MiST 4.0: Microbial Signal Transduction database

Signal transduction systems in bacteria and archaea link environmental stimuli to specific adaptive cellular responses. They control gene expression, motility, biofilm formation, development and other processes that are vital to survival. The microbial signal transduction (MiST) database is an online resource that stores tens of thousands of genomes and allows users to explore their signal transduction profiles, analyze genomes in bulk using the database application programming interface (API) and make testable hypotheses about the functions of newly identified signaling systems. However, signal transduction in metagenomes remained completely unexplored. To lay the foundation for research in metagenomic signal transduction, we have prepared a new release of the MiST database, MiST 4.0, which features over 10 000 metagenome-assembled genomes (MAGs), a scaled representation of proteins and detailed BioSample information. In addition, several thousand new genomes have been processed and added to the database, bringing the total to over 202,000 genomes now available in MiST. A new interface has been developed that allows users to seamlessly switch between genomes and MAGs. Starting from MiST 4.0, the database incorporates updates to the NCBI taxonomy reflecting the inclusion of the rank "phylum" in the International Code of Nomenclature for Prokaryotes, which involved changes to 42 taxa. MiST 4.0 is freely accessible at https://mistdb.com; genomes and MAGs can also be explored using the API available on the same page.

细菌与古菌的信号转导系统（signal transduction system）可将环境刺激与特异性适应性细胞应答相连接，调控基因表达、运动性、生物被膜形成、发育及其他关乎生存的关键生命过程。微生物信号转导数据库（MiST）作为在线资源，存储了数万个基因组，支持用户探索自身的信号转导谱，可通过数据库应用程序编程接口（API）批量分析基因组，并可针对新发现的信号系统功能提出可验证的假说。然而，宏基因组层面的信号转导研究此前仍完全处于空白状态。为宏基因组信号转导研究奠定基础，我们推出了MiST数据库的新版本——MiST 4.0。该版本收录了超过10000个宏基因组组装基因组（metagenome-assembled genomes, MAGs），提供了蛋白质的比例化表征及详细的生物样本信息。此外，本次更新还新增了数千个经过处理的基因组，使MiST数据库中可用的基因组总数现已超过202000个。开发了全新的界面，支持用户在基因组与宏基因组组装基因组之间无缝切换。自MiST 4.0版本起，数据库更新了NCBI分类学（NCBI taxonomy）内容，纳入了《原核生物命名国际准则（International Code of Nomenclature for Prokaryotes）》中新增“门”这一分类阶元的修订，本次更新共涉及42个分类群的调整。用户可通过https://mistdb.com免费访问MiST 4.0；用户亦可通过该页面提供的应用程序编程接口（API）探索基因组与宏基因组组装基因组。

搜集汇总

背景与挑战

背景概述

MiST 4.0是一个微生物信号转导数据库，专注于存储和分析细菌与古菌的基因组及信号转导谱。该版本新增了超过1万个宏基因组组装基因组（MAGs），使总基因组数达到20.2万以上，并提供了包括基因和蛋白质序列在内的详细统计数据。数据库通过新界面支持用户在基因组与宏基因组之间无缝切换，旨在为宏基因组信号转导研究奠定基础。