Forbes Jessica D, Van Domselaar Gary, Bernstein Charles N
*Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Canada; †Bioinformatics Core, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada; and ‡Department of Internal Medicine, IBD Clinical and Research Centre, University of Manitoba, Canada.
Inflamm Bowel Dis. 2016 Apr;22(4):817-25. doi: 10.1097/MIB.0000000000000684.
We aimed to contrast the mucosal microbiota in Crohn's disease (CD) and ulcerative colitis (UC).
We assessed the concept of localized dysbiosis by comparing the bacterial communities of inflamed and noninflamed mucosa of patients with inflammatory bowel disease (IBD) and by analysis of the microbiota composition at distinct gut compartments (ileum, cecum, mid-colon, and rectum). We performed 16S rDNA sequencing to analyze population structures. Quality control and operational taxonomic unit classification of reads were performed using mothur with statistical analyses executed in the R package, phyloseq.
There was no variation in any phyla or genera comparing inflamed to noninflamed mucosa within CD (or UC) or when comparing different gut compartments within CD (or UC). There were differences between the inflamed and noninflamed mucosa between CD and UC: analysis of the inflamed IBD gut at the phylum level indicated that Bacteroidetes (P = 0.002) and Fusobacteria (P < 0.05) were detected more frequently in inflamed CD mucosa than in inflamed UC mucosa. Conversely, Proteobacteria and Firmicutes (P < 0.05) were more frequently observed in the inflamed UC mucosa. At the genus level, the abundance of Faecalibacterium (P ≤ 0.05), Bacteroides (P = 0.003), and Pseudomonas (P < 0.001) were significantly different between the inflamed CD and UC and the abundance of 13 genera were significantly different within the noninflamed mucosa. The noninflamed UC mucosa was the most different from non-IBD mucosa.
Dramatic shifts of microbial communities were not observed between the noninflamed and inflamed mucosa within CD (or UC) although both the inflamed (and noninflamed) mucosa was different between CD and UC.
我们旨在对比克罗恩病（CD）和溃疡性结肠炎（UC）的黏膜微生物群。
我们通过比较炎症性肠病（IBD）患者发炎和未发炎黏膜的细菌群落，并分析不同肠道区域（回肠、盲肠、结肠中段和直肠）的微生物群组成，来评估局部生态失调的概念。我们进行16S rDNA测序以分析种群结构。使用mothur对读数进行质量控制和操作分类单元分类，并在R包phyloseq中进行统计分析。
在CD（或UC）内，将发炎黏膜与未发炎黏膜进行比较时，或在CD（或UC）内比较不同肠道区域时，任何门或属均无差异。CD和UC的发炎黏膜与未发炎黏膜之间存在差异：在门水平上对发炎的IBD肠道进行分析表明，与发炎的UC黏膜相比，在发炎的CD黏膜中更频繁地检测到拟杆菌门（P = 0.002）和梭杆菌门（P < 0.05）。相反，在发炎的UC黏膜中更频繁地观察到变形菌门和厚壁菌门（P < 0.05）。在属水平上，发炎的CD和UC之间，粪杆菌属（P ≤ 0.05）、拟杆菌属（P = 0.003）和假单胞菌属（P < 0.001）的丰度存在显著差异，并且在未发炎黏膜内13个属的丰度存在显著差异。未发炎的UC黏膜与非IBD黏膜差异最大。
尽管CD（或UC）内发炎（和未发炎）黏膜在CD和UC之间存在差异，但在CD（或UC）内未发炎黏膜与发炎黏膜之间未观察到微生物群落的显著变化。
