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Novel high-throughput in vivo approach to define pathobionts driving colitis

定义驱动结肠炎的病原体的新型高通量体内方法

基本信息

批准号：
10195416
负责人：
Janelle C Arthur
金额：
$ 23.33万
依托单位：
UNIV OF NORTH CAROLINA CHAPEL HILL
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-02-13 至 2023-01-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10195416
关键词：
16S ribosomal RNA sequencing Automobile Driving Bacterial Genome Bar Codes Biological Assay Candidate Disease Gene Chromosomes Chronic Clinical Coculture Techniques Colitis Collection Colon Colorectal Cancer Communities Complex Crohn&apos s disease DNA Data Disease Epithelial Cells Escherichia coli Etiology Feces Genome Genomics Germ-Free Gnotobiotic Harvest Health High-Throughput Nucleotide Sequencing Histologic Immune response In Vitro Individual Inflammation Inflammatory Inflammatory Bowel Diseases Insertional Mutagenesis Intestinal Fibrosis Intestinal Mucosa Intestines Invaded Metagenomics Microbe Molecular Molecular Analysis Molecular Profiling Mucous Membrane Mus Pathway interactions Patients Pattern Phenotype Positioning Attribute Rain Resistance Resolution Risk Signal Transduction Technology Testing Tissue Extracts Tissues Variant bacterial community base carcinogenicity comorbidity comparative genomics cost dysbiosis exhaustion experience fecal transplantation genetic signature high risk ileum in vivo inflammatory disease of the intestine innovation interdisciplinary approach macrophage metagenome metatranscriptomics microbial microbiome microbiome composition microbiota molecular marker mouse model novel novel strategies pathobiont screening

项目摘要

ABSTRACT Patients with Inflammatory Bowel Diseases (IBD) experience chronic intestinal inflammation as a consequence of inappropriate immune responses to the microbiota. Patients with IBD, particularly Crohn’s disease (CD), are at a greater risk of developing co-morbidities including intestinal fibrosis/stricturing and IBD-associated colorectal cancer (CRC). These diseases can be driven by specific strains of Escherichia coli. The CD and CRC microbiomes harbor high loads of mucosal E. coli described as “adherent-invasive E. coli” (AIEC). AIEC have no genomic definition, but instead are distinguished by functional attributes tested through exhaustive in vitro co-culture assays: the ability to adhere to and invade cultured epithelial cells and replicate and persist in macrophages. Our preliminary data indicate that this in vitro AIEC definition may not predict in vivo mucosal colonization, and that specific taxa expand with E. coli and contribute to inflammatory disease. The objectives of this proposal are to thoroughly interrogate the AIEC definition in vivo, define microbiome compositional changes driven by high levels of E. coli in colonic and ileal tissues, and identify candidate factors harbored by E. coli that permit colonization of the inflamed intestine. To this end, we have developed a polymicrobial colonization strategy that uses a novel barcoding technology to easily distinguish genetically similar, but functionally distinct sub-strains of clinical E. coli in a complex community. We have developed this strategy using a collection of well-characterized clinical AIEC and non-AIEC strains isolated from the intestinal mucosa of CD and healthy patients. This novel approach overcomes technological limitations associated with profiling bacterial metagenomes intimately associated with host tissues using molecular barcoded bacterial strains, gnotobiotic mouse models well-established in our lab, and barcode-targeted high-throughput sequencing and genomics. This innovative approach positions us to comprehensively interrogate the AIEC definition and identify molecular features required for colonization of the inflamed intestine. We must understand what microbial features promote mucosal colonization with high-risk E. coli strains in order to identify IBD patients at risk for a complicated disease course.

摘要