Metagenomics workflow analysis of endophytic bacteria from oil palm fruits

[摘要] Next-Generation Sequencing (NGS) has become a powerful sequencing tool for microbial study especially to lead the establishment of the field area of metagenomics. This study described a workflow to analyze metagenomics data of a Sequence Read Archive (SRA) file under accession ERP004286 deposited by University of Sao Paulo. It was a direct sequencing data generated by 454 pyrosequencing platform originated from oil palm fruits endophytic bacteria which were cultured using oil-palm enriched medium. This workflow used SortMeRNA to split ribosomal reads sequence, Newbler (GS Assembler and GS Mapper) to assemble and map reads into genome reference, BLAST package to identify and annotate contigs sequence, and QualiMap for statistical analysis. Eight bacterial species were identified in this study. Enterobacter cloacae was the most abundant species followed by Citrobacter koseri, Seratia marcescens, Latococcus lactis subsp. lactis, Klebsiella pneumoniae, Citrobacter amalonaticus, Achromobacter xylosoxidans, and Pseudomonas sp. respectively. All of these species have been reported as endophyte bacteria in various plant species and each has potential as plant growth promoting bacteria or another application in agricultural industries.

[发布机构] Plant Production and Biotechnology Division, PT SMART Tbk., Sinar Mas Land Plaza, 10th Fl., Jl. M.H. Thamrin No. 51, Jakarta; 10350, Indonesia^1

[效力级别] 化学 [学科分类] 生物科学（综合）

[关键词] 454-Pyrosequencing;Agricultural industries;Endophytic bacteria;Enterobacter cloacae;Klebsiella pneumoniae;Next-generation sequencing;Plant growth promoting bacterium;Workflow analysis