ArticleGenome biology2015
Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 128 papers, 2 of them syntheses that pooled it.
What it found
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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.
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.
Who cites it
128 citing papers in PubMed, 2 syntheses or guidelines pooled it, 213 citations in OpenAlex.
- Searching for a Consensus Among Inflammatory Bowel Disease Studies: A Systematic Meta-Analysis.Inflammatory bowel diseases · 2023Pooled it
- Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin.Genome biology · 2022Pooled it
- Probiotics Accelerate Microbiota and Metabolic Pathway Recovery Following Colonoscopy Bowel Preparation in Ulcerative Colitis.Medical science monitor : international medical journal of experimental and clinical research · 2026Trial
- Trial
- Efficacy of curcumin supplementation for the treatment and prevention of pouchitis after ileal pouch-anal anastomosis: a randomized controlled trial.European journal of nutrition · 2025Trial
- Multi-level aggregation analysis of microbiome composition and host gene expression reveals associations with systemic and local immunity.Microbiology spectrum · 2026Article
- Omics-based decoding of molecular and metabolic crosstalk in the skin barrier ecosystem.Cell death and differentiation · 2026Review
- Pterostilbene-mediated microbiota shifts: Implications and opportunities.Journal of traditional and complementary medicine · 2026Review
- Integrative Analysis of Intestinal Transcriptomes UnderscoresBioinformatics and biology insights · 2026Article
- Genomics of host-microbiome interactions in humans.Nature reviews. Genetics · 2026Review
- Article
- Deciphering the personalized functional redundancy hierarchy in the gut microbiome.Microbiome · 2025Article
- Article
- Host transcriptional responses to gut microbiome variation arising from urbanism.bioRxiv : the preprint server for biology · 2025Article
- Dissecting microbial communities with single-cell transcriptome analysis.Science (New York, N.Y.) · 2025Review
- Composition-on-composition regression analysis for multi-omics integration of metagenomic data.Bioinformatics (Oxford, England) · 2025Article
- Power-enhanced two-sample mean tests for high-dimensional microbiome compositional data.Biometrics · 2025Article
- Multiomic analysis reveals cellular, transcriptomic and epigenetic changes in intestinal pouches of ulcerative colitis patients.Nature communications · 2025Article
- Multiomic analysis reveals cellular, transcriptomic and epigenetic changes in intestinal pouches of ulcerative colitis patients.medRxiv : the preprint server for health sciences · 2025Article
- Navigating Chronic Pouchitis: Pathogenesis, Diagnosis, and Management.Gastroenterology & hepatology · 2025Article
68 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundPouchitis 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.
resultsHost 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.
conclusionsThis 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.
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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.