Cell Host & Microbe

Article	Citations
Complex Immune Dysregulation in COVID-19 Patients with Severe Respiratory Failure	1616
Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies	929
Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition	863
A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2	814
Infection and Rapid Transmission of SARS-CoV-2 in Ferrets	765
Heightened Innate Immune Responses in the Respiratory Tract of COVID-19 Patients	759
Type I and Type III Interferons – Induction, Signaling, Evasion, and Application to Combat COVID-19	689
Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization	634
An Infectious cDNA Clone of SARS-CoV-2	594
A Mouse Model of SARS-CoV-2 Infection and Pathogenesis	521
Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization	448
Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite	424
SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity	411
Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation	396
Neutralizing Antibody and Soluble ACE2 Inhibition of a Replication-Competent VSV-SARS-CoV-2 and a Clinical Isolate of SARS-CoV-2	350
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut	335
Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor	310
Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains	299
The variant gambit: COVID-19’s next move	295
SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines	280
D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization	274
Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike	269
BCG Vaccination in Humans Elicits Trained Immunity via the Hematopoietic Progenitor Compartment	266
A Dynamic Immune Response Shapes COVID-19 Progression	256
SARS-CoV-2 human T cell epitopes: Adaptive immune response against COVID-19	241

Retrospective Multicenter Cohort Study Shows Early Interferon Therapy Is Associated with Favorable Clinical Responses in COVID-19 Patients	240
Identification of Human Single-Domain Antibodies against SARS-CoV-2	216
Gut microbiota-derived bile acids in intestinal immunity, inflammation, and tumorigenesis	214
Functional and Genomic Variation between Human-Derived Isolates of Lachnospiraceae Reveals Inter- and Intra-Species Diversity	214
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies	212
Developmental trajectory of the healthy human gut microbiota during the first 5 years of life	209
Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis	199
Favorable Anakinra Responses in Severe Covid-19 Patients with Secondary Hemophagocytic Lymphohistiocytosis	194
A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions	194
Human B Cell Clonal Expansion and Convergent Antibody Responses to SARS-CoV-2	192
Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant	187
Innate immune and inflammatory responses to SARS-CoV-2: Implications for COVID-19	181
The Gut Microbiota and Unhealthy Aging: Disentangling Cause from Consequence	180
The Biology of the HIV-1 Latent Reservoir and Implications for Cure Strategies	172
The Innate Immune System: Fighting on the Front Lines or Fanning the Flames of COVID-19?	166
A Replication-Competent Vesicular Stomatitis Virus for Studies of SARS-CoV-2 Spike-Mediated Cell Entry and Its Inhibition	163
SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera	163
Living in the endosymbiotic world of Wolbachia: A centennial review	162
Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes	159
A single dose of the SARS-CoV-2 vaccine BNT162b2 elicits Fc-mediated antibody effector functions and T cell responses	159
SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape	152
Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level	150
Replication-Competent Vesicular Stomatitis Virus Vaccine Vector Protects against SARS-CoV-2-Mediated Pathogenesis in Mice	148
Enhanced neutralization resistance of SARS-CoV-2 Omicron subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2	148
Real-Time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles	146
Breastmilk Feeding Practices Are Associated with the Co-Occurrence of Bacteria in Mothers’ Milk and the Infant Gut: the CHILD Cohort Study	141
Role of dietary fiber in the recovery of the human gut microbiome and its metabolome	140
An expanded arsenal of immune systems that protect bacteria from phages	138
Induction of alarmin S100A8/A9 mediates activation of aberrant neutrophils in the pathogenesis of COVID-19	137
Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2	136
Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission	133
Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	127
Phages and their satellites encode hotspots of antiviral systems	127
Co-evolution and Co-speciation of Host-Gut Bacteria Systems	125
The Microbiome as a Modifier of Neurodegenerative Disease Risk	122
Kinetics and correlates of the neutralizing antibody response to SARS-CoV-2 infection in humans	122
The Spatial Heterogeneity of the Gut Limits Predation and Fosters Coexistence of Bacteria and Bacteriophages	121
TMEM173 Drives Lethal Coagulation in Sepsis	120
Antibody evasion of SARS-CoV-2 Omicron BA.1, BA.1.1, BA.2, and BA.3 sub-lineages	118
Engineering the Live-Attenuated Polio Vaccine to Prevent Reversion to Virulence	117
Altered Immunity of Laboratory Mice in the Natural Environment Is Associated with Fungal Colonization	116
Commensal microbiota regulates skin barrier function and repair via signaling through the aryl hydrocarbon receptor	116
Microbiota and Fatty Liver Disease—the Known, the Unknown, and the Future	114
A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1	111
The Skin Microbiota: Balancing Risk and Reward	109
Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors	109
Fungal Trans-kingdom Dynamics Linked to Responsiveness to Fecal Microbiota Transplantation (FMT) Therapy in Ulcerative Colitis	108
Oral Microbiome Geography: Micron-Scale Habitat and Niche	107
The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants	107
Rational Vaccine Design in the Time of COVID-19	105

The Impact of the Microbiome on Immunity to Vaccination in Humans	104
Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75	104
Intranasal vaccination with a lentiviral vector protects against SARS-CoV-2 in preclinical animal models	103
Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner	103
Neutralization of SARS-CoV-2 Omicron sub-lineages BA.1, BA.1.1, and BA.2	99
Jasmonate Signaling Enhances RNA Silencing and Antiviral Defense in Rice	96
The immune landscape in tuberculosis reveals populations linked to disease and latency	96
Antibody and B cell responses to SARS-CoV-2 infection and vaccination	95
Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant	94
Global COVID-19 vaccine inequity: The scope, the impact, and the challenges	94
Dual Plasmepsin-Targeting Antimalarial Agents Disrupt Multiple Stages of the Malaria Parasite Life Cycle	93
Approaches and Challenges in SARS-CoV-2 Vaccine Development	93
Shigella ubiquitin ligase IpaH7.8 targets gasdermin D for degradation to prevent pyroptosis and enable infection	93
Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization	93
Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response	92
Acetylation of Cytidine Residues Boosts HIV-1 Gene Expression by Increasing Viral RNA Stability	90
Antibody Feedback Limits the Expansion of B Cell Responses to Malaria Vaccination but Drives Diversification of the Humoral Response	87
High-Fat Diet and Antibiotics Cooperatively Impair Mitochondrial Bioenergetics to Trigger Dysbiosis that Exacerbates Pre-inflammatory Bowel Disease	86
Commensal Staphylococcus epidermidis contributes to skin barrier homeostasis by generating protective ceramides	86
Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp.	85
Human gut bacterial metabolism drives Th17 activation and colitis	85
Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease	84
Organoids and organs-on-chips: Insights into human gut-microbe interactions	83
Bacteria induce skin regeneration via IL-1β signaling	82
The Challenges of Vaccine Development against a New Virus during a Pandemic	80
Robust SARS-CoV-2 infection in nasal turbinates after treatment with systemic neutralizing antibodies	80
Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage	80
The great escape? SARS-CoV-2 variants evading neutralizing responses	77
Gut microbes impact stroke severity via the trimethylamine N-oxide pathway	77
Persistent B cell memory after SARS-CoV-2 vaccination is functional during breakthrough infections	76
Surveillance of European Domestic Pig Populations Identifies an Emerging Reservoir of Potentially Zoonotic Swine Influenza A Viruses	75
SARS-CoV-2 Omicron triggers cross-reactive neutralization and Fc effector functions in previously vaccinated, but not unvaccinated, individuals	74
Neutralization and durability of 2 or 3 doses of the BNT162b2 vaccine against Omicron SARS-CoV-2	74
A complex immune response to flagellin epitope variation in commensal communities	73
Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses	73
Plant immune system activation is necessary for efficient root colonization by auxin-secreting beneficial bacteria	72
Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors	71
HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens	70
Virus vaccines: proteins prefer prolines	70
The Serotonin Neurotransmitter Modulates Virulence of Enteric Pathogens	69
Microbiota regulate innate immune signaling and protective immunity against cancer	69
Antigenic characterization of the SARS-CoV-2 Omicron subvariant BA.2.75	69
Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants	69
The Biology of the Intestinal Intracellular Parasite Cryptosporidium	68
Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation	68
Western diet induces Paneth cell defects through microbiome alterations and farnesoid X receptor and type I interferon activation	67
Dispersal strategies shape persistence and evolution of human gut bacteria	67
Evasion of neutralizing antibody responses by the SARS-CoV-2 BA.2.75 variant	67
Vaccinia virus E3 prevents sensing of Z-RNA to block ZBP1-dependent necroptosis	66
Dynamics of the normal gut microbiota: A longitudinal one-year population study in Sweden	66
Rethinking healthy eating in light of the gut microbiome	66
Programing of an Intravascular Immune Firewall by the Gut Microbiota Protects against Pathogen Dissemination during Infection	65
Pre-existing humoral immunity to human common cold coronaviruses negatively impacts the protective SARS-CoV-2 antibody response	65
Helicobacter pylori CagA elicits BRCAness to induce genome instability that may underlie bacterial gastric carcinogenesis	65
A microbial metabolite remodels the gut-liver axis following bariatric surgery	65
A Bacterial Effector Protein Hijacks Plant Metabolism to Support Pathogen Nutrition	64
Exploration of Bacterial Bottlenecks and Streptococcus pneumoniae Pathogenesis by CRISPRi-Seq	62
An Arabidopsis Secondary Metabolite Directly Targets Expression of the Bacterial Type III Secretion System to Inhibit Bacterial Virulence	62
Bacterial effectors manipulate plant abscisic acid signaling for creation of an aqueous apoplast	62
Early Life Microbiota and Respiratory Tract Infections	61
Anatomy promotes neutral coexistence of strains in the human skin microbiome	61
Ultra-low Dose Aerosol Infection of Mice with Mycobacterium tuberculosis More Closely Models Human Tuberculosis	61
Rewilding Nod2 and Atg16l1 Mutant Mice Uncovers Genetic and Environmental Contributions to Microbial Responses and Immune Cell Composition	61
In vivo commensal control of Clostridioides difficile virulence	60
One year of SARS-CoV-2 evolution	60
The success of SARS-CoV-2 vaccines and challenges ahead	60
The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition	60
Global genome analysis reveals a vast and dynamic anellovirus landscape within the human virome	60
The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping	59
Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota	59
Adherent-invasive E. coli metabolism of propanediol in Crohn’s disease regulates phagocytes to drive intestinal inflammation	59
Gut microbiome dysbiosis contributes to abdominal aortic aneurysm by promoting neutrophil extracellular trap formation	59
Direct comparison of antibody responses to four SARS-CoV-2 vaccines in Mongolia	59
Commensal Bacteria Modulate Immunoglobulin A Binding in Response to Host Nutrition	57
Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice	57
Rethinking next-generation vaccines for coronaviruses, influenzaviruses, and other respiratory viruses	57
Import of Aspartate and Malate by DcuABC Drives H2/Fumarate Respiration to Promote Initial Salmonella Gut-Lumen Colonization in Mice	56
Lysosome Fusion Maintains Phagosome Integrity during Fungal Infection	56
Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2	55
Targeted Depletion of Bacteria from Mixed Populations by Programmable Adhesion with Antagonistic Competitor Cells	55

A calmodulin-binding transcription factor links calcium signaling to antiviral RNAi defense in plants	55
Klebsiella oxytoca causes colonization resistance against multidrug-resistant K. pneumoniae in the gut via cooperative carbohydrate competition	53
Bacteroides thetaiotaomicron-Infecting Bacteriophage Isolates Inform Sequence-Based Host Range Predictions	53
E. coli enhance colonization resistance against Salmonella Typhimurium by competing for galactitol, a context-dependent limiting carbon source	53
Coevolution between bacterial CRISPR-Cas systems and their bacteriophages	52
Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation	52
Proton Motive Force Disruptors Block Bacterial Competence and Horizontal Gene Transfer	52
Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential	52
During Aspergillus Infection, Monocyte-Derived DCs, Neutrophils, and Plasmacytoid DCs Enhance Innate Immune Defense through CXCR3-Dependent Crosstalk	52
Colonization of the live biotherapeutic product VE303 and modulation of the microbiota and metabolites in healthy volunteers	51
SARS-CoV-2 Omicron sublineages exhibit distinct antibody escape patterns	51
Evolutionarily conserved bacterial effectors hijack abscisic acid signaling to induce an aqueous environment in the apoplast	51
Murine model of colonization with fungal pathogen Candida auris to explore skin tropism, host risk factors and therapeutic strategies	51
Detect and destroy: CRISPR-based technologies for the response against viruses	51
Immunoglobulin A Targets a Unique Subset of the Microbiota in Inflammatory Bowel Disease	51
Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike	51
Caudovirales bacteriophages are associated with improved executive function and memory in flies, mice, and humans	50
Alterations in the gut microbiota contribute to cognitive impairment induced by the ketogenic diet and hypoxia	50
Plant roots employ cell-layer-specific programs to respond to pathogenic and beneficial microbes	50
An AAV-based, room-temperature-stable, single-dose COVID-19 vaccine provides durable immunogenicity and protection in non-human primates	50
Phosphorylation-Regulated Activation of the Arabidopsis RRS1-R/RPS4 Immune Receptor Complex Reveals Two Distinct Effector Recognition Mechanisms	49
Prophages encode phage-defense systems with cognate self-immunity	49
Discovery of a Family of Mixed Lineage Kinase Domain-like Proteins in Plants and Their Role in Innate Immune Signaling	49
Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts	49
The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants	48
Microbiota-antibody interactions that regulate gut homeostasis	48
Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution	48
The SMC5/6 complex compacts and silences unintegrated HIV-1 DNA and is antagonized by Vpr	48
An NTD supersite of attack	48
Listeria Phages Induce Cas9 Degradation to Protect Lysogenic Genomes	48
Global, distinctive, and personal changes in molecular and microbial profiles by specific fibers in humans	48
A Combination of Human Broadly Neutralizing Antibodies against Hepatitis B Virus HBsAg with Distinct Epitopes Suppresses Escape Mutations	47
Th1-Th2 Cross-Regulation Controls Early Leishmania Infection in the Skin by Modulating the Size of the Permissive Monocytic Host Cell Reservoir	46
Club Cell TRPV4 Serves as a Damage Sensor Driving Lung Allergic Inflammation	46
Critical Anti-CRISPR Locus Repression by a Bi-functional Cas9 Inhibitor	46
Deep-Learning Resources for Studying Glycan-Mediated Host-Microbe Interactions	45
Signatures of antagonistic pleiotropy in a bacterial flagellin epitope	45
3β-Hydroxysteroid dehydrogenase expressed by gut microbes degrades testosterone and is linked to depression in males	45
Epithelial-Derived Reactive Oxygen Species Enable AppBCX-Mediated Aerobic Respiration of Escherichia coli during Intestinal Inflammation	45
A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection	45
Genomic and functional characterization of a mucosal symbiont involved in early-stage colorectal cancer	44
Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease	44
A Natural Peptide Antigen within the Plasmodium Ribosomal Protein RPL6 Confers Liver TRM Cell-Mediated Immunity against Malaria in Mice	44
Tissue-resident Lachnospiraceae family bacteria protect against colorectal carcinogenesis by promoting tumor immune surveillance	44
Non-neutralizing Antibodies from a Marburg Infection Survivor Mediate Protection by Fc-Effector Functions and by Enhancing Efficacy of Other Antibodies	43
Diet leaves a genetic signature in a keystone member of the gut microbiota	43
Upper and lower respiratory tract correlates of protection against respiratory syncytial virus following vaccination of nonhuman primates	43
Env Exceptionalism: Why Are HIV-1 Env Glycoproteins Atypical Immunogens?	43
Toxoplasma gondii secreted effectors co-opt host repressor complexes to inhibit necroptosis	43
Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA.1 and BA.2	43
Legionella-Infected Macrophages Engage the Alveolar Epithelium to Metabolically Reprogram Myeloid Cells and Promote Antibacterial Inflammation	42
Characterization of gut microbial structural variations as determinants of human bile acid metabolism	42
The vulnerable versatility of Salmonella antibiotic persisters during infection	42
Butyrate-producing Eubacterium rectale suppresses lymphomagenesis by alleviating the TNF-induced TLR4/MyD88/NF-κB axis	42