Evidence map›Paper›PMID 29183332›Full record

ArticleGenome medicine2017

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients.

Andrew Brantley Hall, Moran Yassour, Jenny Sauk, Ashley Garner, Xiaofang Jiang, Timothy Arthur, Georgia K Lagoudas, Tommi Vatanen, Nadine Fornelos, Robin Wilson and 12 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome medicine, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 490 papers, 4 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
490citing papers in PubMed, 4 pooled it
16.6field-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.

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

490 citing papers in PubMed, 4 syntheses or guidelines pooled it, 756 citations in OpenAlex.

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  19. Extensive library ofMicrobiology spectrum · 2026
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430 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

22 authors at 3 institutions in 2 countries.

Andrew Brantley HallBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Moran YassourBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Jenny SaukGastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.
Ashley GarnerBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Xiaofang JiangBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Timothy ArthurBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Georgia K LagoudasBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Tommi VatanenBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Nadine FornelosBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Robin WilsonGastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.
Madeline BerthaEmory University School of Medicine, Emory University, Atlanta, GA, 30322, USA.
Melissa CohenGastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.
John GarberGastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.
Hamed KhaliliGastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.
Dirk GeversBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Ashwin N AnanthakrishnanGastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.
Subra KugathasanEmory University School of Medicine, Emory University, Atlanta, GA, 30322, USA.
Eric S LanderBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Paul BlaineyBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Hera VlamakisBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Ramnik J XavierBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. xavier@molbio.mgh.harvard.edu.
Curtis HuttenhowerBroad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. chuttenh@hsph.harvard.edu.ORCID http://orcid.org/0000-0002-1110-0096
Broad Institute · USHarvard University · USEmory University · US

Funding

Pilot & Feasibility ProgramP30DK043351 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI Ramnik J Xavier · 1991 to 2026
$35.3M
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
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
Autophagy genes and the microbiome in Crohn's DiseaseR01DK092405 · NIDDK · BROAD INSTITUTE, INC. · PI XAVIER, RAMNIK J · 2012 to 2014
$2.0M
Natural history of the infant gut microbiome in health and disease: establishment, feeding & implications for allergyK99DK113224 · NIDDK · BROAD INSTITUTE, INC. · PI YASSOUR, MORAN · 2017 to 2018
$180k
National Institute of Diabetes and Digestive and Kidney Diseases P30DK43351National Institute of Diabetes and Digestive and Kidney Diseases R01DK92405National Institutes of Health (US) U54DE023798National Science Foundation (US) MCB-1453942NIDCR NIH HHS U54 DE023798NIDDK NIH HHS K99 DK113224NIDDK NIH HHS P30 DK043351NIDDK NIH HHS R01 DK092405NIDDK NIH HHS U54 DK102557
6 · The paper itself

Abstract

backgroundInflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functional correlates with IBD outcomes.

methodsWe performed metagenomic sequencing of monthly stool samples from 20 IBD patients and 12 controls (266 total samples). These were taxonomically profiled with MetaPhlAn2 and functionally profiled using HUMAnN2. Differentially abundant species were identified using MaAsLin and strain-specific pangenome haplotypes were analyzed using PanPhlAn.

resultsWe found a significantly higher abundance in patients of facultative anaerobes that can tolerate the increased oxidative stress of the IBD gut. We also detected dramatic, yet transient, blooms of Ruminococcus gnavus in IBD patients, often co-occurring with increased disease activity. We identified two distinct clades of R. gnavus strains, one of which is enriched in IBD patients. To study functional differences between these two clades, we augmented the R. gnavus pangenome by sequencing nine isolates from IBD patients. We identified 199 IBD-specific, strain-specific genes involved in oxidative stress responses, adhesion, iron-acquisition, and mucus utilization, potentially conferring an adaptive advantage for this R. gnavus clade in the IBD gut.

conclusionsThis study adds further evidence to the hypothesis that increased oxidative stress may be a major factor shaping the dysbiosis of the microbiome observed in IBD and suggests that R. gnavus may be an important member of the altered gut community in IBD.

Indexed as

AdultAgedFecesGastrointestinal MicrobiomeGenome, BacterialHumansInflammatory Bowel DiseasesMiddle AgedOxidative StressPhylogenyRuminococcusSpecies SpecificityYoung Adult

Identifiers

PMID29183332
PMCPMC5704459
OpenAlexW2769664962

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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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.