mSystems

Article	Citations
Linking Bacterial-Fungal Relationships to Microbial Diversity and Soil Nutrient Cycling	111
High-Throughput Wastewater SARS-CoV-2 Detection Enables Forecasting of Community Infection Dynamics in San Diego County	107
Rapid, Large-Scale Wastewater Surveillance and Automated Reporting System Enable Early Detection of Nearly 85% of COVID-19 Cases on a University Campus	105
Phylogenetic Distribution of Plastic-Degrading Microorganisms	102
Genome-Resolved Metagenomics Reveals Distinct Phosphorus Acquisition Strategies between Soil Microbiomes	96
Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants	95
Dominant Bacterial Phyla from the Human Gut Show Widespread Ability To Transform and Conjugate Bile Acids	92
Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition	84
High-Fiber, Whole-Food Dietary Intervention Alters the Human Gut Microbiome but Not Fecal Short-Chain Fatty Acids	80
Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment	76
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	75
Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria	74
DOE JGI Metagenome Workflow	72
Short-Chain Fatty Acid-Producing Gut Microbiota Is Decreased in Parkinson’s Disease but Not in Rapid-Eye-Movement Sleep Behavior Disorder	71
Genomic and Chemical Diversity of Bacillus subtilis Secondary Metabolites against Plant Pathogenic Fungi	69
Correlations between α-Linolenic Acid-Improved Multitissue Homeostasis and Gut Microbiota in Mice Fed a High-Fat Diet	69
Distinct Community Assembly Processes of Abundant and Rare Soil Bacteria in Coastal Wetlands along an Inundation Gradient	59
Distinct Responses of Rare and Abundant Microbial Taxa to In Situ Chemical Stabilization of Cadmium-Contaminated Soil	59
Fecal Microbiome Transplantation from Children with Autism Spectrum Disorder Modulates Tryptophan and Serotonergic Synapse Metabolism and Induces Altered Behaviors in Germ-Free Mice	58
Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity	56
Emerging Transcriptional and Genomic Mechanisms Mediating Carbapenem and Polymyxin Resistance in Enterobacteriaceae : a Systematic Review of Current Reports	55
Different Arbuscular Mycorrhizal Fungi Cocolonizing on a Single Plant Root System Recruit Distinct Microbiomes	55
Insights into the Cultured Bacterial Fraction of Corals	55
Deciphering the Mechanisms Shaping the Plastisphere Microbiota in Soil	51
Phylogenetic Distribution of Secondary Metabolites in the Bacillus subtilis Species Complex	51

Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy	51
Transmission of Seed and Soil Microbiota to Seedling	50
Consumption of Dietary Fiber from Different Sources during Pregnancy Alters Sow Gut Microbiota and Improves Performance and Reduces Inflammation in Sows and Piglets	50
Forming Consensus To Advance Urobiome Research	50
Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice	49
Blowing Hot and Cold: Body Temperature and the Microbiome	47
Hydrogen-Oxidizing Bacteria Are Abundant in Desert Soils and Strongly Stimulated by Hydration	46
Phenotypic and Genomic Diversification in Complex Carbohydrate-Degrading Human Gut Bacteria	45
Evaluating and Improving Small Subunit rRNA PCR Primer Coverage for Bacteria, Archaea, and Eukaryotes Using Metagenomes from Global Ocean Surveys	45
Microbiota-Derived Short-Chain Fatty Acids Promote LAMTOR2-Mediated Immune Responses in Macrophages	45
Indoor Dust as a Matrix for Surveillance of COVID-19	44
Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021	44
METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses	44
Effects of ‘Healthy’ Fecal Microbiota Transplantation against the Deterioration of Depression in Fawn-Hooded Rats	44
Emergence of Ceftazidime- and Avibactam-Resistant Klebsiella pneumoniae Carbapenemase-Producing Pseudomonas aeruginosa in China	44
Fusobacterium nucleatum Metabolically Integrates Commensals and Pathogens in Oral Biofilms	43
Integrative Transkingdom Analysis of the Gut Microbiome in Antibiotic Perturbation and Critical Illness	42
AI4AMP: an Antimicrobial Peptide Predictor Using Physicochemical Property-Based Encoding Method and Deep Learning	42
Genomic and Resistance Epidemiology of Gram-Negative Bacteria in Africa: a Systematic Review and Phylogenomic Analyses from a One Health Perspective	42
Impaired Intestinal Akkermansia muciniphila and Aryl Hydrocarbon Receptor Ligands Contribute to Nonalcoholic Fatty Liver Disease in Mice	41
Rice SST Variation Shapes the Rhizosphere Bacterial Community, Conferring Tolerance to Salt Stress through Regulating Soil Metabolites	41
Molecular Evolution and Adaptation of Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) Sequence Type 9	41
Comprehensive Scanning of Prophages in Lactobacillus : Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems	41
Microbial Diversity and Interaction Specificity in Kombucha Tea Fermentations	40
Biogeography, Assembly Patterns, Driving Factors, and Interactions of Archaeal Community in Mangrove Sediments	39
Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data	38
Artificial Selection on Microbiomes To Breed Microbiomes That Confer Salt Tolerance to Plants	38
Recurrent Vulvovaginal Candidiasis: a Dynamic Interkingdom Biofilm Disease of Candida and Lactobacillus	37
Chasing Ghosts: Race, Racism, and the Future of Microbiome Research	37
Bifidobacterium lactis Probio-M8 Adjuvant Treatment Confers Added Benefits to Patients with Coronary Artery Disease via Target Modulation of the Gut-Heart/-Brain Axes	37
Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus	37
Emergence and Expansion of a Carbapenem-Resistant Pseudomonas aeruginosa Clone Are Associated with Plasmid-Borne bla KPC-2 and Virulence-Related G	37
Insights into the Metabolism and Evolution of the Genus Acidiphilium , a Typical Acidophile in Acid Mine Drainage	36
EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets	36
Comparative Molecular and Immunoregulatory Analysis of Extracellular Vesicles from Candida albicans and Candida auris	36
Bridging Rare and Abundant Bacteria with Ecosystem Multifunctionality in Salinized Agricultural Soils: from Community Diversity to Environmental Adaptation	36
Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition	35
Dietary Fiber Ameliorates Lipopolysaccharide-Induced Intestinal Barrier Function Damage in Piglets by Modulation of Intestinal Microbiome	35
Enhanced Biosynthesis of Fatty Acids Is Associated with the Acquisition of Ciprofloxacin Resistance in Edwardsiella tarda	35
Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus “CandidatusAccumulibacter”	34
Plasmids Shape the Current Prevalence of tmexCD1-toprJ1 among Klebsiella pneumoniae in Food Production Chains	33
Functional Insights into the Kelp Microbiome from Metagenome-Assembled Genomes	33
Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community	33
Ecological Succession of Polymicrobial Communities in the Cystic Fibrosis Airways	33
IS 26 Is Responsible for the Evolution and Transmission of bla NDM -Harboring Plasmids in Escherichia coli of Poult	33
Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics	32
Particulate Metabolites and Transcripts Reflect Diel Oscillations of Microbial Activity in the Surface Ocean	32
COVID-19 Pandemic in Lebanon: One Year Later, What Have We Learnt?	32
The Gut Microbiome in Autism: Study-Site Effects and Longitudinal Analysis of Behavior Change	32
High Transcriptional Activity and Diverse Functional Repertoires of Hundreds of Giant Viruses in a Coastal Marine System	32

Sepsis-Induced Gut Dysbiosis Mediates the Susceptibility to Sepsis-Associated Encephalopathy in Mice	32
Maternal Emulsifier P80 Intake Induces Gut Dysbiosis in Offspring and Increases Their Susceptibility to Colitis in Adulthood	32
Lactobacillus acidophilus LA14 Alleviates Liver Injury	32
The Sorghum bicolor Root Exudate Sorgoleone Shapes Bacterial Communities and Delays Network Formation	31
Fungal Communities Are Important Determinants of Bacterial Community Composition in Deadwood	31
Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities	31
AMiGA: Software for Automated Analysis of Microbial Growth Assays	31
Genomic Features Associated with the Degree of Phenotypic Resistance to Carbapenems in Carbapenem-Resistant Klebsiella pneumoniae	31
Intermittent Hypoxia and Hypercapnia Alter Diurnal Rhythms of Luminal Gut Microbiome and Metabolome	31
Genomic Epidemiology and Characterization of Methicillin-Resistant Staphylococcus aureus from Bloodstream Infections in China	30
Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens	30
Genome-Scale Metabolic Models and Machine Learning Reveal Genetic Determinants of Antibiotic Resistance in Escherichia coli and Unravel the Underlying Metabolic Adaptation Mechanisms	30
Genomes of the “ Candidatus Actinomarinales” Order: Highly Streamlined Marine Epipelagic Actinobacteria	30
Marine Community Metabolomes Carry Fingerprints of Phytoplankton Community Composition	30
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	30
Weaning Age and Its Effect on the Development of the Swine Gut Microbiome and Resistome	29
Elucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel Relationships	29
Race, the Vaginal Microbiome, and Spontaneous Preterm Birth	29
Assessing Multiplex Tiling PCR Sequencing Approaches for Detecting Genomic Variants of SARS-CoV-2 in Municipal Wastewater	29
Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities	29
Direct Nanopore Sequencing of mRNA Reveals Landscape of Transcript Isoforms in Apicomplexan Parasites	28
Novel Viral Communities Potentially Assisting in Carbon, Nitrogen, and Sulfur Metabolism in the Upper Slope Sediments of Mariana Trench	28
Gut Dysbiosis and Its Associations with Gut Microbiota-Derived Metabolites in Dogs with Myxomatous Mitral Valve Disease	28
A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog	27
Limited and Strain-Specific Transcriptional and Growth Responses to Acquisition of a Multidrug Resistance Plasmid in Genetically Diverse Escherichia coli Lineages	27
Patterns and Drivers of nirK -Type and nirS -Type Denitrifier Community Assembly along an Elevation Gradient	27
Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria	26
Endophytic Lifestyle of Global Clones of Extended-Spectrum β-Lactamase-Producing Priority Pathogens in Fresh Vegetables: a Trojan Horse Strategy Favoring Human Colonization?	26
BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities	26
Extended Plant Metarhizobiome: Understanding Volatile Organic Compound Signaling in Plant-Microbe Metapopulation Networks	26
Dynamic Bayesian Networks for Integrating Multi-omics Time Series Microbiome Data	26
Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis	26
Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method	26
Urban Wildlife Crisis: Australian Silver Gull Is a Bystander Host to Widespread Clinical Antibiotic Resistance	26
Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil	26
Comparative Analysis of Core Microbiome Assignments: Implications for Ecological Synthesis	25
Serine Metabolism Tunes Immune Responses To Promote Oreochromis niloticus Survival upon Edwardsiella tarda Infection	25
MetaPhage: an Automated Pipeline for Analyzing, Annotating, and Classifying Bacteriophages in Metagenomics Sequencing Data	25
Phylogenomic Analyses of Snodgrassella Isolates from Honeybees and Bumblebees Reveal Taxonomic and Functional Diversity	25
Higher Trimethylamine- N -Oxide Plasma Levels with Increasing Age Are Mediated by Diet and Trimethylamine-Forming Bacteria	25
Deciphering Active Prophages from Metagenomes	25
Identification and Quantification of Bovine Digital Dermatitis-Associated Microbiota across Lesion Stages in Feedlot Beef Cattle	25
Candida Administration Worsens Uremia-Induced Gut Leakage in Bilateral Nephrectomy Mice, an Impact of Gut Fungi and Organismal Molecules in Uremia	25
Molting Alters the Microbiome, Immune Response, and Digestive Enzyme Activity in Mud Crab ( Scylla paramamosain )	25
Inactivation of Nitrite-Dependent Nitric Oxide Biosynthesis Is Responsible for Overlapped Antibiotic Resistance between Naturally and Artificially Evolved Pseudomonas aeruginosa	25
Multi-omics Analysis Revealed Coordinated Responses of Rumen Microbiome and Epithelium to High-Grain-Induced Subacute Rumen Acidosis in Lactating Dairy Cows	25
Comparative Genomics Reveals Thermal Adaptation and a High Metabolic Diversity in “ Candidatus Bathyarchaeia”	24
Free-Living, Psychrotrophic Bacteria of the Genus Psychrobacter Are Descendants of Pathobionts	24
Associations of Genetic Variants Contributing to Gut Microbiota Composition in Immunoglobin A Nephropathy	24
Short-Chain Fatty Acids Reduced Renal Calcium Oxalate Stones by Regulating the Expression of Intestinal Oxalate Transporter SLC26A6	24
Rapid Response of Nitrogen Cycling Gene Transcription to Labile Carbon Amendments in a Soil Microbial Community	24
Struggle To Survive: the Choir of Target Alteration, Hydrolyzing Enzyme, and Plasmid Expression as a Novel Aztreonam-Avibactam Resistance Mechanism	24
A Multiphase Multiobjective Dynamic Genome-Scale Model Shows Different Redox Balancing among Yeast Species of the Saccharomyces Genus in Fermentation	24
Phenotypic and Genomic Comparison of the Two Most Common ExoU-Positive Pseudomonas aeruginosa Clones, PA14 and ST235	24
A Novel Synbiotic Alleviates Autoimmune Hepatitis by Modulating the Gut Microbiota-Liver Axis and Inhibiting the Hepatic TLR4/NF-κB/NLRP3 Signaling Pathway	24
A Reproducible and Tunable Synthetic Soil Microbial Community Provides New Insights into Microbial Ecology	24
Syntrophic Acetate-Oxidizing Microbial Consortia Enriched from Full-Scale Mesophilic Food Waste Anaerobic Digesters Showing High Biodiversity and Functional Redundancy	24
Baseline Gut Metagenomic Functional Gene Signature Associated with Variable Weight Loss Responses following a Healthy Lifestyle Intervention in Humans	23
Species-Level Resolution of Female Bladder Microbiota from 16S rRNA Amplicon Sequencing	23
Elucidating the Beta-Diversity of the Microbiome: from Global Alignment to Local Alignment	23
Common Presence of Phototrophic Gemmatimonadota in Temperate Freshwater Lakes	23
One-Cell Metabolic Phenotyping and Sequencing of Soil Microbiome by Raman-Activated Gravity-Driven Encapsulation (RAGE)	23
Bacterial Microcompartments Coupled with Extracellular Electron Transfer Drive the Anaerobic Utilization of Ethanolamine in Listeria monocytogenes	23
Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort	23
Identification and Characterization of Major Bile Acid 7α-Dehydroxylating Bacteria in the Human Gut	22
Evolutionary Trajectory of the Tet(X) Family: Critical Residue Changes towards High-Level Tigecycline Resistance	22
Host Traits and Phylogeny Contribute to Shaping Coral-Bacterial Symbioses	22
Acinetobacter baumannii Targets Human Carcinoembryonic Antigen-Related Cell Adhesion Molecules (CEACAMs) for Invasion of Pneumocytes	22
Limited Evidence for Microbial Transmission in the Phylosymbiosis between Hawaiian Spiders and Their Microbiota	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
National Prevalence of Salmonella enterica Serotype Kentucky ST198 with High-Level Resistance to Ciprofloxacin and Extended-Spectrum Cephalosporins in China, 2013 to 2017	22
Metagenomic Sequencing of Multiple Soil Horizons and Sites in Close Vicinity Revealed Novel Secondary Metabolite Diversity	22
Metabolic Features of Ganjang (a Korean Traditional Soy Sauce) Fermentation Revealed by Genome-Centered Metatranscriptomics	22
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	22
Comparative Genomics of Exiguobacterium Reveals What Makes a Cosmopolitan Bacterium	21
Whole-Genome Sequencing and Machine Learning Analysis of Staphylococcus aureus from Multiple Heterogeneous Sources in China Reveals Common Genetic Traits of Antimicrobial Resistance	21
Mining of Thousands of Prokaryotic Genomes Reveals High Abundance of Prophages with a Strictly Narrow Host Range	21
Integrated Multi-omics Investigations Reveal the Key Role of Synergistic Microbial Networks in Removing Plasticizer Di-(2-Ethylhexyl) Phthalate from Estuarine Sediments	21
DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid	21
Engineering High-Yield Biopolymer Secretion Creates an Extracellular Protein Matrix for Living Materials	21

Computational Analysis of Microbial Flow Cytometry Data	21
Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure	21
Enhancing Microbiome Research through Genome-Scale Metabolic Modeling	21
Discrimination of Bacterial Community Structures among Healthy, Gingivitis, and Periodontitis Statuses through Integrated Metatranscriptomic and Network Analyses	21
A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation	21
Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn's Disease	21
Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut	21
Global Distribution of mcr Gene Variants in 214K Metagenomic Samples	21
Transcription Inhibitors with XRE DNA-Binding and Cupin Signal-Sensing Domains Drive Metabolic Diversification in Pseudomonas	20
Microbiome Aggregated Traits and Assembly Are More Sensitive to Soil Management than Diversity	20
Refined Quantification of Infection Bottlenecks and Pathogen Dissemination with STAMPR	20
Role of VapBC12 Toxin-Antitoxin Locus in Cholesterol-Induced Mycobacterial Persistence	20
Long-Read Metagenome-Assembled Genomes Improve Identification of Novel Complete Biosynthetic Gene Clusters in a Complex Microbial Activated Sludge Ecosystem	20
Nitric Oxide Impacts Human Gut Microbiota Diversity and Functionalities	20
Cofactor Specificity of Glucose-6-Phosphate Dehydrogenase Isozymes in Pseudomonas putida Reveals a General Principle Underlying Glycolytic Strategies in Bacteria	20
A Novel Virus of Flaviviridae Associated with Sexual Precocity in Macrobrachium rosenbergii	20
Metagenomics and Quantitative Stable Isotope Probing Offer Insights into Metabolism of Polycyclic Aromatic Hydrocarbon Degraders in Chronically Polluted Seawater	20
Diverse Viruses in Deep-Sea Hydrothermal Vent Fluids Have Restricted Dispersal across Ocean Basins	20
Composition, Succession, and Source Tracking of Microbial Communities throughout the Traditional Production of a Farmstead Cheese	20
Host Immunity Alters Community Ecology and Stability of the Microbiome in a Caenorhabditis elegans Model	20
Children with Autism and Their Typically Developing Siblings Differ in Amplicon Sequence Variants and Predicted Functions of Stool-Associated Microbes	20
Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis	20
Cultivating the Bacterial Microbiota of Populus Roots	20
F Plasmid Lineages in Escherichia coli ST95: Implications for Host Range, Antibiotic Resistance, and Zoonoses	20
Compositional and Metabolic Responses of Autotrophic Microbial Community to Salinity in Lacustrine Environments	20
Cross-Scale Analyses of Animal and Human Gut Microbiome Assemblies from Metacommunity to Global Landscape	19
Microbial Functional Diversity Correlates with Species Diversity along a Temperature Gradient	19
High-Content Imaging to Phenotype Antimicrobial Effects on Individual Bacteria at Scale	19
Global Transcriptional Regulators Fine-Tune the Translational and Metabolic Efficiency for Optimal Growth of Escherichia coli	19
Quantifying Live Microbial Load in Human Saliva Samples over Time Reveals Stable Composition and Dynamic Load	19
Long-Term Bacterial and Fungal Dynamics following Oral Lyophilized Fecal Microbiota Transplantation in Clostridioides difficile Infection	19
Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities	19
Phage Diversity in the Human Gut Microbiome: a Taxonomist’s Perspective	19
Harnessing Machine Learning To Unravel Protein Degradation in Escherichia coli	19
The LysR-Type Transcriptional Regulator BsrA (PA2121) Controls Vital Metabolic Pathways in Pseudomonas aeruginosa	19
Host Factors Associated with Gut Mycobiome Structure	19
Role of the Gut Microbiota in the Increased Infant Body Mass Index Induced by Gestational Diabetes Mellitus	18
A High-Throughput Method for Screening for Genes Controlling Bacterial Conjugation of Antibiotic Resistance	18
Fungal Interactions Strengthen the Diversity-Functioning Relationship of Solid-State Fermentation Systems	18
Patient and Microbial Genomic Factors Associated with Carbapenem-Resistant Klebsiella pneumoniae Extraintestinal Colonization and Infection	18
Production and Excretion of Polyamines To Tolerate High Ammonia, a Case Study on Soil Ammonia-Oxidizing Archaeon “ Candidatus Nitrosocosmicus agrestis”	18
Presence of Bromotyrosine Alkaloids in Marine Sponges Is Independent of Metabolomic and Microbiome Architectures	18
Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale	18
Case-Control Microbiome Study of Chronic Otitis Media with Effusion in Children Points at Streptococcus salivarius as a Pathobiont-Inhibiting Species	18
Long-Read-Resolved, Ecosystem-Wide Exploration of Nucleotide and Structural Microdiversity of Lake Bacterioplankton Genomes	18
Network Properties of Local Fungal Communities Reveal the Anthropogenic Disturbance Consequences of Farming Practices in Vineyard Soils	18
Computational Model To Quantify the Growth of Antibiotic-Resistant Bacteria in Wastewater	18
A Peek into the Plasmidome of Global Sewage	18
Cobamide Sharing Is Predicted in the Human Skin Microbiome	18
Elucidating the Diversity and Potential Function of Nonribosomal Peptide and Polyketide Biosynthetic Gene Clusters in the Root Microbiome	18
Alterations in Gut Microbiome Composition and Function in Irritable Bowel Syndrome and Increased Probiotic Abundance with Daily Supplementation	18
Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models	18
Gut-Expressed Vitellogenin Facilitates the Movement of a Plant Virus across the Midgut Wall in Its Insect Vector	18
Inhibition of Antiviral Innate Immunity by Avibirnavirus VP3 via Blocking TBK1-TRAF3 Complex Formation and IRF3 Activation	18
Metagenomic Sequencing Reveals that High-Grain Feeding Alters the Composition and Metabolism of Cecal Microbiota and Induces Cecal Mucosal Injury in Sheep	18
Gut Microbiome Alterations Associated with Diabetes in Mexican Americans in South Texas	18
Gut Microbiome Structure and Association with Host Factors in a Korean Population	18
Characterization of the Plasmidome Encoding Carbapenemase and Mechanisms for Dissemination of Carbapenem-ResistantEnterobacteriaceae	17
Accessory Genomic Epidemiology of Cocirculating Acinetobacter baumannii Clones	17
The Split Personality of Beauveria bassiana: Understanding the Molecular Basis of Fungal Parasitism and Mutualism	17
Gut Microbial Stability is Associated with Greater Endurance Performance in Athletes Undertaking Dietary Periodization	17
The Proportion of Soil-Borne Fungal Pathogens Increases with Elevated Organic Carbon in Agricultural Soils	17
Disentangling the Ecological Processes Shaping the Latitudinal Pattern of Phytoplankton Communities in the Pacific Ocean	17
Bacteria and Archaea Synergistically Convert Glycine Betaine to Biogenic Methane in the Formosa Cold Seep of the South China Sea	17
Comprehensive Large-Scale Integrative Analysis of Omics Data To Accelerate Specialized Metabolite Discovery	17
Lineage-Specific Growth Curves Document Large Differences in Response of Individual Groups of Marine Bacteria to the Top-Down and Bottom-Up Controls	17
BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes	17
Catching SARS-CoV-2 by Sequence Hybridization: a Comparative Analysis	17
A Polysaccharide Biosynthesis Locus in Vibrio parahaemolyticus Important for Biofilm Formation Has Homologs Widely Distributed in Aquatic Bacteria Mainly from Gammaproteobacteria	17
Novel Drivers of Virulence in Clostridioides difficile Identified via Context-Specific Metabolic Network Analysis	17
Aridity Threshold Induces Abrupt Change of Soil Abundant and Rare Bacterial Biogeography in Dryland Ecosystems	17
Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce	17
Metabolic Interactions between Brachypodium and Pseudomonas fluorescens under Controlled Iron-Limited Conditions	17
Evolution of Interbacterial Antagonism in Bee Gut Microbiota Reflects Host and Symbiont Diversification	17
Charting the Lipopeptidome of Nonpathogenic Pseudomonas	17
Revealing the Characteristics of Glucose- and Lactate-Based Chain Elongation for Caproate Production by Caproicibacterium lactatifermentans through Transcriptomic, Bioen	17
Interkingdom Gut Microbiome and Resistome of the Cockroach Blattella germanica	17
The Extracellular Milieu of Toxoplasma 's Lytic Cycle Drives Lab Adaptation, Primarily by Transcriptional Reprogramming	17
Metabolic Diversity and Aero-Tolerance in Anammox Bacteria from Geochemically Distinct Aquifers	17
Precise Species Identification for Acinetobacter: a Genome-Based Study with Description of Two Novel Acinetobacter Species	17
Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level	16
Expanding Culturomics from Gut to Extreme Environmental Settings	16
Comparative Genomics Unveils the Habitat Adaptation and Metabolic Profiles of Clostridium in an Artificial Ecosystem for Liquor Production	16
Identification of c-di-GMP/FleQ-Regulated New Target Genes, Including cyaA , Encoding Adenylate Cyclase, in Pseudomonas putida	16
Microbiome Restructuring: Dominant Coral Bacterium Endozoicomonas Species Respond Differentially to Environmental Changes	16
Infant Skin Bacterial Communities Vary by Skin Site and Infant Age across Populations in Mexico and the United States	16
Symbiotic Bacterium-Derived Organic Acids Protect Delia antiqua Larvae from Entomopathogenic Fungal Infection	16
Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes	16
Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved Metatranscriptomics	16
Long-Read Metagenomics Improves the Recovery of Viral Diversity from Complex Natural Marine Samples	16
Agricultural Management Affects the Active Rhizosphere Bacterial Community Composition and Nitrification	16
Plant Disease Sensing: Studying Plant-Pathogen Interactions at Scale	16
Trehalose Phosphate Synthase Complex-Mediated Regulation of Trehalose 6-Phosphate Homeostasis Is Critical for Development and Pathogenesis in Magnaporthe oryzae	16
Identification and Development of Therapeutics for COVID-19	16
Cervicovaginal DNA Virome Alterations Are Associated with Genital Inflammation and Microbiota Composition	16