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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-04-08

AUTHORS

Xochitl C Morgan, Boyko Kabakchiev, Levi Waldron, Andrea D Tyler, Timothy L Tickle, Raquel Milgrom, Joanne M Stempak, Dirk Gevers, Ramnik J Xavier, Mark S Silverberg, Curtis Huttenhower

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. More... »

PAGES

67

References to SciGraph publications

  • 2011-12-01. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2012-03-08. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2011-07-17. Bayesian community-wide culture-independent microbial source tracking in NATURE METHODS
  • 2009. The Elements of Statistical Learning, Data Mining, Inference, and Prediction in NONE
  • 2012-06-13. Structure, function and diversity of the healthy human microbiome in NATURE
  • 2013-12-11. Diet rapidly and reproducibly alters the human gut microbiome in NATURE
  • 2010-10-07. Supervised classification of microbiota mitigates mislabeling errors in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2013-04-05. High abundance and diversity of antimicrobial resistance determinants among early vancomycin-resistant Enterococcus faecium in Poland in EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
  • 2001-05. Clinical Features of Patients with Invasive Eikenella corrodens Infections and Microbiological Characteristics of the Causative Isolates in EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
  • 2009-02-03. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists in BMC BIOINFORMATICS
  • 2012-09-26. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment in GENOME BIOLOGY
  • 2009-05-29. Gene Set Enrichment Analysis in PROTEIN NETWORKS AND PATHWAY ANALYSIS
  • 2011-03-15. Antibiotic Therapy in Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis in THE AMERICAN JOURNAL OF GASTROENTEROLOGY
  • 2013-03-04. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis in MICROBIOME
  • 2008-03. What is principal component analysis? in NATURE BIOTECHNOLOGY
  • 2010-04-11. QIIME allows analysis of high-throughput community sequencing data in NATURE METHODS
  • 2007-07-12. Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn's disease involving the ileum in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2006-01-01. Breadcrumbs in INTEGRIERTE INFORMATIONSARCHITEKTUR
  • 2010-03. A human gut microbial gene catalogue established by metagenomic sequencing in NATURE
  • 2011-06-24. Metagenomic biomarker discovery and explanation in GENOME BIOLOGY
  • 2008-05-20. Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis in BMC BIOINFORMATICS
  • 2013-11-04. Increased abundance of Sutterella spp. and Ruminococcus torques in feces of children with autism spectrum disorder in MOLECULAR AUTISM
  • 2001-10-01. Ecologically meaningful transformations for ordination of species data in OECOLOGIA
  • 2012-10-31. Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease in NATURE
  • 2006-01-31. The RIN: an RNA integrity number for assigning integrity values to RNA measurements in BMC MOLECULAR AND CELL BIOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13059-015-0637-x

    DOI

    http://dx.doi.org/10.1186/s13059-015-0637-x

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1019300544

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/25887922


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