正当物理学家苦苦寻找宇宙暗物质之际，美国研究人员6月10日报告说，他们完成了对“生命暗物质”的基因组测序。
1996年，科学家首次发现了一种名为“候选门TM6”的细菌。这种细菌广泛存在于水环境中，却无法在实验室中培养，除了其标志性的16S基因外，科学界对它的生命活动特点几乎一无所知。正因此，“候选门TM6”细菌被称为“生命暗物质”。
美国克雷格·文特尔研究所的研究人员在新一期美国《国家科学院学报》报告说，他们采用能从单个细胞中捕获基因组的自动化技术，从一家医院休息室的水槽下水管生物膜上收集了TM6细菌，并使用DNA（脱氧核糖核酸）拼接方法成功重建了该细菌的基因组。
测序结果表明，这种细菌无法制造氨基酸，可能需要寄居在生物膜中或者单细胞微生物内部。不过，目前尚不清楚TM6细菌对人体是否有害。
研究人员表示，该研究成果或将有助于培养和研究类似微生物，从而进一步了解它们的生态特征和功能。（生物谷Bioon.com）
生物谷推荐英文摘要：
Proceedings of the National Academy of Sciences DOI：10.1073/pnas.1219809110
Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum
Jeffrey S. McLeana,b,1, Mary-Jane Lombardoa, Jonathan H. Badgera, Anna Edlunda, Mark Novotnya, Joyclyn Yee-Greenbauma, Nikolay Vyahhic, Adam P. Halla, Youngik Yanga, Christopher L. Duponta, Michael G. Zieglerd, Hamidreza Chitsaze, Andrew E. Allena, Shibu Yoosepha, Glenn Teslerf, Pavel A. Pevznerc,g, Robert M. Friedmana, Kenneth H. Nealsona,b, J. Craig Ventera, and Roger S. Laskena
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.
