Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
University of Chinese Academy of Sciences, Beijing, China.
Gut Microbes. 2022 Jan-Dec;14(1):2100197. doi: 10.1080/19490976.2022.2100197.
Fecal microbiota transplantation (FMT) is a promising treatment for microbiota dysbiosis associated diseases, such as infection (CDI) and inflammatory bowel disease (IBD). The engraftment of donor bacteria is essential for the effectiveness of FMT, which to some extent depends on the matching of donors and recipients. However, how different types of donor-derived bacteria affect FMT efficacy has not been fully dissected. We recruited two longitudinal IBD cohorts of 103 FMT recipients and further analyzed 1,280 microbiota datasets from 14 public CDI and IBD studies to uncover the effect of donor-derived microbiota in recipients. We found that two enterotypes, RCPT/E and RCPT/B (dominated by Enterobacteriaceae and , respectively), consistently exist in both CDI and IBD patients. Based on a time-course-based multi-cohort analysis of FMT fecal samples, we observed the interplay between recipient and donor-derived microbiota during FMT, in which the FMT outcome was significantly associated with the enterotype and microbiota distance between donor and recipient after FMT. We proposed a new measurement, the ratio of colonizers to residents after FMT (C2R), to quantify the engraftment of donor-derived bacteria in the recipients, and then constructed an enterotype-based statistical model for donor-recipient matching, which was validated by both cross-validation and an additional IBD FMT cohort (n = 42). We believe that with the accumulation of FMT multi-omics datasets, machine learning-based methods will be helpful for rational donor selection for improving efficacy and precision FMT practices.
粪便微生物群移植（FMT）是治疗与微生物失调相关疾病的一种很有前途的方法，例如感染（CDI）和炎症性肠病（IBD）。供体细菌的定植对于 FMT 的有效性至关重要，这在某种程度上取决于供体和受者的匹配程度。然而，不同类型的供体衍生细菌如何影响 FMT 的疗效尚未被充分剖析。我们招募了两个 103 名 FMT 受者的纵向 IBD 队列，并进一步分析了来自 14 项公共 CDI 和 IBD 研究的 1280 个微生物组数据集，以揭示供体衍生微生物组在受者中的作用。我们发现，两种肠型，RCPT/E 和 RCPT/B（分别由肠杆菌科和主导），在 CDI 和 IBD 患者中始终存在。基于基于时间的多队列分析 FMT 粪便样本，我们观察到 FMT 过程中受者和供体衍生微生物组之间的相互作用，其中 FMT 结果与供体和受者之间的肠型和微生物组距离显著相关。我们提出了一个新的度量标准，即 FMT 后定植的殖民者与居民的比例（C2R），用于量化供体衍生细菌在受者中的定植情况，然后构建了一个基于肠型的供体-受者匹配统计模型，该模型通过交叉验证和另一个 IBD FMT 队列（n=42）得到了验证。我们相信，随着 FMT 多组学数据集的积累，基于机器学习的方法将有助于合理选择供体，以提高疗效和精准 FMT 实践。
