Evidence map›Paper›PMID 31142855›Full record

ReviewNature2019

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.

Jason Lloyd-Price, Cesar Arze, Ashwin N Ananthakrishnan, Melanie Schirmer, Julian Avila-Pacheco, Tiffany W Poon, Elizabeth Andrews, Nadim J Ajami, Kevin S Bonham, Colin J Brislawn and 30 more

2 registry-linked trialsOpen access · hybridAbstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Nature, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to 2 registered trials, which are not on this map. Cited by 1,845 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
1,845citing papers in PubMed, 1 pooled it
111.1field-weighted citation impact, top 1% of its field
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.

NCT05083091 nacompletednot on this mapstarted 2022, after this paper: background citation

Smartphone Stress Management Training for Irritable Bowel Syndrome

TypeinterventionalSponsorCarnegie Mellon UniversityRan2022 to 2025Enrolled359ConditionsIrritable Bowel SyndromeArmsMindfulness and Attention Training, Mindfulness training, Coping Condition
NCT06124833 recruitingnot on this mapstarted 2023, after this paper: background citation

Building an Integrated Gut Microbiome Data Analysis Platform and Conducting Comparative Clinical Studies in Inflammatory Bowel Disease

Typeobservational_patient_registrySponsorChang Kyun LeeRan2023 to 2028Enrolled900ConditionsInflammatory Bowel Disease (IBD)
3 · Its place in the literature

Who cites it

1,845 citing papers in PubMed, 1 synthesis or guideline pooled it, 3,032 citations in OpenAlex.

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  10. Gut microbes · 2026
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1,785 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

40 authors at 11 institutions in 2 countries.

Jason Lloyd-PriceInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Cesar ArzeDepartment of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
Ashwin N AnanthakrishnanGastroenterology, Massachusetts General Hospital, Boston, MA, USA.
Melanie SchirmerInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Julian Avila-PachecoMetabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Tiffany W PoonInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Elizabeth AndrewsGastroenterology, Massachusetts General Hospital, Boston, MA, USA.
Nadim J AjamiMolecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
Kevin S BonhamInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Colin J BrislawnEarth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA.
David CaseroDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
Holly CourtneyGastroenterology, Massachusetts General Hospital, Boston, MA, USA.
Antonio GonzalezDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Thomas G GraeberMolecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA.
A Brantley HallInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Kathleen LakeDepartment of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
Carol J LandersF. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
Himel MallickInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Damian R PlichtaInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Mahadev PrasadDepartment of Pediatrics, Emory University, Atlanta, GA, USA.
Gholamali RahnavardInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Jenny SaukVatche and Tamar Manoukian Division of Digestive Diseases, University of California Los Angeles, Los Angeles, CA, USA.
Dmitry ShunginInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Yoshiki Vázquez-BaezaJacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
Richard A WhiteEarth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA.
IBDMDB Investigators
Jonathan BraunDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
Lee A DensonDepartment of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
Janet K JanssonEarth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA.
Rob KnightDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Subra KugathasanDepartment of Pediatrics, Emory University, Atlanta, GA, USA.
Dermot P B McGovernF. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
Joseph F PetrosinoMolecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
Thaddeus S StappenbeckDepartment of Pathology & Immunology, Washington University, St. Louis, MO, USA.
Harland S WinterDepartment of Pediatrics, MassGeneral Hospital for Children, Boston, MA, USA.
Clary B ClishMetabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Eric A FranzosaDepartment of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
Hera VlamakisInfectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Ramnik J Xavier *Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Curtis Huttenhower *Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA. chuttenh@hsph.harvard.edu.
Broad Institute · USUniversity of California, Los Angeles · USHarvard University · USMassachusetts General Hospital · USPacific Northwest National Laboratory · USUniversity of California San Diego · USBaylor College of Medicine · USCedars-Sinai Medical Center · USCincinnati Children's Hospital Medical Center · USEmory University · USWashington University in St. Louis · US

Funding

UCLA Clinical Translational Science InstituteUL1TR001881 · NCATS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ARLEEN F. BROWN, ARASH NAEIM · 2016 to 2026
$118.1M
Pilot & Feasibility ProgramP30DK043351 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI RAYMOND T CHUNG · 1991 to 2026
$35.3M
ROLE OF DIETARY CONSTITUENTS ON GENE EXPRESSION IN INTESTINAL EPITHELIUMP30DK040561 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI CHRISTOPHER P DUGGAN · 1994 to 2026
$31.6M
Using polygenic scores to enhance both variant discovery, and understanding of functional consequences of genetic variation in IBD.P01DK046763 · NIDDK · CEDARS-SINAI MEDICAL CENTER · PI TARGAN, STEPHAN R. · 1992 to 2020
$31.1M
Stem Cell/Organoid and Genome Editing CoreP30DK078392 · NIDDK · CINCINNATI CHILDRENS HOSP MED CTR · PI Alexander Miethke · 2007 to 2026
$24.4M
Utilizing the Phenomics of IBD to Enhance Gene DiscoveryU01DK062413 · NIDDK · CEDARS-SINAI MEDICAL CENTER · PI Dermot Patrick McGovern · 2002 to 2026
$12.2M
Characterizing the gut microbial ecosystem for diagnosis and therapy in IBDU54DK102557 · NIDDK · BROAD INSTITUTE, INC. · PI HUTTENHOWER, CURTIS, XAVIER, RAMNIK J · 2014 to 2015
$7.7M
A comprehensive platform for novel therapy development from the microbiomeR24DK110499 · NIDDK · BROAD INSTITUTE, INC. · PI HUTTENHOWER, CURTIS · 2017 to 2021
$7.7M
The Metabolomics Data Center and Workbench (MDCW)U01DK097430 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SUBRAMANIAM, SHANKAR · 2012 to 2017
$7.4M
Characterizing the gut microbial ecosystem for diagnosis and therapy in IBDU54DE023798 · NIDCR · BROAD INSTITUTE, INC. · PI HUTTENHOWER, CURTIS, XAVIER, RAMNIK J · 2013 to 2014
$3.0M
Functional activity and inter-organismal interactions in the human microbiomeR01HG005969 · NHGRI · HARVARD SCHOOL OF PUBLIC HEALTH · PI HUTTENHOWER, CURTIS · 2010 to 2012
$1.3M
NCATS NIH HHS UL1 TR001881NHGRI NIH HHS R01 HG005969NIDCR NIH HHS U54 DE023798NIDDK NIH HHS P01 DK046763NIDDK NIH HHS P30 DK040561NIDDK NIH HHS P30 DK043351NIDDK NIH HHS P30 DK078392NIDDK NIH HHS R24 DK110499NIDDK NIH HHS U01 DK062413NIDDK NIH HHS U54 DK102557
6 · The paper itself

Abstract

Inflammatory bowel diseases, which include Crohn's disease and ulcerative colitis, affect several million individuals worldwide. Crohn's disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (up to 24 time points each; in total 2,965 stool, biopsy, and blood specimens). Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. We demonstrate a characteristic increase in facultative anaerobes at the expense of obligate anaerobes, as well as molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. The study's infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi'omics Database ( http://ibdmdb.org ), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases.

Indexed as

AnimalsFungiGastrointestinal MicrobiomeHealthHumansInflammatory Bowel DiseasesPhylogenySpecies SpecificityTranscriptomeViruses

Identifiers

PMID31142855
PMCPMC6650278
OpenAlexW2947189704

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

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.