Functional analysis of gut microbiome-host interactions during the postnatal window of opportunity by a multiscale sequencing approach

新生儿肠道微生物定植是一个动态的过程，有助于建立肠道免疫和耐受性。在这段时间窗内未能达到体内平衡的宿主-微生物串扰，会影响一生中对炎症性、自身免疫性和代谢性疾病的易感性。尽管产后时期的这一关键作用已被认识到，但对潜在机制的了解仍然很少。在这里，我们加入了我们在微生物组研究、噬菌体生物学和基因组学、新生儿肠道上皮生物学和粘膜免疫学方面的专业知识，以确定微生物在新生儿肠道中的定植动态以及对小鼠先天性和获得性免疫印记的影响。我们提出了一种功能性的方法，其中研究了寄主的定植模式和对宿主的因果影响，这些定植模式和对宿主的因果影响是由确定的最低限度的培养细菌种类重组而成的。特别强调(1)新生儿和成人微生物区系的不同特征，以及(2)鞭毛细菌作为微生物区系的一部分提供主要免疫原性抗原和先天免疫刺激的作用。将研究嗜鞭毛噬菌体，并将其用于细菌群落的精确操作。在多尺度测序方法中，包括微生物组定植动态的元转录和噬菌体分析，组织成熟和肠上皮细胞(IEC)谱系分化的单细胞(Sc)RNAseq，以及淋巴细胞受体测序，我们将对微生物定植在早期生命中的功能重要性提供新的见解。

Microbial colonization of the neonate gut is a dynamic process that contributes to the establishment of intestinal immunity and tolerance. Failure to reach a homeostatic host-microbial crosstalk during this time window influences the susceptibility to inflammatory, autoimmune, and metabolic diseases throughout life. Although this critical role of the postnatal period has been recognized, knowledge about underlying mechanisms is still scant. Here we join our expertise in microbiome research, phage biology and genomics, intestinal epithelium biology in neonates, and mucosal immunology to determine microbial colonization dynamics in the neonatal gut and the impact on innate and adaptive immune imprinting in mice. We propose a functional approach where colonization patterns and causal effects on the host are studied in gnotobiotic mice reconstituted with defined minimal consortia of cultured bacterial species. Particular emphasis is on characterizing (i) differential features of the neonatal and adult microbiota, and (ii) the effect of flagellated bacteria as part of the microbiota providing a dominant immunogenic antigen and innate immune stimulus. Lytic flagellotropic phages will be studied and use for precise manipulation of bacterial communities. In a multiscale sequencing approach including meta-transcriptomic and phageome analysis of microbiome colonization dynamics, single-cell (sc) RNAseq for tissue maturation and differentiation of intestinal epithelial cell (IEC) lineages, and lymphocyte receptor sequencing, we will provide novel insights into the functional importance of microbial colonization in early life.