Cell Host & Microbe

Article	Citations
Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies	949
Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition	887
Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization	645
A Mouse Model of SARS-CoV-2 Infection and Pathogenesis	538
Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization	455
Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite	441
SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity	434
Neutralizing Antibody and Soluble ACE2 Inhibition of a Replication-Competent VSV-SARS-CoV-2 and a Clinical Isolate of SARS-CoV-2	362
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut	361
Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor	326
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	310
The variant gambit: COVID-19’s next move	301
SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines	284
BCG Vaccination in Humans Elicits Trained Immunity via the Hematopoietic Progenitor Compartment	283
D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization	275
Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike	274
Gut microbiota-derived bile acids in intestinal immunity, inflammation, and tumorigenesis	270
SARS-CoV-2 human T cell epitopes: Adaptive immune response against COVID-19	248
Retrospective Multicenter Cohort Study Shows Early Interferon Therapy Is Associated with Favorable Clinical Responses in COVID-19 Patients	243
Functional and Genomic Variation between Human-Derived Isolates of Lachnospiraceae Reveals Inter- and Intra-Species Diversity	242
Developmental trajectory of the healthy human gut microbiota during the first 5 years of life	227
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies	224
Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis	218
A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions	209
The Gut Microbiota and Unhealthy Aging: Disentangling Cause from Consequence	201

Human B Cell Clonal Expansion and Convergent Antibody Responses to SARS-CoV-2	198
Favorable Anakinra Responses in Severe Covid-19 Patients with Secondary Hemophagocytic Lymphohistiocytosis	194
Innate immune and inflammatory responses to SARS-CoV-2: Implications for COVID-19	193
Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant	189
Living in the endosymbiotic world of Wolbachia: A centennial review	189
A Replication-Competent Vesicular Stomatitis Virus for Studies of SARS-CoV-2 Spike-Mediated Cell Entry and Its Inhibition	175
An expanded arsenal of immune systems that protect bacteria from phages	169
Enhanced neutralization resistance of SARS-CoV-2 Omicron subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2	169
Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes	167
SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera	164
A single dose of the SARS-CoV-2 vaccine BNT162b2 elicits Fc-mediated antibody effector functions and T cell responses	164
Role of dietary fiber in the recovery of the human gut microbiome and its metabolome	163
SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape	161
Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level	160
Real-Time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles	157
Replication-Competent Vesicular Stomatitis Virus Vaccine Vector Protects against SARS-CoV-2-Mediated Pathogenesis in Mice	151
Breastmilk Feeding Practices Are Associated with the Co-Occurrence of Bacteria in Mothers’ Milk and the Infant Gut: the CHILD Cohort Study	151
Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	149
Induction of alarmin S100A8/A9 mediates activation of aberrant neutrophils in the pathogenesis of COVID-19	145
Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2	144
Phages and their satellites encode hotspots of antiviral systems	143
Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission	142
Co-evolution and Co-speciation of Host-Gut Bacteria Systems	137
The Microbiome as a Modifier of Neurodegenerative Disease Risk	135
Commensal microbiota regulates skin barrier function and repair via signaling through the aryl hydrocarbon receptor	130
Microbiota and Fatty Liver Disease—the Known, the Unknown, and the Future	127
A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1	127
The Spatial Heterogeneity of the Gut Limits Predation and Fosters Coexistence of Bacteria and Bacteriophages	126
Antibody evasion of SARS-CoV-2 Omicron BA.1, BA.1.1, BA.2, and BA.3 sub-lineages	125
Kinetics and correlates of the neutralizing antibody response to SARS-CoV-2 infection in humans	123
The Skin Microbiota: Balancing Risk and Reward	120
The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants	118
Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors	118
Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75	117
Oral Microbiome Geography: Micron-Scale Habitat and Niche	117
Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant	114
Intranasal vaccination with a lentiviral vector protects against SARS-CoV-2 in preclinical animal models	109
Human gut bacterial metabolism drives Th17 activation and colitis	108
The immune landscape in tuberculosis reveals populations linked to disease and latency	107
Neutralization of SARS-CoV-2 Omicron sub-lineages BA.1, BA.1.1, and BA.2	105
Acetylation of Cytidine Residues Boosts HIV-1 Gene Expression by Increasing Viral RNA Stability	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	104
Jasmonate Signaling Enhances RNA Silencing and Antiviral Defense in Rice	102
Global COVID-19 vaccine inequity: The scope, the impact, and the challenges	100
Antibody and B cell responses to SARS-CoV-2 infection and vaccination	99
Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response	99
Shigella ubiquitin ligase IpaH7.8 targets gasdermin D for degradation to prevent pyroptosis and enable infection	99
Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization	99
Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease	99

Antibody Feedback Limits the Expansion of B Cell Responses to Malaria Vaccination but Drives Diversification of the Humoral Response	98
Commensal Staphylococcus epidermidis contributes to skin barrier homeostasis by generating protective ceramides	98
High-Fat Diet and Antibiotics Cooperatively Impair Mitochondrial Bioenergetics to Trigger Dysbiosis that Exacerbates Pre-inflammatory Bowel Disease	97
Organoids and organs-on-chips: Insights into human gut-microbe interactions	94
Approaches and Challenges in SARS-CoV-2 Vaccine Development	94
Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp.	92
Bacteria induce skin regeneration via IL-1β signaling	89
Plant immune system activation is necessary for efficient root colonization by auxin-secreting beneficial bacteria	87
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	83
A complex immune response to flagellin epitope variation in commensal communities	82
Rethinking healthy eating in light of the gut microbiome	82
Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants	82
Gut microbes impact stroke severity via the trimethylamine N-oxide pathway	81
Rethinking next-generation vaccines for coronaviruses, influenzaviruses, and other respiratory viruses	80
Surveillance of European Domestic Pig Populations Identifies an Emerging Reservoir of Potentially Zoonotic Swine Influenza A Viruses	80
Microbiota regulate innate immune signaling and protective immunity against cancer	79
Dynamics of the normal gut microbiota: A longitudinal one-year population study in Sweden	78
The great escape? SARS-CoV-2 variants evading neutralizing responses	78
SARS-CoV-2 Omicron triggers cross-reactive neutralization and Fc effector functions in previously vaccinated, but not unvaccinated, individuals	78
The Biology of the Intestinal Intracellular Parasite Cryptosporidium	78
Helicobacter pylori CagA elicits BRCAness to induce genome instability that may underlie bacterial gastric carcinogenesis	78
Western diet induces Paneth cell defects through microbiome alterations and farnesoid X receptor and type I interferon activation	78
Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors	77
A microbial metabolite remodels the gut-liver axis following bariatric surgery	77
Gut microbiome dysbiosis contributes to abdominal aortic aneurysm by promoting neutrophil extracellular trap formation	77
Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses	77
Persistent B cell memory after SARS-CoV-2 vaccination is functional during breakthrough infections	77
Antigenic characterization of the SARS-CoV-2 Omicron subvariant BA.2.75	76
Anatomy promotes neutral coexistence of strains in the human skin microbiome	75
Vaccinia virus E3 prevents sensing of Z-RNA to block ZBP1-dependent necroptosis	75
Virus vaccines: proteins prefer prolines	75
Neutralization and durability of 2 or 3 doses of the BNT162b2 vaccine against Omicron SARS-CoV-2	75
Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation	74
Dispersal strategies shape persistence and evolution of human gut bacteria	73
Programing of an Intravascular Immune Firewall by the Gut Microbiota Protects against Pathogen Dissemination during Infection	72
Exploration of Bacterial Bottlenecks and Streptococcus pneumoniae Pathogenesis by CRISPRi-Seq	72
Evasion of neutralizing antibody responses by the SARS-CoV-2 BA.2.75 variant	71
HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens	70
Pre-existing humoral immunity to human common cold coronaviruses negatively impacts the protective SARS-CoV-2 antibody response	70
Early Life Microbiota and Respiratory Tract Infections	70
The Serotonin Neurotransmitter Modulates Virulence of Enteric Pathogens	69
A Bacterial Effector Protein Hijacks Plant Metabolism to Support Pathogen Nutrition	69
The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping	68
The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition	67
Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota	66
In vivo commensal control of Clostridioides difficile virulence	65
Bacterial effectors manipulate plant abscisic acid signaling for creation of an aqueous apoplast	65
Ultra-low Dose Aerosol Infection of Mice with Mycobacterium tuberculosis More Closely Models Human Tuberculosis	65
Tissue-resident Lachnospiraceae family bacteria protect against colorectal carcinogenesis by promoting tumor immune surveillance	65
Global genome analysis reveals a vast and dynamic anellovirus landscape within the human virome	65
The success of SARS-CoV-2 vaccines and challenges ahead	63
E. coli enhance colonization resistance against Salmonella Typhimurium by competing for galactitol, a context-dependent limiting carbon source	63
Gut microbiome lipid metabolism and its impact on host physiology	63
Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2	63
Adherent-invasive E. coli metabolism of propanediol in Crohn’s disease regulates phagocytes to drive intestinal inflammation	63
Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation	62
Klebsiella oxytoca causes colonization resistance against multidrug-resistant K. pneumoniae in the gut via cooperative carbohydrate competition	62
Direct comparison of antibody responses to four SARS-CoV-2 vaccines in Mongolia	62
One year of SARS-CoV-2 evolution	62
Murine model of colonization with fungal pathogen Candida auris to explore skin tropism, host risk factors and therapeutic strategies	61
Alterations in the gut microbiota contribute to cognitive impairment induced by the ketogenic diet and hypoxia	59
A calmodulin-binding transcription factor links calcium signaling to antiviral RNAi defense in plants	59
Colonization of the live biotherapeutic product VE303 and modulation of the microbiota and metabolites in healthy volunteers	59
Evolutionarily conserved bacterial effectors hijack abscisic acid signaling to induce an aqueous environment in the apoplast	59
Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice	59
Butyrate-producing Eubacterium rectale suppresses lymphomagenesis by alleviating the TNF-induced TLR4/MyD88/NF-κB axis	58
Targeted Depletion of Bacteria from Mixed Populations by Programmable Adhesion with Antagonistic Competitor Cells	58
Caudovirales bacteriophages are associated with improved executive function and memory in flies, mice, and humans	58
Prophages encode phage-defense systems with cognate self-immunity	58
During Aspergillus Infection, Monocyte-Derived DCs, Neutrophils, and Plasmacytoid DCs Enhance Innate Immune Defense through CXCR3-Dependent Crosstalk	57
Lysosome Fusion Maintains Phagosome Integrity during Fungal Infection	56
Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential	56
Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts	55
Bacteroides thetaiotaomicron-Infecting Bacteriophage Isolates Inform Sequence-Based Host Range Predictions	55
Microbiota-antibody interactions that regulate gut homeostasis	55
Global, distinctive, and personal changes in molecular and microbial profiles by specific fibers in humans	55
Coevolution between bacterial CRISPR-Cas systems and their bacteriophages	55
SARS-CoV-2 Omicron sublineages exhibit distinct antibody escape patterns	54
3β-Hydroxysteroid dehydrogenase expressed by gut microbes degrades testosterone and is linked to depression in males	54

Immunoglobulin A Targets a Unique Subset of the Microbiota in Inflammatory Bowel Disease	54
Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike	54
The SMC5/6 complex compacts and silences unintegrated HIV-1 DNA and is antagonized by Vpr	53
Plant roots employ cell-layer-specific programs to respond to pathogenic and beneficial microbes	53
An NTD supersite of attack	53
A Combination of Human Broadly Neutralizing Antibodies against Hepatitis B Virus HBsAg with Distinct Epitopes Suppresses Escape Mutations	52
Detect and destroy: CRISPR-based technologies for the response against viruses	52
Discovery of a Family of Mixed Lineage Kinase Domain-like Proteins in Plants and Their Role in Innate Immune Signaling	51
An AAV-based, room-temperature-stable, single-dose COVID-19 vaccine provides durable immunogenicity and protection in non-human primates	51
Fusobacterium nucleatum-derived succinic acid induces tumor resistance to immunotherapy in colorectal cancer	51
A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection	51
The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants	50
Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA.1 and BA.2	50
Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution	50
Deep-Learning Resources for Studying Glycan-Mediated Host-Microbe Interactions	50
Genomic and functional characterization of a mucosal symbiont involved in early-stage colorectal cancer	49
Diet leaves a genetic signature in a keystone member of the gut microbiota	49
Episymbiotic Saccharibacteria suppresses gingival inflammation and bone loss in mice through host bacterial modulation	49
Signatures of antagonistic pleiotropy in a bacterial flagellin epitope	49
Commensal segmented filamentous bacteria-derived retinoic acid primes host defense to intestinal infection	49
Listeria Phages Induce Cas9 Degradation to Protect Lysogenic Genomes	49
Characterization of gut microbial structural variations as determinants of human bile acid metabolism	49
Epithelial-Derived Reactive Oxygen Species Enable AppBCX-Mediated Aerobic Respiration of Escherichia coli during Intestinal Inflammation	48
The vulnerable versatility of Salmonella antibiotic persisters during infection	48
Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites	48
Upper and lower respiratory tract correlates of protection against respiratory syncytial virus following vaccination of nonhuman primates	47
Long-term antibiotic exposure promotes mortality after systemic fungal infection by driving lymphocyte dysfunction and systemic escape of commensal bacteria	47
Anaerobic Respiration of NOX1-Derived Hydrogen Peroxide Licenses Bacterial Growth at the Colonic Surface	46
Ruminococcus gnavus plays a pathogenic role in diarrhea-predominant irritable bowel syndrome by increasing serotonin biosynthesis	46
Autophagy controls mucus secretion from intestinal goblet cells by alleviating ER stress	46
Intestinal mucus and their glycans: A habitat for thriving microbiota	46
Cross-feeding in the gut microbiome: Ecology and mechanisms	46
Key determinants of success in fecal microbiota transplantation: From microbiome to clinic	46
Critical Anti-CRISPR Locus Repression by a Bi-functional Cas9 Inhibitor	46
Toxoplasma gondii secreted effectors co-opt host repressor complexes to inhibit necroptosis	46
The logic of virus evolution	45
TGFβ restricts expansion, survival, and function of T cells within the tuberculous granuloma	45
Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease	44
Structural insights into viral RNA capping and plasma membrane targeting by Chikungunya virus nonstructural protein 1	44
Legionella-Infected Macrophages Engage the Alveolar Epithelium to Metabolically Reprogram Myeloid Cells and Promote Antibacterial Inflammation	44
Anti-CRISPRs go viral: The infection biology of CRISPR-Cas inhibitors	44
Rethinking phage-bacteria-eukaryotic relationships and their influence on human health	44
Gut bacterial isoamylamine promotes age-related cognitive dysfunction by promoting microglial cell death	43
Global mapping of Salmonella enterica-host protein-protein interactions during infection	43
Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease	42
Zooanthroponotic potential of SARS-CoV-2 and implications of reintroduction into human populations	42
Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions	42
Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy	41
The Urinary Tract Microbiome in Older Women Exhibits Host Genetic and Environmental Influences	41
Faecalibaculum rodentium remodels retinoic acid signaling to govern eosinophil-dependent intestinal epithelial homeostasis	41
Human mAbs Broadly Protect against Arthritogenic Alphaviruses by Recognizing Conserved Elements of the Mxra8 Receptor-Binding Site	41
Discovery of ultrapotent broadly neutralizing antibodies from SARS-CoV-2 elite neutralizers	41
A lncRNA fine-tunes salicylic acid biosynthesis to balance plant immunity and growth	41