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通过大规模数据整合揭示全球古菌多样性:仅触及冰山一角

Global Archaeal Diversity Revealed Through Massive Data Integration: Uncovering Just Tip of Iceberg.

作者信息

Kioukis Antonios, Camargo Antonio Pedro, Pavlidis Pavlos, Iliopoulos Ioannis, Kyrpides Nikos C, Lagkouvardos Ilias

机构信息

Department of Clinical Microbiology, School of Medicine, University of Crete, 70013 Heraklion, Greece.

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

出版信息

Microorganisms. 2025 Mar 5;13(3):598. doi: 10.3390/microorganisms13030598.

Abstract

The domain of has gathered significant interest for its ecological and biotechnological potential and its role in helping us to understand the evolutionary history of . In comparison to the bacterial domain, the number of adequately described members in is relatively low, with less than 1000 species described. It is not clear whether this is solely due to the cultivation difficulty of its members or, indeed, the domain is characterized by evolutionary constraints that keep the number of species relatively low. Based on molecular evidence that bypasses the difficulties of formal cultivation and characterization, several novel clades have been proposed, enabling insights into their metabolism and physiology. Given the extent of global sampling and sequencing efforts, it is now possible and meaningful to question the magnitude of global archaeal diversity based on molecular evidence. To do so, we extracted all sequences classified as from 500 thousand amplicon samples available in public repositories. After processing through our highly conservative pipeline, we named this comprehensive resource the 'Global Diversity' (GAD), which encompassed nearly 3 million molecular species clusters at 97% similarity, and organized it into over 500 thousand genera and nearly 100 thousand families. Saline environments have contributed the most to the novel taxa of this previously unseen diversity. The majority of those 16S rRNA gene sequence fragments were verified by matches in metagenomic datasets from IMG/M. These findings reveal a vast and previously overlooked diversity within the , offering insights into their ecological roles and evolutionary importance while establishing a foundation for the future study and characterization of this intriguing domain of life.

摘要

由于其生态和生物技术潜力以及在帮助我们理解[具体生物名称]进化历史方面的作用,[具体生物名称]领域引起了广泛关注。与细菌领域相比,[具体生物名称]中得到充分描述的成员数量相对较少,描述的物种不到1000种。目前尚不清楚这仅仅是由于其成员培养困难,还是实际上该领域具有使物种数量相对较少的进化限制。基于绕过正式培养和表征困难的分子证据,已经提出了几个新的进化枝,从而能够深入了解它们的代谢和生理学。鉴于全球采样和测序工作的规模,现在基于分子证据对全球古菌多样性的规模提出质疑是可能且有意义的。为此,我们从公共数据库中可用的50万个扩增子样本中提取了所有分类为[具体生物名称]的序列。经过我们高度保守的流程处理后,我们将这个综合资源命名为“全球[具体生物名称]多样性”(GAD),它包含了近300万个相似度为97%的分子物种簇,并将其组织成超过50万个属和近10万个科。盐环境对这种前所未见的多样性的新分类群贡献最大。这些16S rRNA基因序列片段中的大多数通过与IMG/M的宏基因组数据集中的匹配得到了验证。这些发现揭示了[具体生物名称]内部一个巨大且以前被忽视的多样性,为深入了解它们的生态作用和进化重要性提供了见解,同时为未来对这个有趣的生命领域的研究和表征奠定了基础。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0307/11944491/6baa6ab47995/microorganisms-13-00598-g001.jpg

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