Cell Host & Microbe

Article	Citations
Complex Immune Dysregulation in COVID-19 Patients with Severe Respiratory Failure	1622
Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies	934
Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition	868
Infection and Rapid Transmission of SARS-CoV-2 in Ferrets	767
Heightened Innate Immune Responses in the Respiratory Tract of COVID-19 Patients	766
Type I and Type III Interferons – Induction, Signaling, Evasion, and Application to Combat COVID-19	695
Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization	636
An Infectious cDNA Clone of SARS-CoV-2	599
A Mouse Model of SARS-CoV-2 Infection and Pathogenesis	526
Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization	451
Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite	428
SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity	418
Neutralizing Antibody and Soluble ACE2 Inhibition of a Replication-Competent VSV-SARS-CoV-2 and a Clinical Isolate of SARS-CoV-2	353
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut	344
Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor	316
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	300
The variant gambit: COVID-19’s next move	296
SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines	281
BCG Vaccination in Humans Elicits Trained Immunity via the Hematopoietic Progenitor Compartment	275
D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization	274
Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike	270
A Dynamic Immune Response Shapes COVID-19 Progression	256
SARS-CoV-2 human T cell epitopes: Adaptive immune response against COVID-19	242
Retrospective Multicenter Cohort Study Shows Early Interferon Therapy Is Associated with Favorable Clinical Responses in COVID-19 Patients	241
Gut microbiota-derived bile acids in intestinal immunity, inflammation, and tumorigenesis	235

Functional and Genomic Variation between Human-Derived Isolates of Lachnospiraceae Reveals Inter- and Intra-Species Diversity	222
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies	218
Identification of Human Single-Domain Antibodies against SARS-CoV-2	218
Developmental trajectory of the healthy human gut microbiota during the first 5 years of life	214
Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis	205
Favorable Anakinra Responses in Severe Covid-19 Patients with Secondary Hemophagocytic Lymphohistiocytosis	195
A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions	195
Human B Cell Clonal Expansion and Convergent Antibody Responses to SARS-CoV-2	193
Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant	188
The Gut Microbiota and Unhealthy Aging: Disentangling Cause from Consequence	185
Innate immune and inflammatory responses to SARS-CoV-2: Implications for COVID-19	184
Living in the endosymbiotic world of Wolbachia: A centennial review	170
The Innate Immune System: Fighting on the Front Lines or Fanning the Flames of COVID-19?	167
A Replication-Competent Vesicular Stomatitis Virus for Studies of SARS-CoV-2 Spike-Mediated Cell Entry and Its Inhibition	166
SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera	163
Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes	160
A single dose of the SARS-CoV-2 vaccine BNT162b2 elicits Fc-mediated antibody effector functions and T cell responses	160
Enhanced neutralization resistance of SARS-CoV-2 Omicron subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2	156
SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape	155
Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level	152
Real-Time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles	150
Replication-Competent Vesicular Stomatitis Virus Vaccine Vector Protects against SARS-CoV-2-Mediated Pathogenesis in Mice	148
Breastmilk Feeding Practices Are Associated with the Co-Occurrence of Bacteria in Mothers’ Milk and the Infant Gut: the CHILD Cohort Study	147
Role of dietary fiber in the recovery of the human gut microbiome and its metabolome	146
An expanded arsenal of immune systems that protect bacteria from phages	145
Induction of alarmin S100A8/A9 mediates activation of aberrant neutrophils in the pathogenesis of COVID-19	140
Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2	139
Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	137
Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission	135
Phages and their satellites encode hotspots of antiviral systems	132
Co-evolution and Co-speciation of Host-Gut Bacteria Systems	128
The Microbiome as a Modifier of Neurodegenerative Disease Risk	124
The Spatial Heterogeneity of the Gut Limits Predation and Fosters Coexistence of Bacteria and Bacteriophages	124
Kinetics and correlates of the neutralizing antibody response to SARS-CoV-2 infection in humans	123
Antibody evasion of SARS-CoV-2 Omicron BA.1, BA.1.1, BA.2, and BA.3 sub-lineages	121
Engineering the Live-Attenuated Polio Vaccine to Prevent Reversion to Virulence	120
Commensal microbiota regulates skin barrier function and repair via signaling through the aryl hydrocarbon receptor	119
Altered Immunity of Laboratory Mice in the Natural Environment Is Associated with Fungal Colonization	117
A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1	116
Microbiota and Fatty Liver Disease—the Known, the Unknown, and the Future	115
Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors	111
The Skin Microbiota: Balancing Risk and Reward	110
Fungal Trans-kingdom Dynamics Linked to Responsiveness to Fecal Microbiota Transplantation (FMT) Therapy in Ulcerative Colitis	110
The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants	110
Oral Microbiome Geography: Micron-Scale Habitat and Niche	110
Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75	108
Rational Vaccine Design in the Time of COVID-19	105
Intranasal vaccination with a lentiviral vector protects against SARS-CoV-2 in preclinical animal models	105
The Impact of the Microbiome on Immunity to Vaccination in Humans	104
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	102
Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant	102
Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response	98
The immune landscape in tuberculosis reveals populations linked to disease and latency	98
Antibody and B cell responses to SARS-CoV-2 infection and vaccination	98
Jasmonate Signaling Enhances RNA Silencing and Antiviral Defense in Rice	97
Acetylation of Cytidine Residues Boosts HIV-1 Gene Expression by Increasing Viral RNA Stability	96
Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization	94
Shigella ubiquitin ligase IpaH7.8 targets gasdermin D for degradation to prevent pyroptosis and enable infection	94
Global COVID-19 vaccine inequity: The scope, the impact, and the challenges	94
Approaches and Challenges in SARS-CoV-2 Vaccine Development	93
Antibody Feedback Limits the Expansion of B Cell Responses to Malaria Vaccination but Drives Diversification of the Humoral Response	91
Human gut bacterial metabolism drives Th17 activation and colitis	90
Commensal Staphylococcus epidermidis contributes to skin barrier homeostasis by generating protective ceramides	90
High-Fat Diet and Antibiotics Cooperatively Impair Mitochondrial Bioenergetics to Trigger Dysbiosis that Exacerbates Pre-inflammatory Bowel Disease	90
Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease	88
Organoids and organs-on-chips: Insights into human gut-microbe interactions	87
Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp.	86
Bacteria induce skin regeneration via IL-1β signaling	84
Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage	83
Robust SARS-CoV-2 infection in nasal turbinates after treatment with systemic neutralizing antibodies	82
The Challenges of Vaccine Development against a New Virus during a Pandemic	80
Gut microbes impact stroke severity via the trimethylamine N-oxide pathway	79
Plant immune system activation is necessary for efficient root colonization by auxin-secreting beneficial bacteria	78
A complex immune response to flagellin epitope variation in commensal communities	78
The great escape? SARS-CoV-2 variants evading neutralizing responses	77
Persistent B cell memory after SARS-CoV-2 vaccination is functional during breakthrough infections	77
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	75
Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses	74
Neutralization and durability of 2 or 3 doses of the BNT162b2 vaccine against Omicron SARS-CoV-2	74
Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants	74
Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors	73
Virus vaccines: proteins prefer prolines	73
Antigenic characterization of the SARS-CoV-2 Omicron subvariant BA.2.75	71
Rethinking healthy eating in light of the gut microbiome	70
Anatomy promotes neutral coexistence of strains in the human skin microbiome	70
Microbiota regulate innate immune signaling and protective immunity against cancer	70
HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens	70
Dynamics of the normal gut microbiota: A longitudinal one-year population study in Sweden	69
The Biology of the Intestinal Intracellular Parasite Cryptosporidium	69
The Serotonin Neurotransmitter Modulates Virulence of Enteric Pathogens	69
Western diet induces Paneth cell defects through microbiome alterations and farnesoid X receptor and type I interferon activation	69
A microbial metabolite remodels the gut-liver axis following bariatric surgery	69
Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation	69
Dispersal strategies shape persistence and evolution of human gut bacteria	68
Vaccinia virus E3 prevents sensing of Z-RNA to block ZBP1-dependent necroptosis	68
Helicobacter pylori CagA elicits BRCAness to induce genome instability that may underlie bacterial gastric carcinogenesis	68
Evasion of neutralizing antibody responses by the SARS-CoV-2 BA.2.75 variant	68
A Bacterial Effector Protein Hijacks Plant Metabolism to Support Pathogen Nutrition	67
Pre-existing humoral immunity to human common cold coronaviruses negatively impacts the protective SARS-CoV-2 antibody response	65
Programing of an Intravascular Immune Firewall by the Gut Microbiota Protects against Pathogen Dissemination during Infection	65
Rethinking next-generation vaccines for coronaviruses, influenzaviruses, and other respiratory viruses	64
Gut microbiome dysbiosis contributes to abdominal aortic aneurysm by promoting neutrophil extracellular trap formation	64
Bacterial effectors manipulate plant abscisic acid signaling for creation of an aqueous apoplast	63
Early Life Microbiota and Respiratory Tract Infections	63
Exploration of Bacterial Bottlenecks and Streptococcus pneumoniae Pathogenesis by CRISPRi-Seq	63
Ultra-low Dose Aerosol Infection of Mice with Mycobacterium tuberculosis More Closely Models Human Tuberculosis	62
The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping	62
The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition	62
Rewilding Nod2 and Atg16l1 Mutant Mice Uncovers Genetic and Environmental Contributions to Microbial Responses and Immune Cell Composition	62
The success of SARS-CoV-2 vaccines and challenges ahead	61
Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota	61
One year of SARS-CoV-2 evolution	61
Adherent-invasive E. coli metabolism of propanediol in Crohn’s disease regulates phagocytes to drive intestinal inflammation	60
Global genome analysis reveals a vast and dynamic anellovirus landscape within the human virome	60
In vivo commensal control of Clostridioides difficile virulence	60
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	59
Import of Aspartate and Malate by DcuABC Drives H2/Fumarate Respiration to Promote Initial Salmonella Gut-Lumen Colonization in Mice	58
Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice	57
Klebsiella oxytoca causes colonization resistance against multidrug-resistant K. pneumoniae in the gut via cooperative carbohydrate competition	57
Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2	56
Lysosome Fusion Maintains Phagosome Integrity during Fungal Infection	56
Targeted Depletion of Bacteria from Mixed Populations by Programmable Adhesion with Antagonistic Competitor Cells	55
E. coli enhance colonization resistance against Salmonella Typhimurium by competing for galactitol, a context-dependent limiting carbon source	55
Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation	55
A calmodulin-binding transcription factor links calcium signaling to antiviral RNAi defense in plants	55
Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts	53
Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential	53

Colonization of the live biotherapeutic product VE303 and modulation of the microbiota and metabolites in healthy volunteers	53
SARS-CoV-2 Omicron sublineages exhibit distinct antibody escape patterns	53
Bacteroides thetaiotaomicron-Infecting Bacteriophage Isolates Inform Sequence-Based Host Range Predictions	53
During Aspergillus Infection, Monocyte-Derived DCs, Neutrophils, and Plasmacytoid DCs Enhance Innate Immune Defense through CXCR3-Dependent Crosstalk	53
Murine model of colonization with fungal pathogen Candida auris to explore skin tropism, host risk factors and therapeutic strategies	53
Evolutionarily conserved bacterial effectors hijack abscisic acid signaling to induce an aqueous environment in the apoplast	53
Alterations in the gut microbiota contribute to cognitive impairment induced by the ketogenic diet and hypoxia	52
Immunoglobulin A Targets a Unique Subset of the Microbiota in Inflammatory Bowel Disease	52
Coevolution between bacterial CRISPR-Cas systems and their bacteriophages	52
Caudovirales bacteriophages are associated with improved executive function and memory in flies, mice, and humans	51
Global, distinctive, and personal changes in molecular and microbial profiles by specific fibers in humans	51
Microbiota-antibody interactions that regulate gut homeostasis	51
Prophages encode phage-defense systems with cognate self-immunity	51
An AAV-based, room-temperature-stable, single-dose COVID-19 vaccine provides durable immunogenicity and protection in non-human primates	51
Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike	51
Detect and destroy: CRISPR-based technologies for the response against viruses	51
The SMC5/6 complex compacts and silences unintegrated HIV-1 DNA and is antagonized by Vpr	50
Discovery of a Family of Mixed Lineage Kinase Domain-like Proteins in Plants and Their Role in Innate Immune Signaling	50
Plant roots employ cell-layer-specific programs to respond to pathogenic and beneficial microbes	50
Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution	50
Tissue-resident Lachnospiraceae family bacteria protect against colorectal carcinogenesis by promoting tumor immune surveillance	49
Phosphorylation-Regulated Activation of the Arabidopsis RRS1-R/RPS4 Immune Receptor Complex Reveals Two Distinct Effector Recognition Mechanisms	49
The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants	49
A Combination of Human Broadly Neutralizing Antibodies against Hepatitis B Virus HBsAg with Distinct Epitopes Suppresses Escape Mutations	48
Listeria Phages Induce Cas9 Degradation to Protect Lysogenic Genomes	48
An NTD supersite of attack	48
Th1-Th2 Cross-Regulation Controls Early Leishmania Infection in the Skin by Modulating the Size of the Permissive Monocytic Host Cell Reservoir	47
Deep-Learning Resources for Studying Glycan-Mediated Host-Microbe Interactions	46
Signatures of antagonistic pleiotropy in a bacterial flagellin epitope	46
Epithelial-Derived Reactive Oxygen Species Enable AppBCX-Mediated Aerobic Respiration of Escherichia coli during Intestinal Inflammation	46
Gut microbiome lipid metabolism and its impact on host physiology	46
3β-Hydroxysteroid dehydrogenase expressed by gut microbes degrades testosterone and is linked to depression in males	46
Critical Anti-CRISPR Locus Repression by a Bi-functional Cas9 Inhibitor	46
Genomic and functional characterization of a mucosal symbiont involved in early-stage colorectal cancer	45
A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection	45
Diet leaves a genetic signature in a keystone member of the gut microbiota	45
Episymbiotic Saccharibacteria suppresses gingival inflammation and bone loss in mice through host bacterial modulation	45
Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA.1 and BA.2	45
Characterization of gut microbial structural variations as determinants of human bile acid metabolism	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
Butyrate-producing Eubacterium rectale suppresses lymphomagenesis by alleviating the TNF-induced TLR4/MyD88/NF-κB axis	44
Commensal segmented filamentous bacteria-derived retinoic acid primes host defense to intestinal infection	43
Non-neutralizing Antibodies from a Marburg Infection Survivor Mediate Protection by Fc-Effector Functions and by Enhancing Efficacy of Other Antibodies	43
Toxoplasma gondii secreted effectors co-opt host repressor complexes to inhibit necroptosis	43
Upper and lower respiratory tract correlates of protection against respiratory syncytial virus following vaccination of nonhuman primates	43
The vulnerable versatility of Salmonella antibiotic persisters during infection	43
Anti-CRISPRs go viral: The infection biology of CRISPR-Cas inhibitors	42
Legionella-Infected Macrophages Engage the Alveolar Epithelium to Metabolically Reprogram Myeloid Cells and Promote Antibacterial Inflammation	42
TGFβ restricts expansion, survival, and function of T cells within the tuberculous granuloma	41
Anaerobic Respiration of NOX1-Derived Hydrogen Peroxide Licenses Bacterial Growth at the Colonic Surface	41
The logic of virus evolution	41
Structural insights into viral RNA capping and plasma membrane targeting by Chikungunya virus nonstructural protein 1	41