Background The healthy human intestine is represented by the presence of bacterial communities predominantly belonging to obligate anaerobes; however disparity and dysanaerobiosis in intestinal microflora may lead to the progression of ulcerative colitis (UC). (qPCR) was performed to determine total bacterial abundances. Results Analysis of 23,927 OTUs exhibited a significant reduction of bacterial diversity consistently from phylum to species level (p?Retapamulin (SB-275833) supplier this age, every individual develops a unique and complex gut microbiota which remains stable throughout adulthood [2,14,16-19]. These complex microbial communities have evolved and developed persistently in shaping up the mucosal immune system during the early phase of life. Absence of these intestinal microbial communities leads to defective cell mediated immune response, discontinuous cytokine production, reduction of total mucosal cell turnover and muscle wall thickness, thereby, giving rise to various autoimmune diseases [3,8,9,16,20,21]. Some of the recent studies have also indicated the crucial role of phyla Proteobacteria in the pathogenesis of UC [22]. Proteobacteria is the largest and most diverse bacterial phyla with known clinical importance in human gastrointestinal diseases, and are implicated in luminal dysbiosis leading to the imbalance between the plausible pathogenic bacteria and functionally defensive commensal bacteria [22-24]. From the experiments performed so far on animal models of IBD, it is apparent that very few signs of inflammation are observed in germ-free animals as compared to the animals that harbour natural microflora [4,8,11]. Many Retapamulin (SB-275833) supplier comparative studies of gut microbiota of patients with IBD and non-IBD controls have been directed towards determination of specific core microbiota or assigning tentatively a particular group, genus, species or strain of microorganism to the prognosis of IBD [8,9,13,25]. These studies have clearly marked the imbalance or dysbiosis in the gut Flt3 microbiota of patients suffering from either CD or UC [8-11,25]. In addition, one of the contemporary study has also proved that this microbiota composition in healthy and diseased individuals is influenced by ethnic and geographical factors [26], thus it becomes more pertinent to study the microbiota composition from different geographical and ethnic niches. Collectively, all these studies confirm the changes which occur in the gut microbial communities in UC patients as compared to healthy controls. [8-11,25] However, these cross-sectional studies in which the disease status is neglected can lead towards complicated outcome, very few studies, have considered the role of mucosal microbiota in relation with the severity of disease [27]. Studies which investigate the compositional microbiota with changes in disease status are currently inadequate. Therefore, the principal aim of the current study is to evaluate and compare the differences between the mucosa associated microbiota of patients manifesting moderate, moderate, and severe stage of UC, as defined by a Simple Clinical Colitis Activity Index (SCCAI)??5 and Baron Score for UC [4,12,28-30]. We adapted two independent techniques to assess and correlate specific bacterial groups in colonic mucosal biopsy samples (collected in a manner that precisely maintained the composition of the microbiota). Amplicon libraries of 16S rRNA genes were generated by Illumina-based deep sequencing method, which were subsequently used to demonstrate the differences in taxonomic diversity of microbial communities in patients suffering from the three different stages of UC. We also applied quantitative real-time polymerase chain reaction (qPCR) to quantify the total bacterial abundance among selected sub-sets of samples. The present findings demonstrate data.