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	960
Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition	904
Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization	650
Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization	458
Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite	453
SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity	447
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut	394
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
Gut microbiota-derived bile acids in intestinal immunity, inflammation, and tumorigenesis	312
The variant gambit: COVID-19’s next move	306
SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines	284
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
Developmental trajectory of the healthy human gut microbiota during the first 5 years of life	248
Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis	241
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies	236
A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions	233
Living in the endosymbiotic world of Wolbachia: A centennial review	212
Innate immune and inflammatory responses to SARS-CoV-2: Implications for COVID-19	207
Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant	195
An expanded arsenal of immune systems that protect bacteria from phages	193
Enhanced neutralization resistance of SARS-CoV-2 Omicron subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2	181
SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape	174
Role of dietary fiber in the recovery of the human gut microbiome and its metabolome	172
Real-Time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles	166

Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways	165
Phages and their satellites encode hotspots of antiviral systems	164
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
Induction of alarmin S100A8/A9 mediates activation of aberrant neutrophils in the pathogenesis of COVID-19	156
Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2	151
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	139
A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1	137
The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants	131
Antibody evasion of SARS-CoV-2 Omicron BA.1, BA.1.1, BA.2, and BA.3 sub-lineages	126
Kinetics and correlates of the neutralizing antibody response to SARS-CoV-2 infection in humans	125
Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75	123
Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant	123
Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors	123
Human gut bacterial metabolism drives Th17 activation and colitis	118
Commensal Staphylococcus epidermidis contributes to skin barrier homeostasis by generating protective ceramides	118
The immune landscape in tuberculosis reveals populations linked to disease and latency	117
Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease	114
Intranasal vaccination with a lentiviral vector protects against SARS-CoV-2 in preclinical animal models	112
Shigella ubiquitin ligase IpaH7.8 targets gasdermin D for degradation to prevent pyroptosis and enable infection	110
Neutralization of SARS-CoV-2 Omicron sub-lineages BA.1, BA.1.1, and BA.2	108
Global COVID-19 vaccine inequity: The scope, the impact, and the challenges	108
Antibody and B cell responses to SARS-CoV-2 infection and vaccination	107
Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner	106
Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization	104
Organoids and organs-on-chips: Insights into human gut-microbe interactions	104
Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp.	103
Bacteria induce skin regeneration via IL-1β signaling	101
Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response	100
Rethinking healthy eating in light of the gut microbiome	97
Rethinking next-generation vaccines for coronaviruses, influenzaviruses, and other respiratory viruses	94
Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage	92
Dynamics of the normal gut microbiota: A longitudinal one-year population study in Sweden	92
Gut microbiome dysbiosis contributes to abdominal aortic aneurysm by promoting neutrophil extracellular trap formation	92
Plant immune system activation is necessary for efficient root colonization by auxin-secreting beneficial bacteria	92
Microbiota regulate innate immune signaling and protective immunity against cancer	91
Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants	89
Western diet induces Paneth cell defects through microbiome alterations and farnesoid X receptor and type I interferon activation	88
A complex immune response to flagellin epitope variation in commensal communities	88
Gut microbes impact stroke severity via the trimethylamine N-oxide pathway	86
Anatomy promotes neutral coexistence of strains in the human skin microbiome	86
Robust SARS-CoV-2 infection in nasal turbinates after treatment with systemic neutralizing antibodies	84
SARS-CoV-2 Omicron triggers cross-reactive neutralization and Fc effector functions in previously vaccinated, but not unvaccinated, individuals	84
Helicobacter pylori CagA elicits BRCAness to induce genome instability that may underlie bacterial gastric carcinogenesis	84
Exploration of Bacterial Bottlenecks and Streptococcus pneumoniae Pathogenesis by CRISPRi-Seq	83
A microbial metabolite remodels the gut-liver axis following bariatric surgery	82
Tissue-resident Lachnospiraceae family bacteria protect against colorectal carcinogenesis by promoting tumor immune surveillance	82
Persistent B cell memory after SARS-CoV-2 vaccination is functional during breakthrough infections	81
Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors	81

Gut microbiome lipid metabolism and its impact on host physiology	80
The great escape? SARS-CoV-2 variants evading neutralizing responses	79
Neutralization and durability of 2 or 3 doses of the BNT162b2 vaccine against Omicron SARS-CoV-2	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	79
Vaccinia virus E3 prevents sensing of Z-RNA to block ZBP1-dependent necroptosis	79
Programing of an Intravascular Immune Firewall by the Gut Microbiota Protects against Pathogen Dissemination during Infection	78
Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation	78
Dispersal strategies shape persistence and evolution of human gut bacteria	78
Bacterial effectors manipulate plant abscisic acid signaling for creation of an aqueous apoplast	78
The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping	78
Virus vaccines: proteins prefer prolines	77
The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition	75
Evasion of neutralizing antibody responses by the SARS-CoV-2 BA.2.75 variant	74
Cross-feeding in the gut microbiome: Ecology and mechanisms	74
Fusobacterium nucleatum-derived succinic acid induces tumor resistance to immunotherapy in colorectal cancer	73
HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens	73
Ultra-low Dose Aerosol Infection of Mice with Mycobacterium tuberculosis More Closely Models Human Tuberculosis	72
Evolutionarily conserved bacterial effectors hijack abscisic acid signaling to induce an aqueous environment in the apoplast	72
In vivo commensal control of Clostridioides difficile virulence	72
Pre-existing humoral immunity to human common cold coronaviruses negatively impacts the protective SARS-CoV-2 antibody response	72
E. coli enhance colonization resistance against Salmonella Typhimurium by competing for galactitol, a context-dependent limiting carbon source	71
Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota	71
Butyrate-producing Eubacterium rectale suppresses lymphomagenesis by alleviating the TNF-induced TLR4/MyD88/NF-κB axis	70
Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2	69
Global genome analysis reveals a vast and dynamic anellovirus landscape within the human virome	68
Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites	67
Klebsiella oxytoca causes colonization resistance against multidrug-resistant K. pneumoniae in the gut via cooperative carbohydrate competition	66
Prophages encode phage-defense systems with cognate self-immunity	66
Alterations in the gut microbiota contribute to cognitive impairment induced by the ketogenic diet and hypoxia	66
Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation	66
Murine model of colonization with fungal pathogen Candida auris to explore skin tropism, host risk factors and therapeutic strategies	65
The success of SARS-CoV-2 vaccines and challenges ahead	64
A calmodulin-binding transcription factor links calcium signaling to antiviral RNAi defense in plants	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
Colonization of the live biotherapeutic product VE303 and modulation of the microbiota and metabolites in healthy volunteers	64
One year of SARS-CoV-2 evolution	63
Caudovirales bacteriophages are associated with improved executive function and memory in flies, mice, and humans	63
Global, distinctive, and personal changes in molecular and microbial profiles by specific fibers in humans	63
Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice	62
3β-Hydroxysteroid dehydrogenase expressed by gut microbes degrades testosterone and is linked to depression in males	61
Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential	61
Key determinants of success in fecal microbiota transplantation: From microbiome to clinic	61
Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA.1 and BA.2	61
Immunoglobulin A Targets a Unique Subset of the Microbiota in Inflammatory Bowel Disease	61
Microbiota-antibody interactions that regulate gut homeostasis	61
Coevolution between bacterial CRISPR-Cas systems and their bacteriophages	60
Lysosome Fusion Maintains Phagosome Integrity during Fungal Infection	59
The SMC5/6 complex compacts and silences unintegrated HIV-1 DNA and is antagonized by Vpr	59
Plant roots employ cell-layer-specific programs to respond to pathogenic and beneficial microbes	58
Intestinal mucus and their glycans: A habitat for thriving microbiota	57
Ruminococcus gnavus plays a pathogenic role in diarrhea-predominant irritable bowel syndrome by increasing serotonin biosynthesis	57
Episymbiotic Saccharibacteria suppresses gingival inflammation and bone loss in mice through host bacterial modulation	56
An NTD supersite of attack	56
Autophagy controls mucus secretion from intestinal goblet cells by alleviating ER stress	56
Deep-Learning Resources for Studying Glycan-Mediated Host-Microbe Interactions	56
Detect and destroy: CRISPR-based technologies for the response against viruses	55
SARS-CoV-2 Omicron sublineages exhibit distinct antibody escape patterns	55
Discovery of a Family of Mixed Lineage Kinase Domain-like Proteins in Plants and Their Role in Innate Immune Signaling	54
Characterization of gut microbial structural variations as determinants of human bile acid metabolism	54
The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants	54
The logic of virus evolution	54
An AAV-based, room-temperature-stable, single-dose COVID-19 vaccine provides durable immunogenicity and protection in non-human primates	54
A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection	53
Long-term antibiotic exposure promotes mortality after systemic fungal infection by driving lymphocyte dysfunction and systemic escape of commensal bacteria	53
Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution	53
Genomic and functional characterization of a mucosal symbiont involved in early-stage colorectal cancer	52
Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions	52
Upper and lower respiratory tract correlates of protection against respiratory syncytial virus following vaccination of nonhuman primates	51
The vulnerable versatility of Salmonella antibiotic persisters during infection	51
Epithelial-Derived Reactive Oxygen Species Enable AppBCX-Mediated Aerobic Respiration of Escherichia coli during Intestinal Inflammation	51
Signatures of antagonistic pleiotropy in a bacterial flagellin epitope	51
TGFβ restricts expansion, survival, and function of T cells within the tuberculous granuloma	50
Diet leaves a genetic signature in a keystone member of the gut microbiota	50
Commensal segmented filamentous bacteria-derived retinoic acid primes host defense to intestinal infection	50
Faecalibaculum rodentium remodels retinoic acid signaling to govern eosinophil-dependent intestinal epithelial homeostasis	49
XBB.1.5 monovalent mRNA vaccine booster elicits robust neutralizing antibodies against XBB subvariants and JN.1	48
Structural insights into viral RNA capping and plasma membrane targeting by Chikungunya virus nonstructural protein 1	48
Toxoplasma gondii secreted effectors co-opt host repressor complexes to inhibit necroptosis	48

Anaerobic Respiration of NOX1-Derived Hydrogen Peroxide Licenses Bacterial Growth at the Colonic Surface	48
Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS	47
Global mapping of Salmonella enterica-host protein-protein interactions during infection	47
Biomarker-responsive engineered probiotic diagnoses, records, and ameliorates inflammatory bowel disease in mice	46
High-fat diet disrupts REG3γ and gut microbial rhythms promoting metabolic dysfunction	46
Anti-CRISPRs go viral: The infection biology of CRISPR-Cas inhibitors	46
Gut bacterial isoamylamine promotes age-related cognitive dysfunction by promoting microglial cell death	46
Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning	46
Human mAbs Broadly Protect against Arthritogenic Alphaviruses by Recognizing Conserved Elements of the Mxra8 Receptor-Binding Site	46
Rethinking phage-bacteria-eukaryotic relationships and their influence on human health	45
The developing infant gut microbiome: A strain-level view	45
A lncRNA fine-tunes salicylic acid biosynthesis to balance plant immunity and growth	45
Gut microbial DL-endopeptidase alleviates Crohn’s disease via the NOD2 pathway	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
Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease	43
A single-cell liver atlas of Plasmodium vivax infection	43
A short prokaryotic Argonaute activates membrane effector to confer antiviral defense	43
Enteric viruses evoke broad host immune responses resembling those elicited by the bacterial microbiome	42
Zooanthroponotic potential of SARS-CoV-2 and implications of reintroduction into human populations	42
Schistosoma mansoni Eggs Modulate the Timing of Granuloma Formation to Promote Transmission	42
Discovery of ultrapotent broadly neutralizing antibodies from SARS-CoV-2 elite neutralizers	42
Antigenic cartography of well-characterized human sera shows SARS-CoV-2 neutralization differences based on infection and vaccination history	41
Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities	41
Arresting microbiome development limits immune system maturation and resistance to infection in mice	40
SARS-CoV-2 Omicron sublineages show comparable cell entry but differential neutralization by therapeutic antibodies	40
Liberation of daidzein by gut microbial β-galactosidase suppresses acetaminophen-induced hepatotoxicity in mice	40
Multi-‘omics of gut microbiome-host interactions in short- and long-term myalgic encephalomyelitis/chronic fatigue syndrome patients	40
Mice with diverse microbial exposure histories as a model for preclinical vaccine testing	40
Two distinct gut microbial pathways contribute to meta-organismal production of phenylacetylglutamine with links to cardiovascular disease	39
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
ACTIVating Resources for the COVID-19 Pandemic: In Vivo Models for Vaccines and Therapeutics	38
Gut bacterial metabolism contributes to host global purine homeostasis	38
Secretory IgA: Linking microbes, maternal health, and infant health through human milk	38
Modulating HIV-1 envelope glycoprotein conformation to decrease the HIV-1 reservoir	38
Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice	38
Non-protective immune imprint underlies failure of Staphylococcus aureus IsdB vaccine	37
HIV-infected macrophages resist efficient NK cell-mediated killing while preserving inflammatory cytokine responses	37
Symbiont-regulated serotonin biosynthesis modulates tick feeding activity	37
Cryptosporidium uses multiple distinct secretory organelles to interact with and modify its host cell	36
Cryptosporidium rhoptry effector protein ROP1 injected during invasion targets the host cytoskeletal modulator LMO7	36
An epithelial-immune circuit amplifies inflammasome and IL-6 responses to SARS-CoV-2	35
Defining antigen targets to dissect vaccinia virus and monkeypox virus-specific T cell responses in humans	35
Mothers of Preterm Infants Have Individualized Breast Milk Microbiota that Changes Temporally Based on Maternal Characteristics	35
Toward a global virus genomic surveillance network	35
Bacteriostatic antibiotics promote CRISPR-Cas adaptive immunity by enabling increased spacer acquisition	35
Regulators of male and female sexual development are critical for the transmission of a malaria parasite	35
Host hepatic metabolism is modulated by gut microbiota-derived sphingolipids	34
RTP4 Is a Potent IFN-Inducible Anti-flavivirus Effector Engaged in a Host-Virus Arms Race in Bats and Other Mammals	33
Cytosolic replication in epithelial cells fuels intestinal expansion and chronic fecal shedding of Salmonella Typhimurium	33
Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria	33
Development of a T cell-based immunodiagnostic system to effectively distinguish SARS-CoV-2 infection and COVID-19 vaccination status	33
Accelerated Preclinical Paths to Support Rapid Development of COVID-19 Therapeutics	32
Dynamic nutrient acquisition from a hydrated apoplast supports biotrophic proliferation of a bacterial pathogen of maize	32
Functional map of SARS-CoV-2 3CL protease reveals tolerant and immutable sites	32
Fusobacterium nucleatum aggravates rheumatoid arthritis through FadA-containing outer membrane vesicles	32
Airway dysbiosis accelerates lung function decline in chronic obstructive pulmonary disease	32
Enteric virome negatively affects seroconversion following oral rotavirus vaccination in a longitudinally sampled cohort of Ghanaian infants	32
Host cells subdivide nutrient niches into discrete biogeographical microhabitats for gut microbes	32
A unique mode of nucleic acid immunity performed by a multifunctional bacterial enzyme	31
Virological characteristics of the SARS-CoV-2 BA.2.86 variant	31
Uncoupling of IL-6 signaling and LC3-associated phagocytosis drives immunoparalysis during sepsis	31
Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronaviruses	31
Airway T cells are a correlate of i.v. Bacille Calmette-Guerin-mediated protection against tuberculosis in rhesus macaques	31
A dissemination-prone morphotype enhances extrapulmonary organ entry by Cryptococcus neoformans	30
Secreted Akkermansia muciniphila threonyl-tRNA synthetase functions to monitor and modulate immune homeostasis	30
Strain-level functional variation in the human gut microbiota based on bacterial binding to artificial food particles	30
Fungal sensing enhances neutrophil metabolic fitness by regulating antifungal Glut1 activity	30
Engineered Escherichia coli for the in situ secretion of therapeutic nanobodies in the gut	30
Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis	30
The Arabidopsis TIR-NBS-LRR protein CSA1 guards BAK1-BIR3 homeostasis and mediates convergence of pattern- and effector-induced immune responses	29
Gut colonization by Proteobacteria alters host metabolism and modulates cocaine neurobehavioral responses	29
Tryptophan metabolites get the gut moving	29
Tet2 deficiency drives liver microbiome dysbiosis triggering Tc1 cell autoimmune hepatitis	29
The bacterial effector GarD shields Chlamydia trachomatis inclusions from RNF213-mediated ubiquitylation and destruction	29
Quantifying rapid bacterial evolution and transmission within the mouse intestine	28
Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes	28
The gut environment regulates bacterial gene expression which modulates susceptibility to bacteriophage infection	28
HIV-1 matrix-tRNA complex structure reveals basis for host control of Gag localization	28
Interspecies commensal interactions have nonlinear impacts on host immunity	27
Maturation of the neonatal oral mucosa involves unique epithelium-microbiota interactions	27
Candida albicans-specific Th17 cell-mediated response contributes to alcohol-associated liver disease	27
Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors	27
Neisseria species as pathobionts in bronchiectasis	27
Spontaneous HIV expression during suppressive ART is associated with the magnitude and function of HIV-specific CD4+ and CD8+ T cells	27
Longitudinal comparison of the developing gut virome in infants and their mothers	27
Antibody escape and cryptic cross-domain stabilization in the SARS-CoV-2 Omicron spike protein	26
The chromatin-remodeling protein BAF60/SWP73A regulates the plant immune receptor NLRs	26
An aberrant inflammatory response in severe COVID-19	26
Enterosignatures define common bacterial guilds in the human gut microbiome	26
The resistance within: Antibiotic disruption of the gut microbiome and resistome dynamics in infancy	25
Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes	25
On-person adaptive evolution of Staphylococcus aureus during treatment for atopic dermatitis	25
Lassa virus glycoprotein nanoparticles elicit neutralizing antibody responses and protection	25