Immune modulation by metagenomic DNA from the gastrointestinal microbiota of newborn infants

胃肠道微生物群与宿主免疫系统之间的干扰相互作用（通常称为生态失调）与多种疾病相关，包括例如炎性肠病、腹泻相关性腹泻和肥胖症。控制胃肠道免疫反应对于正在建立微生物群的新生儿尤其重要，因为他们需要避免过度炎症以应对潜在病原菌的短暂定植。尽管越来越多的证据表明胃肠道微生物群对生态失调的功能作用，但很难确定在微生物群水平上明确定义生态失调的参数。人类宿主可以通过先天免疫受体如Toll样受体组中的TLR 9检测微生物。TLR 9识别微生物DNA的特异性短寡聚体，并参与宿主免疫应答的促炎活化和抗炎调节。通过宏基因组序列分析来定量TLR 9刺激和TLR 9调节序列基序的粪便微生物群表征，与TLR 9依赖性实验免疫测定组合，对于研究宿主-微生物相互作用的动力学是有吸引力的，因为它有可能识别序列-我们的初步数据表明，新生儿粪便微生物群诱导胃肠道菌群失调的能力降低，TLR 9依赖性免疫激活，与成人相比，以及相对于已知TLR 9结合序列基序的相对丰度改变的宏基因组序列组成。因此，我们建议使用新生儿粪便微生物群作为模型来研究DNA依赖的宿主-微生物免疫相互作用。相应地，本提案的目的是收集婴儿和成人的横断面队列，并在体外测量和比较对粪便宏基因组DNA的免疫应答（目的I）对样本进行宏基因组测序，分别计算免疫刺激性和免疫调节性TLR 9结合寡聚体的相对丰度，并建立基于宏基因组序列的免疫激活预测模型（目的II），并测量在无菌小鼠模型中用粪便宏基因组DNA进行胃肠道免疫刺激的效果，以及新生粪便宏基因组DNA减轻化学诱导的结肠炎的鼠模型中的炎症的能力（目的III）。

Disturbed interactions between the gastrointestinal microbiota and the host immune system, commonly referred to as dysbiosis, have been associated with a diverse set of diseases, including for example inflammatory bowel disease, antibiotic-associated diarrhea and obesity. Control over gastrointestinal immune responses is especially important in newborn infants that are in the process of establishing their microbiota, as they need to avoid excessive inflammation in response to transient colonization with potential pathogenic bacteria. In spite of growing evidence for a functional role of the gastrointestinal microbiota for dysbiosis, it has been difficult to identify parameters that would clearly define dysbiosis on the microbiota level. The human host can detect microbes via innate immune receptors such as TLR9 from the group of Toll-like receptors. TLR9 recognizes specific short oligomers of microbial DNA and is involved both in the pro-inflammatory activation and anti-inflammatory modulation of host immune responses. Fecal microbiota characterization by metagenomic sequence analysis to quantify TLR9-stimulating and TLR9-regulating sequence motifs, in combination with TLR9-dependent experimental immune assays, is attractive to study the dynamics of host-microbe interactions, as it has the potential to identify sequence-based diagnostic biomarkers for gastrointestinal dysbiosis.Our preliminary data indicate that the newborn infant fecal microbiota has a reduced capacity to induce TLR9-dependent immune activation, compared to that of adults, as well as an altered metagenomic sequence composition with respect to the relative abundances of known TLR9-binding sequence motifs. We therefore propose to use the newborn fecal microbiota as a model to study DNA-dependent host-microbe immune interactions. Correspondingly, the aims of this proposal are to assemble a cross-sectional cohort of infants and adults and to measure and compare immune responses to fecal metagenomic DNA in vitro (Objective I), to perform metagenomic sequencing on the samples, calculate relative abundances of immunostimulatory and immunoregulatory TLR9-binding oligomers, respectively, and to develop predictive models for metagenomic sequence-based immune activation (Objective II), and to measure the effects of gastrointestinal immune stimulation with fecal metagenomic DNA in a germfree mouse model, as well as the ability of newborn fecal metagenomic DNA to attenuate inflammation in a murine model of chemically induced colitis (Objective III).