|
|||||
|
|
New approaches for archaeal genome-guided cultivation |
|
| Authors: | Wang Yinzhao Kamagata Yoichi Li Meng Han Feifei Wang Fengping Xiao Xiang |
| Institution: | 1.State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China ;2.Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 310-8555, Japan ;3.Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen, 518052, China ;4.Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA ;5.School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, China ;6.State Key Laboratory of Ocean Engineering, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China ; |
| Abstract: | Archaea, one of the three domains of life along with Bacteria and Eukarya, contains ancient life forms such as methanogen that are observed today on Earth, and one lineage Asgard archaea is also considered the closest ancestor of Eukarya.Recently, with the development of interdisciplinary studies from Earth and Life sciences, archaeal organisms are considered to play pivotal roles in geochemical cycling in nature. However, our understanding of the attributes, origin and evolution, geochemical and ecological functions of Archaea is hampered by the scarcity of archaeal isolates, which has represented a challenge to researchers for the last 40 years. Cultivation-independent sequencing and phylogenomic analyses have demonstrated a considerable diversity of Archaea with more than 20 novel phyla. However, only four archaeal phyla have cultured representatives, leaving large gaps in our knowledge of the metabolic capabilities and ecological functions of the majority of archaeal strains identified exclusively by DNA sequencing. In this review, we summarize the discovery and development of archaeal research, highlight the knowledge gap between uncultured and cultured archaeal microbes, and call on the importance of devoting greater research efforts to archaeal cultivation. Finally, we outlined new ideas and strategic approaches, namely,(1)genome-based methods,(2) microbial network information-based methods,(3) genome-scale model-guided methods, and(4)machine learning methods, to enable the cultivation of uncultivated archaeal microbes using accumulated high-throughput sequencing data. |
| Keywords: | |
| 本文献已被 CNKI SpringerLink 等数据库收录！ | |