Zhou Jiayin, Yu Xiaoli, Liu Jihua, Qin Wei, He Zhili, Stahl David, Jiao Nianzhi, Zhou Jizhong, Tu Qichao
Institute of Marine Science and Technology, Shandong University, Qingdao, China.
Joint Laboratory for Ocean Research and Education of Dalhousie University, Shandong University and Xiamen University, Qingdao, China.
mSystems. 2021 Jun 29;6(3):e0049721. doi: 10.1128/mSystems.00497-21. Epub 2021 Jun 1.
Cobalamin (vitamin B12; VB) is an indispensable nutrient for all living entities in the Earth's biosphere and plays a vital role in both natural and host environments. Currently in the metagenomic era, gene families of interest are extracted and analyzed based on functional profiles by searching shotgun metagenomes against public databases. However, critical issues exist in applying public databases for specific processes such as VB biosynthesis pathways. We developed a curated functional gene database termed VBPath for accurate metagenomic profiling of VB biosynthesis gene families of microbial communities in complex environments. VBPath contains a total of 60 VB synthesis gene families, 287,731 sequences, and 21,154 homology groups, and it aims to provide accurate functional and taxonomic profiles of VB synthesis pathways for shotgun metagenomes and minimize false-positive assignments. VBPath was applied to characterize cobalamin biosynthesis gene families in human intestines and marine environments. The results demonstrated that ocean and human intestine had dramatically different VB synthesis processes and that gene families belonging to salvage and remodeling pathway dominated human intestine but were lowest in the ocean ecosystem. VBPath is expected to be a useful tool to study cobalamin biosynthesis processes via shotgun metagenome sequencing in both environmental and human microbiome research. Vitamin B12 (VB) is an indispensable nutrient for all living entities in the world but can only be synthesized by a small subset of prokaryotes. Therefore, this small subset of prokaryotes controls ecosystem stability and host health to some extent. However, critical accuracy and comprehensiveness issues exist in applying public databases to profile VB synthetic gene families and taxonomic groups in complex metagenomes. In this study, we developed a curated functional gene database termed VBPath for accurate metagenomic profiling of VB communities in complex environments. VBPath is expected to serve as a valuable tool to uncover the hidden microbial communities producing this precious nutrient on Earth.
钴胺素（维生素B12；VB）是地球生物圈中所有生物不可或缺的营养素，在自然环境和宿主环境中都起着至关重要的作用。在当前的宏基因组时代，通过将鸟枪法宏基因组与公共数据库进行比对，根据功能概况提取和分析感兴趣的基因家族。然而，在将公共数据库应用于特定过程（如VB生物合成途径）时存在关键问题。我们开发了一个经过整理的功能基因数据库，称为VBPath，用于对复杂环境中微生物群落的VB生物合成基因家族进行准确的宏基因组分析。VBPath总共包含60个VB合成基因家族、287,731个序列和21,154个同源组，旨在为鸟枪法宏基因组提供VB合成途径准确的功能和分类概况，并尽量减少假阳性分配。VBPath被应用于表征人类肠道和海洋环境中的钴胺素生物合成基因家族。结果表明，海洋和人类肠道的VB合成过程有显著差异，属于补救和重塑途径的基因家族在人类肠道中占主导地位，但在海洋生态系统中含量最低。VBPath有望成为环境和人类微生物组研究中通过鸟枪法宏基因组测序研究钴胺素生物合成过程的有用工具。维生素B12（VB）是世界上所有生物不可或缺的营养素，但只能由一小部分原核生物合成。因此，这一小部分原核生物在一定程度上控制着生态系统的稳定性和宿主的健康。然而，在将公共数据库应用于复杂宏基因组中VB合成基因家族和分类群的分析时，存在关键的准确性和全面性问题。在本研究中，我们开发了一个经过整理的功能基因数据库，称为VBPath，用于对复杂环境中VB群落进行准确的宏基因组分析。VBPath有望成为一个有价值的工具，用于揭示地球上产生这种珍贵营养素的隐藏微生物群落。
