Paired mucosal j-pouch and afferent limb samples from postoperative ulcerative colitis and familial ademonatous polyposis patients from Mount Sinai Hospital, Toronto. Samples were collected during pouch endoscopy and 16S sequenced.

Dataset overview

Participants 204

Samples 652

Reuse readiness 8.9/10 evidence-backed score

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease.

Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, et al. · Genome biology · 2015

Abstract

<h4>Background</h4>Pouchitis is common after ileal pouch-anal anastomosis (IPAA) surgery for ulcerative colitis (UC). Similar to inflammatory bowel disease (IBD), both host genetics and the microbiota are implicated in its pathogenesis. We use the IPAA model of IBD to associate mucosal host gene expression with mucosal microbiomes and clinical outcomes. We analyze host transcriptomic data and 16S rRNA gene sequencing data from paired biopsies from IPAA patients with UC and familial adenomatous polyposis. To achieve power for a genome-wide microbiome-transcriptome association study, we use principal component analysis for transcript and clade reduction, and identify significant co-variation between clades and transcripts.<h4>Results</h4>Host transcripts co-vary primarily with biopsy location and inflammation, while microbes co-vary primarily with antibiotic use. Transcript-microbe associations are surprisingly modest, but the most strongly microbially-associated host transcript pattern is enriched for complement cascade genes and for the interleukin-12 pathway. Activation of these host processes is inversely correlated with Sutterella, Akkermansia, Bifidobacteria, and Roseburia abundance, and positively correlated with Escherichia abundance.<h4>Conclusions</h4>This study quantifies the effects of inflammation, antibiotic use, and biopsy location upon the microbiome and host transcriptome during pouchitis. Understanding these effects is essential for basic biological insights as well as for well-designed and adequately-powered studies. Additionally, our study provides a method for profiling host-microbe interactions with appropriate statistical power using high-throughput sequencing, and suggests that cross-sectional changes in gut epithelial transcription are not a major component of the host-microbiome regulatory interface during pouchitis.

doi:10.1186/s13059-015-0637-x ↗ PMID 25887922 ↗ PMC4414286 ↗

Study facts

Organism: human gut metagenome
Platform: Illumina MiSeq
Age group: adult
Disease groups: —
Anatomical sites: —

Data availability

Analysis code

Strengths & limitations for reuse

Strengths

Raw reads are advertised
Feature/OTU tables are advertised
Taxonomic tables are advertised
Analysis code is available
Participant-to-sample mapping is available
Participant counts are documented
Sample counts are documented

Extraction evidence & provenance

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

Assay

Field	Value	Evidence
`assay.paired_end`	True	generating paired-end reads of 175 bp in length in each direction Section `Methods—16S profiling and sequencing`, offset 42000
`assay.platform`	Illumina MiSeq from source	ENA instrument_model=Illumina MiSeq Section `ENA study report`, offset —
`assay.primers_reported`	True	Primers: 515 F [GTGCCAGCMGCCGCGGTAA] and 806R [GGACTACHVGGGTWTCTAAT] Section `Methods—16S profiling and sequencing`, offset 41400
`assay.read_depth_reported`	29914	A mean sequence depth of 29,914 sequences/sample was obtained Section `Methods—Bioinformatic processing of sequences`, offset 43200
`assay.read_length`	175	generating paired-end reads of 175 bp in length in each direction Section `Methods—16S profiling and sequencing`, offset 42000
`assay.sequencing_type`	amplicon_16s	Samples were collected during pouch endoscopy and 16S sequenced. Section `study description`, offset —
`assay.target_region`	V4	The 16S gene dataset consists of Illumina MiSeq sequences targeting the V4 variable region. Section `Methods—16S profiling and sequencing`, offset 41000

Cohort

Field	Value	Evidence
`cohort.age_group`	adult	Patients who had surgical management of UC or FAP were included... aged between 18 and 78 years Section `Results`, offset 4750
`cohort.disease_activity_metadata_available`	True	to numerically score inflammation, the severity of objective traits was graded... and the inflammation score was defined as the sum of these traits Section `Methods—Patient cohort`, offset 35000
`cohort.study_design`	cross_sectional	a large, metadata-rich, cross-sectional cohort Section `Results`, offset 4700
`cohort.total_participants`	204	After quality control, there was host gene expression and microbiome data obtained by microarray and 16S analysis from a total of 255 samples representing 204 individuals Section `Results`, offset 4900
`cohort.treatment_exposure_documented`	True	antibiotic use was reported as ‘true’ if patients had taken antibiotics in the 30 days prior to biopsy collections Section `Methods—Patient cohort`, offset 36500

Data_Assets

Field	Value	Evidence
`data_assets.analysis_code`	True	This analysis was performed by the associated corpower.Rnw script. Section `Methods—Power calculations`, offset 44700
`data_assets.feature_or_otu_table`	True	this pipeline picks OTUs using a reference-based method and constructs an OTU table Section `Methods—Bioinformatic processing of sequences`, offset 42800
`data_assets.open_access`	True from source	"license": "cc by" Section `publication metadata`, offset —
`data_assets.pipeline_or_tool_versions`	True	further processed in a data curation pipeline implemented in QIIME 1.5.0 Section `Methods—Bioinformatic processing of sequences`, offset 42600
`data_assets.qc_or_negative_controls_reported`	True	The resulting OTU tables are checked for mislabeling and contamination Section `Methods—Bioinformatic processing of sequences`, offset 43000
`data_assets.raw_reads`	True	16S sequence data for this project have been filtered to remove human sequences and are publicly available as Bioproject PRJNA269954 Section `Data availability`, offset 47800
`data_assets.sample_metadata`	True	Metadata are available at [74]. Section `Data availability`, offset 48100
`data_assets.taxonomic_table`	True	Taxonomy is assigned using the Greengenes predefined taxonomy map of reference sequence OTUs to taxonomy Section `Methods—Bioinformatic processing of sequences`, offset 42900

Specimens

Field	Value	Evidence
`specimens.body_site`	mucosal biopsies from the ileal J-pouch and pre-pouch ileum (afferent limb)	Tissue biopsies were obtained from the mid-portion of the pouch and the PPI during pouchoscopy. Section `Methods—Sample collection`, offset 38100
`specimens.inflamed_status_available`	True	any score over 3 was considered inflamed Section `Methods—Patient cohort`, offset 35200
`specimens.longitudinal_sampling`	False inferred	a large, metadata-rich, cross-sectional cohort Section `Results`, offset 4700
`specimens.number_of_samples`	652 from source	ENA sample_count=652 Section `ENA study report`, offset —
`specimens.participant_to_sample_mapping_available`	True	255 samples representing 204 individuals; these comprised 196 PPI samples and 59 pouch samples Section `Results`, offset 4900
`specimens.sample_type`	mucosal_biopsy	Tissue biopsies were obtained from the mid-portion of the pouch and the PPI during pouchoscopy. Section `Methods—Sample collection`, offset 38100