KARAKTERISASI DAN BIOPROSPEKSI BERBASIS GENOM VIRGIBACILLUS SALARIUS DARI LAUT JAWA SECARA IN SILICO

• Main Author: Steven, Ray
• Format: Final Project
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/65974
• Institution: Institut Teknologi Bandung

The sea is a dynamic and complex ecosystem to survive for various microorganisms. Marine microorganisms, such as bacteria, can produce various compounds belonging to secondary metabolites with various biological functions that provide survival advantages. There have been many secondary metabolites from marine bacteria that have been used in various industries because they have functions that can provide added value to human life. Marine bacteria from Indonesia, such as Virgibacillus salarius, have been widely studied for their potential to produce secondary metabolites such as carotenoids, antimicrobial compounds, and antiviral compounds. However, so far, there have been no studies related to whole genome sequencing (WGS) and genome-based secondary metabolite search studies from Indonesian marine Virgibacillus salarius. The purpose of this study was to determine the genomic characteristics of Virgibacillus salarius isolates from the Java Sea, characterize secondary metabolite gene clusters, and their bioprospects for industry. The method used in this study includes taxonomic determination by calculating overall genome relatedness indices (OGRI) with FastANI (ANI value) and GGDC (dDDH value) and their phylogenetic position using OrthoFinder and visualized in tree form using iTOL. After that, the quality of the sequencing was determined using CheckM and the general characteristics of the genome were determined using Biopython. Pangenomic analysis of the Virgibacillus genus was performed using GET_HOMOLOGUES and genomic island content analysis was performed using IslandViewer. Analysis of the presence of secondary metabolite gene clusters was performed with antiSMASH and visualization of the reaction pathway was performed with KEGG Reconstructor. Gene cluster families were grouped using BiG-SCAPE and visualized in the form of a network using Cytoscape. Coordinate data and genome annotations were combined with Biopython and visualized into a circular genome map using Proksee. Based on the results of the WGS analysis, the identified bacterial isolates were Virgibacillus salarius after calculating ANI and dDDH, and supported by the results of phylogenetic analysis. The quality of the genome obtained from the sequencing results is "high-quality draft". The general characteristic of this genome is 4.45 Mb in size and the function of each gene has been mapped into the COG (Cluster of Orthologous Groups) category. The results of the pangenomic analysis showed that Virgibacillus had an "open" pangenome type and Virgibacillus salarius isolates from the Java Sea had the highest number of unique genes compared to other Virgibacillus bacteria. The number of genomic islands in the genome has also been successfully calculated, but the determination of the type of genomic island needs to be carried out with further studies. Eight secondary metaboliteproducing gene clusters were obtained which were divided into NRPS, PKS (type III), RiPPs, terpenes, and ectoines. Ectoine and squalene (terpene) gene clusters have complete genes and high economic value so that these gene clusters can be utilized for further production processes. The two NRPS clusters found also have the potential to be utilized but still require further study. The results of this characterization can be used as a basis for the production of secondary metabolites in Virgibacillus bacteria.