| # | Title | Journal | Year | Citations |
|---|
|
| 1 | Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys | MSystems | 2016 | 1,461 |
| 2 | Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns | MSystems | 2017 | 1,441 |
| 3 | SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases | MSystems | 2020 | 699 |
| 4 | American Gut: an Open Platform for Citizen Science Microbiome Research | MSystems | 2018 | 632 |
| 5 | Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research | MSystems | 2017 | 596 |
| 6 | Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes | MSystems | 2016 | 407 |
| 7 | Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information | MSystems | 2018 | 407 |
| 8 | Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies | MSystems | 2016 | 392 |
| 9 | 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 | 372 |
| 10 | Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre | MSystems | 2016 | 360 |
| 11 | Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling | MSystems | 2017 | 355 |
| 12 | Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data | MSystems | 2017 | 350 |
| 13 | A Novel Sparse Compositional Technique Reveals Microbial Perturbations | MSystems | 2019 | 332 |
| 14 | Evaluating the Information Content of Shallow Shotgun Metagenomics | MSystems | 2018 | 327 |
| 15 | 2019 Novel Coronavirus (COVID-19) Pandemic: Built Environment Considerations To Reduce Transmission | MSystems | 2020 | 320 |
| 16 | Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes | MSystems | 2018 | 296 |
| 17 | Balance Trees Reveal Microbial Niche Differentiation | MSystems | 2017 | 294 |
| 18 | Salinity Is a Key Determinant for Soil Microbial Communities in a Desert Ecosystem | MSystems | 2019 | 263 |
| 19 | Meta-analysis To Define a Core Microbiota in the Swine Gut | MSystems | 2017 | 260 |
| 20 | Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults | MSystems | 2019 | 237 |
| 21 | q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data | MSystems | 2018 | 228 |
| 22 | Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction | MSystems | 2018 | 226 |
| 23 | Total Lipopolysaccharide from the Human Gut Microbiome Silences Toll-Like Receptor Signaling | MSystems | 2017 | 217 |
| 24 | Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir | MSystems | 2016 | 213 |
| 25 | Balances: a New Perspective for Microbiome Analysis | MSystems | 2018 | 212 |
| 26 | Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing | MSystems | 2018 | 211 |
| 27 | phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes | MSystems | 2020 | 211 |
| 28 | SARS-CoV-2 and ORF3a: Nonsynonymous Mutations, Functional Domains, and Viral Pathogenesis | MSystems | 2020 | 210 |
| 29 | Depletion of Blautia Species in the Microbiota of Obese Children Relates to Intestinal Inflammation and Metabolic Phenotype Worsening | MSystems | 2020 | 209 |
| 30 | Gut Microbiota and Metabolome Alterations Associated with Parkinson’s Disease | MSystems | 2020 | 186 |
| 31 | Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments | MSystems | 2019 | 179 |
| 32 | MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses | MSystems | 2016 | 178 |
| 33 | Insights into Butyrate Production in a Controlled Fermentation System via Gene Predictions | MSystems | 2017 | 178 |
| 34 | Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity | MSystems | 2018 | 176 |
| 35 | Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation | MSystems | 2016 | 173 |
| 36 | Probiotic Bifidobacterium lactis V9 Regulates the Secretion of Sex Hormones in Polycystic Ovary Syndrome Patients through the Gut-Brain Axis | MSystems | 2019 | 172 |
| 37 | Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition | MSystems | 2016 | 163 |
| 38 | Significant Impacts of Increasing Aridity on the Arid Soil Microbiome | MSystems | 2017 | 162 |
| 39 | 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 | 160 |
| 40 | Open-Source Sequence Clustering Methods Improve the State Of the Art | MSystems | 2016 | 159 |
| 41 | Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota | MSystems | 2017 | 159 |
| 42 | Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries | MSystems | 2020 | 151 |
| 43 | MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota | MSystems | 2020 | 147 |
| 44 | Core Microbiota in Agricultural Soils and Their Potential Associations with Nutrient Cycling | MSystems | 2019 | 146 |
| 45 | Development of the Human Mycobiome over the First Month of Life and across Body Sites | MSystems | 2018 | 141 |
| 46 | Quantifying and Understanding Well-to-Well Contamination in Microbiome Research | MSystems | 2019 | 138 |
| 47 | Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities | MSystems | 2019 | 133 |
| 48 | Clostridium difficile Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut Microbiomes | MSystems | 2017 | 131 |
| 49 | Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass | MSystems | 2019 | 130 |
| 50 | Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life? | MSystems | 2018 | 128 |
