Mining Functional Genes And Gene Clusters In Tara Oceans Metagenomic Data

Microbial secondary metabolites are a major sources of clinical-use antibiotics.Due to the presence of antibiotic resistance,it has been more and more important to search for novel antimicrobial compounds.Studies on secondary metabolite biosynthetic gene clusters in environmental(like marine)microbial genomes could provide insights for researchers into novel drug development.Metagenomics,as an approach to investigate microbial communities,could assist researchers to perform their researches at a larger scale and explore the environments at a deeper layer.Microbial antibiotic resistance is a big problem we are currently facing.Studies on antibiotic resistance could help researchers make new strategies on how to use and develop anti-pathogen drugs.For example,it is possible to engineer the biosynthetic gene clusters of known antibiotics to increase the compounds' activity or confer novel activity.Therefore,studies on microbial secondary metabolite biosynthetic gene clusters an antibiotic resistance genes are of great significance.In this study,it has been planned to mining open marine microbial metagenomic data to shed light on functional genes and gene clusters.Tara Oceans Expedition was led by EMBL and is a project aiming at sampling and sequencing planktons in global oceans.This project provides us with a great opportunity to predict and mine the genes and gene clusters in an open environment like global oceans.In this study,the metagenomics data from Tara Oceans ERP001736,a component project of PRJEB1787,were downloaded and analyzed.Several studies were conducted and results were obtained:(1)The metagenomics reads from 135 Tara Oceans samples were assembled and mapped.High quality sequences were obtained after several other steps.These sequences are ready-to-use data for mining functional genes and gene clusters and other studies related to metagenomics.(2)antiSMASH was used to identify,annotate and analyse secondary metabolite biosynthesis gene clusters,and many clusters with great novelty were discovered.The key domains and modification domains were explore,and the backbone structures of the products from some clusters were predicted.The numbers and composition of clusters in samples were analyzed by statistical tests,and it is shown that depth is a major factor that affect the distribution of clusters.(3)Based on reference sequences in ARDB,antibiotic resistance genes in the data were identified,annotated,and classified.Thousands of antibiotic resistance gene sequences were discovered,which could be divided into 70 categories.Their distribution in environments and enrichment in microbial genus were studied,and depth is still a major factor.Some genus are more enriched in antibiotic resistance genes.