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	956
Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition	899
Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization	643
Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization	457
Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite	452
SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity	443
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut	389
Neutralizing Antibody and Soluble ACE2 Inhibition of a Replication-Competent VSV-SARS-CoV-2 and a Clinical Isolate of SARS-CoV-2	362
Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor	327
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	316
The variant gambit: COVID-19’s next move	305
Gut microbiota-derived bile acids in intestinal immunity, inflammation, and tumorigenesis	301
SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines	283
Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike	276
D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization	276
SARS-CoV-2 human T cell epitopes: Adaptive immune response against COVID-19	252
Retrospective Multicenter Cohort Study Shows Early Interferon Therapy Is Associated with Favorable Clinical Responses in COVID-19 Patients	246
Developmental trajectory of the healthy human gut microbiota during the first 5 years of life	243
Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis	234
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies	232
A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions	223
Living in the endosymbiotic world of Wolbachia: A centennial review	207
Human B Cell Clonal Expansion and Convergent Antibody Responses to SARS-CoV-2	203
Innate immune and inflammatory responses to SARS-CoV-2: Implications for COVID-19	203
Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant	193

An expanded arsenal of immune systems that protect bacteria from phages	189
Enhanced neutralization resistance of SARS-CoV-2 Omicron subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2	179
A Replication-Competent Vesicular Stomatitis Virus for Studies of SARS-CoV-2 Spike-Mediated Cell Entry and Its Inhibition	177
SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape	172
Role of dietary fiber in the recovery of the human gut microbiome and its metabolome	171
Real-Time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles	165
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
Phages and their satellites encode hotspots of antiviral systems	161
Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	159
Induction of alarmin S100A8/A9 mediates activation of aberrant neutrophils in the pathogenesis of COVID-19	156
Replication-Competent Vesicular Stomatitis Virus Vaccine Vector Protects against SARS-CoV-2-Mediated Pathogenesis in Mice	155
Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2	150
Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission	147
Commensal microbiota regulates skin barrier function and repair via signaling through the aryl hydrocarbon receptor	137
A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1	136
The Spatial Heterogeneity of the Gut Limits Predation and Fosters Coexistence of Bacteria and Bacteriophages	130
The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants	128
Kinetics and correlates of the neutralizing antibody response to SARS-CoV-2 infection in humans	125
Antibody evasion of SARS-CoV-2 Omicron BA.1, BA.1.1, BA.2, and BA.3 sub-lineages	123
Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors	122
Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant	122
Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75	120
The immune landscape in tuberculosis reveals populations linked to disease and latency	116
Commensal Staphylococcus epidermidis contributes to skin barrier homeostasis by generating protective ceramides	113
Human gut bacterial metabolism drives Th17 activation and colitis	112
Intranasal vaccination with a lentiviral vector protects against SARS-CoV-2 in preclinical animal models	112
Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease	108
Global COVID-19 vaccine inequity: The scope, the impact, and the challenges	107
Antibody Feedback Limits the Expansion of B Cell Responses to Malaria Vaccination but Drives Diversification of the Humoral Response	107
Neutralization of SARS-CoV-2 Omicron sub-lineages BA.1, BA.1.1, and BA.2	107
Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner	106
Shigella ubiquitin ligase IpaH7.8 targets gasdermin D for degradation to prevent pyroptosis and enable infection	106
Antibody and B cell responses to SARS-CoV-2 infection and vaccination	105
Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization	104
Organoids and organs-on-chips: Insights into human gut-microbe interactions	101
Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response	100
Bacteria induce skin regeneration via IL-1β signaling	100
Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp.	100
Rethinking healthy eating in light of the gut microbiome	95
Approaches and Challenges in SARS-CoV-2 Vaccine Development	94
Rethinking next-generation vaccines for coronaviruses, influenzaviruses, and other respiratory viruses	93
Plant immune system activation is necessary for efficient root colonization by auxin-secreting beneficial bacteria	91
Dynamics of the normal gut microbiota: A longitudinal one-year population study in Sweden	90
Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage	90
Gut microbiome dysbiosis contributes to abdominal aortic aneurysm by promoting neutrophil extracellular trap formation	88
Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants	87
Western diet induces Paneth cell defects through microbiome alterations and farnesoid X receptor and type I interferon activation	86
Microbiota regulate innate immune signaling and protective immunity against cancer	86
Robust SARS-CoV-2 infection in nasal turbinates after treatment with systemic neutralizing antibodies	84

A complex immune response to flagellin epitope variation in commensal communities	84
Surveillance of European Domestic Pig Populations Identifies an Emerging Reservoir of Potentially Zoonotic Swine Influenza A Viruses	84
SARS-CoV-2 Omicron triggers cross-reactive neutralization and Fc effector functions in previously vaccinated, but not unvaccinated, individuals	83
Gut microbes impact stroke severity via the trimethylamine N-oxide pathway	82
Anatomy promotes neutral coexistence of strains in the human skin microbiome	82
Helicobacter pylori CagA elicits BRCAness to induce genome instability that may underlie bacterial gastric carcinogenesis	82
The Biology of the Intestinal Intracellular Parasite Cryptosporidium	82
A microbial metabolite remodels the gut-liver axis following bariatric surgery	81
Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors	81
Exploration of Bacterial Bottlenecks and Streptococcus pneumoniae Pathogenesis by CRISPRi-Seq	81
Neutralization and durability of 2 or 3 doses of the BNT162b2 vaccine against Omicron SARS-CoV-2	79
Tissue-resident Lachnospiraceae family bacteria protect against colorectal carcinogenesis by promoting tumor immune surveillance	79
The great escape? SARS-CoV-2 variants evading neutralizing responses	79
Persistent B cell memory after SARS-CoV-2 vaccination is functional during breakthrough infections	79
Antigenic characterization of the SARS-CoV-2 Omicron subvariant BA.2.75	79
Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses	78
Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation	77
Programing of an Intravascular Immune Firewall by the Gut Microbiota Protects against Pathogen Dissemination during Infection	77
Dispersal strategies shape persistence and evolution of human gut bacteria	76
Gut microbiome lipid metabolism and its impact on host physiology	76
Vaccinia virus E3 prevents sensing of Z-RNA to block ZBP1-dependent necroptosis	76
Virus vaccines: proteins prefer prolines	75
The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition	74
Bacterial effectors manipulate plant abscisic acid signaling for creation of an aqueous apoplast	74
Evasion of neutralizing antibody responses by the SARS-CoV-2 BA.2.75 variant	73
A Bacterial Effector Protein Hijacks Plant Metabolism to Support Pathogen Nutrition	72
The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping	72
HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens	72
Ultra-low Dose Aerosol Infection of Mice with Mycobacterium tuberculosis More Closely Models Human Tuberculosis	72
In vivo commensal control of Clostridioides difficile virulence	71
Pre-existing humoral immunity to human common cold coronaviruses negatively impacts the protective SARS-CoV-2 antibody response	71
Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota	70
E. coli enhance colonization resistance against Salmonella Typhimurium by competing for galactitol, a context-dependent limiting carbon source	70
Global genome analysis reveals a vast and dynamic anellovirus landscape within the human virome	68
Evolutionarily conserved bacterial effectors hijack abscisic acid signaling to induce an aqueous environment in the apoplast	68
Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2	67
Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation	66
Fusobacterium nucleatum-derived succinic acid induces tumor resistance to immunotherapy in colorectal cancer	66
Butyrate-producing Eubacterium rectale suppresses lymphomagenesis by alleviating the TNF-induced TLR4/MyD88/NF-κB axis	66
Klebsiella oxytoca causes colonization resistance against multidrug-resistant K. pneumoniae in the gut via cooperative carbohydrate competition	66
Murine model of colonization with fungal pathogen Candida auris to explore skin tropism, host risk factors and therapeutic strategies	65
Alterations in the gut microbiota contribute to cognitive impairment induced by the ketogenic diet and hypoxia	65
Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites	65
Prophages encode phage-defense systems with cognate self-immunity	64
Adherent-invasive E. coli metabolism of propanediol in Crohn’s disease regulates phagocytes to drive intestinal inflammation	64
Direct comparison of antibody responses to four SARS-CoV-2 vaccines in Mongolia	64
The success of SARS-CoV-2 vaccines and challenges ahead	64
One year of SARS-CoV-2 evolution	63
Cross-feeding in the gut microbiome: Ecology and mechanisms	63
Caudovirales bacteriophages are associated with improved executive function and memory in flies, mice, and humans	62
Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice	62
A calmodulin-binding transcription factor links calcium signaling to antiviral RNAi defense in plants	62
Global, distinctive, and personal changes in molecular and microbial profiles by specific fibers in humans	61
Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential	60
Colonization of the live biotherapeutic product VE303 and modulation of the microbiota and metabolites in healthy volunteers	60
Immunoglobulin A Targets a Unique Subset of the Microbiota in Inflammatory Bowel Disease	60
Coevolution between bacterial CRISPR-Cas systems and their bacteriophages	59
Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA.1 and BA.2	59
3β-Hydroxysteroid dehydrogenase expressed by gut microbes degrades testosterone and is linked to depression in males	59
Microbiota-antibody interactions that regulate gut homeostasis	58
Lysosome Fusion Maintains Phagosome Integrity during Fungal Infection	58
Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts	57
Bacteroides thetaiotaomicron-Infecting Bacteriophage Isolates Inform Sequence-Based Host Range Predictions	57
Plant roots employ cell-layer-specific programs to respond to pathogenic and beneficial microbes	57
The SMC5/6 complex compacts and silences unintegrated HIV-1 DNA and is antagonized by Vpr	56
Deep-Learning Resources for Studying Glycan-Mediated Host-Microbe Interactions	55
Ruminococcus gnavus plays a pathogenic role in diarrhea-predominant irritable bowel syndrome by increasing serotonin biosynthesis	55
Intestinal mucus and their glycans: A habitat for thriving microbiota	55
SARS-CoV-2 Omicron sublineages exhibit distinct antibody escape patterns	55
An NTD supersite of attack	54
Episymbiotic Saccharibacteria suppresses gingival inflammation and bone loss in mice through host bacterial modulation	54
Detect and destroy: CRISPR-based technologies for the response against viruses	54
An AAV-based, room-temperature-stable, single-dose COVID-19 vaccine provides durable immunogenicity and protection in non-human primates	54
Key determinants of success in fecal microbiota transplantation: From microbiome to clinic	54
The logic of virus evolution	54
The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants	54
Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike	54
A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection	53
Discovery of a Family of Mixed Lineage Kinase Domain-like Proteins in Plants and Their Role in Innate Immune Signaling	53
Autophagy controls mucus secretion from intestinal goblet cells by alleviating ER stress	53

Genomic and functional characterization of a mucosal symbiont involved in early-stage colorectal cancer	52
Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution	51
Characterization of gut microbial structural variations as determinants of human bile acid metabolism	51
TGFβ restricts expansion, survival, and function of T cells within the tuberculous granuloma	50
Epithelial-Derived Reactive Oxygen Species Enable AppBCX-Mediated Aerobic Respiration of Escherichia coli during Intestinal Inflammation	50
Commensal segmented filamentous bacteria-derived retinoic acid primes host defense to intestinal infection	50
Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions	49
Long-term antibiotic exposure promotes mortality after systemic fungal infection by driving lymphocyte dysfunction and systemic escape of commensal bacteria	49
Diet leaves a genetic signature in a keystone member of the gut microbiota	49
Upper and lower respiratory tract correlates of protection against respiratory syncytial virus following vaccination of nonhuman primates	49
Signatures of antagonistic pleiotropy in a bacterial flagellin epitope	49
Anaerobic Respiration of NOX1-Derived Hydrogen Peroxide Licenses Bacterial Growth at the Colonic Surface	48
The vulnerable versatility of Salmonella antibiotic persisters during infection	48
Toxoplasma gondii secreted effectors co-opt host repressor complexes to inhibit necroptosis	48
Global mapping of Salmonella enterica-host protein-protein interactions during infection	47
Structural insights into viral RNA capping and plasma membrane targeting by Chikungunya virus nonstructural protein 1	47
Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease	46
Anti-CRISPRs go viral: The infection biology of CRISPR-Cas inhibitors	46
Human mAbs Broadly Protect against Arthritogenic Alphaviruses by Recognizing Conserved Elements of the Mxra8 Receptor-Binding Site	46
Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS	45
Gut bacterial isoamylamine promotes age-related cognitive dysfunction by promoting microglial cell death	45
Rethinking phage-bacteria-eukaryotic relationships and their influence on human health	45
Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning	44
Faecalibaculum rodentium remodels retinoic acid signaling to govern eosinophil-dependent intestinal epithelial homeostasis	44
Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy	44
Legionella-Infected Macrophages Engage the Alveolar Epithelium to Metabolically Reprogram Myeloid Cells and Promote Antibacterial Inflammation	44
A lncRNA fine-tunes salicylic acid biosynthesis to balance plant immunity and growth	43
High-fat diet disrupts REG3γ and gut microbial rhythms promoting metabolic dysfunction	43
Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease	42
Schistosoma mansoni Eggs Modulate the Timing of Granuloma Formation to Promote Transmission	42
The developing infant gut microbiome: A strain-level view	42
Biomarker-responsive engineered probiotic diagnoses, records, and ameliorates inflammatory bowel disease in mice	42
Discovery of ultrapotent broadly neutralizing antibodies from SARS-CoV-2 elite neutralizers	42
Zooanthroponotic potential of SARS-CoV-2 and implications of reintroduction into human populations	42
A single-cell liver atlas of Plasmodium vivax infection	42
Antigenic cartography of well-characterized human sera shows SARS-CoV-2 neutralization differences based on infection and vaccination history	41
Enteric viruses evoke broad host immune responses resembling those elicited by the bacterial microbiome	41
A short prokaryotic Argonaute activates membrane effector to confer antiviral defense	41
XBB.1.5 monovalent mRNA vaccine booster elicits robust neutralizing antibodies against XBB subvariants and JN.1	40
Liberation of daidzein by gut microbial β-galactosidase suppresses acetaminophen-induced hepatotoxicity in mice	40
Gut microbial DL-endopeptidase alleviates Crohn’s disease via the NOD2 pathway	40
Mice with diverse microbial exposure histories as a model for preclinical vaccine testing	40
Multi-‘omics of gut microbiome-host interactions in short- and long-term myalgic encephalomyelitis/chronic fatigue syndrome patients	40
SARS-CoV-2 Omicron sublineages show comparable cell entry but differential neutralization by therapeutic antibodies	40
Dosing a synbiotic of human milk oligosaccharides and B. infantis leads to reversible engraftment in healthy adult microbiomes without antibiotics	39
Oral polymicrobial communities: Assembly, function, and impact on diseases	39
Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities	39
Clostridioides difficile Senses and Hijacks Host Heme for Incorporation into an Oxidative Stress Defense System	39
Host Adaptation Predisposes Pseudomonas aeruginosa to Type VI Secretion System-Mediated Predation by the Burkholderia cepacia Complex	38
An Enteric Pathogen Subverts Colonization Resistance by Evading Competition for Amino Acids in the Gut	38
Arresting microbiome development limits immune system maturation and resistance to infection in mice	38
Non-protective immune imprint underlies failure of Staphylococcus aureus IsdB vaccine	37
Symbiont-regulated serotonin biosynthesis modulates tick feeding activity	37
ACTIVating Resources for the COVID-19 Pandemic: In Vivo Models for Vaccines and Therapeutics	37