Amir Kovacs

Genotype Is a Stronger Determinant than Sex of the Mouse Gut Microbiota

The mammalian gut microbiota is considered to be determined mostly by diet, while the effect of genotype is still controversial. Here, we examined the effect of genotype on the gut microbiota in normal populations, exhibiting only natural polymorphisms, and evaluated this effect in comparison to the effect of sex. DNA fingerprinting approaches were used to profile the gut microbiota of eight different recombinant inbred mouse lines of the collaborative cross consortium, whose level of genetic diversity mimics that of a natural human population. Analyses based on automated ribosomal internal transcribed spacer analysis demonstrated significant higher similarity of the gut microbiota composition within mouse lines than between them or within same-gender groups. Thus, genetic background significantly impacts the microbiota composition and is a stronger determinant than gender. These findings imply that genetic polymorphisms help shape the intestinal microbiota of mammals and consequently could affect host susceptibility to diseases.

Composition and dynamics of the gill microbiota of an invasive Indo-Pacific oyster in the eastern Mediterranean Sea.

Gill bacterial communities of Chama pacifica, an Indo-Pacific invasive oyster to the eastern Mediterranean Sea, were compared with those of Chama savignyi, its northern Red Sea congeneric species. Summer and winter bacterial populations were characterized and compared using 16S rDNA clone libraries, and seasonal population dynamics were monitored by automated ribosomal intergenic spacer analysis (ARISA). Clone libraries revealed a specific clade of bacteria, closely related to marine endosymbionts from the Indo-Pacific, found in both ecosystems, of which one taxon was conserved in oysters from both sites. This taxon was dominant in summer libraries and was weakly present in winter ones, where other members of this group were dominant. ARISA results revealed significant seasonal variation in bacterial populations of Mediterranean Sea oysters, as opposed to Red Sea ones that were stable throughout the year. We suggest that this conserved association between bacteria and oyster reflects either a symbiosis between the oyster host and some of its bacteria, a co-invasion of both parties, or both.

Pouch Inflammation Is Associated With a Decrease in Specific Bacterial Taxa

BACKGROUND & AIMS Pouchitis is a common long-term complication in patients with ulcerative colitis (UC) undergoing proctocolectomy with ileal pouch-anal anastomosis. Because the inflammation occurs in a previously normal small bowel, studies of this process might provide information about the development of Crohns disease. Little is known about the intestinal microbiome of patients with pouchitis. We investigated whether specific bacterial populations correlate with the pouch disease phenotype and inflammatory activity. METHODS We performed a prospective study of patients with UC who underwent pouch surgery (N = 131) from 1981 through 2012 and were followed at Tel Aviv Medical Center. Patients were assigned to groups based on their degree and type of pouch inflammation. Patients with familial adenomatous polyposis after pouch surgery (n = 9), individuals with intact colons undergoing surveillance colonoscopy (n = 10), and patients with UC who did not undergo surgery (n = 9) served as controls. We collected demographic and disease activity data (based on the Pouchitis Disease Activity Index) and measured levels of C-reactive protein. Fecal samples were collected, levels of calprotectin were measured, and microbiota were analyzed by 16S ribosomal RNA gene amplicon pyrosequencing. RESULTS Increased proportions of the Fusobacteriaceae family correlated with increased disease activity and levels of C-reactive protein in patients with UC who underwent pouch surgery. In contrast, proportions of Faecalibacterium were reduced in patients with pouchitis vs controls; there was a negative correlation between proportion of Faecalibacterium and level of C-reactive protein. There was an association between antibiotic treatment, but not biologic or immunomodulatory therapy, with reduced proportions of 11 genera and with increased proportions of Enterococcus and Enterobacteriaceae. CONCLUSIONS Reductions in protective bacteria and increases in inflammatory bacteria are associated with pouch inflammation in patients with UC who underwent pouch surgery. The finding that antibiotics exacerbate dysbiosis indicates that these drugs might not provide long-term benefit for patients with pouchitis. Additional studies of this form of dysbiosis could provide information about the pathogenesis of Crohns disease.

Tu1772 Intestinal Microbiota Is Different in Crohn's Ileitis Compared to Crohn's Colitis and Ulcerative Colitis

at the genus level demonstrate that control and preservative samples are comparable at day 0. Preservative samples remain stable at room temperature for as long as 5 days. Control samples kept in sterile water had marked shifts within 24 hours, with a significant increase in Enterobacteriaceae on day 1 that persisted throughout the remainder of the experiment and blooms of Lysinibacillus and Bacillus by days 3 and 4, respectively. (B) Principal component analysis plot demonstrates that all preservative samples (blue) cluster closely around the two baseline control samples (red: D0C1 and D0C2). Subsequent control samples increasingly deviate from day 1 (D1C1, D1C2) to day 7 (D7C1, D7C2).

Intestinal Microbiota and Intestinal Disease: Inflammatory Bowel Diseases

The two major inflammatory bowel diseases (IBD), Crohn’s disease (CD), and ulcerative colitis (UC) are idiopathic relapsing disorders characterized by chronic inflammation of the gastrointestinal tract. It is increasingly evident that the commensal intestinal microbiota plays a role in the pathogenesis of IBD, as multiple lines of evidence, both from rodent and human studies, support microbial involvement in the etiology of these diseases. In general, it is thought that IBD are driven by an irregular immune response to the commensal microbiota in genetically susceptible individuals. A leading hypothesis, concerning the nature of the role that bacteria play in the pathogenesis of IBD, suggests that the disease state is promoted by dysbiosis, a shift in the balance of healthy microbiota in favor of pro-inflammatory microbial species. Numerous studies have described a reduction in the biodiversity of the Firmicutes phylum in CD patients, particularly clostridial species. This phylogenetic group contains many bacteria that produce butyrate, a short chain fatty acid considered to have anti-inflammatory properties. Moreover, recent data suggest that clostridial species are involved in multiple regulatory processes of the innate immune system. Further research, elucidating the interactions between the gut microbiota and the immune system could potentially provide the key for understanding IBD.

Can Colonoscopy Aspirates be a Substitute for Fecal Samples in Analyses of the Intestinal Microbiota

There is a growing interest in the study of the human gut microbiota, as correlations between changes in bacterial profiles and diseases are increasingly discovered. Studies in this field generally use fecal samples, but it is often easier to obtain colon content aspirates during colonoscopy. This study used automated ribosomal internal spacer analysis (ARISA) to examine the extent to which the microbiota of colon aspirate samples obtained after bowel cleansing can reflect interindividual differences and serve as a proxy for fecal samples. Pre-bowel preparation fecal samples as well as colonoscopy aspirate samples from the cecum and rectum were obtained from 19 subjects. DNA was extracted from all samples, and comparative analysis was performed, including analysis of similarity (ANOSIM) and nonmetric multidimensional scaling. ANOSIM confirmed that samples from the same individual were well separated from samples from different individuals. Significantly larger differences were found between samples from different individuals than between samples of the same individual (R = 0.7605, p < 0.0001). These findings show that post-bowel preparation aspirates maintain a strong individual signature. Colonoscopy aspirates can therefore serve as a substitute for fecal samples in studies comparing the microbiota of different clinical study groups, especially when fecal samples are unavailable.