Indentification of probotic-related genes from pediococcus acidilactici through genome sequencing

Sammuel Ungkan Anak Jimbau (2018) Indentification of probotic-related genes from pediococcus acidilactici through genome sequencing. Masters thesis, Universiti Malaysia Sabah.

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Abstract

Pediococcus acidilactici, a species of lactic acid bacteria (LAB) is used in food fermentation and bioprocessing. The purposes of this research were to assemble and annotate the short-read sequence of Pediococcus acidilactici strain isolated from beef and to identify genes attribute to probiotic properties based on the assembled and annotated genome. Initial steps for genome assembly were quality control, trimming of the raw sequenced genome through FastQC and Trimmomatic. De novo genome assembly was performed using SPAdes, while genome annotation was done by using Prokka and RAST. Genome assembly produced 239 contigs with length of 1,954,278 bp. The NSO reported was 31,626 with GC content of 42.06%. Probiotic related genes identified such as choloylglycine hydrolase and xylulose-5-phosphate phosphoketolase are responsible for fermentation process and gastrointestinal resistance. Efflux pump Lde gene and teichoic acid production genes were also identified which are responsible for antibiotic resistance and adhesion ability. These functional genes identified can attribute to the probiotic properties of the P. acidi!acticistrain. Further validation of these genes and genomic comparison between different species or strains can be done in future research in order to identify the niches of probiotic bacteria.

Item Type:	Thesis (Masters)
Keyword:	Pediococcus acidi, Actici, Beef meat, De novo assembly, Genome annotation, Probiotic genes
Subjects:	Q Science > QR Microbiology > QR1-502 Microbiology
Department:	INSTITUTE > Biotechnology Research Institute (BRI)
Depositing User:	DG MASNIAH AHMAD -
Date Deposited:	13 Jun 2025 14:59
Last Modified:	13 Jun 2025 14:59
URI:	https://eprints.ums.edu.my/id/eprint/44040

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