| # | Title | Journal | Year | Citations |
|---|
| 1 | Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities | Applied and Environmental Microbiology | 2009 | 18,390 |
| 2 | Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform | Applied and Environmental Microbiology | 2013 | 5,923 |
| 3 | Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition) | Autophagy | 2016 | 4,701 |
| 4 | Guidelines for the use and interpretation of assays for monitoring autophagy | Autophagy | 2012 | 3,122 |
| 5 | Drug delivery strategy utilizing conjugation via reversible disulfide linkages: role and site of cellular reducing activities | Advanced Drug Delivery Reviews | 2003 | 1,270 |
| 6 | Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella | Cell Metabolism | 2015 | 1,190 |
| 7 | Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome | PLoS Computational Biology | 2012 | 939 |
| 8 | Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection | Nature Communications | 2014 | 817 |
| 9 | Dynamics and associations of microbial community types across the human body | Nature | 2014 | 723 |
| 10 | Enteric bacteria promote human and mouse norovirus infection of B cells | Science | 2014 | 689 |
| 11 | Campylobacter jejuni: molecular biology and pathogenesis | Nature Reviews Microbiology | 2007 | 662 |
| 12 | Comparison of the Respiratory Microbiome in Healthy Nonsmokers and Smokers | American Journal of Respiratory and Critical Care Medicine | 2013 | 655 |
| 13 | The Genetics and Regulation of Heat-Shock Proteins | Annual Review of Genetics | 1984 | 647 |
| 14 | Defining a Healthy Human Gut Microbiome: Current Concepts, Future Directions, and Clinical Applications | Cell Host and Microbe | 2012 | 615 |
| 15 | The Gut Microbiome Modulates Colon Tumorigenesis | MBio | 2013 | 582 |
| 16 | A three-dimensional model to analyze drug-drug interactions | Antiviral Research | 1990 | 543 |
| 17 | IL-12– and IL-23–modulated T cells induce distinct types of EAE based on histology, CNS chemokine profile, and response to cytokine inhibition | Journal of Experimental Medicine | 2008 | 528 |
| 18 | Integration host factor: A protein for all reasons | Cell | 1988 | 523 |
| 19 | Ribosomes as sensors of heat and cold shock in Escherichia coli. | Proceedings of the National Academy of Sciences of the United States of America | 1990 | 523 |
| 20 | Reproducible Community Dynamics of the Gastrointestinal Microbiota following Antibiotic Perturbation | Infection and Immunity | 2009 | 489 |
| 21 | MicroRNA-132–mediated loss of p120RasGAP activates the endothelium to facilitate pathological angiogenesis | Nature Medicine | 2010 | 477 |
| 22 | Bacteroides in the Infant Gut Consume Milk Oligosaccharides via Mucus-Utilization Pathways | Cell Host and Microbe | 2011 | 474 |
| 23 | The Human Gut Microbiome as a Screening Tool for Colorectal Cancer | Cancer Prevention Research | 2014 | 463 |
| 24 | Diversity of Bacterial Populations on the Tongue Dorsa of Patients with Halitosis and Healthy Patients | Journal of Clinical Microbiology | 2003 | 454 |
| 25 | Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome | MBio | 2016 | 430 |
| 26 | Periodontal Disease as a Specific, albeit Chronic, Infection: Diagnosis and Treatment | Clinical Microbiology Reviews | 2001 | 383 |
| 27 | Detection of prokaryotic mRNA signifies microbial viability and promotes immunity | Nature | 2011 | 378 |
| 28 | Plasminogen Is a Critical Host Pathogenicity Factor for Group A Streptococcal Infection | Science | 2004 | 365 |
| 29 | Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing | Nature Biotechnology | 2012 | 365 |
| 30 | OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units | MSphere | 2017 | 365 |
| 31 | From Structure to Function: the Ecology of Host-Associated Microbial Communities | Microbiology and Molecular Biology Reviews | 2010 | 339 |
| 32 | Mycobacterial phagosome maturation, rab proteins, and intracellular trafficking | Electrophoresis | 1997 | 320 |
| 33 | The Intermucosal Connection between the Mouth and Gut in Commensal Pathobiont-Driven Colitis | Cell | 2020 | 314 |
| 34 | Mechanisms That Control Bacterial Populations in Continuous-Flow Culture Models of Mouse Large Intestinal Flora | Infection and Immunity | 1983 | 305 |
| 35 | COVID-19 Coronavirus Vaccine Design Using Reverse Vaccinology and Machine Learning | Frontiers in Immunology | 2020 | 301 |
| 36 | Proteinaceous Bacterial Adhesins and Their Receptors | CRC Critical Reviews in Microbiology | 1982 | 293 |
| 37 | Survival and Implantation of Escherichia coli in the Intestinal Tract | Infection and Immunity | 1983 | 289 |
| 38 | Engineering and Characterization of Functional Human Microvessels in Immunodeficient Mice | Laboratory Investigation | 2001 | 280 |
| 39 | HIV-1 infects multipotent progenitor cells causing cell death and establishing latent cellular reservoirs | Nature Medicine | 2010 | 279 |
| 40 | Identifying control mechanisms of granuloma formation during M. tuberculosis infection using an agent-based model | Journal of Theoretical Biology | 2004 | 275 |
| 41 | Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions | Genome Medicine | 2016 | 272 |
| 42 | Gut Microbiota and Colonization Resistance against Bacterial Enteric Infection | Microbiology and Molecular Biology Reviews | 2019 | 272 |
| 43 | Structure of the gut microbiome following colonization with human feces determines colonic tumor burden | Microbiome | 2014 | 268 |
| 44 | Recovery of the Gut Microbiome following Fecal Microbiota Transplantation | MBio | 2014 | 267 |
| 45 | Microbiome Data Distinguish Patients with Clostridium difficile Infection and Non-C. difficile-Associated Diarrhea from Healthy Controls | MBio | 2014 | 263 |
| 46 | Interactions Between the Gastrointestinal Microbiome and Clostridium difficile | Annual Review of Microbiology | 2015 | 256 |
| 47 | Prolonged Severe Acute Respiratory Syndrome Coronavirus 2 Replication in an Immunocompromised Patient | Journal of Infectious Diseases | 2021 | 256 |
| 48 | A Legionella pneumophila gene encoding a species-specific surface protein potentiates initiation of intracellular infection | Infection and Immunity | 1989 | 255 |
| 49 | NLRP6 Protects Il10 Mice from Colitis by Limiting Colonization of Akkermansia muciniphila | Cell Reports | 2017 | 250 |
| 50 | Recasting nonlinear differential equations as S-systems: a canonical nonlinear form | Mathematical Biosciences | 1987 | 248 |
