Global marine microbial diversity and its potential in bioprospecting

• 成果类型: Article
• 署名作者: Chen, Jianwei; Jia, Yangyang; Sun, Ying; Liu, Kun; Zhou, Changhao; Liu, Chuan; Li, Denghui; Liu, Guilin; Zhang, Chengsong; Yang, Tao; Huang, Lei; Zhuang, Yunyun; Wang, Dazhi; Xu, Dayou; Zhong, Qiaoling; Guo, Yang; Li, Anduo; Seim, Inge; Jiang, Ling; Wang, Lushan; Lee, Simon Ming Yuen; Liu, Yujing; Wang, Dantong; Zhang, Guoqiang; Liu, Shanshan; Wei, Xiaofeng; Yue, Zhen; Zheng, Shanmin; Shen, Xuechun; Wang, Sen; Qi, Chen; Chen, Jing; Ye, Chen; Zhao, Fang; Wang, Jun; Fan, Jie; Li, Baitao; Sun, Jiahui; Jia, Xiaodong; Xia, Zhangyong; Zhang, He; Liu, Junnian; Zheng, Yue; Liu, Xin; Wang, Jian; Yang, Huanming; Kristiansen, Karsten; Xu, Xun; Mock, Thomas; Li, Shengying; Zhang, Wenwei; Fan, Guangyi
• 署名单位: Beijing Genomics Institute (BGI); University of Copenhagen; Shandong University; Beijing Genomics Institute (BGI); Ocean University of China; Xiamen University; Chinese Academy of Sciences; Chinese Academy of Sciences; Institute of Deep-Sea Science & Engineering, CAS; Nanjing Tech University; Hong Kong Polytechnic University; Hong Kong Polytechnic University; Beijing Genomics Institute (BGI); University of East Anglia
• 刊物名称: Nature
• ISSN/ISSBN: 0028-6356
• DOI: 10.1038/s41586-024-07891-2
• 发表日期: 2024-09-12
• 关键词: crispr-cas; assembled genomes; bacterial; identification; community; biodegradation; annotation; EVOLUTION; insight; genes

摘要

The past two decades has witnessed a remarkable increase in the number of microbial genomes retrieved from marine systems1,2. However, it has remained challenging to translate this marine genomic diversity into biotechnological and biomedical applications3,4. Here we recovered 43,191 bacterial and archaeal genomes from publicly available marine metagenomes, encompassing a wide range of diversity with 138 distinct phyla, redefining the upper limit of marine bacterial genome size and revealing complex trade-offs between the occurrence of CRISPR-Cas systems and antibiotic resistance genes. In silico bioprospecting of these marine genomes led to the discovery of a novel CRISPR-Cas9 system, ten antimicrobial peptides, and three enzymes that degrade polyethylene terephthalate. In vitro experiments confirmed their effectiveness and efficacy. This work provides evidence that global-scale sequencing initiatives advance our understanding of how microbial diversity has evolved in the oceans and is maintained, and demonstrates how such initiatives can be sustainably exploited to advance biotechnology and biomedicine. Analysis of 43,191 genomes obtained from publicly available marine bacterial and archaeal metagenome data provides insights into marine bacterial evolution, CRISPR-Cas defence and antibiotic resistance genes, and demonstrates the potential of marine metagenomes for biotechnological applications.