Nature Reviews Microbiology

(The TQCC of Nature Reviews Microbiology is 21. 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.)
Characteristics of SARS-CoV-2 and COVID-193126
SARS-CoV-2 variants, spike mutations and immune escape2586
Coronavirus biology and replication: implications for SARS-CoV-21973
Gut microbiota in human metabolic health and disease1962
Plant–microbiome interactions: from community assembly to plant health1368
Long COVID: major findings, mechanisms and recommendations1088
The gut microbiota–brain axis in behaviour and brain disorders866
Antibiotic resistance in the environment786
Nanomaterial-based therapeutics for antibiotic-resistant bacterial infections627
Considerations for diagnostic COVID-19 tests552
Gut microbial metabolites as multi-kingdom intermediates548
Infectious disease in an era of global change514
Transmissibility and transmission of respiratory viruses434
Biofilm dispersion433
SARS-CoV-2 pathogenesis411
Regulation of peptidoglycan synthesis and remodelling342
The biofilm life cycle: expanding the conceptual model of biofilm formation331
Tolerance and resistance of microbial biofilms325
Tackling the emerging threat of antifungal resistance to human health320
An evolving view on biogeochemical cycling of iron298
Bat-borne virus diversity, spillover and emergence294
Life and death in the soil microbiome: how ecological processes influence biogeochemistry291
The population genetics of pathogenic Escherichia coli270
Unique and common traits in mycorrhizal symbioses263
Mechano-bactericidal actions of nanostructured surfaces262
Structural biology of SARS-CoV-2 and implications for therapeutic development260
The human virome: assembly, composition and host interactions258
The evolution of SARS-CoV-2254
Host–microbiota interactions in immune-mediated diseases252
Innovations to culturing the uncultured microbial majority250
Prevotella diversity, niches and interactions with the human host250
Pathogenesis of human cytomegalovirus in the immunocompromised host247
Microbial volatile organic compounds in intra-kingdom and inter-kingdom interactions235
The role of vaccines in combatting antimicrobial resistance232
Electromicrobiology: the ecophysiology of phylogenetically diverse electroactive microorganisms228
Tara Oceans: towards global ocean ecosystems biology227
Diversity within species: interpreting strains in microbiomes216
Pseudomonas aeruginosa adaptation and evolution in patients with cystic fibrosis212
Horizontal gene transfer and adaptive evolution in bacteria210
Bacillus subtilis biofilm formation and social interactions209
Molecular mechanisms of antibiotic resistance revisited205
The stringent response and physiological roles of (pp)pGpp in bacteria203
Ecology and genomics of Actinobacteria: new concepts for natural product discovery192
Beyond horizontal gene transfer: the role of plasmids in bacterial evolution191
Interactions between bacterial and phage communities in natural environments190
Influenza virus and SARS-CoV-2: pathogenesis and host responses in the respiratory tract189
Xanthomonas diversity, virulence and plant–pathogen interactions182
Priority effects in microbiome assembly182
Biology and evolution of bacterial toxin–antitoxin systems175
The structural basis of herpesvirus entry171
Antimicrobial use, drug-resistant infections and COVID-19170
Soil microbiomes and one health170
Bacterial motility: machinery and mechanisms169
Skeletal infections: microbial pathogenesis, immunity and clinical management168
Microbiome-based therapeutics164
Crop microbiome and sustainable agriculture163
Infections at the maternal–fetal interface: an overview of pathogenesis and defence160
Reconstructing organisms in silico: genome-scale models and their emerging applications158
SARS-CoV-2 variant biology: immune escape, transmission and fitness156
Microbial diversity in extreme environments155
The microbiome-shaping roles of bacteriocins149
Mass spectrometry-based metabolomics in microbiome investigations146
The rumen microbiome: balancing food security and environmental impacts145
Anti-tuberculosis treatment strategies and drug development: challenges and priorities144
Nutritional immunity: the battle for nutrient metals at the host–pathogen interface144
Bile acids and the gut microbiota: metabolic interactions and impacts on disease141
Treatment strategies for cryptococcal infection: challenges, advances and future outlook140
The biofilm matrix: multitasking in a shared space139
Carbohydrate-active enzymes (CAZymes) in the gut microbiome138
Examining horizontal gene transfer in microbial communities138
Proximate and ultimate causes of the bactericidal action of antibiotics134
Evasion of plant immunity by microbial pathogens133
Human papillomaviruses: diversity, infection and host interactions130
Antibiofilm activity of host defence peptides: complexity provides opportunities130
Immune evasion and provocation by Mycobacterium tuberculosis129
SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies129
Microbial evolution and transitions along the parasite–mutualist continuum126
Microbial production of advanced biofuels126
Epstein–Barr virus and multiple sclerosis123
The host-associated archaeome121
Learning from the past: development of safe and effective COVID-19 vaccines118
Evolutionary causes and consequences of bacterial antibiotic persistence115
Physical properties of the bacterial outer membrane114
Formation and function of bacterial organelles112
Interactions between Borrelia burgdorferi and ticks110
Salmonella Typhimurium and inflammation: a pathogen-centric affair109
When anaerobes encounter oxygen: mechanisms of oxygen toxicity, tolerance and defence106
Ecology, evolution and spillover of coronaviruses from bats106
Ecology and impacts of white-nose syndrome on bats106
Staphylococcus aureus host interactions and adaptation103
Resisting antimicrobial resistance103
Climate change impacts on plant pathogens, food security and paths forward102
Nanomaterials arising amid antibiotic resistance102
Toxoplasma gondii infection and its implications within the central nervous system102
Target protection as a key antibiotic resistance mechanism98
The dynamic lung microbiome in health and disease98
Architecture of bacterial respiratory chains97
Antigenic evolution will lead to new SARS-CoV-2 variants with unpredictable severity92
Epigenetic and epitranscriptomic regulation of viral replication89
The marine nitrogen cycle: new developments and global change88
Gradients and consequences of heterogeneity in biofilms84
Monkeypox virus: a neglected zoonotic pathogen spreads globally82
Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle82
Influenza lineage extinction during the COVID-19 pandemic?82
Towards SARS-CoV-2 serotypes?81
Trichoderma: a multipurpose, plant-beneficial microorganism for eco-sustainable agriculture81
Structural biology of CRISPR–Cas immunity and genome editing enzymes81
Predictive biology: modelling, understanding and harnessing microbial complexity80
Host specificity of the gut microbiome79
Diversity and evolution of the animal virome78
Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota78
Revisiting the rules of life for viruses of microorganisms75
Composition and functions of bacterial membrane vesicles74
The ecological roles of bacterial chemotaxis73
The effects of the COVID-19 pandemic on community respiratory virus activity72
The LUCA and its complex virome71
A lasting symbiosis: how the Hawaiian bobtail squid finds and keeps its bioluminescent bacterial partner71
The WHO fungal priority pathogens list as a game-changer71
Structural insights into RNA polymerases of negative-sense RNA viruses70
Diverse and unified mechanisms of transcription initiation in bacteria68
A lasting symbiosis: how Vibrio fischeri finds a squid partner and persists within its natural host68
Microbiota succession throughout life from the cradle to the grave68
Microbially mediated metal corrosion65
Clostridioides difficile toxins: mechanisms of action and antitoxin therapeutics64
Viral and host heterogeneity and their effects on the viral life cycle63
Marine biofilms: diversity, interactions and biofouling60
Architecture of the dynamic fungal cell wall58
Genomic and fossil windows into the secret lives of the most ancient fungi56
The physiology and genetics of bacterial responses to antibiotic combinations55
Physiological limitations and opportunities in microbial metabolic engineering54
The highly diverse antiphage defence systems of bacteria53
Optimizing antimicrobial use: challenges, advances and opportunities52
Population bottlenecks and founder effects: implications for mosquito-borne arboviral emergence52
Staphylococcus epidermidis and its dual lifestyle in skin health and infection52
Microbiota-mediated colonization resistance: mechanisms and regulation51
Anti-trypanosomatid drug discovery: progress and challenges51
SARS-CoV-2 viral load and shedding kinetics50
Structure and function of retroviral integrase50
Author Correction: Long COVID: major findings, mechanisms and recommendations50
Giant virus biology and diversity in the era of genome-resolved metagenomics49
Mutualistic interplay between bacteriophages and bacteria in the human gut49
Interspecific hybridization as a driver of fungal evolution and adaptation48
Alternative functions of CRISPR–Cas systems in the evolutionary arms race47
From the soil to the clinic: the impact of microbial secondary metabolites on antibiotic tolerance and resistance44
Type VII secretion systems: structure, functions and transport models44
Pathogenesis, epidemiology and control of Group A Streptococcus infection41
The gut–liver axis and gut microbiota in health and liver disease40
The National Microbiome Data Collaborative: enabling microbiome science40
Prospects for SARS-CoV-2 diagnostics, therapeutics and vaccines in Africa40
Author Correction: Plant–microbiome interactions: from community assembly to plant health39
Forest microbiome and global change39
Soil viral diversity, ecology and climate change39
Microbial oxidation of atmospheric trace gases38
Lipid biomarkers: molecular tools for illuminating the history of microbial life38
Bacterial defences: mechanisms, evolution and antimicrobial resistance36
Lassa fever — the road ahead34
Crimean–Congo haemorrhagic fever virus31
Innate immune evasion strategies of SARS-CoV-231
Shaping bacterial gene expression by physiological and proteome allocation constraints31
Viral genomics in Ebola virus research30
Impact of enteric bacterial infections at and beyond the epithelial barrier29
The biogeography of infection revisited29
Genomics and epidemiological surveillance29
RNA-targeting CRISPR–Cas systems27
The interplay between microbial communities and soil properties26
Respiratory syncytial virus infection and novel interventions26
Surveying membrane landscapes: a new look at the bacterial cell surface24
Bacterial DNA excision repair pathways24
Prevention, treatment and cure of HIV infection21
The importance of molecular diagnostics for infectious diseases in low-resource settings21