mSystems

Article	Citations
SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases	489
SARS-CoV-2 and ORF3a: Nonsynonymous Mutations, Functional Domains, and Viral Pathogenesis	174
phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes	164
Gut Microbiota and Metabolome Alterations Associated with Parkinson’s Disease	161
High-Throughput Wastewater SARS-CoV-2 Detection Enables Forecasting of Community Infection Dynamics in San Diego County	104
Precise Species Identification for Enterobacter : a Genome Sequence-Based Study with Reporting of Two Novel Species, Enterobacter quasiroggenkampii	95
Oscillations in U.S. COVID-19 Incidence and Mortality Data Reflect Diagnostic and Reporting Factors	94
Soil Carbon, Nitrogen, and Phosphorus Cycling Microbial Populations and Their Resistance to Global Change Depend on Soil C:N:P Stoichiometry	94
Rapid, Large-Scale Wastewater Surveillance and Automated Reporting System Enable Early Detection of Nearly 85% of COVID-19 Cases on a University Campus	93
Coupling Bacterial Community Assembly to Microbial Metabolism across Soil Profiles	91
Phylogenetic Distribution of Plastic-Degrading Microorganisms	91
Linking Bacterial-Fungal Relationships to Microbial Diversity and Soil Nutrient Cycling	88
Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants	84
Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes	83
Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition	77
Pivotal Roles for pH, Lactate, and Lactate-Utilizing Bacteria in the Stability of a Human Colonic Microbial Ecosystem	73
Dominant Bacterial Phyla from the Human Gut Show Widespread Ability To Transform and Conjugate Bile Acids	73
Space Is More Important than Season when Shaping Soil Microbial Communities at a Large Spatial Scale	73
Genome-Resolved Metagenomics Reveals Distinct Phosphorus Acquisition Strategies between Soil Microbiomes	69
High-Fiber, Whole-Food Dietary Intervention Alters the Human Gut Microbiome but Not Fecal Short-Chain Fatty Acids	69
Administration of Exogenous Melatonin Improves the Diurnal Rhythms of the Gut Microbiota in Mice Fed a High-Fat Diet	68
Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria	68
Abundant and Diverse RNA Viruses in Insects Revealed by RNA-Seq Analysis: Ecological and Evolutionary Implications	67
High-Frequency, High-Throughput Quantification of SARS-CoV-2 RNA in Wastewater Settled Solids at Eight Publicly Owned Treatment Works in Northern California Shows Strong Association with COVID-19 Inci	67
Short-Chain Fatty Acid-Producing Gut Microbiota Is Decreased in Parkinson’s Disease but Not in Rapid-Eye-Movement Sleep Behavior Disorder	64

RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery	63
Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment	63
Correlations between α-Linolenic Acid-Improved Multitissue Homeostasis and Gut Microbiota in Mice Fed a High-Fat Diet	59
DOE JGI Metagenome Workflow	58
Genomic and Chemical Diversity of Bacillus subtilis Secondary Metabolites against Plant Pathogenic Fungi	57
Alterations in the Gut Microbiome in the Progression of Cirrhosis to Hepatocellular Carcinoma	56
Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Reveals Mosaic Pattern of Phylogeographical Distribution	56
The Gut Microbiome and Individual-Specific Responses to Diet	55
Impact of Glyphosate on the Honey Bee Gut Microbiota: Effects of Intensity, Duration, and Timing of Exposure	53
Distinct Community Assembly Processes of Abundant and Rare Soil Bacteria in Coastal Wetlands along an Inundation Gradient	52
Biofilm Structure Promotes Coexistence of Phage-Resistant and Phage-Susceptible Bacteria	51
Long-Term Chemical-Only Fertilization Induces a Diversity Decline and Deep Selection on the Soil Bacteria	51
Temperature-Induced Annual Variation in Microbial Community Changes and Resulting Metabolome Shifts in a Controlled Fermentation System	50
Emerging Transcriptional and Genomic Mechanisms Mediating Carbapenem and Polymyxin Resistance in Enterobacteriaceae : a Systematic Review of Current Reports	50
Insights into the Cultured Bacterial Fraction of Corals	49
Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean	49
Fecal Microbiome Transplantation from Children with Autism Spectrum Disorder Modulates Tryptophan and Serotonergic Synapse Metabolism and Induces Altered Behaviors in Germ-Free Mice	49
High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy	47
Coexistence of Antibiotic Resistance Genes and Virulence Factors Deciphered by Large-Scale Complete Genome Analysis	47
Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice	47
Reclassification of the Taxonomic Framework of Orders Cellvibrionales, Oceanospirillales, Pseudomonadales , and Alteromonadales in Class	47
Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms	47
Different Arbuscular Mycorrhizal Fungi Cocolonizing on a Single Plant Root System Recruit Distinct Microbiomes	46
Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity	45
Distinct Responses of Rare and Abundant Microbial Taxa to In Situ Chemical Stabilization of Cadmium-Contaminated Soil	45
Evolutionary Timeline and Genomic Plasticity Underlying the Lifestyle Diversity in Rhizobiales	44
Consumption of Dietary Fiber from Different Sources during Pregnancy Alters Sow Gut Microbiota and Improves Performance and Reduces Inflammation in Sows and Piglets	43
Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function	43
Phylogenetic Distribution of Secondary Metabolites in the Bacillus subtilis Species Complex	43
Stability of the Virome in Lab- and Field-Collected Aedes albopictus Mosquitoes across Different Developmental Stages and Possible Core Viruses in the Publicly Available Virome Data of	42
Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems	42
Hydrogen-Oxidizing Bacteria Are Abundant in Desert Soils and Strongly Stimulated by Hydration	42
Forming Consensus To Advance Urobiome Research	42
GapMind: Automated Annotation of Amino Acid Biosynthesis	42
Emergence of Ceftazidime- and Avibactam-Resistant Klebsiella pneumoniae Carbapenemase-Producing Pseudomonas aeruginosa in China	41
Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021	41
Deciphering the Mechanisms Shaping the Plastisphere Microbiota in Soil	41
Blowing Hot and Cold: Body Temperature and the Microbiome	41
Microbiota-Derived Short-Chain Fatty Acids Promote LAMTOR2-Mediated Immune Responses in Macrophages	39
Comparative Genomics and Metabolomics in the Genus Nocardia	39
Indoor Dust as a Matrix for Surveillance of COVID-19	39
Phenotypic and Genomic Diversification in Complex Carbohydrate-Degrading Human Gut Bacteria	39
Transmission of Seed and Soil Microbiota to Seedling	39
Gut Microbiota and Host Thermoregulation in Response to Ambient Temperature Fluctuations	38
Stool Samples of Acute Diarrhea Inpatients as a Reservoir of ST11 Hypervirulent KPC-2-Producing Klebsiella pneumoniae	38
Molecular Evolution and Adaptation of Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) Sequence Type 9	38
Roles of Organohalide-RespiringDehalococcoidiain Carbon Cycling	38
Rice SST Variation Shapes the Rhizosphere Bacterial Community, Conferring Tolerance to Salt Stress through Regulating Soil Metabolites	37
Predicting Phenotypic Polymyxin Resistance in Klebsiella pneumoniae through Machine Learning Analysis of Genomic Data	37
Impaired Intestinal Akkermansia muciniphila and Aryl Hydrocarbon Receptor Ligands Contribute to Nonalcoholic Fatty Liver Disease in Mice	37

Siderophore-Mediated Interactions Determine the Disease Suppressiveness of Microbial Consortia	37
Integrative Transkingdom Analysis of the Gut Microbiome in Antibiotic Perturbation and Critical Illness	36
Plant Hosts Modify Belowground Microbial Community Response to Extreme Drought	36
PqsE Is Essential for RhlR-Dependent Quorum Sensing Regulation in Pseudomonas aeruginosa	36
METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses	36
Evaluating and Improving Small Subunit rRNA PCR Primer Coverage for Bacteria, Archaea, and Eukaryotes Using Metagenomes from Global Ocean Surveys	36
Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy	36
Recurrent Vulvovaginal Candidiasis: a Dynamic Interkingdom Biofilm Disease of Candida and Lactobacillus	35
Comprehensive Scanning of Prophages in Lactobacillus : Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems	35
Genomic Analysis of Bovine Staphylococcus aureus Isolates from Milk To Elucidate Diversity and Determine the Distributions of Antimicrobial and Virulence Genes and Their Association with Mastitis	35
Distinct Bacterial Pathways Influence the Efficacy of Antibiotics against Mycobacterium tuberculosis	35
Chasing Ghosts: Race, Racism, and the Future of Microbiome Research	35
The Gut Microbiota Communities of Wild Arboreal and Ground-Feeding Tropical Primates Are Affected Differently by Habitat Disturbance	34
HapX, an Indispensable bZIP Transcription Factor for Iron Acquisition, Regulates Infection Initiation by Orchestrating Conidial Oleic Acid Homeostasis and Cytomembrane Functionality in Mycopathogen Be	34
Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture	34
Soil Bacterial Communities Exhibit Strong Biogeographic Patterns at Fine Taxonomic Resolution	34
Biogeography, Assembly Patterns, Driving Factors, and Interactions of Archaeal Community in Mangrove Sediments	34
Genomic and Resistance Epidemiology of Gram-Negative Bacteria in Africa: a Systematic Review and Phylogenomic Analyses from a One Health Perspective	34
The Killing Mechanism of Teixobactin against Methicillin-Resistant Staphylococcus aureus: an Untargeted Metabolomics Study	33
The Gut Microbiota-Produced Indole-3-Propionic Acid Confers the Antihyperlipidemic Effect of Mulberry-Derived 1-Deoxynojirimycin	33
Bridging Rare and Abundant Bacteria with Ecosystem Multifunctionality in Salinized Agricultural Soils: from Community Diversity to Environmental Adaptation	33
Emergence and Expansion of a Carbapenem-Resistant Pseudomonas aeruginosa Clone Are Associated with Plasmid-Borne bla KPC-2 and Virulence-Related G	33
EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets	33
Artificial Selection on Microbiomes To Breed Microbiomes That Confer Salt Tolerance to Plants	33
Systematic Reconstruction of the Complete Two-Component Sensorial Network in Staphylococcus aureus	32
Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus	32
COVID-19 Pandemic in Lebanon: One Year Later, What Have We Learnt?	32
Insights into the Metabolism and Evolution of the Genus Acidiphilium , a Typical Acidophile in Acid Mine Drainage	32
Beneficial Chromosomal Integration of the Genes for CTX-M Extended-Spectrum β-Lactamase in Klebsiella pneumoniae for Stable Propagation	31
Lactobacillus acidophilus LA14 Alleviates Liver Injury	31
AI4AMP: an Antimicrobial Peptide Predictor Using Physicochemical Property-Based Encoding Method and Deep Learning	31
Ecological Succession of Polymicrobial Communities in the Cystic Fibrosis Airways	31
Maternal Emulsifier P80 Intake Induces Gut Dysbiosis in Offspring and Increases Their Susceptibility to Colitis in Adulthood	30
Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community	30
COVID-19 and the Gut Microbiome: More than a Gut Feeling	30
Quantification of Lysogeny Caused by Phage Coinfections in Microbial Communities from Biophysical Principles	30
Particulate Metabolites and Transcripts Reflect Diel Oscillations of Microbial Activity in the Surface Ocean	30
Fusobacterium nucleatum Metabolically Integrates Commensals and Pathogens in Oral Biofilms	30
High Transcriptional Activity and Diverse Functional Repertoires of Hundreds of Giant Viruses in a Coastal Marine System	29
Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data	29
IS 26 Is Responsible for the Evolution and Transmission of bla NDM -Harboring Plasmids in Escherichia coli of Poult	29
Characterizing the Mechanism of Action of an Ancient Antimicrobial, Manuka Honey, against Pseudomonas aeruginosa Using Modern Transcriptomics	29
The Gut Microbiome in Autism: Study-Site Effects and Longitudinal Analysis of Behavior Change	28
Plasmids Shape the Current Prevalence of tmexCD1-toprJ1 among Klebsiella pneumoniae in Food Production Chains	28
Bifidobacterium lactis Probio-M8 Adjuvant Treatment Confers Added Benefits to Patients with Coronary Artery Disease via Target Modulation of the Gut-Heart/-Brain Axes	28
Fungal Communities Are Important Determinants of Bacterial Community Composition in Deadwood	28
Genomic Epidemiology and Characterization of Methicillin-Resistant Staphylococcus aureus from Bloodstream Infections in China	28
Privatization of Biofilm Matrix in Structurally Heterogeneous Biofilms	28
Host Genetic Factors Associated with Vaginal Microbiome Composition in Kenyan Women	28
Intermittent Hypoxia and Hypercapnia Alter Diurnal Rhythms of Luminal Gut Microbiome and Metabolome	28
Genome-Scale Metabolic Models and Machine Learning Reveal Genetic Determinants of Antibiotic Resistance in Escherichia coli and Unravel the Underlying Metabolic Adaptation Mechanisms	28
Functional Insights into the Kelp Microbiome from Metagenome-Assembled Genomes	28
Increasing the Hindgut Carbohydrate/Protein Ratio by Cecal Infusion of Corn Starch or Casein Hydrolysate Drives Gut Microbiota-Related Bile Acid Metabolism To Stimulate Colonic Barrier Function	28
Comparative Molecular and Immunoregulatory Analysis of Extracellular Vesicles from Candida albicans and Candida auris	28
Direct Nanopore Sequencing of mRNA Reveals Landscape of Transcript Isoforms in Apicomplexan Parasites	27
Assessing Multiplex Tiling PCR Sequencing Approaches for Detecting Genomic Variants of SARS-CoV-2 in Municipal Wastewater	27
Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics	27
Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations	27
Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method	27
Dietary Fiber Ameliorates Lipopolysaccharide-Induced Intestinal Barrier Function Damage in Piglets by Modulation of Intestinal Microbiome	27
Initial Mapping of the New York City Wastewater Virome	27
Citrobacter Species Increase Energy Harvest by Modulating Intestinal Microbiota in Fish: Nondominant Species Play Important Functions	27
Extended Plant Metarhizobiome: Understanding Volatile Organic Compound Signaling in Plant-Microbe Metapopulation Networks	26
Emergence of mcr-9.1 in Extended-Spectrum-β-Lactamase-Producing Clinical Enterobacteriaceae in Pretoria, South Africa: Global Evolutionary	26
Genomic Features Associated with the Degree of Phenotypic Resistance to Carbapenems in Carbapenem-Resistant Klebsiella pneumoniae	26
Characterization of the Vaginal Microbiome in Women with Infertility and Its Potential Correlation with Hormone Stimulation during In Vitro Fertilization Surgery	26
Bioinformatic Mapping of Opine-Like Zincophore Biosynthesis in Bacteria	26
Weaning Age and Its Effect on the Development of the Swine Gut Microbiome and Resistome	26
Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities	26
In Silico Analysis Highlights the Diversity and Novelty of Circular Bacteriocins in Sequenced Microbial Genomes	26
Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil	26
Isolation and Characterization of the Novel Phage JD032 and Global Transcriptomic Response during JD032 Infection of Clostridioides difficile Ribotype 078	26
Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities	25
Enhanced Biosynthesis of Fatty Acids Is Associated with the Acquisition of Ciprofloxacin Resistance in Edwardsiella tarda	25
Endophytic Lifestyle of Global Clones of Extended-Spectrum β-Lactamase-Producing Priority Pathogens in Fresh Vegetables: a Trojan Horse Strategy Favoring Human Colonization?	25
Elucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel Relationships	25
Genomes of the “ Candidatus Actinomarinales” Order: Highly Streamlined Marine Epipelagic Actinobacteria	25
Marine Sediments Hold an Untapped Potential for Novel Taxonomic and Bioactive Bacterial Diversity	25
Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis	25
Marine Community Metabolomes Carry Fingerprints of Phytoplankton Community Composition	25

Sepsis-Induced Gut Dysbiosis Mediates the Susceptibility to Sepsis-Associated Encephalopathy in Mice	25
Limited and Strain-Specific Transcriptional and Growth Responses to Acquisition of a Multidrug Resistance Plasmid in Genetically Diverse Escherichia coli Lineages	24
Microbial Strategies for Survival in the Glass Sponge Vazella pourtalesii	24
Serine Metabolism Tunes Immune Responses To Promote Oreochromis niloticus Survival upon Edwardsiella tarda Infection	24
A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog	24
Microbial Diversity and Interaction Specificity in Kombucha Tea Fermentations	24
Race, the Vaginal Microbiome, and Spontaneous Preterm Birth	24
Parallel Analysis of Cystic Fibrosis Sputum and Saliva Reveals Overlapping Communities and an Opportunity for Sample Decontamination	24
Candida Administration Worsens Uremia-Induced Gut Leakage in Bilateral Nephrectomy Mice, an Impact of Gut Fungi and Organismal Molecules in Uremia	24
The Stringent Stress Response Controls Proteases and Global Regulators under Optimal Growth Conditions in Pseudomonas aeruginosa	23
Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin	23
A Family of Viral Satellites Manipulates Invading Virus Gene Expression and Can Affect Cholera Toxin Mobilization	23
Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens	23
Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus “CandidatusAccumulibacter”	23
Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds	23
Free-Living, Psychrotrophic Bacteria of the Genus Psychrobacter Are Descendants of Pathobionts	23
Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition	23
The Sorghum bicolor Root Exudate Sorgoleone Shapes Bacterial Communities and Delays Network Formation	23
BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities	23
Novel Viral Communities Potentially Assisting in Carbon, Nitrogen, and Sulfur Metabolism in the Upper Slope Sediments of Mariana Trench	23
Gut Dysbiosis and Its Associations with Gut Microbiota-Derived Metabolites in Dogs with Myxomatous Mitral Valve Disease	23
Urban Wildlife Crisis: Australian Silver Gull Is a Bystander Host to Widespread Clinical Antibiotic Resistance	23
An Expanded Genetic Code Enables Trimethylamine Metabolism in Human Gut Bacteria	23
Common Presence of PhototrophicGemmatimonadotain Temperate Freshwater Lakes	22
Mucosal Microbiota and Metabolome along the Intestinal Tract Reveal a Location-Specific Relationship	22
AMiGA: Software for Automated Analysis of Microbial Growth Assays	22
Viral Ecogenomics of Arctic Cryopeg Brine and Sea Ice	22
Patterns and Drivers of nirK -Type and nirS -Type Denitrifier Community Assembly along an Elevation Gradient	22
T3SEpp: an Integrated Prediction Pipeline for Bacterial Type III Secreted Effectors	22
Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2	22
Host Traits and Phylogeny Contribute to Shaping Coral-Bacterial Symbioses	22
Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria	22
Proteomic Study of the Survival and Resuscitation Mechanisms of Filamentous Persisters in an Evolved Escherichia coli Population from Cyclic Ampicillin Treatment	22
Deciphering Active Prophages from Metagenomes	22
Struggle To Survive: the Choir of Target Alteration, Hydrolyzing Enzyme, and Plasmid Expression as a Novel Aztreonam-Avibactam Resistance Mechanism	22
The Evolutionary Success of the Marine Bacterium SAR11 Analyzed through a Metagenomic Perspective	22
Effects of ‘Healthy’ Fecal Microbiota Transplantation against the Deterioration of Depression in Fawn-Hooded Rats	21
Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models	21
Spatial Compartmentalization of the Microbiome between the Lumen and Crypts Is Lost in the Murine Cecum following the Process of Surgery, Including Overnight Fasting and Exposure to Antibiotics	21
Subspecies Niche Specialization in the Oral Microbiome Is Associated with Nasopharyngeal Carcinoma Risk	21
Identification and Quantification of Bovine Digital Dermatitis-Associated Microbiota across Lesion Stages in Feedlot Beef Cattle	21
Phylogenomic Analyses of Snodgrassella Isolates from Honeybees and Bumblebees Reveal Taxonomic and Functional Diversity	21
Comparative Genomics Reveals Thermal Adaptation and a High Metabolic Diversity in “ Candidatus Bathyarchaeia”	21
Inactivation of Nitrite-Dependent Nitric Oxide Biosynthesis Is Responsible for Overlapped Antibiotic Resistance between Naturally and Artificially Evolved Pseudomonas aeruginosa	21
One-Cell Metabolic Phenotyping and Sequencing of Soil Microbiome by Raman-Activated Gravity-Driven Encapsulation (RAGE)	21
A Multiphase Multiobjective Dynamic Genome-Scale Model Shows Different Redox Balancing among Yeast Species of theSaccharomycesGenus in Fermentation	21
RNA-Protein Interaction Analysis of SARS-CoV-2 5′ and 3′ Untranslated Regions Reveals a Role of Lysosome-Associated Membrane Protein-2a during Viral Infection	20
Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure	20
DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid	20
CRISPR-CBEI: a Designing and Analyzing Tool Kit for Cytosine Base Editor-Mediated Gene Inactivation	20
Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design	20
In Silico Structure-Based Repositioning of Approved Drugs for Spike Glycoprotein S2 Domain Fusion Peptide of SARS-CoV-2: Rationale from Molecular Dynamics and Binding Free Energy Ca	20
Evidence for Succession and Putative Metabolic Roles of Fungi and Bacteria in the Farming Mutualism of the Ambrosia Beetle Xyleborus affinis	20
Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort	20
Dynamic Bayesian Networks for Integrating Multi-omics Time Series Microbiome Data	20
Baseline Gut Metagenomic Functional Gene Signature Associated with Variable Weight Loss Responses following a Healthy Lifestyle Intervention in Humans	20
Higher Trimethylamine- N -Oxide Plasma Levels with Increasing Age Are Mediated by Diet and Trimethylamine-Forming Bacteria	20
Virulence of the Pathogen Porphyromonas gingivalis Is Controlled by the CRISPR-Cas Protein Cas3	20
Continental-Scale Microbiome Study Reveals Different Environmental Characteristics Determining Microbial Richness, Composition, and Quantity in Hotel Rooms	20
National Prevalence of Salmonella enterica Serotype Kentucky ST198 with High-Level Resistance to Ciprofloxacin and Extended-Spectrum Cephalosporins in China, 2013 to 2017	20
Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut	20
Menopause Is Associated with an Altered Gut Microbiome and Estrobolome, with Implications for Adverse Cardiometabolic Risk in the Hispanic Community Health Study/Study of Latinos	20
Short-Chain Fatty Acids Reduced Renal Calcium Oxalate Stones by Regulating the Expression of Intestinal Oxalate Transporter SLC26A6	20
Rapid Response of Nitrogen Cycling Gene Transcription to Labile Carbon Amendments in a Soil Microbial Community	20
Phenotypic and Genomic Comparison of the Two Most Common ExoU-Positive Pseudomonas aeruginosa Clones, PA14 and ST235	19
Cross-Scale Analyses of Animal and Human Gut Microbiome Assemblies from Metacommunity to Global Landscape	19
End-to-End Protocol for the Detection of SARS-CoV-2 from Built Environments	19
Quantifying Live Microbial Load in Human Saliva Samples over Time Reveals Stable Composition and Dynamic Load	19
Multi-omics Analysis Revealed Coordinated Responses of Rumen Microbiome and Epithelium to High-Grain-Induced Subacute Rumen Acidosis in Lactating Dairy Cows	19
Genome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and Promoters	19
F Plasmid Lineages in Escherichia coli ST95: Implications for Host Range, Antibiotic Resistance, and Zoonoses	19
Respiratory Bacteria Stabilize and Promote Airborne Transmission of Influenza A Virus	19
Transcription Inhibitors with XRE DNA-Binding and Cupin Signal-Sensing Domains Drive Metabolic Diversification in Pseudomonas	19
Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn's Disease	19
Shifts in the Bacterial Population and Ecosystem Functions in Response to Vegetation in the Yellow River Delta Wetlands	19
Molting Alters the Microbiome, Immune Response, and Digestive Enzyme Activity in Mud Crab ( Scylla paramamosain )	19
Acinetobacter baumannii Targets Human Carcinoembryonic Antigen-Related Cell Adhesion Molecules (CEACAMs) for Invasion of Pneumocytes	19
Apoptosis in a Whitefly Vector Activated by a Begomovirus Enhances Viral Transmission	19
Species-Level Resolution of Female Bladder Microbiota from 16S rRNA Amplicon Sequencing	19
Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides	19
Integrated Multi-omics Investigations Reveal the Key Role of Synergistic Microbial Networks in Removing Plasticizer Di-(2-Ethylhexyl) Phthalate from Estuarine Sediments	19
Global Distribution of mcr Gene Variants in 214K Metagenomic Samples	18
Comparison of Oral Microbiota Collected Using Multiple Methods and Recommendations for New Epidemiologic Studies	18
Cofactor Specificity of Glucose-6-Phosphate Dehydrogenase Isozymes in Pseudomonas putida Reveals a General Principle Underlying Glycolytic Strategies in Bacteria	18
Computational Analysis of Microbial Flow Cytometry Data	18
Presence of Bromotyrosine Alkaloids in Marine Sponges Is Independent of Metabolomic and Microbiome Architectures	18
Associations of Genetic Variants Contributing to Gut Microbiota Composition in Immunoglobin A Nephropathy	18
The Behavior of Amphibians Shapes Their Symbiotic Microbiomes	18
The Inactivation of Enzymes Belonging to the Central Carbon Metabolism Is a Novel Mechanism of Developing Antibiotic Resistance	18
Metabolic Features of Ganjang (a Korean Traditional Soy Sauce) Fermentation Revealed by Genome-Centered Metatranscriptomics	18
Cultivating the Bacterial Microbiota of Populus Roots	18
Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities	18
Children with Autism and Their Typically Developing Siblings Differ in Amplicon Sequence Variants and Predicted Functions of Stool-Associated Microbes	18
Evolutionary Trajectory of the Tet(X) Family: Critical Residue Changes towards High-Level Tigecycline Resistance	18
Harnessing Machine Learning To Unravel Protein Degradation in Escherichia coli	18