Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ
Journal
Cell host & microbe
Year
2014
Inflammatory bowel diseases (IBDs), including Crohn's disease (CD), are genetically linked to host pathways that implicate an underlying role for aberrant immune responses to intestinal microbiota. However, patterns of gut microbiome dysbiosis in IBD patients are inconsistent among published studies. Using samples from multiple gastrointestinal locations collected prior to treatment in new-onset cases, we studied the microbiome in the largest pediatric CD cohort to date. An axis defined by an increased abundance in bacteria which include Enterobacteriaceae, Pasteurellacaea, Veillonellaceae, and Fusobacteriaceae, and decreased abundance in Erysipelotrichales, Bacteroidales, and Clostridiales, correlates strongly with disease status. Microbiome comparison between CD patients with and without antibiotic exposure indicates that antibiotic use amplifies the microbial dysbiosis associated with CD. Comparing the microbial signatures between the ileum, the rectum, and fecal samples indicates that at this early stage of disease, assessing the rectal mucosal-associated microbiome offers unique potential for convenient and early diagnosis of CD.
Experiment 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-16
Curated date: 2023/03/13
Curator: Khadeeejah
Revision editor(s): Chloe, Claregrieve1, Khadeeejah, Atrayees, Aiyshaaaa, Victoria
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Ileum , Rectum Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum,Intestinum rectum,Rectal sac,Terminal portion of intestine,Terminal portion of large intestine,Rectum,rectum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Crohn's disease Colitis, Granulomatous,CROHN DIS,Crohn Disease,Crohn disease,Crohn's associated gastritis,Crohn's disease,Crohn's disease of colon,Crohn's disease of large bowel,CROHNS DIS,Crohns Disease,Enteritis, Granulomatous,Enteritis, Regional,Gastritis Associated with Crohn Disease,Gastritis Associated with Crohn's Disease,granulomatous colitis,Ileitis, Regional,Ileitis, Terminal,Ileocolitis,pediatric Crohn's disease,regional enteritis,crohn disease,crohn's disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Crohn's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Treatment-naive pediatric patients (ages 3-17) with new-onset Crohn's disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 221
- Group 1 sample size Number of subjects in the case (exposed) group
- 447
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- Linear Regression
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, antibiotic exposure, race, sex, Confounders controlled for: "subject" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.subject, Confounders controlled for: "diagnosis" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.diagnosis, Confounders controlled for: "ulcering" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.ulcering, Confounders controlled for: "PCDAI" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.PCDAI, Confounders controlled for: "biopsy location" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.biopsy location, Confounders controlled for: "ileal involvement" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.ileal involvement
Alpha Diversity
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-16
Curated date: 2023/03/13
Curator: Khadeeejah
Revision editor(s): Khadeeejah, Atrayees, Chloe, Aiyshaaaa
Source: Table S2A
Description: Alteration in the abundance of several taxa in the ileal and rectal samples, in the diagnosis variable.
Abundance in Group 1: increased abundance in Crohn's disease
Revision editor(s): Khadeeejah, Atrayees, Chloe, Aiyshaaaa
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-16
Curated date: 2023/03/13
Curator: Khadeeejah
Revision editor(s): Khadeeejah, Aiyshaaaa, Chloe, Atrayees
Source: Table S2A
Description: Alteration in the abundance of several taxa in the ileal and rectal samples, in the diagnosis variable.
Abundance in Group 1: decreased abundance in Crohn's disease
Revision editor(s): Khadeeejah, Aiyshaaaa, Chloe, Atrayees
Experiment 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-16
Curated date: 2023/04/04
Curator: Khadeeejah
Revision editor(s): Khadeeejah, Aiyshaaaa, Atrayees, Victoria
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, antibiotic exposure, race, sex, Confounders controlled for: "ulcering" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.ulcering, Confounders controlled for: "subject" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.subject, Confounders controlled for: "diagnosis" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.diagnosis, Confounders controlled for: "PCDAI" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.PCDAI, Confounders controlled for: "biopsy location" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.biopsy location, Confounders controlled for: "ileal involvement" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.ileal involvement
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-16
Source: Table S2B
Description: Taxa in stool samples significantly associated with disease.
Abundance in Group 1: increased abundance in Crohn's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae | ||
| Ruminococcus | ||
| Dorea | ||
| Blautia producta | ||
| [Ruminococcus] torques |
Revision editor(s): Khadeeejah, Aiyshaaaa, Atrayees
Experiment 3
Reviewed Marked as Reviewed by Atrayees on 2023-6-16
Curated date: 2023/04/04
Curator: Khadeeejah
Revision editor(s): Khadeeejah, Aiyshaaaa, Atrayees, Victoria
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Ileum , Rectum , Feces Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum,Intestinum rectum,Rectal sac,Terminal portion of intestine,Terminal portion of large intestine,Rectum,rectum,Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, antibiotic exposure, race, sex, Confounders controlled for: "PCDAI" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.PCDAI, Confounders controlled for: "diagnosis" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.diagnosis, Confounders controlled for: "subject" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.subject, Confounders controlled for: "ileal involvement" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.ileal involvement, Confounders controlled for: "ulcering" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.ulcering, Confounders controlled for: "biopsy location" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.biopsy location
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-16
Source: Table S2C
Description: precise differences between the mucosal tissue and stool samples within patients with new-onset CD
Abundance in Group 1: increased abundance in Crohn's disease
Revision editor(s): Khadeeejah, Aiyshaaaa, Atrayees
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-16
Source: Tabls S2C
Description: precise differences between the mucosal tissue and stool samples within patients with new-onset CD
Abundance in Group 1: decreased abundance in Crohn's disease
Revision editor(s): Khadeeejah, Aiyshaaaa, Atrayees
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