Significant progress has been made in the knowledge of gut microbiome (GM) and no doubt seems to remain on the association of dysbiosis with inflammatory bowel diseases (IBD). Although it is not clear whether this bacterial imbalance is a cause or consequence of symptoms, modulation of intestinal bacteria is viewed as a therapeutic strategy for IBD. However, any approach of reversing dysbiosis should take in account inter-individual differences in GM's structure and function. These variations are among the reasons for different outcomes of culture based bacteriotherapy and fecal transplantation for the disease management. By analyzing the mucosal associated GM of a group adult ulcerative colitis (UC) and Crohn's disease (CD) patients, this study aimed to contribute with additional data on dysbiosis in IBD.Methods:
Gut mucosal biopsies from 23 controls (Co), 19 CD and 14 UC patients were subjected to DNA purification and PCR amplification using primers specific for the V6 region of 16S ribosomal rRNA gene (16SV6rDNA). The resulting amplicons were sequenced by the Ion torrent PGM machine, processed and analyzed with bioinformatics tools available at MG-Rast server (http://metagenomics.anl.gov/), having as a reference the RDP database. The patients comprised adult (61 ± 12, 38 ± 14 and 39 ± 18 Y/O, respectively for Co, CD and UC group) attending the Endoscopy Unit of the Botucatu Medical School, State University of São Paulo, who were not under antibiotic therapy within 3 months preceding the colonoscopy examination. A single biopsy was sampled from each subject (from ileum or right colon, in Co and CD groups and from any part of the large bowel in UC).Results:
Both UC and CD patients presented gut dysbiosis, reflected in reduced mean a-diversity in bacterial population as compared with corresponding a-diversity of controls. Dysbiosis was more evident among CD patients and characterized by a >50% negative difference in the average number of Firmicutes (17,566 in Co × 6842 in CD, P = 0.03) and a ca. twice higher positive difference in that of unclassified (4046 in Co × 12,018 in CD, P = 0.03) 16SV6rDNA reads. In UC, dysbiosis was marked by a reduction in Firmicutes reads only (17,566 in Co ×, 4974 in UC P = 0.03). Lower numbers of Clostridia and Bacilli accounted for most of Firmicutes dysbiosis in CD and of Clostridia for Firmicutes dysbiosis in UC. However, Bacteroides thetaiotaomicron (Bacilli) was reduced both in UC and CD (567 reads in Co × 180 reads in CD [P = 0.04] and 82.5 reads in UC [P = 0.03]). Eubacterium hallii (Clostridia) contributed for Firmicutes dysbiosis in both CD and UC (reads: 148 in Co × 44.5 in CD, P = 0.02, and 28 in UC, P = 0.01). In CD, but not in UC, a number of other species, such as Roseburia inulinivorans (reads: 320 × 69, P = 0.03), contributed for Firmicutes dysbiosis.Conclusions:
In conclusion, for the studied population, dysbiosis was more pronounced among CD than UC patients, and was characterized by a higher number of unclassified bacterial sequences.