| # | Title | Journal | Year | Citations |
|---|
| 1 | Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy | Applied and Environmental Microbiology | 2007 | 17,125 |
| 2 | A communal catalogue reveals Earth’s multiscale microbial diversity | Nature | 2017 | 1,942 |
| 3 | The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists | Journal of Eukaryotic Microbiology | 2005 | 1,476 |
| 4 | Microbial seed banks: the ecological and evolutionary implications of dormancy | Nature Reviews Microbiology | 2011 | 1,365 |
| 5 | Extracellular electron transfer mechanisms between microorganisms and minerals | Nature Reviews Microbiology | 2016 | 1,224 |
| 6 | Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation | Nature Reviews Genetics | 2003 | 1,179 |
| 7 | Genome evolution and adaptation in a long-term experiment with Escherichia coli | Nature | 2009 | 1,038 |
| 8 | Decreased Diversity of the Fecal Microbiome in RecurrentClostridium difficile–Associated Diarrhea | Journal of Infectious Diseases | 2008 | 954 |
| 9 | Fe(II)/α-Ketoglutarate-Dependent Hydroxylases and Related Enzymes | Critical Reviews in Biochemistry and Molecular Biology | 2004 | 828 |
| 10 | Lactobacilli Differentially Modulate Expression of Cytokines and Maturation Surface Markers in Murine Dendritic Cells | Journal of Immunology | 2002 | 796 |
| 11 | Deoxynivalenol: mechanisms of action, human exposure, and toxicological relevance | Archives of Toxicology | 2010 | 786 |
| 12 | Historical contingency and the evolution of a key innovation in an experimental population ofEscherichia coli | Proceedings of the National Academy of Sciences of the United States of America | 2008 | 728 |
| 13 | Comparison of the Respiratory Microbiome in Healthy Nonsmokers and Smokers | American Journal of Respiratory and Critical Care Medicine | 2013 | 655 |
| 14 | Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity | MBio | 2014 | 549 |
| 15 | Genome Sequence of Yersinia pestis KIM | Journal of Bacteriology | 2002 | 534 |
| 16 | Genomic analysis of a key innovation in an experimental Escherichia coli population | Nature | 2012 | 527 |
| 17 | Pre-B-cell colony-enhancing factor, whose expression is up-regulated in activated lymphocytes, is a nicotinamide phosphoribosyltransferase, a cytosolic enzyme involved in NAD biosynthesis | European Journal of Immunology | 2002 | 499 |
| 18 | Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population | Science | 2011 | 497 |
| 19 | Reproducible Community Dynamics of the Gastrointestinal Microbiota following Antibiotic Perturbation | Infection and Immunity | 2009 | 489 |
| 20 | Epigenetic Modification and Antibody-Dependent Expansion of Memory-like NK Cells in Human Cytomegalovirus-Infected Individuals | Immunity | 2015 | 469 |
| 21 | Long-Term Dynamics of Adaptation in Asexual Populations | Science | 2013 | 447 |
| 22 | Intravenous Administration of Self-complementary AAV9 Enables Transgene Delivery to Adult Motor Neurons | Molecular Therapy | 2009 | 444 |
| 23 | Ascending Migration of Endophytic Rhizobia, from Roots to Leaves, inside Rice Plants and Assessment of Benefits to Rice Growth Physiology | Applied and Environmental Microbiology | 2005 | 442 |
| 24 | Valid publication of the names of forty-two phyla of prokaryotes | International Journal of Systematic and Evolutionary Microbiology | 2021 | 435 |
| 25 | Incompatible and sterile insect techniques combined eliminate mosquitoes | Nature | 2019 | 430 |
| 26 | Prospects for a bio-based succinate industry | Applied Microbiology and Biotechnology | 2007 | 416 |
| 27 | Nickel uptake and utilization by microorganisms | FEMS Microbiology Reviews | 2003 | 413 |
| 28 | Systematic artifacts in metagenomes from complex microbial communities | ISME Journal | 2009 | 412 |
| 29 | Distinguishing Nitrous Oxide Production from Nitrification and Denitrification on the Basis of Isotopomer Abundances | Applied and Environmental Microbiology | 2006 | 411 |
| 30 | Repeatability and Contingency in the Evolution of a Key Innovation in Phage Lambda | Science | 2012 | 401 |
| 31 | rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea | Nucleic Acids Research | 2009 | 398 |
| 32 | Wolbachia Invades Anopheles stephensi Populations and Induces Refractoriness to Plasmodium Infection | Science | 2013 | 393 |
| 33 | ProbioticL. reuteriTreatment Prevents Bone Loss in a Menopausal Ovariectomized Mouse Model | Journal of Cellular Physiology | 2014 | 374 |
| 34 | Harvesting energy from the marine sediment–water interface II | Biosensors and Bioelectronics | 2006 | 371 |
| 35 | New Strategies for Cultivation and Detection of Previously Uncultured Microbes | Applied and Environmental Microbiology | 2004 | 369 |
| 36 | Role of the Intestinal Microbiota in Resistance to Colonization by Clostridium difficile | Gastroenterology | 2014 | 369 |
| 37 | Histamine Derived from Probiotic Lactobacillus reuteri Suppresses TNF via Modulation of PKA and ERK Signaling | PLoS ONE | 2012 | 363 |
| 38 | Land-use history has a stronger impact on soil microbial community composition than aboveground vegetation and soil properties | Soil Biology and Biochemistry | 2011 | 362 |
| 39 | Anopheles gambiae: historical population decline associated with regional distribution of insecticide-treated bed nets in western Nyanza Province, Kenya | Malaria Journal | 2010 | 361 |
| 40 | Diversity is the question, not the answer | ISME Journal | 2017 | 358 |
| 41 | Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis | PLoS Biology | 2010 | 348 |
| 42 | Ecological patterns of seed microbiome diversity, transmission, and assembly | Current Opinion in Microbiology | 2017 | 331 |
| 43 | Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3) | Journal of Molecular Biology | 2009 | 316 |
| 44 | Isolation and Characterization of Soil Bacteria That Define Terriglobus gen. nov., in the Phylum Acidobacteria | Applied and Environmental Microbiology | 2007 | 301 |
| 45 | Second-Order Selection for Evolvability in a Large Escherichia coli Population | Science | 2011 | 300 |
| 46 | Harnessing mosquito–Wolbachia symbiosis for vector and disease control | Acta Tropica | 2014 | 284 |
| 47 | Nomenclature and taxonomy of the genus Salmonella | International Journal of Systematic and Evolutionary Microbiology | 2005 | 283 |
| 48 | Host-microbial symbiosis in the vertebrate gastrointestinal tract and the Lactobacillus reuteri paradigm | Proceedings of the National Academy of Sciences of the United States of America | 2011 | 283 |
| 49 | The Class Mesomycetozoea: A Heterogeneous Group of Microorganisms at the Animal-Fungal Boundary | Annual Review of Microbiology | 2002 | 282 |
| 50 | Antibiotic-Associated Diarrhea Accompanied by Large-Scale Alterations in the Composition of the Fecal Microbiota | Journal of Clinical Microbiology | 2004 | 282 |
