Whole Genome Analysis of Limosilactobacillus fermentum MCC0552 for Probiotic Functionalities and Comparative Genomic Study with Reference Strains

Krishna, Komatwar and Aravind, Sundararaman and Steji, Raphel and Prakash, M. Halami (2025) Whole Genome Analysis of Limosilactobacillus fermentum MCC0552 for Probiotic Functionalities and Comparative Genomic Study with Reference Strains. Probiotics and Antimicrobial Proteins. pp. 1-16.

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Abstract

Limosilactobacillus fermentum MCC0552, a potential probiotic was isolated from a dairy source. L. fermentum MCC0552 has been proven earlier to enhance immuno-modulatory response by alleviating inflammatory and diabetic effects. The objective of this study is to analyse the whole genome sequence of L. fermentum MCC0552 for probiotic functionalities and to compare it with the reference strains. The general genomic features of L. fermentum strain MCC0552 were analysed and a phylogenetic dendrogram was generated by considering the genome sequences of reference strains (L. fermentum IFO 3956, F-6, MTCC 5898 and ATCC 14931 or B1 28) which elucidates their evolutionary lineage. Functional analysis of MCC0552 reveals that the strain possess vitamin biosynthesis gene (thiamine and riboflavin) and mucin binding protein (mubp) with comparatively larger in size. HPLC analysis suggests that the strain MCC0552 synthesises class B vitamins (B1, B2, B6, B9 and B12) which increases its significance in nutritional and nutraceutical applications. Genomic island (GI) prediction shows 19 GI in strain MCC0552 genome were identified. GI regions possessed CRISPR cluster genes, mainly type IE, cas2 and type III-A, nucleotide sugar biosynthesis gene, TA system genes, heavy metal associated genes, etc. On further analysis, the strain exhibited the presence of 2 intact prophage regions which ensure its supplementary probiotic attribute. Thus, the present study elaborates on the probiotic potential of strain MCC0552 at the genome level, revealing its remarkable genomic potential and presenting novel prospects for utilising its unique genetic features in diverse scientific fields.

Item Type:	Article
Uncontrolled Keywords:	Probiotics · Reference strains · Whole genome analysis · Vitamins · Genomic islands · Prophage region
Subjects:	600 Technology > 08 Food technology > 10 Food Microorganisms
Divisions:	Food Microbiology
Depositing User:	Somashekar K S
Date Deposited:	28 Nov 2025 05:01
Last Modified:	28 Nov 2025 05:01
URI:	http://ir.cftri.res.in/id/eprint/20135

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