Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum.
Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum.
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DOI：
10.1073/pnas.1219809110
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发表时间：
2013-06-25
影响因子：
11.1
通讯作者：
Lasken, Roger S
中科院分区：
文献类型：
--
作者：
McLean, Jeffrey S;Lombardo, Mary-Jane;Lasken, Roger S
“生命的暗物质”描述了微生物，甚至是细菌门的整个部门，这些部门已经逃避了培养，还没有被测序。我们提出了一个基因组从全球分布，但难以捉摸的候选门TM6，并揭示其代谢潜力。通过使用高度自动化的单细胞基因组学平台分析细胞，在来自医院洗手间内的水槽排水管的生物膜中检测到TM6。我们开发了一种方法，用于增加通量并有效地提高基于单流分选细胞的小型随机池的采样罕见事件的可能性，通过多重置换扩增扩增其DNA并对池中的所有细胞进行测序，从而创建“迷你宏基因组”。“最近开发的单细胞组装程序SPAdes与重叠群分箱方法相结合，允许从这些微型宏基因组重建基因组。在该TM6成员（JCVI TM6SC1）的7个重叠群中回收了总共1.07 Mb，估计代表其基因组的90%。从独立捕获、扩增和组装的池产生的总共三个TM6基因组草图之间的高核苷酸同一性提供了正确基因组序列的强有力的确认。TM6可能是革兰氏阴性生物，并且可能是未知宿主（非自由生活）的共生体，部分基于其小基因组，低GC含量，以及缺乏大多数氨基酸和维生素的生物合成途径。保守的单拷贝基因的系统基因组学分析证实，TM6SC1是一个深分支的门。
The "dark matter of life" describes microbes and even entire divisions of bacterial phyla that have evaded cultivation and have yet to be sequenced. We present a genome from the globally distributed but elusive candidate phylum TM6 and uncover its metabolic potential. TM6 was detected in a biofilm from a sink drain within a hospital restroom by analyzing cells using a highly automated single-cell genomics platform. We developed an approach for increasing throughput and effectively improving the likelihood of sampling rare events based on forming small random pools of single-flow-sorted cells, amplifying their DNA by multiple displacement amplification and sequencing all cells in the pool, creating a "mini-metagenome." A recently developed single-cell assembler, SPAdes, in combination with contig binning methods, allowed the reconstruction of genomes from these mini-metagenomes. A total of 1.07 Mb was recovered in seven contigs for this member of TM6 (JCVI TM6SC1), estimated to represent 90% of its genome. High nucleotide identity between a total of three TM6 genome drafts generated from pools that were independently captured, amplified, and assembled provided strong confirmation of a correct genomic sequence. TM6 is likely a Gram-negative organism and possibly a symbiont of an unknown host (nonfree living) in part based on its small genome, low-GC content, and lack of biosynthesis pathways for most amino acids and vitamins. Phylogenomic analysis of conserved single-copy genes confirms that TM6SC1 is a deeply branching phylum.