現(xiàn)有基因組序列只能讓我們對微生物引人注目的多樣性有一個(gè)很有限的認(rèn)識(shí)，因?yàn)樗鼈冎薪^大部分從未被培養(yǎng)出純培養(yǎng)物,。在這項(xiàng)研究中,，Tanja Woyke及其同事利用單細(xì)胞基因組學(xué)方法來研究和測序來自九個(gè)多樣化生境的201種未培養(yǎng)的古生菌和細(xì)菌細(xì)胞。該信息顯示了無數(shù)的“門”內(nèi)和“門”間關(guān)系以及若干出乎意料的代謝特征,。在這些新數(shù)據(jù)的基礎(chǔ)上,，作者提出了對古生菌域和細(xì)菌域的分類修正，包括提議將古生菌重新歸入三個(gè)“超級(jí)門”（superphyla）中,。（生物谷Bioon.com）
生物谷推薦英文摘要：
Nature doi:10.1038/nature12352
Insights into the phylogeny and coding potential of microbial dark matter
Christian Rinke, Patrick Schwientek, Alexander Sczyrba, Natalia N. Ivanova, Iain J. Anderson, Jan-Fang Cheng, Aaron Darling, Stephanie Malfatti, Brandon K. Swan, Esther A. Gies, Jeremy A. Dodsworth, Brian P. Hedlund, George Tsiamis, Stefan M. Sievert, Wen-Tso Liu, Jonathan A. Eisen, Steven J. Hallam, Nikos C. Kyrpides, Ramunas Stepanauskas, Edward M. Rubin, Philip Hugenholtz & Tanja Woyke
Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201?uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29?major mostly uncharted branches of the tree of life, so-called ‘microbial dark matter’. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.
