Mechanisms of adaptation to interbacterial antagonism by the human gut microbiota

肠道微生物群对人类健康的影响取决于物种的身份 在其中导致人与人之间微生物群组成差异的机制是 没有被很好地理解。我们专注于优势菌群成员之间的细菌间相互作用， 在西方成年人的肠道中的分类单元，拟杆菌目。这些细菌争夺空间 和营养物质通过一个称为VI型分泌系统（T6 SS）的分子载体。有毒 通过T6 SS在相邻拟杆菌目细胞之间传递的蛋白质效应物导致细胞停滞， 或裂解，我们和其他人以前已经揭示，这种竞争导致应变水平 通过杀死目标细菌来排除微生物群的差异。由于效应器可以 当T6 SS编码细菌被不加区别地传递到亲属细胞时， 特异性中和同源效应物。我们之前已经确认了 在类杆菌目的大型基因组阵列中编码的“孤儿”免疫因子 缺乏同源效应子的基因组。这些获得的细菌间防御（AID）系统 通过中和同源效应物使T6 SS无效，并促进应变- 排除微生物。在这一建议中，我们试图了解 孤儿免疫基因被捕获并聚集到最常见的AID系统中， 重组酶相关AID（rAID）系统，使用细菌遗传学的强大组合， 生物化学、宏基因组学和基因生物学。我们进一步寻求理解该法规 通过一个假设的“竞争感应”， 涉及混合传感器-激酶途径的机制。我们的目标是共同理解 拟杆菌目防御T6 SS对肠道微生物组的影响。

The impact of the gut microbiota on human health depends on the identity of the species therein. The mechanisms that lead to differences in microbiota composition between people is not well understood. We focus on interbacterial interactions between members of the dominant taxon in the gut of Western adults, the order Bacteroidales. These bacteria compete for space and nutrients via a molecular nanoweapon known as the type VI secretion system (T6SS). Toxic protein effectors delivered between adjacent Bacteroidales cells by the T6SS result in cell statis or lysis, and we and others have previously revealed that this competition results in strain-level differences in the microbiota through exclusion of target bacteria via killing. Since effectors can be delivered indiscriminately to kin cells, T6SS-encoding bacteria produce immunity factors that specifically neutralize cognate effectors. We have previously identified the pervasive presence of “orphan” immunity factors encoded within large genomic arrays within Bacteroidales genomes that lack cognate effectors. These acquired interbacterial defense (AID) systems render the T6SS ineffective through neutralization of cognate effectors and facilitate strain- exclusion from microbiomes. In this proposal, we seek to understand the mechanism by which orphan immunity genes are captured aggregated into the most common type of AID system, the recombinase-associated AID (rAID) system, using a powerful combination of bacterial genetics, biochemistry, metagenomics, and gnotobiology. We further seek to understand the regulation and biogeographical role of rAID systems through a hypothesized “competition-sensing” mechanism that involves a hybrid sensor-kinase pathway. Together, we aim to understand the impact of Bacteroidales defense against the T6SS on the gut microbiome.