SCycDB: A curated functional gene database for metagenomic profiling of sulphur cycling pathways. (30th December 2020)

• Record Type: Journal Article
• Authors: Yu, Xiaoli; Zhou, Jiayin; Song, Wen; Xu, Mengzhao; He, Qiang; Peng, Yisheng; Tian, Yun; Wang, Cheng; Shu, Longfei; Wang, Shanquan; Yan, Qingyun; Liu, Jihua; Tu, Qichao; He, Zhili
• Is Part Of: Molecular ecology resources. Volume 21:Number 3(2021)
• Page Start: 924
• Page End: 940
• Publication Date: 2020-12-30
• Subjects: functional gene database -- metagenome sequencing -- microbial community -- sulphur cycling; Molecular ecology -- Periodicals; 572.8
• DOI: 10.1111/1755-0998.13306
• Languages: English
• ISSNs: 1755-098X

Abstract

Abstract: 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.