Evidence map›Paper›PMID 34789871›Full record

ReviewNature medicine2021

Reporting guidelines for human microbiome research: the STORMS checklist.

Chloe Mirzayi, Audrey Renson, Genomic Standards Consortium, Massive Analysis and Quality Control Society, Fatima Zohra, Shaimaa Elsafoury, Ludwig Geistlinger, Lora J Kasselman, Kelly Eckenrode, Janneke van de Wijgert and 95 more

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Nature medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 352 papers, 18 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
352citing papers in PubMed, 18 pooled it
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

352 citing papers in PubMed, 18 syntheses or guidelines pooled it.

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  4. Zearalenone exposure and the mammalian gut microbiome: a systematic review of the literature.Toxicological sciences : an official journal of the Society of Toxicology · 2026
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  8. Impacts of Lifestyle and Microbiota-Targeted Interventions for Overweight and Obesity on the Human Gut Microbiome: A Systematic Review.Obesity reviews : an official journal of the International Association for the Study of Obesity · 2026
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292 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

105 authors.

Chloe MirzayiCUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA.
Audrey RensonUniversity of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Genomic Standards Consortium
Massive Analysis and Quality Control Society
Fatima ZohraCUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA.
Shaimaa ElsafouryCUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA.
Ludwig GeistlingerCUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA.
Lora J KasselmanCUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA.
Kelly EckenrodeCUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA.
Janneke van de WijgertJulius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
Amy LoughmanFood & Mood Centre, The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Victoria, Australia.
Francine Z MarquesHypertension Research Laboratory, School of Biological Sciences, Faculty of Science, Monash University, Melbourne, Victoria, Australia.ORCID http://orcid.org/0000-0003-4920-9991
David A MacIntyreDepartment of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK.
Manimozhiyan ArumugamNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Rimsha AzharCUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA.
Francesco BeghiniDepartment CIBIO, University of Trento, Trento, Italy.
Kirk BergstromDepartment of Biology, University of British Columbia-Okanagan Campus, Kelowna, British Columbia, Canada.
Ami BhattDivision of Hematology and Division of Bone Marrow Transplantation, Department of Medicine, and Department of Genetics, Stanford University, Stanford, CA, USA.
Jordan E BisanzDepartment of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
Jonathan BraunDivision of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
Hector Corrada BravoGenentech, South San Francisco, CA, USA.
Gregory A BuckCenter for Microbiome Engineering and Data Analysis, Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA.ORCID http://orcid.org/0000-0003-4621-3987
Frederic BushmanUniversity of Pennsylvania, Philadelphia, PA, USA.
David CaseroF. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
Gerard ClarkeDepartment of Psychiatry and Neurobehavioural Science, and APC Microbiome Ireland, University College Cork, Cork, Ireland.
Maria Carmen ColladoInstitute of Agrochemistry and Food Technology-National Research Council, Valencia, Spain.
Paul D CotterTeagasc Food Research Centre-Moorepark, Cork, Ireland.
John F CryanAPC Microbiome Ireland, University College Cork, Cork, Ireland.
Ryan T DemmerSchool of Public Health, University of Minnesota, Minneapolis, MN, USA.
Suzanne DevkotaF. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
Eran ElinavImmunology Department, Weizmann Institute of Science, Rehovot, Israel.
Juan S EscobarVidarium-Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia.
Jennifer FettweisCenter for Microbiome Engineering and Data Analysis, Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA.
Robert D FinnEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
Anthony A FodorDepartment of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA.
Sofia ForslundExperimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité University Hospital, Berlin, Germany.
Andre FrankeInstitute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
Cesare FurlanelloHK3 Lab, Rovereto, Italy.
Jack GilbertDepartment of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
Elizabeth GriceDepartment of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Benjamin Haibe-KainsPrincess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
Scott HandleyDepartment of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
Pamela HerdMcCourt School of Public Policy, Georgetown University, Washington, DC, USA.
Susan HolmesDepartment of Statistics, Stanford University, Stanford, CA, USA.
Jonathan P JacobsDivision of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
Lisa KarstensDepartment of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA.
Rob KnightCenter for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
Dan KnightsDepartment of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.
Omry KorenAzrieli Faculty of Medicine, Bar Ilan University, Safed, Israel.
Douglas S KwonDivision of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
Morgan LangilleDepartment of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada.
Brianna LindsayUniversity of Maryland School of Medicine, Institute of Human Virology, Baltimore, MD, USA.
Dermot McGovernF. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
Alice C McHardyDepartment of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Brunswick, Germany.
Shannon McWeeneyOHSU Knight Cancer Institute, Portland, OR, USA.
Noel T MuellerDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
Luigi NeziDepartment of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico-Istituto Europeo di Oncologia, Milan, Italy.
Matthew OlmDepartment of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
Noah PalmDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
Edoardo PasolliDepartment of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
Jeroen RaesDepartment of Microbiology and Immunology, Rega institute, KU Leuven and VIB Center for Microbiology, Leuven, Belgium.
Matthew R RedinboDepartment of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Malte RühlemannInstitute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany.
R Balfour SartorCenter for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Patrick D SchlossDepartment of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA.
Lynn SchrimlUniversity of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA.
Eran SegalDepartment of Computer Science, Weizmann Institute of Science, Rehovot, Israel.
Michelle ShardellUniversity of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA.
Thomas SharptonDepartment of Microbiology and Department of Statistics, Oregon State University, Corvallis, OR, USA.
Ekaterina SmirnovaDepartment of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA.
Harry SokolGastroenterology Department, Centre de Recherche Saint-Antoine, INSERM, Assistance Publique-Hôpitaux de Paris, Saint Antoine Hospital, Sorbonne Université, Paris, France.
Justin L SonnenburgDepartment of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
Sujatha SrinivasanVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
Louise B ThingholmInstitute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany.
Peter J TurnbaughDepartment of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.
Vaibhav UpadhyayDepartment of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.
Ramona L WallsCritical Path Institute, Tucson, AZ, USA.
Paul WilmesLuxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.ORCID http://orcid.org/0000-0002-6478-2924
Takuji YamadaDepartment of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.ORCID http://orcid.org/0000-0002-9622-1849
Georg ZellerStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Mingyu ZhangDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
Ni ZhaoDepartment of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
Liping ZhaoDepartment of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, USA.
Wenjun BaoJMP Life Sciences, SAS Institute, Cary, NC, USA.
Aedin CulhaneDepartment of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
Viswanath DevanarayanEisai, Woodcliff Lake, NJ, USA.
Joaquin DopazoClinical Bioinformatics Area, Hospital Virgen del Rocio, Sevilla, Spain.
Xiaohui FanCollege of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
Matthias FischerExperimental Pediatric Oncology, University Children's Hospital, Cologne, Germany.
Wendell JonesQ2 Solutions-EA Genomics, Durham, NC, USA.
Rebecca KuskoImmuneering, Cambridge, MA, USA.
Christopher E MasonWeill Cornell Medicine, New York, NY, USA.
Tim R MercerAustralian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia.
Susanna-Assunta SansoneOxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UK.
Andreas SchererInstitute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.
Leming ShiState Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China.
Shraddha ThakkarOffice of Computational Science, Office of Translational Sciences, Center for Drug Evaluation and Research, Washington, DC, USA.
Weida TongDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food & Drug Administration, Jefferson, AR, USA.
Russ WolfingerScientific Discovery and Genomics, SAS Institute, Cary, NC, USA.
Christopher HunterGigaScience Database, BGI Hong Kong, Hong Kong, China.
Nicola SegataDepartment CIBIO, University of Trento, Trento, Italy.ORCID http://orcid.org/0000-0002-1583-5794
Curtis Huttenhower *Harvard T. H. Chan School of Public Health, Boston, MA, USA.ORCID http://orcid.org/0000-0002-1110-0096
Jennifer B Dowd *Department of Sociology, Leverhulme Centre for Demographic Science, University of Oxford, Oxford, UK.
Heidi E Jones *CUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA.ORCID http://orcid.org/0000-0002-4285-3752
Levi Waldron *CUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA. levi.waldron@sph.cuny.edu.ORCID http://orcid.org/0000-0003-2725-0694

Funding

Translational Research Support CoreP30ES005022 · NIEHS · UNIV OF MED/DENT NJ-R W JOHNSON MED SCH · PI PANOS G. GEORGOPOULOS · 1988 to 2026
$47.4M
UCSF Nutrition Obesity Research CenterP30DK098722 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHRISTIAN VAISSE · 2015 to 2026
$14.6M
Impact of Diet on Intestinal Microbiota-Host DynamicsR01DK085025 · NIDDK · STANFORD UNIVERSITY · PI JUSTIN L SONNENBURG · 2010 to 2026
$6.4M
Exploiting Public Metagenomic Data to Uncover Cancer-Microbiome RelationshipsR01CA230551 · NCI · GRADUATE SCHOOL OF PUBLIC HEALTH AND HEALTH POLICY · PI Levi Waldron · 2020 to 2026
$3.9M
Structural Basis for Hormone and Neurotransmitter Processing by Gut Microbial EnzymesR01GM135218 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI REDINBO, MATTHEW R · 2019 to 2022
$1.5M
Exploiting public metagenomic data to uncover cancer-microbiome relationshipsU01CA230551 · NCI · GRADUATE SCHOOL OF PUBLIC HEALTH AND HEALTH POLICY · PI WALDRON, LEVI · 2019 to 2019
$464k
Biotechnology and Biological Sciences Research Council BB/E025080/1NCI NIH HHS R01 CA230551NCI NIH HHS U01 CA230551NIDDK NIH HHS P30 DK098722NIDDK NIH HHS R01 DK085025NIEHS NIH HHS P30 ES005022NIGMS NIH HHS R01 GM135218
6 · The paper itself

Abstract

The particularly interdisciplinary nature of human microbiome research makes the organization and reporting of results spanning epidemiology, biology, bioinformatics, translational medicine and statistics a challenge. Commonly used reporting guidelines for observational or genetic epidemiology studies lack key features specific to microbiome studies. Therefore, a multidisciplinary group of microbiome epidemiology researchers adapted guidelines for observational and genetic studies to culture-independent human microbiome studies, and also developed new reporting elements for laboratory, bioinformatics and statistical analyses tailored to microbiome studies. The resulting tool, called 'Strengthening The Organization and Reporting of Microbiome Studies' (STORMS), is composed of a 17-item checklist organized into six sections that correspond to the typical sections of a scientific publication, presented as an editable table for inclusion in supplementary materials. The STORMS checklist provides guidance for concise and complete reporting of microbiome studies that will facilitate manuscript preparation, peer review, and reader comprehension of publications and comparative analysis of published results.

Indexed as

Research DesignComputational BiologyDysbiosisHumansMicrobiotaObservational Studies as TopicTranslational Science, Biomedical

Identifiers

PMID34789871
PMCPMC9105086

What OpenQuestion holds

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Read underepoch 390

Registered trials

None linked

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.