Genomic Profiling of Pediococcus acidilactici LBP: A Potential Probiotic Isolate from Indonesian ethnic Food Lemea

Rashid, Muhammad Naeem and Prof. Agustin Krisna Wardani,, STP., M.Si., Ph.D. and Dian Widya Ningtyas, STP., MP., Ph.D. (2024) Genomic Profiling of Pediococcus acidilactici LBP: A Potential Probiotic Isolate from Indonesian ethnic Food Lemea. Magister thesis, Universitas Brawijaya.

Abstract

Lemea, a traditional fermented food from the Rejang tribe of Bengkulu, Indonesia, is made with chopped bamboo shoots and fish. The study aimed to Annotate the whole genome of P. acidilactici isolated from Lemea and compare it to other bacterial strains in the Pediococcus genus. In order to demonstrate the diversity within this species, a phylogenetic tree constructed using every core gene in the genus was employed to analyze the connections between every strain. Pan-genome analysis was performed utilizing eight assemblies obtained from the NCBI database. The investigation further sought to identify the bacteriocins produced by the isolate, provide a functional characterization within the Pediococcus genus, and provide a meta-analysis. Genomics data were also utilized to evaluate the effectiveness of using P. acidilactici in food and beverage fermentation. The isolate's safety was assessed using whole genome sequencing. The strain was identified as Pediococcus acidilactici LBP using 16S rRNA gene sequencing and was capable of generating bacteriocin. The genome of P. acidilactici LBP consisted roughly 2 million base pairs in a single chromosome, 1,860 coding sequences, 71 ribonucleic acids, a guanine-cytosine composition of 42.01%, a protein operon cluster predicted as pediocin (estimated molecular weight: 6600 Da) and no plasmid was detected. The Pediococcus acidilactici LBP encoded a pediocin operon, a full Clustered regularly interspaced short palindromic repeats-Cas system, and a restriction modification system, all of which are extremely beneficial and can prevent food spoilage. These systems have the ability to prevent the growth of harmful bacteria that lead to food deterioration and illnesses caused by food contamination. Furthermore, throughout evolution, these systems prevent the horizontal transfer of virulent genes, and resistant antimicrobial genes. Beside the genes aiding food safety, Pediococcus acidilactici LBP strain also encoded genes that foster fermentation to produce functional fermented foods prolonging food storage life and improving the organoleptic qualities. The absence of matches for proteins linked to pathogenic families further supports the probiotic nature of Pediococcus acidilactici LBP. The investigation of the Pediococcus acidilactici LBP strain for safety revealed that it has coding sequences associated with antibacterial resistance genes and hemolytic toxins produced by B. cerus group. The Pediococcus acidilactici LBP strain contained coding sequences derived from bacteriophage infection and were able to rearrange their genomes, as evidenced by the discovery of twentyseven insertion sequences and single prophage region in the Pediococcus acidilactici LBP's gene pool but safety analysis predicted that isolate is unable to transfer undesirable genes to other microbes. The greatest percentage of Glycoside Hydrolases was found in four families of CAZymes, with 57 genes in total. A number of proteases have been found, including penicillin amidase, aminopeptidase YscS, oligoendopeptidase F, lysine decarboxylase, and Xaa-Pro aminopeptidase. Further evidence of the Pediococcus acidilactici LBP’s probiotic activity comes from the presence of glutamate carboxypeptidase and glutaminyl-peptide cyclotransferase, which help the host absorb and digest proteins and amino acids from food. Pediococcus acidilactici's carbohydrate metabolic capabilities confirmed by the presence of glycoside hydrolases, glycosyltransferases and carbohydrate estrases indicated its ability to ferment D-ribose, D-mannose, fructose, and cellobiose and its proficiency in carbohydratexv fermentation. These findings indicate that P. acidilactici LBP is an excellent candidate as a starter culture for fermented foods and beverages of various natures, improving probiotic content, sensory qualities, and shelf life.

Item Type:	Thesis (Magister)
Identification Number:	042410
Uncontrolled Keywords:	P. acidilactici, bacteriocin, whole genome analysis, biopreservative, food safety
Divisions:	S2/S3 > Magister Keteknikan Pertanian, Fakultas Teknologi Pertanian
Depositing User:	Unnamed user with username nova
Date Deposited:	23 Sep 2024 06:57
Last Modified:	23 Sep 2024 06:57
URI:	http://repository.ub.ac.id/id/eprint/225842

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