Cell Host & Microbe

(The TQCC of Cell Host & Microbe is 39. 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 2020-01-01 to 2024-01-01.)
Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China1652
Complex Immune Dysregulation in COVID-19 Patients with Severe Respiratory Failure1579
Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies905
Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition844
A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2794
Infection and Rapid Transmission of SARS-CoV-2 in Ferrets748
Heightened Innate Immune Responses in the Respiratory Tract of COVID-19 Patients739
Type I and Type III Interferons – Induction, Signaling, Evasion, and Application to Combat COVID-19668
Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization615
An Infectious cDNA Clone of SARS-CoV-2580
A Mouse Model of SARS-CoV-2 Infection and Pathogenesis490
Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization441
Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite408
SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity380
Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation348
Neutralizing Antibody and Soluble ACE2 Inhibition of a Replication-Competent VSV-SARS-CoV-2 and a Clinical Isolate of SARS-CoV-2337
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut307
Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor299
Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains290
The variant gambit: COVID-19’s next move288
Precision Microbiome Modulation with Discrete Dietary Fiber Structures Directs Short-Chain Fatty Acid Production275
SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines274
D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization266
Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike259
A Dynamic Immune Response Shapes COVID-19 Progression252
BCG Vaccination in Humans Elicits Trained Immunity via the Hematopoietic Progenitor Compartment247
Retrospective Multicenter Cohort Study Shows Early Interferon Therapy Is Associated with Favorable Clinical Responses in COVID-19 Patients235
SARS-CoV-2 human T cell epitopes: Adaptive immune response against COVID-19230
Identification of Human Single-Domain Antibodies against SARS-CoV-2207
Favorable Anakinra Responses in Severe Covid-19 Patients with Secondary Hemophagocytic Lymphohistiocytosis192
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies192
Functional and Genomic Variation between Human-Derived Isolates of Lachnospiraceae Reveals Inter- and Intra-Species Diversity191
Developmental trajectory of the healthy human gut microbiota during the first 5 years of life189
Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant183
Human B Cell Clonal Expansion and Convergent Antibody Responses to SARS-CoV-2182
A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions180
Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis179
Gut microbiota-derived bile acids in intestinal immunity, inflammation, and tumorigenesis169
Innate immune and inflammatory responses to SARS-CoV-2: Implications for COVID-19167
The Innate Immune System: Fighting on the Front Lines or Fanning the Flames of COVID-19?161
SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera160
The Gut Microbiota and Unhealthy Aging: Disentangling Cause from Consequence158
The Biology of the HIV-1 Latent Reservoir and Implications for Cure Strategies157
A Replication-Competent Vesicular Stomatitis Virus for Studies of SARS-CoV-2 Spike-Mediated Cell Entry and Its Inhibition154
A single dose of the SARS-CoV-2 vaccine BNT162b2 elicits Fc-mediated antibody effector functions and T cell responses151
Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes149
Replication-Competent Vesicular Stomatitis Virus Vaccine Vector Protects against SARS-CoV-2-Mediated Pathogenesis in Mice144
Living in the endosymbiotic world of Wolbachia: A centennial review144
SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape137
Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level133
Breastmilk Feeding Practices Are Associated with the Co-Occurrence of Bacteria in Mothers’ Milk and the Infant Gut: the CHILD Cohort Study130
Induction of alarmin S100A8/A9 mediates activation of aberrant neutrophils in the pathogenesis of COVID-19129
Enhanced neutralization resistance of SARS-CoV-2 Omicron subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2128
Role of dietary fiber in the recovery of the human gut microbiome and its metabolome126
Roseburia spp. Abundance Associates with Alcohol Consumption in Humans and Its Administration Ameliorates Alcoholic Fatty Liver in Mice122
Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2121
Kinetics and correlates of the neutralizing antibody response to SARS-CoV-2 infection in humans119
Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission118
Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways116
Co-evolution and Co-speciation of Host-Gut Bacteria Systems116
The Spatial Heterogeneity of the Gut Limits Predation and Fosters Coexistence of Bacteria and Bacteriophages114
Fecal IgA Levels Are Determined by Strain-Level Differences in Bacteroides ovatus and Are Modifiable by Gut Microbiota Manipulation113
TMEM173 Drives Lethal Coagulation in Sepsis111
The Microbiome as a Modifier of Neurodegenerative Disease Risk110
A Bioinformatic Analysis of Integrative Mobile Genetic Elements Highlights Their Role in Bacterial Adaptation107
An expanded arsenal of immune systems that protect bacteria from phages107
Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors106
Altered Immunity of Laboratory Mice in the Natural Environment Is Associated with Fungal Colonization106
Antibody evasion of SARS-CoV-2 Omicron BA.1, BA.1.1, BA.2, and BA.3 sub-lineages106
Rational Vaccine Design in the Time of COVID-19105
Fungal Trans-kingdom Dynamics Linked to Responsiveness to Fecal Microbiota Transplantation (FMT) Therapy in Ulcerative Colitis103
Phages and their satellites encode hotspots of antiviral systems102
Engineering the Live-Attenuated Polio Vaccine to Prevent Reversion to Virulence102
The Impact of the Microbiome on Immunity to Vaccination in Humans100
Intranasal vaccination with a lentiviral vector protects against SARS-CoV-2 in preclinical animal models99
The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants98
Microbiota and Fatty Liver Disease—the Known, the Unknown, and the Future98
A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A197
Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner97
Commensal microbiota regulates skin barrier function and repair via signaling through the aryl hydrocarbon receptor96
Oral Microbiome Geography: Micron-Scale Habitat and Niche95
Neutralization of SARS-CoV-2 Omicron sub-lineages BA.1, BA.1.1, and BA.294
Approaches and Challenges in SARS-CoV-2 Vaccine Development93
The Skin Microbiota: Balancing Risk and Reward93
Global COVID-19 vaccine inequity: The scope, the impact, and the challenges88
Jasmonate Signaling Enhances RNA Silencing and Antiviral Defense in Rice88
The immune landscape in tuberculosis reveals populations linked to disease and latency87
Dual Plasmepsin-Targeting Antimalarial Agents Disrupt Multiple Stages of the Malaria Parasite Life Cycle87
Fermentation Products of Commensal Bacteria Alter Enterocyte Lipid Metabolism87
Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.7584
Antibody and B cell responses to SARS-CoV-2 infection and vaccination83
Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization83
Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response82
Acetylation of Cytidine Residues Boosts HIV-1 Gene Expression by Increasing Viral RNA Stability80
Staphylococcus epidermidis Contributes to Healthy Maturation of the Nasal Microbiome by Stimulating Antimicrobial Peptide Production80
Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp.79
The Challenges of Vaccine Development against a New Virus during a Pandemic79
High-Fat Diet and Antibiotics Cooperatively Impair Mitochondrial Bioenergetics to Trigger Dysbiosis that Exacerbates Pre-inflammatory Bowel Disease78
Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant77
Robust SARS-CoV-2 infection in nasal turbinates after treatment with systemic neutralizing antibodies77
Shigella ubiquitin ligase IpaH7.8 targets gasdermin D for degradation to prevent pyroptosis and enable infection76
Antibody Feedback Limits the Expansion of B Cell Responses to Malaria Vaccination but Drives Diversification of the Humoral Response75
The great escape? SARS-CoV-2 variants evading neutralizing responses75
Human gut bacterial metabolism drives Th17 activation and colitis74
Salmonella-Driven Polarization of Granuloma Macrophages Antagonizes TNF-Mediated Pathogen Restriction during Persistent Infection72
Gut microbes impact stroke severity via the trimethylamine N-oxide pathway72
Organoids and organs-on-chips: Insights into human gut-microbe interactions72
Changes in Microbiome Confer Multigenerational Host Resistance after Sub-toxic Pesticide Exposure71
Surveillance of European Domestic Pig Populations Identifies an Emerging Reservoir of Potentially Zoonotic Swine Influenza A Viruses71
Functional and Computational Genomics Reveal Unprecedented Flexibility in Stage-Specific Toxoplasma Metabolism71
SARS-CoV-2 Omicron triggers cross-reactive neutralization and Fc effector functions in previously vaccinated, but not unvaccinated, individuals71
Persistent B cell memory after SARS-CoV-2 vaccination is functional during breakthrough infections71
Salmonella Effector SteE Converts the Mammalian Serine/Threonine Kinase GSK3 into a Tyrosine Kinase to Direct Macrophage Polarization69
A complex immune response to flagellin epitope variation in commensal communities69
Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses68
Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage68
Neutralization and durability of 2 or 3 doses of the BNT162b2 vaccine against Omicron SARS-CoV-268
Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease68
HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens67
Commensal Staphylococcus epidermidis contributes to skin barrier homeostasis by generating protective ceramides67
Bacteria induce skin regeneration via IL-1β signaling67
Virus vaccines: proteins prefer prolines66
Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation66
Outer Membrane Vesiculation Facilitates Surface Exchange and In Vivo Adaptation of Vibrio cholerae64
The Serotonin Neurotransmitter Modulates Virulence of Enteric Pathogens62
Antigenic characterization of the SARS-CoV-2 Omicron subvariant BA.2.7562
Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors61
Western diet induces Paneth cell defects through microbiome alterations and farnesoid X receptor and type I interferon activation61
Programing of an Intravascular Immune Firewall by the Gut Microbiota Protects against Pathogen Dissemination during Infection60
Pre-existing humoral immunity to human common cold coronaviruses negatively impacts the protective SARS-CoV-2 antibody response60
Plant immune system activation is necessary for efficient root colonization by auxin-secreting beneficial bacteria60
A Bacterial Effector Protein Hijacks Plant Metabolism to Support Pathogen Nutrition60
Microbiota regulate innate immune signaling and protective immunity against cancer60
A microbial metabolite remodels the gut-liver axis following bariatric surgery59
Dispersal strategies shape persistence and evolution of human gut bacteria59
Co-transmission of Related Malaria Parasite Lineages Shapes Within-Host Parasite Diversity59
The Biology of the Intestinal Intracellular Parasite Cryptosporidium58
The success of SARS-CoV-2 vaccines and challenges ahead58
An Arabidopsis Secondary Metabolite Directly Targets Expression of the Bacterial Type III Secretion System to Inhibit Bacterial Virulence57
One year of SARS-CoV-2 evolution56
Exploration of Bacterial Bottlenecks and Streptococcus pneumoniae Pathogenesis by CRISPRi-Seq56
Xenosiderophore Utilization Promotes Bacteroides thetaiotaomicron Resilience during Colitis56
Bacterial effectors manipulate plant abscisic acid signaling for creation of an aqueous apoplast56
Rewilding Nod2 and Atg16l1 Mutant Mice Uncovers Genetic and Environmental Contributions to Microbial Responses and Immune Cell Composition56
Dynamics of the normal gut microbiota: A longitudinal one-year population study in Sweden55
Targeted Depletion of Bacteria from Mixed Populations by Programmable Adhesion with Antagonistic Competitor Cells55
Rethinking healthy eating in light of the gut microbiome54
Vaccinia virus E3 prevents sensing of Z-RNA to block ZBP1-dependent necroptosis54
Lysosome Fusion Maintains Phagosome Integrity during Fungal Infection54
Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants54
Direct comparison of antibody responses to four SARS-CoV-2 vaccines in Mongolia54
Adherent-invasive E. coli metabolism of propanediol in Crohn’s disease regulates phagocytes to drive intestinal inflammation53
Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice53
Atypical Resistance Protein RPW8/HR Triggers Oligomerization of the NLR Immune Receptor RPP7 and Autoimmunity53
In vivo commensal control of Clostridioides difficile virulence53
Commensal Bacteria Modulate Immunoglobulin A Binding in Response to Host Nutrition53
Ultra-low Dose Aerosol Infection of Mice with Mycobacterium tuberculosis More Closely Models Human Tuberculosis52
Global genome analysis reveals a vast and dynamic anellovirus landscape within the human virome52
Early Life Microbiota and Respiratory Tract Infections52
The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition51
Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike51
An AAV-based, room-temperature-stable, single-dose COVID-19 vaccine provides durable immunogenicity and protection in non-human primates49
A calmodulin-binding transcription factor links calcium signaling to antiviral RNAi defense in plants49
Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota49
Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-248
A Combination of Human Broadly Neutralizing Antibodies against Hepatitis B Virus HBsAg with Distinct Epitopes Suppresses Escape Mutations47
During Aspergillus Infection, Monocyte-Derived DCs, Neutrophils, and Plasmacytoid DCs Enhance Innate Immune Defense through CXCR3-Dependent Crosstalk46
Bacteroides thetaiotaomicron-Infecting Bacteriophage Isolates Inform Sequence-Based Host Range Predictions46
An NTD supersite of attack46
Detect and destroy: CRISPR-based technologies for the response against viruses46
Phosphorylation-Regulated Activation of the Arabidopsis RRS1-R/RPS4 Immune Receptor Complex Reveals Two Distinct Effector Recognition Mechanisms46
Immunoglobulin A Targets a Unique Subset of the Microbiota in Inflammatory Bowel Disease45
Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution45
Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential45
Plant roots employ cell-layer-specific programs to respond to pathogenic and beneficial microbes45
Discovery of a Family of Mixed Lineage Kinase Domain-like Proteins in Plants and Their Role in Innate Immune Signaling45
Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation45
Coevolution between bacterial CRISPR-Cas systems and their bacteriophages45
SARS-CoV-2 Omicron sublineages exhibit distinct antibody escape patterns45
Murine model of colonization with fungal pathogen Candida auris to explore skin tropism, host risk factors and therapeutic strategies45
Import of Aspartate and Malate by DcuABC Drives H2/Fumarate Respiration to Promote Initial Salmonella Gut-Lumen Colonization in Mice45
Microbiota-antibody interactions that regulate gut homeostasis44
Structural Analysis of Rabies Virus Glycoprotein Reveals pH-Dependent Conformational Changes and Interactions with a Neutralizing Antibody44
Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease44
E. coli enhance colonization resistance against Salmonella Typhimurium by competing for galactitol, a context-dependent limiting carbon source44
Evolutionarily conserved bacterial effectors hijack abscisic acid signaling to induce an aqueous environment in the apoplast44
Alterations in the gut microbiota contribute to cognitive impairment induced by the ketogenic diet and hypoxia44
Critical Anti-CRISPR Locus Repression by a Bi-functional Cas9 Inhibitor44
Th1-Th2 Cross-Regulation Controls Early Leishmania Infection in the Skin by Modulating the Size of the Permissive Monocytic Host Cell Reservoir44
Klebsiella oxytoca causes colonization resistance against multidrug-resistant K. pneumoniae in the gut via cooperative carbohydrate competition43
Caudovirales bacteriophages are associated with improved executive function and memory in flies, mice, and humans43
lncRNA Sensing of a Viral Suppressor of RNAi Activates Non-canonical Innate Immune Signaling in Drosophila43
Epithelial-Derived Reactive Oxygen Species Enable AppBCX-Mediated Aerobic Respiration of Escherichia coli during Intestinal Inflammation43
Deep-Learning Resources for Studying Glycan-Mediated Host-Microbe Interactions43
Rethinking next-generation vaccines for coronaviruses, influenzaviruses, and other respiratory viruses42
Colonization of the live biotherapeutic product VE303 and modulation of the microbiota and metabolites in healthy volunteers42
Regulatory Considerations for Fecal Microbiota Transplantation Products42
Gut microbiome dysbiosis contributes to abdominal aortic aneurysm by promoting neutrophil extracellular trap formation42
A Natural Peptide Antigen within the Plasmodium Ribosomal Protein RPL6 Confers Liver TRM Cell-Mediated Immunity against Malaria in Mice42
The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants42
Env Exceptionalism: Why Are HIV-1 Env Glycoproteins Atypical Immunogens?42
Toxoplasma gondii secreted effectors co-opt host repressor complexes to inhibit necroptosis41
Signatures of antagonistic pleiotropy in a bacterial flagellin epitope41
Structural insights into viral RNA capping and plasma membrane targeting by Chikungunya virus nonstructural protein 140
Club Cell TRPV4 Serves as a Damage Sensor Driving Lung Allergic Inflammation40
Non-neutralizing Antibodies from a Marburg Infection Survivor Mediate Protection by Fc-Effector Functions and by Enhancing Efficacy of Other Antibodies40
Discovery of ultrapotent broadly neutralizing antibodies from SARS-CoV-2 elite neutralizers39
Global, distinctive, and personal changes in molecular and microbial profiles by specific fibers in humans39
Legionella-Infected Macrophages Engage the Alveolar Epithelium to Metabolically Reprogram Myeloid Cells and Promote Antibacterial Inflammation39
Human Cytomegalovirus miRNAs Regulate TGF-β to Mediate Myelosuppression while Maintaining Viral Latency in CD34+ Hematopoietic Progenitor Cells39
The vulnerable versatility of Salmonella antibiotic persisters during infection39