Evidence map›Paper›PMID 30531976›Full record

ArticleNature microbiology2019

Gut microbiome structure and metabolic activity in inflammatory bowel disease.

Eric A Franzosa, Alexandra Sirota-Madi, Julian Avila-Pacheco, Nadine Fornelos, Henry J Haiser, Stefan Reinker, Tommi Vatanen, A Brantley Hall, Himel Mallick, Lauren J McIver and 17 more

Erratum issued Registry-linked trialAbstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature microbiology, 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 trial NCT04165265 (Reduction in Length of Hospitalization in Patients With Acute Severe Ulcerative Colitis Treated With Rescue Therapy With Infliximab by the Use of Web-app Constant-Care. One Year Follow-up, Inclusive Colectomy Rate.), which is not on this map. Cited by 1,149 papers, 4 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
1,149citing papers in PubMed, 4 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.

NCT04165265 naunknown statusnot on this map

Reduction in Length of Hospitalization in Patients With Acute Severe Ulcerative Colitis Treated With Rescue Therapy With Infliximab by the Use of Web-app Constant-Care. One Year Follow-up, Inclusive Colectomy Rate.

TypeinterventionalSponsorNordsjaellands HospitalRan2019 to 2021Enrolled28ConditionsUlcerative Colitis, TelemedicineArmsConstant-Care
3 · Its place in the literature

Who cites it

1,149 citing papers in PubMed, 4 syntheses or guidelines pooled it.

  1. Pooled it
  2. Pooled it
  3. Pooled it
  4. Pooled it
  5. Trial
  6. Gut microbes · 2026
    Article
  7. Article
  8. Review
  9. Review
  10. Article
  11. Review
  12. Phenolic-Rich Extract fromFoods (Basel, Switzerland) · 2026
    Article
  13. Article
  14. Article
  15. Article
  16. Docosahexaenoic acid alleviates DSS-induced colitis by regulating the gut microbiota and restoring the gut barrier.International microbiology : the official journal of the Spanish Society for Microbiology · 2026
    Article
  17. Review
  18. Article
  19. Article
  20. Article

1,089 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

27 authors.

Eric A FranzosaBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-8798-7068
Alexandra Sirota-MadiBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Julian Avila-PachecoBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Nadine FornelosBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Henry J HaiserNovartis Institute for Biomedical Research Inc., Cambridge, MA, USA.
Stefan ReinkerNovartis Institute for Biomedical Research Inc., Cambridge, MA, USA.
Tommi VatanenBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-0949-1291
A Brantley HallBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Himel MallickBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Lauren J McIverBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Jenny S SaukGastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Robin G WilsonGastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Betsy W StevensGastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Justin M ScottBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Kerry PierceBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Amy A DeikBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Kevin BullockBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Floris ImhannDepartment of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.ORCID http://orcid.org/0000-0001-5278-903X
Jeffrey A PorterNovartis Institute for Biomedical Research Inc., Basel, Switzerland.
Alexandra ZhernakovaDepartment of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.
Jingyuan FuDepartment of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.
Rinse K WeersmaDepartment of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.
Cisca WijmengaDepartment of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.
Clary B ClishBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-8259-9245
Hera VlamakisBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Curtis HuttenhowerBroad Institute of MIT and Harvard, Cambridge, MA, USA. chuttenh@hsph.harvard.edu.ORCID http://orcid.org/0000-0002-1110-0096
Ramnik J XavierBroad Institute of MIT and Harvard, Cambridge, MA, USA. xavier@molbio.mgh.harvard.edu.ORCID http://orcid.org/0000-0002-5630-5167

Funding

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
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
Autophagy genes and the microbiome in Crohn's DiseaseR01DK092405 · NIDDK · BROAD INSTITUTE, INC. · PI XAVIER, RAMNIK J · 2012 to 2014
$2.0M
NIDDK NIH HHS P30 DK040561NIDDK NIH HHS P30 DK043351NIDDK NIH HHS R01 DK092405NIDDK NIH HHS R24 DK110499NIDDK NIH HHS U01 DK097430NIDDK NIH HHS U54 DK102557
6 · The paper itself

Abstract

The inflammatory bowel diseases (IBDs), which include Crohn's disease (CD) and ulcerative colitis (UC), are multifactorial chronic conditions of the gastrointestinal tract. While IBD has been associated with dramatic changes in the gut microbiota, changes in the gut metabolome-the molecular interface between host and microbiota-are less well understood. To address this gap, we performed untargeted metabolomic and shotgun metagenomic profiling of cross-sectional stool samples from discovery (n = 155) and validation (n = 65) cohorts of CD, UC and non-IBD control patients. Metabolomic and metagenomic profiles were broadly correlated with faecal calprotectin levels (a measure of gut inflammation). Across >8,000 measured metabolite features, we identified chemicals and chemical classes that were differentially abundant in IBD, including enrichments for sphingolipids and bile acids, and depletions for triacylglycerols and tetrapyrroles. While > 50% of differentially abundant metabolite features were uncharacterized, many could be assigned putative roles through metabolomic 'guilt by association' (covariation with known metabolites). Differentially abundant species and functions from the metagenomic profiles reflected adaptation to oxidative stress in the IBD gut, and were individually consistent with previous findings. Integrating these data, however, we identified 122 robust associations between differentially abundant species and well-characterized differentially abundant metabolites, indicating possible mechanistic relationships that are perturbed in IBD. Finally, we found that metabolome- and metagenome-based classifiers of IBD status were highly accurate and, like the vast majority of individual trends, generalized well to the independent validation cohort. Our findings thus provide an improved understanding of perturbations of the microbiome-metabolome interface in IBD, including identification of many potential diagnostic and therapeutic targets.

Indexed as

Gastrointestinal MicrobiomeBiodiversityBiomarkersColitis, UlcerativeCrohn DiseaseFecesHumansInflammationInflammatory Bowel DiseasesLeukocyte L1 Antigen ComplexMetabolomeMetagenomeBiomarkersLeukocyte L1 Antigen Complex

Identifiers

PMID30531976
PMCPMC6342642

What OpenQuestion holds

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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.