| # | Title | Journal | Year | Citations |
|---|
| 1 | OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units | MSphere | 2017 | 365 |
| 2 | Antibiotic-Induced Alterations of the Gut Microbiota Alter Secondary Bile Acid Production and Allow for Clostridium difficile Spore Germination and Outgrowth in the Large Intestine | MSphere | 2016 | 349 |
| 3 | Effectiveness of Face Masks in Preventing Airborne Transmission of SARS-CoV-2 | MSphere | 2020 | 293 |
| 4 | Extreme Dysbiosis of the Microbiome in Critical Illness | MSphere | 2016 | 283 |
| 5 | The Case for Adopting the “Species Complex” Nomenclature for the Etiologic Agents of Cryptococcosis | MSphere | 2017 | 274 |
| 6 | Increasing Temperature and Relative Humidity Accelerates Inactivation of SARS-CoV-2 on Surfaces | MSphere | 2020 | 265 |
| 7 | Comparative Pathogenicity of United Kingdom Isolates of the Emerging Pathogen Candida auris and Other Key Pathogenic Candida Species | MSphere | 2016 | 242 |
| 8 | Metagenomic Evidence for the Presence of Comammox Nitrospira -Like Bacteria in a Drinking Water System | MSphere | 2016 | 229 |
| 9 | Molecular Epidemiology of Colonizing and Infecting Isolates of Klebsiella pneumoniae | MSphere | 2016 | 204 |
| 10 | Rampant C→U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses: Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories | MSphere | 2020 | 204 |
| 11 | SCC mec Finder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence Data | MSphere | 2018 | 197 |
| 12 | IS 26 -Mediated Formation of Transposons Carrying Antibiotic Resistance Genes | MSphere | 2016 | 194 |
| 13 | A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection | MSphere | 2018 | 187 |
| 14 | Escherichia coli Sequence Type 410 Is Causing New International High-Risk Clones | MSphere | 2018 | 183 |
| 15 | Infant Gut Microbiota Development Is Driven by Transition to Family Foods Independent of Maternal Obesity | MSphere | 2016 | 175 |
| 16 | Candida albicans Gene Deletion with a Transient CRISPR-Cas9 System | MSphere | 2016 | 174 |
| 17 | Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi | MSphere | 2018 | 173 |
| 18 | Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units | MSphere | 2018 | 168 |
| 19 | Persistence of Supplemented Bifidobacterium longum subsp. infantis EVC001 in Breastfed Infants | MSphere | 2017 | 158 |
| 20 | A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses | MSphere | 2016 | 151 |
| 21 | Transcriptome Assembly and Profiling of Candida auris Reveals Novel Insights into Biofilm-Mediated Resistance | MSphere | 2018 | 151 |
| 22 | The Gut Microbiota of Healthy Aged Chinese Is Similar to That of the Healthy Young | MSphere | 2017 | 141 |
| 23 | Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing | MSphere | 2021 | 140 |
| 24 | Whole-Genome Sequencing of Human Clinical Klebsiella pneumoniae Isolates Reveals Misidentification and Misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae | MSphere | 2017 | 139 |
| 25 | Oral Administration of Porphyromonas gingivalis Alters the Gut Microbiome and Serum Metabolome | MSphere | 2018 | 134 |
| 26 | A Simple and Universal System for Gene Manipulation in Aspergillus fumigatus: In Vitro -Assembled Cas9-Guide RNA Ribonucleoproteins Coupled with Microhomology Repair Templates | MSphere | 2017 | 130 |
| 27 | The Mucosal Vaccine Adjuvant LT(R192G/L211A) or dmLT | MSphere | 2018 | 127 |
| 28 | Efficacy of T-705 (Favipiravir) in the Treatment of Infections with Lethal Severe Fever with Thrombocytopenia Syndrome Virus | MSphere | 2016 | 124 |
| 29 | Importance of Resolving Fungal Nomenclature: the Case of Multiple Pathogenic Species in the Cryptococcus Genus | MSphere | 2017 | 124 |
| 30 | COVID-19: Knowns, Unknowns, and Questions | MSphere | 2020 | 124 |
| 31 | Metabolic and Community Synergy of Oral Bacteria in Colorectal Cancer | MSphere | 2016 | 123 |
| 32 | Global Assessment of the Activity of Tigecycline against Multidrug-Resistant Gram-Negative Pathogens between 2004 and 2014 as Part of the Tigecycline Evaluation and Surveillance Trial | MSphere | 2017 | 116 |
| 33 | Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean | MSphere | 2017 | 114 |
| 34 | Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides | MSphere | 2016 | 109 |
| 35 | Characterization of Aspergillus fumigatus Isolates from Air and Surfaces of the International Space Station | MSphere | 2016 | 108 |
| 36 | The Microbiome and Metabolome of Preterm Infant Stool Are Personalized and Not Driven by Health Outcomes, Including Necrotizing Enterocolitis and Late-Onset Sepsis | MSphere | 2018 | 107 |
| 37 | Elevated Fecal pH Indicates a Profound Change in the Breastfed Infant Gut Microbiome Due to Reduction of Bifidobacterium over the Past Century | MSphere | 2018 | 106 |
| 38 | Food Starch Structure Impacts Gut Microbiome Composition | MSphere | 2018 | 106 |
| 39 | pH-Mediated Microbial and Metabolic Interactions in Fecal Enrichment Cultures | MSphere | 2017 | 105 |
| 40 | The Gut Commensal Microbiome of Drosophila melanogaster Is Modified by the Endosymbiont Wolbachia | MSphere | 2017 | 105 |
| 41 | Rescue of the 1947 Zika Virus Prototype Strain with a Cytomegalovirus Promoter-Driven cDNA Clone | MSphere | 2016 | 104 |
| 42 | Use of RNA-Protein Complexes for Genome Editing in Non- albicans Candida Species | MSphere | 2017 | 100 |
| 43 | COVID-19 Hyperinflammation: What about Neutrophils? | MSphere | 2020 | 99 |
| 44 | Separate F-Type Plasmids Have Shaped the Evolution of the H 30 Subclone of Escherichia coli Sequence Type 131 | MSphere | 2016 | 98 |
| 45 | CRISPR-Cas and Restriction-Modification Act Additively against Conjugative Antibiotic Resistance Plasmid Transfer in Enterococcus faecalis | MSphere | 2016 | 95 |
| 46 | Potential Roles of Fungal Extracellular Vesicles during Infection | MSphere | 2016 | 95 |
| 47 | Daily Vaginal Microbiota Fluctuations Associated with Natural Hormonal Cycle, Contraceptives, Diet, and Exercise | MSphere | 2020 | 95 |
| 48 | Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis | MSphere | 2016 | 94 |
| 49 | High-Fat Diet Changes Fungal Microbiomes and Interkingdom Relationships in the Murine Gut | MSphere | 2017 | 94 |
| 50 | Aedes aegypti Piwi4 Is a Noncanonical PIWI Protein Involved in Antiviral Responses | MSphere | 2017 | 92 |
