Old Mike posted a study yesterday that may be useful when reviewing the American Gut Project results.A Modular Organization of the Human Intestinal Mucosal Microbiota and Its Association with Inflammatory Bowel Disease
The IBD-associated dysbiosis of mucosal microbiota has been delineated in detail in several investigations [9,32,35]. Specifically, IBD patients have fewer Firmicutes and a concomitant increase in Proteobacteria, validated in several independent cohorts [36,37]. To determine whether previously reported alterations were also observed in our dataset, we compared the relative abundances of each phylum between disease states using analysis of variance (ANOVA). In contrast to controls, IBD patients harbored relatively more abundant Actinobacteria (FDR corrected P = 0.006 for UC, < 0.0001 for CD), accompanied with the depletion of Firmicutes (FDR corrected P = 0.056 for UC, 0.25 for CD) in these subjects (Figure 2A, Dataset S1 and S2). The increases of Proteobacteria (FDR corrected P = 0.254 for UC, 0.143 for CD) and Tenericutes (FDR corrected P = 0.115 for UC, 0.157 for CD) were also observed in IBD patients, although not statistically significant. Taken together, microbial composition represented by this study cohort, and captured by lavage sampling, reflected the changes of relative abundances of enteric microbiota in IBD subjects at phylum level observed in other datasets and sampling methods.
The reduction in bacterial diversity in IBD patients is a consistent finding across studies [32,38,39], although it is still unknown whether this alteration is causative or a secondary effect of IBD. Compared with controls, the phylogenetic diversities of UC and CD subjects at 97% OTU level were significantly lower (Figure 2B), and the difference was more evident in CD (t-test, P = 0.0003) than that in UC subjects (t-test, P = 0.0056) at the depth of 3,000 reads per sample. This data indicates that the lower microbial diversity previously observed in patients with active IBD also persists in clinically quiescent phases of disease.