ArticleNature biotechnology2019
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
Erratum issued 3 registry-linked trialsAbstract readLetter
In one paragraph
Article in Nature biotechnology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. It is linked to 3 registered trials, which are not on this map. Cited by 11,982 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
11,982citing papers in PubMed, 1 pooled it
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Fiber-rich Foods, Weight Status, and the Gut Microbiota: A Comparative Study in NH Hispanic Adults at Risk for Food Insecurity
Biomarkers and Respiratory Omics as New CHildren Opportunities - Study of Clinical Outcomes and Predictivity Evaluation - a Multi-cohort, Multi-center Study
Trial Comparing the Efficacy of Transanal Irrigation Versus Standard Bowel Care in Patients With Parkinson's Disease and Severe Constipation. Impact on Gut Microbiome and Motor Disorders. TAI-PD Study.
Who cites it
11,982 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Functional Redundancy Enables Stable Treatment Performance Across Taxonomically Diverse Dairy Wastewater Microbiomes.Environmental microbiology reports · 2026Pooled it
- Fecal filtrate transplantation as salvage therapy for fulminantGut microbes · 2026Trial
- The impact of prophylactic azithromycin on the developing preterm gut microbiome and resistome.Gut microbes · 2026Trial
- Heat-treatedJournal of microbiology and biotechnology · 2026Trial
- Effect of Abrocitinib on the Skin Microbiome in Patients With Moderate-to-Severe Atopic Dermatitis.Allergy · 2026Trial
- Effects of Heat-KilledNutrients · 2026Trial
- Integrative Analysis of Gut Microbiota in Alpha-Gal Research.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Rectal ozone insufflation modulates gut microbiota: improving lung function in mice with chronic obstructive pulmonary disease.Medical gas research · 2027Article
- Gut microbiota profile in school-aged children with vitamin A depletion and vitamin E deficiency: A cross-sectional study.Gut microbes reports · 2027Article
- Article
- Compositional and functional differences of gut microbiome and metabolome inform pathogenesis of cholestatic liver disease.Gut microbes · 2026Article
- Gut microbes mediate the synergistic effects of dietary cholesterol and saturated fat in driving fibrosing MASH.Gut microbes · 2026Article
- Article
- Article
- Human fecal transplantation from stunted children promotes metabolic dysfunction in mice fed with a high-fat and high-fructose corn syrup diet.Gut microbes · 2026Article
- Article
- High-fat diet-derived metabolite uridine diphosphate (UDP) impairs epithelial regeneration by P2YGut microbes · 2026Article
- From gut dysbiosis to eubiosis: understanding microbiome recovery as an ecological process.Gut microbes · 2026Review
- Article
- IgA deficiency reveals a microbiota-dependent pathway to gluten sensitivity.Gut microbes · 2026Article
11,922 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
112 authors.
Evan BolyenCenter for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.ORCID http://orcid.org/0000-0002-5362-6782
Jai Ram RideoutCenter for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.ORCID http://orcid.org/0000-0003-2587-1454
Matthew R DillonCenter for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.ORCID http://orcid.org/0000-0002-7713-1952
Nicholas A BokulichCenter for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.ORCID http://orcid.org/0000-0002-1784-8935
Christian C AbnetMetabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA.ORCID http://orcid.org/0000-0002-3008-7843
Gabriel A Al-GhalithDepartment of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.ORCID http://orcid.org/0000-0002-6953-6319
Harriet AlexanderBiology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
Eric J AlmDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-8294-9364
Manimozhiyan ArumugamNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-0886-9101
Francesco AsnicarCentre for Integrative Biology, University of Trento, Trento, Italy.ORCID http://orcid.org/0000-0003-3732-1468
Yang BaiState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.ORCID http://orcid.org/0000-0003-2652-7022
Jordan E BisanzDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-8649-1706
Kyle BittingerDivision of Gastroenterology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Asker BrejnrodNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Colin J BrislawnEarth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
C Titus BrownDepartment of Population Health and Reproduction, University of California, Davis, Davis, CA, USA.ORCID http://orcid.org/0000-0001-6001-2677
Benjamin J CallahanDepartment of Population Health & Pathobiology, North Carolina State University, Raleigh, NC, USA.ORCID http://orcid.org/0000-0002-8752-117X
Andrés Mauricio Caraballo-RodríguezCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.ORCID http://orcid.org/0000-0001-5499-2728
John ChaseCenter for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
Emily K CopeCenter for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
Ricardo Da SilvaCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
Christian DienerInstitute for Systems Biology, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-7476-0868
Pieter C DorresteinCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.ORCID http://orcid.org/0000-0002-3003-1030
Gavin M DouglasDepartment of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada.
Daniel M DurallIrving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, British Columbia, Canada.ORCID http://orcid.org/0000-0001-7414-4443
Claire DuvalletDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-8093-8394
Christian F EdwardsonA. Watson Armour III Center for Animal Health and Welfare, Aquarium Microbiome Project, John G. Shedd Aquarium, Chicago, IL, USA.ORCID http://orcid.org/0000-0001-7524-7209
Madeleine ErnstCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
Mehrbod EstakiDepartment of Biology, University of British Columbia Okanagan, Okanagan, British Columbia, Canada.
Jennifer FouquierComputational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.ORCID http://orcid.org/0000-0002-0975-8235
Julia M GauglitzCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
Sean M GibbonsInstitute for Systems Biology, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-8724-7916
Deanna L GibsonIrving K. Barber School of Arts and Sciences, Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada.
Antonio GonzalezDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Kestrel GorlickCenter for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
Jiarong GuoCenter for Microbial Ecology, Michigan State University, East Lansing, MI, USA.
Benjamin HillmannDepartment of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.
Susan HolmesStatistics Department, Stanford University, Palo Alto, CA, USA.ORCID http://orcid.org/0000-0002-2208-8168
Hannes HolsteDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-7739-6590
Curtis HuttenhowerDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.ORCID http://orcid.org/0000-0002-1110-0096
Gavin A HuttleyResearch School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.
Stefan JanssenDepartment of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Dusseldorf, Germany.ORCID http://orcid.org/0000-0003-0955-0589
Alan K JarmuschCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
Lingjing JiangDepartment of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA.
Benjamin D KaehlerResearch School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.
Kyo Bin KangCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.ORCID http://orcid.org/0000-0003-3290-1017
Christopher R KeefeCenter for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.ORCID http://orcid.org/0000-0002-4289-0991
Paul KeimCenter for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
Scott T KelleyDepartment of Biology, San Diego State University, San Diego, CA, USA.
Dan KnightsDepartment of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.
Irina KoesterCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
Tomasz KosciolekDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA.ORCID http://orcid.org/0000-0002-9915-7387
Jorden KrepsCenter for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.ORCID http://orcid.org/0000-0003-3758-6458
Morgan G I LangilleDepartment of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada.
Joslynn LeeScience Education, Howard Hughes Medical Institute, Ashburn, VA, USA.
Ruth LeyDepartment of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.
Yong-Xin LiuState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.ORCID http://orcid.org/0000-0003-1832-9835
Erikka LoftfieldMetabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA.ORCID http://orcid.org/0000-0002-3573-8748
Catherine LozuponeDepartment of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.ORCID http://orcid.org/0000-0003-4786-7202
Massoud MaherDepartment of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA.
Clarisse MarotzDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-1520-8854
Bryan D MartinDepartment of Statistics, University of Washington, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-8002-5296
Daniel McDonaldDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-0876-9060
Lauren J McIverDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Alexey V MelnikCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.ORCID http://orcid.org/0000-0002-4645-8880
Jessica L MetcalfDepartment of Animal Science, Colorado State University, Fort Collins, CO, USA.
Sydney C MorganIrving K. Barber School of Arts and Sciences, Unit 2 (Biology), University of British Columbia, Kelowna, British Columbia, Canada.
Jamie T MortonDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Ahmad Turan NaimeyCenter for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
Jose A Navas-MolinaDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-4595-920X
Louis Felix NothiasCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
Stephanie B OrchanianCenter for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-2491-1074
Talima PearsonCenter for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.ORCID http://orcid.org/0000-0003-3696-041X
Samuel L PeoplesSchool of Information Studies, Syracuse University, Syracuse, NY, USA.
Daniel PetrasCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.ORCID http://orcid.org/0000-0002-6561-3022
Mary Lai PreussDepartment of Biological Sciences, Webster University, St. Louis, MO, USA.
Elmar PruesseDepartment of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
Lasse Buur RasmussenNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Adam RiversAgricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA.ORCID http://orcid.org/0000-0002-3703-834X
Michael S RobesonCollege of Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.ORCID http://orcid.org/0000-0001-7119-6301
Patrick RosenthalDepartment of Biological Sciences, Webster University, St. Louis, MO, USA.
Nicola SegataCentre for Integrative Biology, University of Trento, Trento, Italy.ORCID http://orcid.org/0000-0002-1583-5794
Michael ShafferComputational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
Arron ShifferCenter for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
Rashmi SinhaMetabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA.
Se Jin SongDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-0750-5709
John R SpearDepartment of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA.
Austin D SwaffordCenter for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
Luke R ThompsonDepartment of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, USA.ORCID http://orcid.org/0000-0002-3911-1280
Pedro J TorresDepartment of Biology, San Diego State University, San Diego, CA, USA.
Pauline TrinhDepartment of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA.
Anupriya TripathiCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
Peter J TurnbaughDepartment of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-0888-2875
Sabah Ul-HasanQuantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, USA.
Justin J J van der HooftBioinformatics Group, Wageningen University, Wageningen, the Netherlands.ORCID http://orcid.org/0000-0002-9340-5511
Fernando VargasDivision of Biological Sciences, University of California San Diego, San Diego, CA, USA.
Yoshiki Vázquez-BaezaDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Emily VogtmannMetabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA.ORCID http://orcid.org/0000-0003-1355-5593
Max von HippelDepartment of Mathematics, University of Arizona, Tucson, AZ, USA.ORCID http://orcid.org/0000-0003-0288-5802
William WaltersDepartment of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.
Yunhu WanMetabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA.
Mingxun WangCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
Jonathan WarrenNational Laboratory Service, Environment Agency, Starcross, UK.ORCID http://orcid.org/0000-0003-3381-3852
Kyle C WeberAgricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA.
Charles H D WilliamsonPathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
Amy D WillisDepartment of Biostatistics, University of Washington, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-2802-4317
Zhenjiang Zech XuDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Jesse R ZaneveldSchool of STEM, Division of Biological Sciences, University of Washington Bothell, Bothell, WA, USA.
Yilong ZhangMerck & Co. Inc., Kenilworth, NJ, USA.
Qiyun ZhuDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-3568-6271
Rob KnightDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-0975-9019
J Gregory CaporasoCenter for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA. greg.caporaso@nau.edu.ORCID http://orcid.org/0000-0002-8865-1670
Funding
SSCIMA: Integrating Analysis of Socio-economic Sub-population Dynamics to Improve Spatial Models of Infectious DiseaseU54MD012388 · NIMHD · NORTHERN ARIZONA UNIVERSITY · PI Julie A. Baldwin · 2017 to 2026
$49.7MTraining/Career Development and Education Core and PlansU54CA143925 · NCI · NORTHERN ARIZONA UNIVERSITY · PI Jason A Wilder · 2009 to 2026
$27.5MBiostatistics, Epidemiologic & Bioinformatic Training in Environmental HealthT32ES015459 · NIEHS · UNIVERSITY OF WASHINGTON · PI June T. Spector · 2009 to 2026
$10.6MLower Gastrointestinal Cancer StudiesZIACP010198 · NCI · DIVISION OF CANCER EPIDEMIOLOGY AND GENETICS · PI SINHA, RASHMI · 2009 to 2025
$6.6MStatistical methods to enhance reproducible microbiome discoveryR35GM133420 · NIGMS · UNIVERSITY OF WASHINGTON · PI Amy D Willis · 2019 to 2026
$2.8MIntramural NIH HHS Z99 CA999999NCI NIH HHS U54 CA143925NIEHS NIH HHS T32 ES015459NIGMS NIH HHS R35 GM133420NIMHD NIH HHS U54 MD012388
Abstract
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.