Domestication and characterization of TM7-the most elusive oral phylum

摘要 本申请的总体目标是表征新发现的超小寄生细菌， 在牙龈炎和牙周炎中，基因组的数量大大减少，并且显示出增加的丰度。上一 资金周期，我们成功地培养和测序TM 7 x，第一个成员的未培养的TM 7 从人类进化而来。菌株TM 7 x在所有细菌中是独特的，它具有超小的尺寸（200-300 nm）， 生活在宿主细菌的表面，这种关系在人类微生物组中从未被报道过 或在细菌域中。由于基因组高度简化，TM 7 x不能合成任何自身的氨基酸， 维生素或细胞壁前体，并且必须寄生于影响其生长的其他口腔细菌。特别 值得注意的是，TM 7属于候选辐射门（CPR），这是最近发现的一个分支， 包括超过26%的已知细菌多样性，估计有70个未培养的门 基因组数量减少迄今为止，TM 7 x仍然是整个CPR中唯一报道的培养代表， 使我们的团队处于一个独特的位置，在该领域取得重大进展，并促进基本的 这些超小的人类相关细菌的发现，以及整个CPR组。 我们的初步研究结果表明，TM 7 x与其宿主口腔放线菌的关系 菌株XH 001是一个高度调节的共生相互作用，其中TM 7 x表现出共生 阶段（与宿主共存）和毒性寄生阶段（诱导宿主细胞死亡）。这种耐人寻味的关系 类似于观察到的温和噬菌体及其宿主，其中噬菌体能够 在溶原性和溶解性周期之间切换，并引起生理和生态后果。在这 我们的目标是实现以下两个目标。1)为了确定分子组成和调节 TM 7 x与宿主关系的调控途径; 2）研究TM 7 x与宿主关系的细菌范围， TM 7 x与。特别地，在具有一个或多个抗原的细菌寄生虫内编码的宿主杀伤机制是已知的。 简化的基因组在根本上是新颖的并且与临床相关。能够感染并杀死多个 细菌宿主可能允许TM 7 x影响口腔群落动态和结构，从而调节 在健康和疾病期间影响微生物组。 这项研究的成功将大大推进这些超小细菌的研究领域， 扩大我们对这种在人类中发现的新型微生物共生的知识，以及 CPR微生物对口腔微生物生态学的影响。

Abstract The overall goal of this application is to characterize newly discovered ultra-small parasitic bacteria that have extremely reduced genomes and show increased abundance in gingivitis and periodontitis. In the previous funding cycle, we successfully cultivated and sequenced TM7x, the first member of the uncultivated TM7 phylum from humans. Strain TM7x is unique among all bacteria, it has an ultrasmall size (200-300 nm) and lives on the surface of a host bacterium, a relationship that had never been reported in the human microbiome or in the Bacteria domain. With a highly-reduced genome, TM7x cannot synthesize any of its own amino acids, vitamins or cell wall precursors and must parasitize other oral bacteria which impacts their growth. Of particular note is that TM7 belongs to the Candidate Phyla Radiation (CPR), a recently discovered subdivision in the domain Bacteria that comprises >26% of the known bacterial diversity with an estimated 70 uncultivated Phyla with reduced genomes. To date, TM7x is still the only reported cultivated representative of the entire CPR, putting our team in a unique position to make significant advancements in the field and facilitate fundamental discoveries on these ultra-small human associated bacteria, as well as the CPR group as a whole. Our preliminary data revealed that the relationship of TM7x and its bacterial host, an oral Actinomyces odontolyticus strain XH001 is a highly-regulated symbiotic interaction in which TM7x displays both symbiotic phase (co-existing with host) and virulent parasitic phase (inducing host cell death). This intriguing relationship is similar to the one observed for temperate bacteriophages and their hosts where phages are capable of switching between lysogenic and lytic cycle, and entails physiological and ecological consequences. In this application, we aim to achieve the following two goals. 1) To identify the molecular components and regulatory pathways governing the relationship between TM7x and its host; 2) To investigate the range of bacteria that TM7x interacts with. In particular, the mechanism of host killing encoded within a bacterial parasite with a reduced genome is both fundamentally novel and clinically relevant. The ability to infect and kill multiple bacterial hosts may allow TM7x to influence the oral community dynamics and structure, thus modulating community and impacting microbiome during health and diseases. The success of the study would greatly advance the developing research field of these ultra-small bacteria, expand our knowledge on this novel microbial symbiosis found in humans, as well as the potential impact of CPR organisms on oral microbiome ecology.