Table_1_Amish (Rural) vs. non-Amish (Urban) Infant Fecal Microbiotas Are Highly Diverse and Their Transplantation Lead to Differences in Mucosal Immune Maturation in a Humanized Germfree Piglet Model.DOCX

The gut microbiome plays an important role in the immune system development, maintenance of normal health status, and in disease progression. In this study, we comparatively examined the fecal microbiomes of Amish (rural) and non-Amish (urban) infants and investigated how they could affect the mucosal immune maturation in germ-free piglets that were inoculated with the two types of infant fecal microbiota (IFM). Differences in microbiome diversity and structure were noted between the two types of fecal microbiotas. The fecal microbiota of the non-Amish (urban) infants had a greater relative abundance of Actinobacteria and Bacteroidetes phyla, while that of the Amish (rural) counterparts was dominated by Firmicutes. Amish infants had greater species richness compared with the non-Amish infants' microbiota. The fecal microbiotas of the Amish and the non-Amish infants were successfully transplanted into germ-free piglets, and the diversity and structure of the microbiota in the transplanted piglets remained similar at phylum level but not at the genus level. Principal coordinates analysis (PCoA) based on Weighted-UniFrac distance revealed distinct microbiota structure in the intestines of the transplanted piglets. Shotgun metagenomic analysis also revealed clear differences in functional diversity of fecal microbiome between Amish and non-Amish donors as well as microbiota transplanted piglets. Specific functional features were enriched in either of the microbiota transplanted piglet groups directly corresponding to the predominance of certain bacterial populations in their gut environment. Some of the colonized bacterial genera were correlated with the frequency of important lymphoid and myeloid immune cells in the ileal submucosa and mesenteric lymph nodes (MLN), both important for mucosal immune maturation. Overall, this study demonstrated that transplantation of diverse IFM into germ-free piglets largely recapitulates the differences in gut microbiota structure between rural (Amish) and urban (non-Amish) infants. Thus, fecal microbiota transplantation to germ-free piglets could be a useful large animal model system for elucidating the impact of gut microbiota on the mucosal immune system development. Future studies can focus on determining the additional advantages of the pig model over the rodent model.

肠道微生物群在免疫系统发育、维持正常健康状况以及疾病进展中发挥着重要作用。在本研究中，我们比较研究了阿米什（农村）和非阿米什（城市）婴儿的粪便微生物群，并探讨了它们如何影响接种两种类型婴儿粪便微生物群（IFM）的无菌猪的黏膜免疫成熟。两种粪便微生物群在微生物群多样性和结构上存在差异。非阿米什（城市）婴儿的粪便微生物群中，放线菌门和拟杆菌门的比例相对较高，而阿米什（农村）婴儿的粪便微生物群则以厚壁菌门为主。与非阿米什婴儿的微生物群相比，阿米什婴儿的物种丰富度更高。阿米什和非阿米什婴儿的粪便微生物群成功移植到无菌猪体内，移植猪的微生物群在门水平上保持相似性，但在属水平上则不相似。基于加权UniFrac距离的主坐标分析（PCoA）揭示了移植猪肠道中微生物群结构的独特性。射箭宏基因组分析也揭示了阿米什和非阿米什捐赠者以及移植猪的粪便微生物群在功能多样性上的明显差异。两组移植猪的微生物群中，特定的功能特征得到富集，直接对应其肠道环境中某些细菌群体的主导地位。一些定植的细菌属与回肠亚黏膜和肠系膜淋巴结（MLN）中重要淋巴和髓系免疫细胞的频率相关，这两者对黏膜免疫成熟至关重要。总体而言，这项研究证明了将多样化的IFM移植到无菌猪体内，在很大程度上再现了农村（阿米什）和城市（非阿米什）婴儿肠道微生物群结构上的差异。因此，粪便微生物群移植到无菌猪体内可能是一个用于阐明肠道微生物群对黏膜免疫系统发育影响的实用的大型动物模型系统。未来的研究可以着重于确定猪模型相对于啮齿动物模型的额外优势。