Nature Microbiology

(The TQCC of Nature Microbiology is 62. The table below lists those papers that are above that threshold based on CrossRef citation counts. The publications cover those that have been published in the past four years, i.e., from 2019-03-01 to 2023-03-01.)
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-24436
The neuroactive potential of the human gut microbiota in quality of life and depression865
Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus505
The current and future global distribution and population at risk of dengue440
Defining and combating antibiotic resistance from One Health and Global Health perspectives391
Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease344
Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread338
Global diversity and biogeography of bacterial communities in wastewater treatment plants332
Emergence of plasmid-mediated high-level tigecycline resistance genes in animals and humans314
Decoding type I and III interferon signalling during viral infection246
Plasmid-encoded tet(X) genes that confer high-level tigecycline resistance in Escherichia coli229
The high prevalence of antibiotic heteroresistance in pathogenic bacteria is mainly caused by gene amplification199
Gut pathobionts underlie intestinal barrier dysfunction and liver T helper 17 cell immune response in primary sclerosing cholangitis188
FtsW is a peptidoglycan polymerase that is functional only in complex with its cognate penicillin-binding protein181
Dampened NLRP3-mediated inflammation in bats and implications for a special viral reservoir host181
Intestinal serotonin and fluoxetine exposure modulate bacterial colonization in the gut181
HIV-1 reservoirs in urethral macrophages of patients under suppressive antiretroviral therapy175
Peptostreptococcus anaerobius promotes colorectal carcinogenesis and modulates tumour immunity165
Defective viral genomes are key drivers of the virus–host interaction160
Drug repurposing for antimicrobial discovery159
Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea158
Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes149
Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail147
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage137
Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate131
Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome131
An automated Raman-based platform for the sorting of live cells by functional properties128
The structure of the influenza A virus genome122
Antibody responses to viral infections: a structural perspective across three different enveloped viruses121
Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology120
A genomic view of the reef-building coral Porites lutea and its microbial symbionts120
A systematic review of biomarkers to detect active tuberculosis117
Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism114
Enabling genetic analysis of diverse bacteria with Mobile-CRISPRi114
Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection113
Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance112
Megaphages infect Prevotella and variants are widespread in gut microbiomes111
Transmission of human-associated microbiota along family and social networks110
Non-specific degradation of transcripts promotes plasmid clearance during type III-A CRISPR–Cas immunity107
Reactive oxygen species induce antibiotic tolerance during systemic Staphylococcus aureus infection107
Defective Epstein–Barr virus in chronic active infection and haematological malignancy106
Mucin glycans attenuate the virulence of Pseudomonas aeruginosa in infection105
Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi104
Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms103
Control of nitrogen fixation in bacteria that associate with cereals101
Quantitative microbiome profiling disentangles inflammation- and bile duct obstruction-associated microbiota alterations across PSC/IBD diagnoses100
The global distribution of Bacillus anthracis and associated anthrax risk to humans, livestock and wildlife99
Expanding anaerobic alkane metabolism in the domain of Archaea96
Pseudomonas aeruginosa orchestrates twitching motility by sequential control of type IV pili movements90
Genome mining identifies cepacin as a plant-protective metabolite of the biopesticidal bacterium Burkholderia ambifaria89
A jumbo phage that forms a nucleus-like structure evades CRISPR–Cas DNA targeting but is vulnerable to type III RNA-based immunity89
Characterization of a filovirus (Měnglà virus) from Rousettus bats in China88
Sulfonate-based networks between eukaryotic phytoplankton and heterotrophic bacteria in the surface ocean87
Complex N-glycan breakdown by gut Bacteroides involves an extensive enzymatic apparatus encoded by multiple co-regulated genetic loci85
Cooking shapes the structure and function of the gut microbiome83
Modelling approaches for studying the microbiome82
Phosphatidic acid governs natural egress in Toxoplasma gondii via a guanylate cyclase receptor platform81
Bacillus subtilis cell diameter is determined by the opposing actions of two distinct cell wall synthetic systems81
Influenza A variants with reduced susceptibility to baloxavir isolated from Japanese patients are fit and transmit through respiratory droplets80
Life cycle progression and sexual development of the apicomplexan parasite Cryptosporidium parvum79
Direct interactions with influenza promote bacterial adherence during respiratory infections78
Defining the human gut host–phage network through single-cell viral tagging78
Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens78
Type I interferon-driven susceptibility to Mycobacterium tuberculosis is mediated by IL-1Ra77
Intracellular bacteria engage a STING–TBK1–MVB12b pathway to enable paracrine cGAS–STING signalling77
Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation75
Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice74
Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche72
Consistent trade-offs in fungal trait expression across broad spatial scales72
Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota72
Viral complementation of immunodeficiency confers protection against enteric pathogens via interferon-λ70
Cyclophilin A protects HIV-1 from restriction by human TRIM5α70
Evolutionary genomics of anthroponosis in Cryptosporidium69
Airborne microbial transport limitation to isolated Antarctic soil habitats69
A conjugative plasmid that augments virulence in Klebsiella pneumoniae67
Antibiotic combinations that exploit heteroresistance to multiple drugs effectively control infection67
The Toxoplasma effector TEEGR promotes parasite persistence by modulating NF-κB signalling via EZH267
An RNA-centric dissection of host complexes controlling flavivirus infection66
Evidence for phospholipid export from the bacterial inner membrane by the Mla ABC transport system66
The impact of antimicrobials on gonococcal evolution65
Molecular architecture, polar targeting and biogenesis of the Legionella Dot/Icm T4SS64
Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice64
Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels63
Fungal biofilm morphology impacts hypoxia fitness and disease progression63
Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria62
CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria62
The intestinal regionalization of acute norovirus infection is regulated by the microbiota via bile acid-mediated priming of type III interferon62