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SCycDB: A curated functional gene database for metagenomic profiling of sulphur cycling pathways
Molecular Ecology Resources ( IF 7.7 ) Pub Date : 2020-12-07 , DOI: 10.1111/1755-0998.13306
Xiaoli Yu 1 , Jiayin Zhou 2 , Wen Song 2 , Mengzhao Xu 2 , Qiang He 3 , Yisheng Peng 1 , Yun Tian 4 , Cheng Wang 1 , Longfei Shu 1 , Shanquan Wang 1 , Qingyun Yan 1 , Jihua Liu 2 , Qichao Tu 2 , Zhili He 1, 5
Affiliation  

Microorganisms play important roles in the biogeochemical cycling of sulphur (S), an essential element in the Earth's biosphere. Shotgun metagenome sequencing has opened a new avenue to advance our understanding of S cycling microbial communities. However, accurate metagenomic profiling of S cycling microbial communities remains technically challenging, mainly due to low coverage and inaccurate definition of S cycling gene families in public orthology databases. Here we developed a manually curated S cycling database (SCycDB) to profile S cycling functional genes and taxonomic groups for shotgun metagenomes. The developed SCycDB contains 207 gene families and 585,055 representative sequences affiliated with 52 phyla and 2684 genera of bacteria/archaea, and 20,761 homologous orthology groups were also included to reduce false positive sequence assignments. SCycDB was applied for functional and taxonomic analysis of S cycling microbial communities from four habitats (freshwater, hot spring, marine sediment and soil). Gene families and microorganisms involved in S reduction were abundant in the marine sediment, while those of S oxidation and dimethylsulphoniopropionate transformation were abundant in the soil. SCycDB is expected to be a useful tool for fast and accurate metagenomic analysis of S cycling microbial communities in the environment.

中文翻译:

SCycDB:精选的功能基因数据库,用于硫循环途径的宏基因组分析

微生物在硫(S)的生物地球化学循环中起着重要作用,硫是地球生物圈中必不可少的元素。gun弹枪的基因组测序为我们加深对S循环微生物群落的了解开辟了一条新途径。但是,S自行车微生物群落的精确宏基因组学分析在技术上仍然具有挑战性,这主要是由于公共矫形数据库中S自行车基因家族的覆盖率低和定义不准确。在这里,我们开发了一个手动管理的S循环数据库(SCycDB),以描述shot弹枪基因组的S循环功能基因和分类学组。已开发的SCycDB包含207个基因家族和585,055个代表性序列,这些序列与52种细菌和2684个细菌/古细菌属相关,以及20种,还包括761个同源矫正组,以减少假阳性序列分配。SCycDB用于来自四个生境(淡水,温泉,海洋沉积物和土壤)的S循环微生物群落的功能和分类学分析。海洋沉积物中富含S的基因家族和微生物丰富,而土壤中有丰富的S氧化和丙二酸二甲基磺酸盐转化的家族。SCycDB有望成为快速准确地对环境中S循环微生物群落进行宏基因组学分析的有用工具。海洋沉积物中富含S的基因家族和微生物丰富,而土壤中有丰富的S氧化和丙二酸二甲基磺酸盐转化的家族。SCycDB有望成为快速准确地对环境中S循环微生物群落进行宏基因组学分析的有用工具。海洋沉积物中富含S的基因家族和微生物丰富,而土壤中有丰富的S氧化和丙二酸二甲基磺酸盐转化的家族。SCycDB有望成为快速准确地对环境中S循环微生物群落进行宏基因组学分析的有用工具。
更新日期:2020-12-07
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