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Title: Analysis and characterisation of the faecal microbial degradome in inflammatory bowel disease. : Multi 'omic analysis of the gut microbiome in IBD      
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ID:
PRJEB13266
description:
Background. The gut microbiota is recognised as a contributory factor for IBD to develop, however, the method by which it does so still remains unclear. Dysbiosis of the microbiota has been suggested as one route by which the microbiota can trigger an abnormal immunological response and thus lead to the pathologies of IBD. However, the dysbiotic state has only been observed in individuals with IBD and not as a prodromal. Here we suggest that another feature of the microbiome, the active proteome, may be responsible for disease initiation and relapse. In particular the degradome, or proteolytic portion of the proteome. Here we measure the proteolytic activity, types and affected on tight junction integrity of proteins isolated from faeces of IBD and healthy volunteers. Methods. Faecal water and proteases (FWP) were isolated from stool samples taken from healthy (n=11) and IBD patients (Crohn’s disease n=7 and Ulcerative colitis n=6) and total proteins were extracted using a mechanical beadbeating lysis and normalized to 1mg/ml final concentration. The proteolytic activity was measured using a fluorescent substrate and types of proteases assessed using specific protease inhibitors. Tight junction integrity was assessed, in vitro, in the absence or presence of FWP, and with specific protease inhibitors, by trans epithelial resistance (TER). Metataxonomic and metagenomic analysis of the microbiota and microbiome were undertaken. Results. No significant difference in total proteins between either groups was measured, but there was a significantly higher levels of proteases, in FWP, in the IBD cohort when compared to healthy (P < 0.001 for azocasein and <0.001 for Keratin azure). Specific protease inhibitors showed greatest inhibition for the bacterial class. Mammalian specific inhibitors also reduced activity, while fungal protease inhibitors only inhibited IBD samples. No significant signatures relating to proteases were seen in the microbiome from analysis of the metagenomes, but there was a decrease in OTUs from the Verrumicrobia in samples with low levels of proteolytic activity. Tight junction integrity was compromised by the FWP and there was a strong inverse correlation with high levels of FWP and TER, which was abrogated by addition of inhibitors of bacterial proteases. Conclusions. The proteolytic fraction of the gut metaproteome is responsible for affecting the tight junction integrity of colonocytes and positively correlates with reduction in TER. We conclude that the levels of microbial proteases in the colon are associated with disease severity, but currently this is a trend and not a significant association.
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJEB13266
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abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject