National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning, 530007, China.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China.
Sci Rep. 2023 May 19;13(1):8126. doi: 10.1038/s41598-023-34995-y.
Shotgun metagenome sequencing provides the opportunity to recover underexplored rare populations and identify difficult-to-elucidate biochemical pathways. However, information on sulfur genes, including their sequences, is scattered in public databases. Here, we introduce SMDB ( https://smdb.gxu.edu.cn/ )-a manually curated database of sulfur genes based on an in-depth review of the scientific literature and orthology database. The SMDB contained a total of 175 genes and covered 11 sulfur metabolism processes with 395,737 representative sequences affiliated with 110 phyla and 2340 genera of bacteria/archaea. The SMDB was applied to characterize the sulfur cycle from five habitats and compared the microbial diversity of mangrove sediments with that of other habitats. The structure and composition of microorganism communities and sulfur genes were significantly different among the five habitats. Our results show that microorganism alpha diversity in mangrove sediments was significantly higher than in other habitats. Genes involved in dissimilatory sulfate reduction were abundant in subtropical marine mangroves and deep-sea sediments. The neutral community model results showed that microbial dispersal was higher in the marine mangrove ecosystem than in others habitats. The Flavilitoribacter of sulfur-metabolizing microorganism becomes a reliable biomarker in the five habitats. SMDB will assist researchers to analyze genes of sulfur cycle from the metagenomic efficiently.
shotgun 宏基因组测序为探索未被充分研究的稀有种群和鉴定难以阐明的生化途径提供了机会。然而，关于硫基因的信息，包括它们的序列，分散在公共数据库中。在这里，我们介绍了 SMDB（https://smdb.gxu.edu.cn/）-一个基于对科学文献和同源性数据库的深入审查的硫基因人工 curated 数据库。SMDB 共包含 175 个基因，涵盖 11 个硫代谢过程，有 395737 个代表序列隶属于 110 个门和 2340 个细菌/古菌属。SMDB 被用于从五个生境中表征硫循环，并将红树林沉积物与其他生境的微生物多样性进行比较。五个生境中微生物群落和硫基因的结构和组成有显著差异。我们的结果表明，红树林沉积物中微生物的 alpha 多样性显著高于其他生境。在亚热带海洋红树林和深海沉积物中，异化硫酸盐还原相关基因丰富。中性群落模型结果表明，海洋红树林生态系统中微生物的扩散性高于其他生境。硫代谢微生物中的 Flavilitoribacter 成为五个生境中的可靠生物标志物。SMDB 将有助于研究人员从宏基因组中有效地分析硫循环基因。
