Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia.
Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050, Tomsk, Russia.
Syst Appl Microbiol. 2019 Jan;42(1):67-76. doi: 10.1016/j.syapm.2018.08.013. Epub 2018 Sep 3.
Candidate bacterial phylum BRC1 has been identified in a broad range of mostly organic-rich oxic and anoxic environments through molecular analysis of microbial communities. None of the members of BRC1 have been cultivated and only a few draft genome sequences have been obtained from metagenomes or as a result of single-cell sequencing. We have reconstructed complete genome of BRC1 bacterium, BY40, from metagenome of the microbial community of a deep subsurface thermal aquifer in the Tomsk Region of the Western Siberia, Russia, and used it for metabolic reconstruction and comparison with existing genomic data. Analysis of 3.3Mb genome of BY40 bacterium revealed numerous glycoside hydrolases that could enable utilization of carbohydrates, including enzymes of chitin-degradation pathway. The bacterium lacks flagellar machinery but the twitching motility is encoded. The reconstructed central metabolism revealed pathways enabling the fermentation of organic substrates, as well as their complete oxidation through aerobic and anaerobic respiration. Phylogenetic analysis using BY40 genome supported the phylum level classification of BRC1 lineage. Based on phylogenetic and genomic analyses, the novel bacterium is proposed to be classified as Candidatus Sumerlaea chitinivorans, within a candidate phylum Sumerlaeota.
通过对微生物群落的分子分析，在广泛的主要富含有机物的好氧和缺氧环境中发现了候选细菌门 BRC1。BRC1 的成员都没有被培养，只有少数基因组草图序列是从宏基因组或单细胞测序中获得的。我们从俄罗斯西伯利亚西部托木斯克地区深部地下热含水层微生物群落的宏基因组中重建了 BRC1 细菌 BY40 的完整基因组，并将其用于代谢重建和与现有基因组数据的比较。对 BY40 细菌 3.3Mb 基因组的分析揭示了大量糖苷水解酶，这些酶可以利用碳水化合物，包括几丁质降解途径的酶。该细菌缺乏鞭毛机制，但编码了蠕动运动。重建的中心代谢途径显示了发酵有机底物的途径，以及通过需氧和厌氧呼吸进行的完全氧化。使用 BY40 基因组进行的系统发育分析支持了 BRC1 谱系的门水平分类。基于系统发育和基因组分析，提议将新型细菌分类为 Candidatus Sumerlaea chitinivorans，属于候选门 Sumerlaeota。
