Topic · Gut microbiota and health
Most cited papers in Gut microbiota and health
What are the most cited papers in Gut microbiota and health?
The most cited paper in Gut microbiota and health is "DADA2: High-resolution sample inference from Illumina amplicon data" (Benjamin J. Callahan, Paul J. McMurdie, Michael Rosen et al., 2016), with 37,958 citations. Next come "Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2" (25,165) and "Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities" (22,073).
Showing 50 of 100 papers. Every paper with more than 3,491 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | DADA2: High-resolution sample inference from Illumina amplicon data Benjamin J. Callahan, Paul J. McMurdie, Michael Rosen et al. · Nature Methods | 23 May 2016 | 37,958 |
| 2 | Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 Evan K Bolyen et al. · Nature Biotechnology | 24 Jul 2019 | 25,165 |
| 3 | Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities Patrick D. Schloss, Sarah L. Westcott, Thomas Ryabin et al. · Applied and Environmental Microbiology | 3 Oct 2009 | 22,073 |
| 4 | Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy Qiong Wang, George M Garrity, James M. Tiedje et al. · Applied and Environmental Microbiology | 22 Jun 2007 | 20,801 |
| 5 | UPARSE: highly accurate OTU sequences from microbial amplicon reads R. C. Edgar · Nature Methods | 18 Aug 2013 | 17,573 |
| 6 | Metagenomic biomarker discovery and explanation Nicola Segata, Jacques Izard, Levi D. Waldron et al. · Genome biology | 24 Jun 2011 | 17,136 |
| 7 | CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Donovan H. Parks, Michael Imelfort, Connor T. Skennerton et al. · Genome Research | 14 May 2015 | 13,397 |
| 8 | An obesity-associated gut microbiome with increased capacity for energy harvest Peter James Turnbaugh, Ruth E. Ley, Michael A. Mahowald et al. · Nature | Dec 2006 | 12,679 |
| 9 | Structure, function and diversity of the healthy human microbiome Curtis Huttenhower et al. · Nature | Jun 2012 | 12,195 |
| 10 | A human gut microbial gene catalogue established by metagenomic sequencing Junjie Qin et al. · Nature | Mar 2010 | 11,892 |
| 11 | Diet rapidly and reproducibly alters the human gut microbiome Lawrence A. David, Corinne F. Maurice, Rachel N. Carmody et al. · Nature | 11 Dec 2013 | 10,461 |
| 12 | Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences Morgan G. I. Langille, Jesse Zaneveld, J. Gregory Caporaso et al. · Nature Biotechnology | 25 Aug 2013 | 9,519 |
| 13 | The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic Colin Hill, Francisco Guarner, Gregor Reid et al. · Nature Reviews Gastroenterology & Hepatology | 10 Jun 2014 | 9,518 |
| 14 | Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms J. Gregory Caporaso, Christian L. Lauber, William Anton Walters et al. · The ISME Journal | 8 Mar 2012 | 9,285 |
| 15 | Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies Anna Klindworth, Elmar Pruesse, Timmy Schweer et al. · Nucleic Acids Research | 28 Aug 2012 | 9,235 |
| 16 | Human gut microbes associated with obesity Ruth E. Ley, Peter James Turnbaugh, Samuel Klein et al. · Nature | 20 Dec 2006 | 8,887 |
| 17 | UniFrac: a New Phylogenetic Method for Comparing Microbial Communities Catherine Lozupone, Rob Knight · Applied and Environmental Microbiology | Dec 2005 | 8,691 |
| 18 | Human gut microbiome viewed across age and geography Tanya Yatsunenko et al. · Nature | 8 May 2012 | 8,081 |
| 19 | A core gut microbiome in obese and lean twins Peter James Turnbaugh, Micah Hamady, Tanya Yatsunenko et al. · Nature | 30 Nov 2008 | 7,978 |
| 20 | Diversity of the Human Intestinal Microbial Flora Paul B. Eckburg, Elisabeth M. Bik, Charles Noah Bernstein et al. · Science | 14 Apr 2005 | 7,956 |
| 21 | Enterotypes of the human gut microbiome Manimozhiyan Arumugam et al. · Nature | 19 Apr 2011 | 7,806 |
| 22 | Dietary Modulation of the Human Colonic Microbiota: Introducing the Concept of Prebiotics Glenn R. Gibson, Marcel B. Roberfroid · Journal of Nutrition | Jun 1995 | 7,690 |
| 23 | Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform James J. Kozich, Sarah L. Westcott, Nielson T. Baxter et al. · Applied and Environmental Microbiology | 21 Jun 2013 | 7,674 |
| 24 | From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites Ara Koh, Filipe De Vadder, Petia Kovatcheva‐Datchary et al. · Cell | Jun 2016 | 7,123 |
| 25 | A metagenome-wide association study of gut microbiota in type 2 diabetes Junjie Qin et al. · Nature | 25 Sep 2012 | 7,088 |
| 26 | PICRUSt2 for prediction of metagenome functions Gavin M. Douglas, Vincent J. Maffei, Jesse Zaneveld et al. · Nature Biotechnology | Jun 2020 | 7,006 |
| 27 | Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes Gary D. Wu, Jun Chen, Christian Hoffmann et al. · Science | Sep 2011 | 6,707 |
| 28 | Metabolic Endotoxemia Initiates Obesity and Insulin Resistance Patrice D. Cani et al. · Diabetes | 27 Jun 2007 | 6,653 |
| 29 | Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin Nicholas A. Bokulich, Benjamin D. Kaehler, Jai Ram Rideout et al. · Microbiome | 17 May 2018 | 6,258 |
| 30 | Obesity alters gut microbial ecology Ruth E. Ley, Fredrik Bäckhed, Peter James Turnbaugh et al. · Proceedings of the National Academy of Sciences | 20 Jul 2005 | 6,243 |
| 31 | The Human Microbiome Project Peter James Turnbaugh, Ruth E. Ley, Micah Hamady et al. · Nature | 17 Oct 2007 | 6,235 |
| 32 | Biofilms: an emergent form of bacterial life Hans‐Curt Flemming, Jost Wingender, Ulrich Szewzyk et al. · Nature Reviews Microbiology | 11 Aug 2016 | 6,029 |
| 33 | Diversity, stability and resilience of the human gut microbiota Catherine Lozupone, Jesse Stombaugh, Jeffrey I. Gordon et al. · Nature | Sep 2012 | 5,727 |
| 34 | Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa Carlotta De Filippo, Duccio Cavalieri, Monica Di Paola et al. · Proceedings of the National Academy of Sciences | 2 Aug 2010 | 5,726 |
| 35 | Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors Bertrand Routy et al. · Science | 2 Nov 2017 | 5,679 |
| 36 | Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells Yukihiro Furusawa et al. · Nature | 13 Nov 2013 | 5,575 |
| 37 | Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics Glenn R. Gibson, Robert W. Hutkins, Mary Ellen Sanders et al. · Nature Reviews Gastroenterology & Hepatology | 14 Jun 2017 | 5,560 |
| 38 | Role of the Microbiota in Immunity and Inflammation Yasmine Belkaid, Timothy Wesley Hand · Cell | Mar 2014 | 5,511 |
| 39 | The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic T reg Cell Homeostasis Patrick M. Smith, Michael R. Howitt, Nicolai S. Panikov et al. · Science | 5 Jul 2013 | 5,478 |
| 40 | Host-Bacterial Mutualism in the Human Intestine Fredrik Bäckhed, Ruth E. Ley, Justin Laine Sonnenburg et al. · Science | 24 Mar 2005 | 5,363 |
| 41 | Revised Estimates for the Number of Human and Bacteria Cells in the Body Ron Sender, Shai Fuchs, Ron Milo · PLoS Biology | 19 Aug 2016 | 5,258 |
| 42 | The Microbiota-Gut-Brain Axis John F. Cryan et al. · Physiological Reviews | 28 Aug 2019 | 5,217 |
| 43 | The gut microbiota shapes intestinal immune responses during health and disease June L. Round, Sarkis K. Mazmanian · Nature reviews. Immunology | 3 Apr 2009 | 5,124 |
| 44 | The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism Gijs den Besten, Karen van Eunen, Albert Kornelis Groen et al. · Journal of Lipid Research | 3 Jul 2013 | 5,091 |
| 45 | metaSPAdes: a new versatile metagenomic assembler Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov et al. · Genome Research | 15 Mar 2017 | 5,016 |
| 46 | Kraken: ultrafast metagenomic sequence classification using exact alignments Derrick E. Wood, Steven L. Salzberg · Genome biology | 3 Mar 2014 | 4,992 |
| 47 | Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease Luke Jostins et al. · Nature | 31 Oct 2012 | 4,928 |
| 48 | Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation Nicholas Arpaia, Clarissa Campbell, Xiying Fan et al. · Nature | 13 Nov 2013 | 4,892 |
| 49 | The Ribosomal Database Project: improved alignments and new tools for rRNA analysis James R. Cole, Qi Wang, Erick Cardenas et al. · Nucleic Acids Research | 12 Nov 2008 | 4,882 |
| 50 | Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients Vancheswaran Gopalakrishnan et al. · Science | 2 Nov 2017 | 4,849 |
Citations are OpenAlex's own counts, from its 2026-09-23 snapshot, so the ranking can differ from Google Scholar or Web of Science. A paper is listed for a field when OpenAlex files it under one of the field's topics; retracted papers and papers whose citation count cannot be traced to citing works are left out, and a preprint and the article it became are shown once. Release dates are OpenAlex's: where a source gave only a month or a year, that is what is shown. How the lists are chosen.