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Comparative Probiogenomics Analysis of Limosilactobacillus fermentum 3872

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Abstract

Limosilactobacillus fermentum is an important member of the lactic acid bacteria group and holds immense potential for probiotic properties in human health and relevant industries. In this study, a comparative probiogenomic approach was applied to analyze the genome sequence of L. fermentum 3872, which was extracted from a commercially available yogurt sample, along with 20 different publicly available strains. Results indicate that the genome size of the characterized L. fermentum 3892 strain is 2,057,839 bp, with a single- and circular-type chromosome possessing a G + C content of 51.69%. The genome of L. fermentum 3892 strain comprises a total of 2120 open reading frames (ORFs), two genes encoding rRNAs, and 53 genes encoding tRNAs. Upon comparative probiogenomic analysis, two plasmid sequences were detected among the study strains, including one for the L. fermentum 3872 genome, which was found between position 1,288,203 and 1,289,237 with an identity of 80.98. The whole-genome alignment revealed 2223 identical sites and a pairwise identity of 98.9%, indicating a significant difference of 1.1% among genome strains. Comparison of amino acid encoding genes among strains included in this study suggests that the strain 3872 exhibited the highest degree of amino acids present, including glutamine, glutamate, aspartate, asparagine, lysine, threonine, methionine, and cysteine. The comparative antibiotic resistome profiling revealed that strain 3872 exhibited a high resistant capacity only to ciprofloxacin antibiotics as compared to other strains. This study provides a genomic-based evaluation approach for comparative probiotic strain analysis in commercial foods and their significance to human health.

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Data Availability

The raw sequencing data used in this study has been submitted to NCBI with the Accession number PRJNA795894. The detailed information of the strains used for comparative probiogenomics is given in Table 1.

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Funding

This work was supported by the National Key Research and Development Program of China (2021YFC2103004).

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Authors and Affiliations

  1. School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China

    Mati Ullah, Jianda Han, Yanzhen Chen, Mingchen Yan, Yi Ma, Zhong Ni & Huayou Chen

  2. College of Fisheries, Huazhong Agriculture University, Wuhan, 430070, Hubei, China

    Muhammad Rizwan

  3. School of Life Sciences, University of Science and Technology of China, Hefei, China

    Ali Raza

  4. Gen’Omics Research Hub (GENOMAC HUB), Ogbomoso, Nigeria

    Oluwaseyi Abraham Olawale

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  1. Mati Ullah
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  9. Oluwaseyi Abraham Olawale
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  10. Huayou Chen
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Contributions

MU and HC design the project. MU performed the experiments. MU, MR, JH, AR, YC, MY, YM, ZN, OAO analyzed the data. MU wrote the initial manuscript draft. HC provided suggestion to improve the initial article draft. MU wrote the final draft. All authors approved the final draft.

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Correspondence to Huayou Chen.

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Ullah, M., Rizwan, M., Han, J. et al. Comparative Probiogenomics Analysis of Limosilactobacillus fermentum 3872. Probiotics & Antimicro. Prot. (2024). https://doi.org/10.1007/s12602-024-10286-4

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