| 1 | Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys | MSystems | 2016 | 1,861 |
| 2 | Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns | MSystems | 2017 | 1,727 |
| 3 | American Gut: an Open Platform for Citizen Science Microbiome Research | MSystems | 2018 | 780 |
| 4 | SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases | MSystems | 2020 | 764 |
| 5 | Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research | MSystems | 2017 | 691 |
| 6 | New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract | MSystems | 2018 | 501 |
| 7 | Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information | MSystems | 2018 | 483 |
| 8 | Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes | MSystems | 2016 | 474 |
| 9 | A Novel Sparse Compositional Technique Reveals Microbial Perturbations | MSystems | 2019 | 455 |
| 10 | Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies | MSystems | 2016 | 450 |
| 11 | Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data | MSystems | 2017 | 426 |
| 12 | Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre | MSystems | 2016 | 425 |
| 13 | Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling | MSystems | 2017 | 412 |
| 14 | Evaluating the Information Content of Shallow Shotgun Metagenomics | MSystems | 2018 | 407 |
| 15 | Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes | MSystems | 2018 | 372 |
| 16 | Salinity Is a Key Determinant for Soil Microbial Communities in a Desert Ecosystem | MSystems | 2019 | 362 |
| 17 | 2019 Novel Coronavirus (COVID-19) Pandemic: Built Environment Considerations To Reduce Transmission | MSystems | 2020 | 352 |
| 18 | Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults | MSystems | 2019 | 318 |
| 19 | Meta-analysis To Define a Core Microbiota in the Swine Gut | MSystems | 2017 | 314 |
| 20 | Balance Trees Reveal Microbial Niche Differentiation | MSystems | 2017 | 308 |
| 21 | q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data | MSystems | 2018 | 287 |
| 22 | phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes | MSystems | 2020 | 287 |
| 23 | Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction | MSystems | 2018 | 282 |
| 24 | Depletion of
Blautia
Species in the Microbiota of Obese Children Relates to Intestinal Inflammation and Metabolic Phenotype Worsening | MSystems | 2020 | 278 |
| 25 | Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing | MSystems | 2018 | 262 |
| 26 | Gut Microbiota and Metabolome Alterations Associated with Parkinson’s Disease | MSystems | 2020 | 258 |
| 27 | Total Lipopolysaccharide from the Human Gut Microbiome Silences Toll-Like Receptor Signaling | MSystems | 2017 | 257 |
| 28 | Balances: a New Perspective for Microbiome Analysis | MSystems | 2018 | 249 |
| 29 | Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir | MSystems | 2016 | 242 |
| 30 | Probiotic
Bifidobacterium lactis
V9 Regulates the Secretion of Sex Hormones in Polycystic Ovary Syndrome Patients through the Gut-Brain Axis | MSystems | 2019 | 240 |
| 31 | Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments | MSystems | 2019 | 233 |
| 32 | Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity | MSystems | 2018 | 229 |
| 33 | MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota | MSystems | 2020 | 228 |
| 34 | Core Microbiota in Agricultural Soils and Their Potential Associations with Nutrient Cycling | MSystems | 2019 | 220 |
| 35 | Insights into Butyrate Production in a Controlled Fermentation System via Gene Predictions | MSystems | 2017 | 218 |
| 36 | SARS-CoV-2 and ORF3a: Nonsynonymous Mutations, Functional Domains, and Viral Pathogenesis | MSystems | 2020 | 216 |
| 37 | MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses | MSystems | 2016 | 215 |
| 38 | Linking Bacterial-Fungal Relationships to Microbial Diversity and Soil Nutrient Cycling | MSystems | 2021 | 204 |
| 39 | Significant Impacts of Increasing Aridity on the Arid Soil Microbiome | MSystems | 2017 | 201 |
| 40 | Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition | MSystems | 2016 | 200 |
| 41 | Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes | MSystems | 2020 | 195 |
| 42 | A Prospective Metagenomic and Metabolomic Analysis of the Impact of Exercise and/or Whey Protein Supplementation on the Gut Microbiome of Sedentary Adults | MSystems | 2018 | 193 |
| 43 | Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries | MSystems | 2020 | 193 |
| 44 | Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota | MSystems | 2017 | 185 |
| 45 | Soil Carbon, Nitrogen, and Phosphorus Cycling Microbial Populations and Their Resistance to Global Change Depend on Soil C:N:P Stoichiometry | MSystems | 2020 | 184 |
| 46 | Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation | MSystems | 2016 | 183 |
| 47 | Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities | MSystems | 2019 | 180 |
| 48 | Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India | MSystems | 2019 | 174 |
| 49 | Open-Source Sequence Clustering Methods Improve the State Of the Art | MSystems | 2016 | 172 |
| 50 | Genome-Resolved Metagenomics Reveals Distinct Phosphorus Acquisition Strategies between Soil Microbiomes | MSystems | 2022 | 169 |
