Foundry120 atlas

← IBD microbiome

Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients.

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Dataset overview

Participants 183
Samples 183
Reuse readiness 7.1/10 evidence-backed score

Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients.

Santoru ML, Piras C, Murgia A, Palmas V, Camboni T, Liggi S, Ibba I, Lai MA, et al. · Scientific reports · 2017

Abstract

Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract of uncertain origin, which includes ulcerative colitis (UC) and Crohn's disease (CD). The composition of gut microbiota may change in IBD affected individuals, but whether dysbiosis is the cause or the consequence of inflammatory processes in the intestinal tissue is still unclear. Here, the composition of the microbiota and the metabolites in stool of 183 subjects (82 UC, 50 CD, and 51 healthy controls) were determined. The metabolites content and the microbiological profiles were significantly different between IBD and healthy subjects. In the IBD group, Firmicutes, Proteobacteria, Verrucomicrobia, and Fusobacteria were significantly increased, whereas Bacteroidetes and Cyanobacteria were decreased. At genus level Escherichia, Faecalibacterium, Streptococcus, Sutterella and Veillonella were increased, whereas Bacteroides, Flavobacterium, and Oscillospira decreased. Various metabolites including biogenic amines, amino acids, lipids, were significantly increased in IBD, while others, such as two B group vitamins, were decreased in IBD compared to healthy subjects. This study underlines the potential role of an inter-omics approach in understanding the metabolic pathways involved in IBD. The combined evaluation of metabolites and fecal microbiome can be useful to discriminate between healthy subjects and patients with IBD.

doi:10.1038/s41598-017-10034-5 ↗ PMID 28842640 ↗ PMC5573342 ↗

Study facts

Organism
—
Platform
Illumina MiSeq
Age group
adult
Disease groups
Crohn's disease, Non-IBD controls, Ulcerative colitis
Anatomical sites
—

Data availability

Specific data assets have not been resolved from the source yet — see the source repository below for the full file listing.

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised
  • Taxonomic tables are advertised
  • Participant-to-sample mapping is available
  • Participant counts are documented
  • Sample counts are documented

Limitations

  • Not documented: feature/otu tables are advertised
Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

FieldValueEvidence
assay.platform Illumina MiSeq
analysis on the Illumina MiSeq platform

Section Library preparation and sequencing, offset 26300
assay.primers_reported True
primers targeting the V3 and V4 hypervariable region of the bacterial 16S rRNA gene

Section Library preparation and sequencing, offset 26300
assay.sequencing_type amplicon_16s
Barcoded amplicon libraries ... primers targeting the V3 and V4 hypervariable region of the bacterial 16S rRNA gene

Section Library preparation and sequencing, offset 26300
assay.target_region V3-V4
primers targeting the V3 and V4 hypervariable region of the bacterial 16S rRNA gene

Section Library preparation and sequencing, offset 26300

Cohort

FieldValueEvidence
cohort.age_group adult
the exclusion criteria were as follows: (a) age >80 or <20 years

Section Patients, offset 23800
cohort.crohns_disease_participants 50
183 subjects (82 UC, 50 CD, and 51 healthy controls)

Section study description, offset —
cohort.disease_activity_metadata_available True
Disease activity was verified by well-established criteria, including endoscopic grading according to the CDEIS and Rutgeerts scores for CD patients, and the Mayo score for UC patients

Section Patients, offset 23600
cohort.non_ibd_controls 51
183 subjects (82 UC, 50 CD, and 51 healthy controls)

Section study description, offset —
cohort.study_design cross_sectional
Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients.

Section study metadata, offset —
cohort.total_participants 183
the composition of the microbiota and the metabolites in stool of 183 subjects (82 UC, 50 CD, and 51 healthy controls) were determined.

Section study description, offset —
cohort.treatment_exposure_documented True
Therapy Mesalazine/Salazopyrin/Steroids ... Azatioprine ... Infliximab/Adalimumab ... No IBD therapy

Section Patients, offset 24200
cohort.ulcerative_colitis_participants 82
183 subjects (82 UC, 50 CD, and 51 healthy controls)

Section study description, offset —

Data_Assets

FieldValueEvidence
data_assets.open_access True
"license": "cc by"

Section publication metadata, offset 1350
data_assets.raw_reads True
All Illumina sequence data ... are available from the corresponding author on reasonable request.

Section Availability of data and material, offset 31000
data_assets.taxonomic_table True
The datasets (classification, number of reads, percentages, Spearman correlations) supporting the conclusions of this work are included within the article as additional files.

Section Availability of data and material, offset 31000

Specimens

FieldValueEvidence
specimens.longitudinal_sampling False
one fecal sample from each subject was collected

Section Patients, offset 23880
specimens.number_of_samples 183
A total of 18,899,323 sequencing reads were obtained from the 183 fecal samples.

Section Microbiota analysis, offset 4200
specimens.participant_to_sample_mapping_available True
one fecal sample from each subject was collected

Section Patients, offset 23880
specimens.sample_type stool
one fecal sample from each subject was collected

Section Patients, offset 23880