Gut bacteria play a key role in initiating and maintaining the inflammatory process in the gut tissues of inflammatory bowel disease (IBD) patients, by supplying antigens or other stimulatory factors that trigger immune cell activation. Changes in the composition of the intestinal microbiota in IBD patients compared to that in healthy controls and a reduced diversity of intestinal microbial species are linked to the pathogenesis of IBD.

Intestinal dysbiosis in inflammatory bowel disease (IBD) patients depend on disease activity. We aimed to characterize the microbiota after 7 years of follow-up in an unselected cohort of IBD patients according to disease activity and disease severity. Fifty eight Crohn’s disease (CD) and 82 ulcerative colitis (UC) patients were included. Disease activity was assessed by the Harvey-Bradshaw Index for CD and Simple Clinical Colitis Activity Index for UC. Microbiota diversity was assessed by 16S rDNA MiSeq sequencing. In UC patients with active disease and in CD patients with aggressive disease the richness (number of OTUs, p = 0.018 and p = 0.013, respectively) and diversity (Shannons index, p = 0.017 and p = 0.023, respectively) were significantly decreased. In the active UC group there was a significant decrease in abundance of the phylum Firmicutes (p = 0.018). The same was found in CD patients with aggressive disease (p = 0.05) while the abundance of Proteobacteria phylum showed a significant increase (p = 0.03) in CD patients. We found a change in the microbial abundance in UC patients with active disease and in CD patients with aggressive disease. These results suggest that dysbiosis of the gut in IBD patients is not only related to current activity but also to the course of the disease.

Ulcerative colitis (UC) is a chronic inflammatory bowel disease. The probiotic bacterium Escherichia coli Nissle 1917 (EcN) has been used to maintain and induce clinical remission in UC. Our aim was to test the effect of Ciprofloxacin and/or orally administered EcN as add-on to conventional therapies in patients with active UC. Our single center double-blinded randomized placebo controlled study included patients with a Colitis Activity Index (CAI) score of at least 6. Patients were randomized to Ciprofloxacin or placebo for 1week followed by EcN or placebo for 7weeks. All 4 treatments were given as add-on treatments. One hundred subjects with active UC were recruited. In the per-protocol analysis we, surprisingly, found that in the group receiving placebo/EcN fewer patients, 54%, reached remission compared to the group receiving placebo/placebo, 89%, p<0.05. Among patients treated with Cipro/placebo and Cipro/EcN, 78% and 66% reached remission, respectively. Furthermore, the group receiving placebo/EcN had the largest number of withdrawals, 11 of 25 (44%), compared to 15 of 75 (20%) in any of the other groups, p<0.05. Indication of lack of mucosal healing was found in the group treated with placebo/Nissle, since only 4 (29%) of the 14 patients, who completed the study, reported no blood in stools at week 12 (p<0.02), compared to 63%, 67% and 65% in groups treated with Cipro/Nissle, Cipro/placebo and placebo/placebo, respectively. Our data suggest that there is no benefit in the use of E. coli Nissle as an add-on treatment to conventional therapies for active ulcerative colitis. Furthermore, treatment with E. coli Nissle without a previous antibiotic cure resulted in fewer patients reaching clinical remission.

There are challenges, when extracting bacterial DNA from specimens for molecular diagnostics, since fecal samples also contain DNA from human cells and many different substances derived from food, cell residues and medication that can inhibit downstream PCR. The purpose of the study was to evaluate two different DNA extraction methods in order to choose the most efficient method for studying intestinal bacterial diversity using Denaturing Gradient Gel Electrophoresis (DGGE).

Escherichia coli have been found in increased numbers in tissues from patients with Inflammatory Bowel Disease (IBD) and adherent-invasive E. coli have been found in resected ileum from patients with Crohn's disesae. This study aimed to characterize possible differences in phylogenetic group (triplex PCR), extraintestinal pathogenic E. coli (ExPEC) genes and multilocus sequence type (MLST) between E. coli strains isolated from IBD patients with past or present involvement of the left side of the colon and from controls.