate symbionts escape vomocytosis by host cell immune suppression35
Keystone taxa indispensable for microbiome recovery35
Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites34
Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation34
A cell surface-exposed protein complex with an essential virulence function in Ustilago maydis34
Listeria monocytogenes upregulates mitochondrial calcium signalling to inhibit LC3-associated phagocytosis as a survival strategy34
Bacteriophage genome engineering with CRISPR–Cas13a33
Regulation of host and virus genes by neuronal miR-138 favours herpes simplex virus 1 latency33
DNA methylation enzymes and PRC1 restrict B-cell Epstein–Barr virus oncoprotein expression33
Gut-inhabiting Clostridia build human GPCR ligands by conjugating neurotransmitters with diet- and human-derived fatty acids33
Lysogenic host–virus interactions in SAR11 marine bacteria33
Platform for isolation and characterization of SARS-CoV-2 variants enables rapid characterization of Omicron in Australia33
Prophage integration into CRISPR loci enables evasion of antiviral immunity in Streptococcus pyogenes33
The cell biology of archaea33
Epigenetic cell fate in Candida albicans is controlled by transcription factor condensates acting at super-enhancer-like elements33
Single-molecule imaging of LexA degradation in Escherichia coli elucidates regulatory mechanisms and heterogeneity of the SOS response33
Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network33
The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice33
Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships33
Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants33
Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity32
Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes32
Variation and transmission of the human gut microbiota across multiple familial generations32
The Rcs stress response inversely controls surface and CRISPR–Cas adaptive immunity to discriminate plasmids and phages32
A heat-shock response regulated by the PfAP2-HS transcription factor protects human malaria parasites from febrile temperatures32
Patient-derived monoclonal antibody neutralizes SARS-CoV-2 Omicron variants and confers full protection in monkeys32
Coinfection by influenza A virus and respiratory syncytial virus produces hybrid virus particles32
Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia32
Cell wall synthesis and remodelling dynamics determine division site architecture and cell shape in Escherichia coli32
Collective interactions augment influenza A virus replication in a host-dependent manner31
Spatiotemporal proteomics uncovers cathepsin-dependent macrophage cell death during Salmonella infection31
Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape31
Identification of Tse8 as a Type VI secretion system toxin from Pseudomonas aeruginosa that targets the bacterial transamidosome to inhibit protein synthesis in prey cells31
The evolutionary origin of host association in the Rickettsiales30
Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments30
PCRCR complex is essential for invasion of human erythrocytes by Plasmodium falciparum30
Adaptation of the small intestine to microbial enteropathogens in Zambian children with stunting30
Viral biogeography of the mammalian gut and parenchymal organs29
Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex29
SARS-CoV-2-specific T-cell epitope repertoire in convalescent and mRNA-vaccinated individuals29
Widespread divergent transcription from bacterial and archaeal promoters is a consequence of DNA-sequence symmetry29
Interaction dynamics and virus–host range for estuarine actinophages captured by epicPCR29
Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon29