State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
Suzhou Research Institute, Shandong University, Suzhou, 215123, China.
Microbiome. 2020 Sep 16;8(1):134. doi: 10.1186/s40168-020-00903-z.
Sequencing prokaryotic genomes has revolutionized our understanding of the many roles played by microorganisms. However, the cell and taxon proportions of genome-sequenced bacteria or archaea on earth remain unknown. This study aimed to explore this basic question using large-scale alignment between the sequences released by the Earth Microbiome Project and 155,810 prokaryotic genomes from public databases.
Our results showed that the median proportions of the genome-sequenced cells and taxa (at 100% identities in the 16S-V4 region) in different biomes reached 38.1% (16.4-86.3%) and 18.8% (9.1-52.6%), respectively. The sequenced proportions of the prokaryotic genomes in biomes were significantly negatively correlated with the alpha diversity indices, and the proportions sequenced in host-associated biomes were significantly higher than those in free-living biomes. Due to a set of cosmopolitan OTUs that are found in multiple samples and preferentially sequenced, only 2.1% of the global prokaryotic taxa are represented by sequenced genomes. Most of the biomes were occupied by a few predominant taxa with a high relative abundance and much higher genome-sequenced proportions than numerous rare taxa.
These results reveal the current situation of prokaryotic genome sequencing for earth biomes, provide a more reasonable and efficient exploration of prokaryotic genomes, and promote our understanding of microbial ecological functions. Video Abstract.
对原核生物基因组进行测序极大地改变了我们对微生物所扮演的众多角色的理解。然而，地球上测序细菌或古菌的细胞和分类群比例仍然未知。本研究旨在使用地球微生物组计划发布的序列与公共数据库中的 155810 个原核基因组之间的大规模比对来探索这一基本问题。
我们的结果表明，不同生物群中测序细胞和分类群（在 16S-V4 区域具有 100%同一性）的中位数比例分别达到 38.1%（16.4-86.3%）和 18.8%（9.1-52.6%）。生物群中原核基因组的测序比例与 alpha 多样性指数呈显著负相关，宿主相关生物群中的测序比例明显高于自由生活生物群。由于一组在多个样本中发现并优先测序的世界性 OTUs，只有 2.1%的全球原核分类群由测序基因组代表。大多数生物群都被少数具有高相对丰度和远高于大量稀有分类群的测序比例的优势分类群占据。
这些结果揭示了地球生物群中原核生物基因组测序的现状，为原核生物基因组的更合理、更有效的探索提供了依据，并促进了我们对微生物生态功能的理解。视频摘要。
