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Comparative Genomic and Functional Characterization of Lactobacillus casei Group (LCG) Probiotic Strains Isolated from Traditional Yogurts by Next-Generation Sequencing

Comparative Genomic and Functional Characterization of Lactobacillus casei Group (LCG) Probiotic Strains Isolated from Traditional Yogurts by Next-Generation Sequencing

Mati Ullah1*, Muhammad Rizwan2, Ali Raza3, Xianlin Zhao4, Yanling Sun4, Sarah Gul5, Muhammad Ihtesham Waheed6, Muhammad Nadeem Khan7, Alvina Gul8, Sami Ullah Jan9* and Chao Huang4*

1Department of Microbiology, Faculty of Veterinary & Animal Sciences, The University of Agriculture, Dera Ismail Khan, Pakistan
2College of Animal Sciences and Technology, Anhui Agricultural University, Hefei, Anhui, China
3Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
4Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
5Department of Biological Sciences, Faculty of Basic and Applied Sciences, International Islamic University, Islamabad, Pakistan
6Department of Plant Breeding and Genetics, University of Agriculture, Peshawar
7Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
8Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, H-12 Campus, Islamabad, Pakistan
9Department of Bioinformatics and Biosciences, Faculty of Health & Life Sciences, Capital University of Science and Technology, Islamabad, Pakistan
 
*      Corresponding author: samiullahjan@gmail.com

ABSTRACT

Lactobacillus casei group which is consists of Lactobacillus rhamnosus, Lactobacillus casei, and Lactobacillus paracaseiis an important group of probiotic lactic acid bacteria with numerous commercial and applied health applications. In the present study, we comparatively analysed the genomes of three strains (Lactobacillus rhamnosus ATCC 53103, Lactobacillus casei L9, and Lactobacillus paracasei W56) of LCG isolated from traditional yogurt samples using the next-generation sequencing approach. The GC contents of the characterized strains were in the range of 46.03 to 46.52% while the protein-coding sequences (CDS) were in the range of 2544 to 2888. The pan-genome analysis of the three strains identified a total of 5449 genes with 377 as core genes. The functional characterization by subsystem category distribution analysis revealed “Carbohydrates” is the largest subsystem followed by “protein metabolism” while the biological pathway analysis by the Kyoto encyclopedia of genes and genomes (KEGG) database identified the “metabolic and biosynthesis of secondary metabolites pathway” as the dominant one. Similarly, the functional characterization by eggNOG database revealed that the COGs associated with “Carbohydrate transport and metabolism” were dominant. These find-ings provide a broader understanding of the genome features as well as their functional characterization of the famous probiotic bacterial group.

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Pakistan Journal of Zoology

June

Pakistan J. Zool., Vol. 56, Iss. 3, pp. 1001-1500

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