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In silico prospection of Lactobacillus acidophilus strains with potential probiotic activity

  • Biotechnology and Industrial Microbiology - Research Paper
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Abstract

Lactic acid bacteria (LAB) are fermentative microorganisms and perform different roles in biotechnological processes, mainly in the food and pharmaceutical industries. Among the LAB, Lactobacillus acidophilus is a species that deserves to be highlighted for being used both in prophylaxis and in the treatment of pathologies. Most of the metabolites produced by this species are linked to the inhibition of pathogens. In this study, we utilized a pangenomic and metabolic annotation analysis using Roary and BlastKOALA, ML-based probiotic activity prediction with iProbiotic and whole-genome similarity using ANI to identify strains of L. acidophilus with potential probiotic activity. According to the results in BlastKOALA and iProbiotics, L. acidophilus NCTC 13721 had the greatest potential among the 64 strains tested, both in terms of its ability to be a Lactobacillus spp. probiotic, when in the amount of genes involved in the metabolism of organic acids and quorum sensing. In addition, DSM 20079 proved to be promising for prospecting new probiotic Lactobacillus from BlastKOALA analyses, as they presented similar results in the number of genes involved in the production of lactic acid, acetic acid, hydrogen peroxide, except for quorum sensing where the NCTC 13721 strain had 14 more genes. L. acidophilus NCTC 13721 and L. acidophilus La-5 strains showed greater ability to be Lactobacillus spp. probiotic capacity, showing 84.8% and 51.9% capacity in the iProbiotics tool, respectively. When analyzed in ANI, none of the evaluated strains showed genomic similarity with NCTC 13721. In contrast, the DSM 20079 strain showed genomic similarity with all evaluated strains except NCTC 13721. Furthermore, eight strains with characteristics with approximately 100% genomic similarity to La-5 were listed: S20_1, LA-5, FSI4, APC2845, LA-G80-111, DS1_1A, LA1, and BCRC 14065. Therefore, according to the findings in iProbiotics and BlastKoala, among the 64 strains evaluated, NCTC 13721 is the most promising strain to be used for future in vitro studies.

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Acknowledgements

We are grateful to Fábio Pereira Leivas Leite, Daniela Peres Martinez, and Carlos James Scaini for the contribution in the manuscript revision and the Omixlab (Bioinformatics Laboratory of the Federal University of Pelotas) team for all the analysis support. We also thank CAPES and the Post-Graduate Program in Health Sciences of Federal University of Rio Grande for the scholarship granted, which made this work possible.

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  1. Post-Graduate Program in Health Sciences, Universidade Federal do Rio Grande – FURG, Faculty of Medicine, Academic Area of the University Hospital, Rio Grande, RS, Brazil

    Rafaella Sinnott Dias & Luciana Farias da Costa de Avila

  2. Bioinformatics Laboratory, Technological Development Center, Federal University of Pelotas, Capão do Leão, Rio Grande do Sul, Brazil

    Frederico Schmitt Kremer

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Dias, R.S., Kremer, F.S. & da Costa de Avila, L.F. In silico prospection of Lactobacillus acidophilus strains with potential probiotic activity. Braz J Microbiol 54, 2733–2743 (2023). https://doi.org/10.1007/s42770-023-01139-3

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