Complete Genomes of Clade G6 Saccharibacteria Suggest a Divergent Ecological Niche and Lifestyle.
Complete Genomes of Clade G6 Saccharibacteria Suggest a Divergent Ecological Niche and Lifestyle.
复制标题
G6分支糖杆菌的完整基因组表明其具有不同的生态位和生活方式。
DOI：
10.1128/msphere.00530-21
复制
发表时间：
2021-08-25
期刊：
影响因子：
4.8
通讯作者：
Baker JL
中科院分区：
文献类型：
--
作者：
Baker JL
Saccharomyces细菌（以前称为TM 7）具有减少的基因组和小的细胞大小，并且似乎具有依赖于细菌宿主的寄生生活方式。虽然存在至少6个主要的Saccharomyces细菌分支栖息在人类口腔中，但口腔Saccharomyces细菌的完整基因组先前仅限于G1分支。在这项研究中，使用纳米孔测序从进化枝G6获得三个完整的基因组序列。系统发育分析表明，G6内至少存在3至5个不同的物种，其中两个独立的类群由3个完整的基因组代表。G6 Saccharomyces细菌与更好研究的进化枝G1高度不同，并且在所有Saccharomyces细菌中具有最小的基因组和最低的GC含量。泛基因组分析表明，尽管97%的泛酵母菌共有核心基因和89%的G1特异核心基因具有推定功能，但244个G6特异核心基因中只有50%具有推定功能，突出了这一群体的新奇。与G1相比，G6具有不同的代谢途径。G6基因组缺乏F1 Fo ATP酶、戊糖磷酸途径和参与核苷酸代谢的几个基因，这些基因都是G1的核心基因。G6基因组与G1基因组相比也是独特的，因为它们编码d-乳酸脱氢酶、腺苷酸环化酶、有限的甘油脂质代谢、脂阿拉伯甘露聚糖生物合成酶的同系物以及降解淀粉的方法。这些差异在关键代谢步骤表明一个独特的生活方式和生态位的进化枝G6，可能与替代主机和/或主机的依赖性，这将有显着的生态，进化，并可能致病的影响。重要的是，寄生菌是超小的寄生菌，是口腔微生物群的常见成员，并且越来越多地与疾病和炎症有关。然而，对Saccharomyces细菌的生活方式和对人类健康的影响仍然知之甚少，特别是对于没有完整基因组的进化枝（G2至G6）或培养的分离株（G2和G4至G6）。获得完整的基因组对于Saccharomyces细菌特别重要，因为它们缺乏许多用于确定基因组草图完整性的“必需”核心基因，并且在进化枝G1之外存在很少的参考文献。在这项研究中，3 G6菌株，代表两个候选物种，获得和分析的完整基因组。G6基因组与G1基因组高度不同，并且神秘，其中50%的G6核心基因没有推定的功能。编码的功能途径的显着差异是一个独特的生活方式和生态位，可能与替代主机和/或主机的依赖性，这将有重大影响的生态，进化和发病机制。
Saccharibacteria (formerly TM7) have reduced genomes and a small cell size and appear to have a parasitic lifestyle dependent on a bacterial host. Although there are at least 6 major clades of Saccharibacteria inhabiting the human oral cavity, complete genomes of oral Saccharibacteria were previously limited to the G1 clade. In this study, nanopore sequencing was used to obtain three complete genome sequences from clade G6. Phylogenetic analysis suggested the presence of at least 3 to 5 distinct species within G6, with two discrete taxa represented by the 3 complete genomes. G6 Saccharibacteria were highly divergent from the more-well-studied clade G1 and had the smallest genomes and lowest GC content of all Saccharibacteria. Pangenome analysis showed that although 97% of shared pan-Saccharibacteria core genes and 89% of G1-specific core genes had putative functions, only 50% of the 244 G6-specific core genes had putative functions, highlighting the novelty of this group. Compared to G1, G6 harbored divergent metabolic pathways. G6 genomes lacked an F1Fo ATPase, the pentose phosphate pathway, and several genes involved in nucleotide metabolism, which were all core genes for G1. G6 genomes were also unique compared to that of G1 in that they encoded d-lactate dehydrogenase, adenylate cyclase, limited glycerolipid metabolism, a homolog to a lipoarabinomannan biosynthesis enzyme, and the means to degrade starch. These differences at key metabolic steps suggest a distinct lifestyle and ecological niche for clade G6, possibly with alternative hosts and/or host dependencies, which would have significant ecological, evolutionary, and likely pathogenic implications. IMPORTANCESaccharibacteria are ultrasmall parasitic bacteria that are common members of the oral microbiota and have been increasingly linked to disease and inflammation. However, the lifestyle and impact on human health of Saccharibacteria remain poorly understood, especially for the clades with no complete genomes (G2 to G6) or cultured isolates (G2 and G4 to G6). Obtaining complete genomes is of particular importance for Saccharibacteria, because they lack many of the “essential” core genes used for determining draft genome completeness, and few references exist outside clade G1. In this study, complete genomes of 3 G6 strains, representing two candidate species, were obtained and analyzed. The G6 genomes were highly divergent from that of G1 and enigmatic, with 50% of the G6 core genes having no putative functions. The significant difference in encoded functional pathways is suggestive of a distinct lifestyle and ecological niche, probably with alternative hosts and/or host dependencies, which would have major implications in ecology, evolution, and pathogenesis.