In silico prediction and in vitro analysis of bacteriocin and probiotic properties of Weissella cibaria NM1 isolated from Asian sea bass

Ahmad Zuhairi Abdul Malek; Nur Amalina Ahmad Lokman; Boon Chin Tan; Yin Sze Lim

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In silico prediction and in vitro analysis of bacteriocin and probiotic properties of Weissella cibaria NM1 isolated from Asian sea bass

Author: Ahmad Zuhairi Abdul Malek ¹ ; Nur Amalina Ahmad Lokman ¹ ; Boon Chin Tan ² ; Yin Sze Lim ¹
Author Information

1. School of Biosciences, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.
2. Centre for Research in Biotechnology for Agriculture (CEBAR), Level 3, Research Management and Innovation Complex, University of Malaya, 50603 Kuala Lumpur, Malaysia.
Publication Type:Journal Article
Keywords: Weissella cibaria; Bacteriocin; Probiotic; In silico prediction; Machine learning
MeSH: Bacteriocins; Probiotics; Weissella; Asian; Computer Simulation; In Vitro Techniques
From:Malaysian Journal of Microbiology 2021;17(6):708-719
CountryMalaysia
Language:English
Abstract: Aims:This study aims to predict the presence of bacteriocin- and probiotic-associated genes in the genome of Weissella cibaria NM1 isolated from Asian sea bass using a machine learning-based NeuBI prediction approach, followed by the investigation of the crude bacteriocin antimicrobial and probiotic properties via in vitro analysis.
Methodology and results:This study utilized the machine learning-based NeuBI prediction approach with a homology search of highly conserved bacteriocin-associated genes present in the genome of W. cibaria NM1. This approach discovered a putative bacteriocin gene (WC_2064) and bacteriocin operon with complete immunity, transporter, regulator and modifier genes. Furthermore, the genome of W. cibaria NM1 was found to harboured specific probiotic*associated genes that would contribute to acid and bile tolerance, adhesion on thehost cell and exhibited cholesterolreducing ability. On top of that, the genome also shows the absence of virulence and antibiotic resistance genes, which signifies the safety of W. cibaria NM1 as a potential probiotic candidate. In vitro study has confirmed the antipseudomonal activity of crude bacteriocin NM1 with MIC of 62.5 mg/mL. Weissella cibaria NM1 can tolerate 0.3% (v/v) of bile salt condition and the transit through the simulated gastric (pH 3 and 4) and small intestinal (pH 8) tract.
Conclusion, significance and impact of study:Current findings suggested in silico approach can speed up the search for putative bacteriocin and probiotic-associated genes from the genome of W. cibaria NM1. Nevertheless, further verification through experimental works will be deemed essential.
Full text:20.2021my0071.pdf