Relationship between rectal swab and tissue samples for analysis of mucosa-associated microbiota in patients with inflammatory bowel disease

Background: Gut mucosa-associated microbiota correlates better with disease phenotypes than fecal microbiota, but the sampling via tissue biopsy is more invasive and uncomfortable. Rectal swab may be a suitable substitute for tissue biopsy, but their effectiveness is controversial. This study aims to evaluate the differences in the microbiota at these sites in patients with inflammatory bowel disease (IBD). Methods: IBD patients and a control group were enrolled when surveillance colonoscopy was scheduled. Samples of colon biopsy tissues, rectal swabs during colonoscopy, and feces before bowel preparation were collected for analyzing microbial composition. To explore the short-term effects of bowel preparation on swab microbiota, pre-preparation swab samples were also collected from 27 IBD patients. Results: A total of 33 Crohn’s disease (CD), 54 ulcerative colitis (UC), and 21 non-IBD patients were enrolled. In the beta diversity analysis, fecal microbiota differed clearly from swab and tissue microbiota in the three disease groups. The swab microbiota was closer to, but still different from, the tissue microbiota. Consistently, we identified several differentially abundant genera between the swab and tissue sites. The beta diversity analysis did not reveal a difference in swab microbiota before and after bowel preparation, but the genus composition of most individuals varied markedly. Conclusion: Swab microbiota resembled tissue microbiota relative to fecal microbiota, but they still differed. Bowel preparation did not alter the overall swab microbiota in the short term but changed the microbial composition markedly in most patients Contact: Chiao-Hsiung Chuang [e-mail]. This submission was powered by METAGENOTE (https://metagenote.niaid.nih.gov).

背景：与粪便微生物群相比，肠道黏膜相关微生物群与疾病表型的相关性更强，但通过组织活检获取样本的侵入性更强、舒适度更低。直肠拭子或可作为组织活检的合适替代方案，但其有效性尚存争议。本研究旨在评估炎症性肠病（inflammatory bowel disease, IBD）患者不同采样部位的微生物群差异。方法：本研究纳入计划接受监测性结肠镜检查的炎症性肠病患者及对照组人群。采集结肠活检组织、结肠镜检查期间获取的直肠拭子以及肠道准备前的粪便样本，以分析微生物群落组成。为探究肠道准备对拭子微生物群的短期影响，本研究还从27名炎症性肠病患者中采集了肠道准备前的拭子样本。结果：本研究共纳入33例克罗恩病（Crohn’s disease, CD）患者、54例溃疡性结肠炎（ulcerative colitis, UC）患者以及21例非炎症性肠病患者。β多样性分析结果显示，三类疾病组的粪便微生物群与拭子微生物群、组织微生物群均存在显著差异。直肠拭子微生物群与组织微生物群的相似度更高，但二者仍存在差异。与之一致的是，本研究在拭子与组织采样部位之间鉴定出多个丰度存在显著差异的菌属。β多样性分析未发现肠道准备前后拭子微生物群存在整体差异，但多数受试者的菌属组成发生了显著变化。结论：相较于粪便微生物群，直肠拭子微生物群与组织微生物群更为相似，但二者仍存在差异。肠道准备短期内未改变拭子微生物群的整体构成，但可使多数患者的微生物群落组成发生显著改变。联系方式：庄乔雄（Chiao-Hsiung Chuang），邮箱：[e-mail]。本稿件由METAGENOTE平台（https://metagenote.niaid.nih.gov）支持撰写。