Metagenomic analysis of Crohn’s Disease

Sammanfattning

Inflammatory Bowel Disease (IBD) is a chronic and incurable condition that is increasing inprevalence across the globe. This illness consist of two forms: Crohn’s Disease (CD) andUlcerative Colitis (UC). CD is characterised by a patch inflammation pattern across the gut anda multitude of different factors, such as diet. Contemporary research has found a link betweengut dysbiosis and the development of IBD, suggesting that the microbial flora colonising the guthave a vital part to play in the development of CD.This paper aims to identify taxa associated with CD. This is done through the application ofmachine learning algorithms as standard univariate statistical methods fail to apply in the highlyinterdependent domain of the gut microbiome. The compositionally of the data and externalfactors influencing variance in the data will be taken into account.After applying a Center Log ratio transformation (CLR) to a MetaPhlAn3 taxonomic profile andusing a random forest classifier the following five taxa were identified as the most important inthe association to CD: Ruminococcaceae bacterium, Akkermansia muciniphila, Streptococcusparasanguinis, Flavonifractor plautii and Bifidobacterium bifidum.