ESKtides: a comprehensive database and mining method for ESKAPE-derived peptides
ESKtides: a comprehensive database and mining method for ESKAPE-derived peptides
Abstract Under the concept of one health, Super-drug resistant bacteria are getting more and more attention from scientists, in particular, ESKAPE bacteria directly killed more than 1,270,000 people in 2019. Recent studies have proposed that phage PGHs(peptidoglycan hydrolases) and antimicrobial peptides can be the new antibacterial agents against multi-drug resistant bacteria. However, Methods for mining antimicrobial peptides based on phages or phages PGHs are in need to develop. Here, using ESKAPE strains and ESKAPE phages in total of 6,809 samples from National Center for Biotechnology Information (NCBI), PhagesDB, Microbe Versus Phage (MVP) and Virus-Host Database, we systematically identified PGHs across ESKAPE strains prophages and phages, mined peptides and scored peptides based on PGHs. As a result, a total of 1,000 high antibacterial activity peptides and 1,200 medium antibacterial activity peptides were identified. In order to reduce the impact of different methods on comments, we used a unified process to comment ESKAPE strains and phages. In addition, we designed an online tool to predict the peptides antibacterial activity. Calculations of peptides phylogeny, peptides physicochemical property and peptides secondary structure are also included into our online tools. Finally, we developed ESKtides, a user-friendly and intuitive database (http://www.phageonehealth.cn:9000/ESKtides) for data browsing, searching, and downloading. ESKtides will significantly provide a rich peptide library based on ESKAPE strains and phages.
Zou Geng、Wu Hongfang、Zhang Yue、Zhou Yang、Chen Huanchun、Li David Runze、Li Jinquan、Li Xuejian
State Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University||Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural UniversityState Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University||Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural UniversityState Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University||Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural UniversityState Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural UniversityState Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural UniversityState Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University||Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural UniversityState Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University||Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University||Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesState Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University||Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University
医学研究方法微生物学生物科学研究方法、生物科学研究技术
Zou Geng,Wu Hongfang,Zhang Yue,Zhou Yang,Chen Huanchun,Li David Runze,Li Jinquan,Li Xuejian.ESKtides: a comprehensive database and mining method for ESKAPE-derived peptides[EB/OL].(2025-03-28)[2025-05-21].https://www.biorxiv.org/content/10.1101/2023.05.03.538019.点此复制
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