Genome-Based in silico Evaluation of the Biosafety and Probiotic Traits of Limosilactobacillus fermentum J23 Isolated from Artisanal Mexican Cheese

References

• Alayande, K. A., O. A. Aiyegoro, T. M. Nengwekhulu, L. Katata-Seru, C. N. Ateba, and Y.-F. Chang. 2020. Integrated genome-based probiotic relevance and safety evaluation of lactobacillus reuteri PNW1. PLoS One 15 (7):e0235873. doi:10.1371/journal.pone.0235873.
   PubMed Web of Science ®Google Scholar
• Alcock, B. P., A. R. Raphenya, T. T. Y. Lau, K. K. Tsang, M. Bouchard, A. Edalatmand, W. Huynh, A.L.V. Nguyen, A.A. Cheng, S. Liu, et al. 2020. CARD 2020: Antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 48 (D1):D517–D525. doi:10.1093/nar/gkz935.
   PubMed Web of Science ®Google Scholar
• Alizadeh, M., M. Jalal, K. Hamed, A. Saber, S. Kheirouri, F. Pourteymour Fard Tabrizi, and N. Kamari. 2020. Recent updates on anti-inflammatory and antimicrobial effects of furan natural derivatives. J. Inflamm. Res. 13:451–463. doi:10.2147/JIR.S262132.
   PubMed Web of Science ®Google Scholar
• Andrews, S. 2019. FastQC a quality control tool for high throughput sequence data. Accessed June 30, 2022. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
   Google Scholar
• Arndt, D., J. R. Grant, A. Marcu, T. Sajed, A. Pon, Y. Liang, and D. S. Wishart. 2016. PHASTER: A better, faster version of the PHAST phage search tool. Nucleic Acids Res. 44 (W1):W16–W21. doi:10.1093/nar/gkw387.
   PubMed Web of Science ®Google Scholar
• Aziz, R. K., D. Bartels, A. A. Best, M. DeJongh, T. Disz, R. A. Edwards, K. Formsma, S. Gerdes, E.M. Glass, M. Kubal, et al. 2008. The RAST server: Rapid annotations using subsystems technology. BMC Genom. 9(1):75. doi:10.1186/1471-2164-9-75.
   PubMed Web of Science ®Google Scholar
• Bankevich, A., S. Nurk, D. Antipov, A. A. Gurevich, M. Dvorkin, A. S. Kulikov, V. M. Lesin, S. I. Nikolenko, S. Pham, A. D. Prjibelski, et al. 2012. Spades: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19(5):455–477. doi:10.1089/cmb.2012.0021.
   PubMed Web of Science ®Google Scholar
• Barbieri, F., C. Montanari, F. Gardini, and G. Tabanelli. 2019. Biogenic amine production by lactic acid bacteria: A review. Foods 8 (1):17. doi:10.3390/foods8010017.
   PubMed Web of Science ®Google Scholar
• Batool, Z., D. Xu, X. Zhang, X. Li, Y. Li, Z. Chen, B. Li, and L. Li. 2021. A review on furan: Formation, analysis, occurrence, carcinogenicity, genotoxicity and reduction methods. Crit. Rev. Food Sci. Nutr. 61 (3):395–406. doi:10.1080/10408398.2020.1734532.
   PubMed Web of Science ®Google Scholar
• Benini, S. 2020. Carbohydrate-active enzymes: Structure, activity, and reaction products. Int. J. Mol .Sci. 21 (8):2727. doi:10.3390/ijms21082727.
   PubMed Web of Science ®Google Scholar
• Bertelli, C., M. R. Laird, K. P. Williams, B. Y. Lau, G. Hoad, G. L. Winsor, and F. S. L. Brinkman. 2017. IslandViewer 4: Expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res. 45 (W1):W30–W35. doi:10.1093/nar/gkx343.
   PubMed Web of Science ®Google Scholar
• Bertelli, C., K. E. Tilley, and F. S. L. Brinkman. 2019. Microbial genomic island discovery, visualization and analysis. Brief. Bioinform. 20 (5):1685–1698. doi:10.1093/bib/bby042.
   PubMed Web of Science ®Google Scholar
• Blin, K., S. Shaw, K. Steinke, R. Villebro, N. Ziemert, S. Y. Lee, M. H. Medema, and T. Weber. 2019. antiSMASH 5.0: Updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 47 (W1):W81–W87. doi:10.1093/nar/gkz310.
   PubMed Web of Science ®Google Scholar
• Bolger, A. M., M. Lohse, and B. Usadel. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30 (15):2114–2120. doi:10.1093/bioinformatics/btu170.
   PubMed Web of Science ®Google Scholar
• Brandt, K., M. A. Nethery, S. O’Flaherty, and R. Barrangou. 2020. Genomic characterization of lactobacillus fermentum DSM 20052. BMC Genom 21 (1):328. doi:10.1186/s12864-020-6740-8.
   PubMed Web of Science ®Google Scholar
• Camacho, C., G. Coulouris, V. Avagyan, N. Ma, J. Papadopoulos, K. Bealer, and T. L. Madden. 2009. BLAST + : Architecture and applications. BMC Bioinform. 10 (1):421. doi:10.1186/1471-2105-10-421.
   PubMed Web of Science ®Google Scholar
• Castro‑López, C., C. Pascacio‑Villafán, M. Aluja, H. S. García, A. F. González-Córdova, B. Vallejo-Cordoba, and A. Hernández-Mendoza. forthcoming. Safety assessment of the potential probiotic bacterium Limosilactobacillus fermentum J23 using the Mexican fruit fly (Anastrepha ludens Loew, Diptera: Tephritidae) as a novel in vivo model. Probiotics Antimicrob. Proteins. doi:10.1007/s12602-022-10034-6.
   Web of Science ®Google Scholar
• Castro-López, C., H. S. García, G. C. G. Martínez-Ávila, A. F. González-Córdova, B. Vallejo-Cordoba, and A. Hernández-Mendoza. 2021. Genomics-based approaches to identify and predict the health-promoting and safety activities of promising probiotic strains – a probiogenomics review. Trends Food Sci. Technol. 108:148–163. doi:10.1016/j.tifs.2020.12.017.
   Web of Science ®Google Scholar
• Chatterjee, M., A. C. Pushkaran, A. K. Vasudevan, K. K. N. Menon, R. Biswas, and C. G. Mohan. 2018. Understanding the adhesion mechanism of a mucin binding domain from Lactobacillus fermentum and its role in enteropathogen exclusion. Int. J. Biol. Macromol. 110:598–607. doi:10.1016/j.ijbiomac.2017.10.107.
   PubMed Web of Science ®Google Scholar
• Chen, L., Q. Gu, P. Li, S. Chen, and Y. Li. 2019. Genomic analysis of Lactobacillus reuteri WHH1689 reveals its probiotic properties and stress resistance. Food Sci. Nutr. 7 (2):844–857. doi:10.1002/fsn3.934.
   PubMed Web of Science ®Google Scholar
• Chokesajjawatee, N., P. Santiyanont, K. Chantarasakha, K. Kocharin, C. Thammarongtham, S. Lertampaiporn, T. Vorapreeda, T. Srisuk, T. Wongsurawat, P. Jenjaroenpun et al. 2020. Safety assessment of a Nham starter culture Lactobacillus plantarum BCC9546 via whole-genome analysis. Sci. Rep. 10(1):10241. doi:10.1038/s41598-020-66857-2.
   PubMed Web of Science ®Google Scholar
• Chun, J., A. Oren, A. Ventosa, H. Christensen, D. R. Arahal, M. S. da Costa, A.P. Rooney, H. Yi, X.W. Xu, S. De Meyer, et al. 2018. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int. J. Syst. Evol. Microbiol. 68 (1):461–466. doi:10.1099/ijsem.0.002516.
   PubMed Web of Science ®Google Scholar
• Cosentino, S., M. Voldby Larsen, F. Møller Aarestrup, and O. Lund. 2013. PathogenFinder ‒ distinguishing friend from foe using bacterial whole genome sequence data. PLoS One 8 (10):e77302. doi:10.1371/journal.pone.0077302.
   PubMed Web of Science ®Google Scholar
• Couvin, D., A. Bernheim, C. Toffano-Nioche, M. Touchon, J. Michalik, B. Néron, E. P. C. Rocha, G. Vergnaud, D. Gautheret, C. Pourcel, et al. 2018. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res. 46(W1):W246–W251. doi:10.1093/nar/gky425.
   PubMed Web of Science ®Google Scholar
• Crawley, A. B., E. D. Henriksen, E. Stout, K. Brandt, and R. Barrangou. 2018. Characterizing the activity of abundant, diverse and active CRISPR-Cas systems in Lactobacilli. Sci. Rep. 8 (1):11544. doi:10.1038/s41598-018-29746-3.
   PubMedGoogle Scholar
• da Silva Filho, A. C., R. T. Raittz, D. Guizelini, C. R. De Pierri, D. W. Augusto, I. C. R. dos Santos-Weiss, and J. N. Marchaukoski. 2018. Comparative analysis of genomic island prediction tools. Front Genet. 9:619. doi:10.3389/fgene.2018.00619.
   PubMed Web of Science ®Google Scholar
• Dabaj, F. K., O. Lasekan, M. Y. A. Manap, and F. H. Ling. 2020. Evaluation of the volatilomic potentials of the Lactobacillus casei 431 and Lactobacillus acidophilus La-5 in fermented milk. CYTA J. Food 18 (1):291–300. doi:10.1080/19476337.2020.1741688.
   Web of Science ®Google Scholar
• Dos Santos, C. I., C. D. L. Campos, W. R. Nunes-Neto, M. S. Do Carmo, F. A. B. Nogueira, R. M. Ferreira, E. P. S. Costa, L.F. Gonzaga, J.M. Araújo, J.M. Monteiro et al. 2021. Genomic analysis of Limosilactobacillus fermentum ATCC 23271, a potential probiotic strain with anti-Candida activity. J. Fungi 7(10):794. doi:10.3390/jof7100794.
   Web of Science ®Google Scholar
• Drula, E., M.-L. Garron, S. Dogan, V. Lombard, B. Henrissat, and N. Terrapon. 2022. The carbohydrate-active enzyme database: Functions and literature. Nucleic Acids Res. 50 (D1):D571–D577. doi:10.1093/nar/gkab1045.
   PubMed Web of Science ®Google Scholar
• Duar, R. M., X. B. Lin, J. Zheng, M. E. Martino, T. Grenier, M. E. Pérez-Muñoz, F. Leulier, M. Gänzle, and J. Walter. 2017. Lifestyles in transition: Evolution and natural history of the genus lactobacillus. FEMS Microbiol. Rev. 41 (S1):S27–S48. doi:10.1093/femsre/fux030.
   PubMedGoogle Scholar
• Florensa, A. F., R. S. Kaas, P. T. L. C. Clausen, D. Aytan-Aktug, and F. M. Aarestrup. 2022. ResFinder ‒ an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes. Microb. Genom. 8 (1):000748. doi:10.1099/mgen.0.000748.
   PubMed Web of Science ®Google Scholar
• Food and Drug Administration, FDA. 2018. Microorganisms & microbial-derived ingredients used in food (partial list). Last Modified April 1. Accessed July 13, 2023. https://www.fda.gov/food/generally-recognized-safe-gras/microorganisms-microbial-derived-ingredients-used-food-partial-list.
   Google Scholar
• Gao, X., J. Kong, H. Zhu, B. Mao, S. Cui, and J. Zhao. 2021. Lactobacillus, Bifidobacterium and Lactococcus response to environmental stress: Mechanisms and application of cross‐protection to improve resistance against freeze‐drying. J. Appl. Microbiol. 132 (2):802–821. doi:10.1111/jam.15251.
   PubMed Web of Science ®Google Scholar
• Ghattargi, V. C., M. A. Gaikwad, B. S. Meti, Y. S. Nimonkar, K. Dixit, O. Prakash, Y. S. Shouche, S. P. Pawar, and D. P. Dhotre. 2018. Comparative genome analysis reveals key genetic factors associated with probiotic property in enterococcus faecium strains. BMC. Genom 19 (1):652. doi:10.1186/s12864-018-5043-9.
   PubMedGoogle Scholar
• Goel, A., P. M. Halami, and J. P. Tamang. 2020. Genome analysis of lactobacillus plantarum isolated from some Indian fermented foods for bacteriocin production and probiotic marker genes. Front. Microbiol. 11:40. doi:10.3389/fmicb.2020.00040.
   PubMed Web of Science ®Google Scholar
• Golubov, A. 2021. Genome instability in bacteria: Causes and consequences. In Genome stability: From virus to human application, ed. I. Kovalchuk and O. Kovalchuk, Vol. 26, 2nd ed., 73–90. Amsterdam: Elsevier B.V. & Academic Press.
   Google Scholar
• Gurevich, A., V. Saveliev, N. Vyahhi, and G. Tesler. 2013. QUAST: Quality assessment tool for genome assemblies. Bioinformatics 29 (8):1072–1075. doi:10.1093/bioinformatics/btt086.
   PubMed Web of Science ®Google Scholar
• Gutiérrez-Chávez, C., N. Benaud, and B. C. Ferrari. 2021. The ecological roles of microbial lipopeptides: Where are we going? Comput. Struct. Biotechnol. J. 19:1400–1413. doi:10.1016/j.csbj.2021.02.017.
   PubMed Web of Science ®Google Scholar
• Heredia-Castro, P. Y., J. I. Méndez-Romero, A. Hernández-Mendoza, E. Acedo-Félix, A. F. González-Córdova, and B. Vallejo-Cordoba. 2015. Antimicrobial activity and partial characterization of bacteriocin-like inhibitory substances produced by Lactobacillus spp. isolated from artisanal Mexican cheese. J. Dairy Sci. 98 (12):8285–8293. doi:10.3168/jds.2015-10104.
   PubMed Web of Science ®Google Scholar
• Heredia-Castro, P. Y., R. Reyes-Díaz, M. A. Rendón-Rosales, L. M. Beltrán-Barrientos, M. J. Torres-Llanez, M. C. Estrada-Montoya, A. Hernández-Mendoza, A. F. González-Córdova, and B. Vallejo-Cordoba. 2021. Novel bacteriocins produced by Lactobacillus fermentum strains with bacteriostatic effects in milk against selected indicator microorganisms. J. Dairy Sci. 104 (4):4033–4043. doi:10.3168/jds.2020-19531.
   PubMed Web of Science ®Google Scholar
• Hill, C., F. Guarner, G. Reid, G. R. Gibson, D. J. Merenstein, B. Pot, L. Morelli, R. B. Canani, H. J. Flint, S. Salminen, et al. 2014. The international scientific association for probiotics and prebiotics consensus on the scope and appropriate use of the term probiotic. Nat. Rev. Gastroenterol. Hepatol. 11(8):506–514. doi:10.1038/nrgastro.2014.66.
   PubMed Web of Science ®Google Scholar
• Hossain, T. L. 2022. Functional genomics of the lactic acid bacterium Limosilactobacillus fermentum LAB-1: Metabolic, probiotic and biotechnological perspectives. Heliyon 8 (11):e11412. doi:10.1016/j.heliyon.2022.e11412.
   PubMed Web of Science ®Google Scholar
• Hsu, H.-Y., Y.-C. Liao, S.-H. Lin, J.-S. Lin, C.-C. Lee, and K. Watanabe. 2022. Safety assessment of Lactiplantibacillus plantarum TWK10 based on whole-genome sequencing, phenotypic, and oral toxicity analysis. Microorganisms 10:784. doi:10.3390/microorganisms10040784.
   PubMed Web of Science ®Google Scholar
• Hymes, J. P., and T. R. Klaenhammer. 2016. Stuck in the middle: Fibronectin-binding proteins in gram-positive bacteria. Front Microbiol. 7:1504. doi:10.3389/fmicb.2016.01504.
   PubMed Web of Science ®Google Scholar
• Jian, Z., L. Zeng, T. Xu, S. Sun, S. Yan, L. Yang, Y. Huang, J. Jia, and T. Dou. 2021. Antibiotic resistance genes in bacteria: Occurrence, spread, and control. J. Basic Microbiol. 61 (12):1049–1070. doi:10.1002/jobm.202100201.
   PubMed Web of Science ®Google Scholar
• Kim, H., Y.-S. Lee, H.-Y. Yu, M. Kwon, K.-K. Kim, G. In, S.-K. Hong, and S.-K. Kim. 2022. Anti-inflammatory effects of Limosilactobacillus fermentum KGC1601 isolated from Panax ginseng and its probiotic characteristics. Foods 11:1707. doi:10.3390/foods11121707.
   PubMed Web of Science ®Google Scholar
• Knutsen, H. K., J. Alexander, L. Barregård, M. Bignami, B. Brüschweiler, S. Ceccatelli, B. Cottrill, M. Dinovi, L. Edler, B. Grasl‐Kraupp, et al. 2017. Risks for public health related to the presence of furan and methylfurans in food. EFSA. J. 15(10):e05005. doi:10.2903/j.efsa.2017.5005.
   PubMed Web of Science ®Google Scholar
• Kothari, D., S. Patel, and S.-K. Kim. 2019. Probiotic supplements might not be universally-effective and safe: A review. Biomed. Pharmacother. 111:537–547. doi:10.1016/j.biopha.2018.12.104.
   PubMed Web of Science ®Google Scholar
• Kumar, R., T. M. Feltrup, R. V. Kukreja, K. B. Patel, S. Cai, and B. R. Singh. 2019. Evolutionary features in the structure and function of bacterial toxins. Toxins 11 (1):15. doi:10.3390/toxins11010015.
   PubMed Web of Science ®Google Scholar
• Lacerda, D. C., P. C. Trindade da Costa, P. B. Pontes, L. A. Carneiro Dos Santos, J. P. R. Cruz Neto, C. C. Silva Luis, V. P. de Sousa Brito, and J. L. de Brito Alves. 2022. Potential role of Limosilactobacillus fermentum as a probiotic with anti-diabetic properties: A review. World J. Diabetes 13 (9):717–728. doi:10.4239/wjd.v13.i9.717.
   PubMed Web of Science ®Google Scholar
• Lee, B. S., O.-H. Ban, W. Y. Bang, S. A. Chae, S. Oh, C. Park, M. Lee, S.J. Kim, J. Yang, and Y.H. Jung. 2021. Safety assessment of Lactobacillus reuteri IDCC 3701 based on phenotypic and genomic analysis. Ann. Microbiol. 71(1):10. doi:10.1186/s13213-021-01622-y.
   Web of Science ®Google Scholar
• Lehri, B., A. M. Seddon, and A. V. Karlyshev. 2017. Potential probiotic-associated traits revealed from completed high quality genome sequence of Lactobacillus fermentum 3872. Stand Genomic. Sci. 12 (1):19. doi:10.1186/s40793-017-0228-4.
   PubMedGoogle Scholar
• Lemke, R. A. S., S. M. Olson, K. Morse, S. D. Karlen, A. Higbee, E. T. Beebe, J. Ralph, J. J. Coon, B. G. Fox, and T. J. Donohue. 2020. A bacterial biosynthetic pathway for methylated furan fatty acids. J. Biol. Chem. 295 (29):9786–9801. doi:10.1074/jbc.RA120.013697.
   PubMed Web of Science ®Google Scholar
• Leuschner, R. G. K., T. P. Robinson, M. Hugas, P. S. Cocconcelli, F. Richard-Forget, G. Klein, and M. Richardson. 2010. Qualified presumption of safety (QPS): A generic risk assessment approach for biological agents notified to the European Food Safety Authority (EFSA). Trends Food Sci. Technol. 21 (9):425–435. doi:10.1016/j.tifs.2010.07.003.
   Web of Science ®Google Scholar
• Lipszyc, A., M. Szuplewska, and D. Bartosik. 2022. How do transposable elements activate expression of transcriptionally silent antibiotic resistance genes? Int J. Mol. Sci. 23:8063. doi:10.3390/ijms23158063.
   PubMed Web of Science ®Google Scholar
• Liu, B., D. Zheng, Q. Jin, L. Chen, and J. Yang. 2019. VFDB 2019: A comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res. 47 (D1):D687–D692. doi:10.1093/nar/gky1080.
   PubMed Web of Science ®Google Scholar
• Liu, D.-M., Y.-Y. Huang, and M.-H. Liang. 2022. Analysis of the probiotic characteristics and adaptability of Lactiplantibacillus plantarum DMDL 9010 to gastrointestinal environment by complete genome sequencing and corresponding phenotypes. LWT - Food Sci. Technol. 158:113129. doi:10.1016/j.lwt.2022.113129.
   Web of Science ®Google Scholar
• Masiá, C., A. Geppel, P. E. Jensen, and P. Buldo. 2021. Effect of lactobacillus rhamnosus on physicochemical properties of fermented plant-based raw materials. Foods 10 (3):573. doi:10.3390/foods10030573.
   PubMed Web of Science ®Google Scholar
• Moriya, Y., M. Itoh, S. Okuda, A. C. Yoshizawa, and M. Kanehisa. 2007. KAAS: An automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35:W182–W185. doi:10.1093/nar/gkm321.
   PubMed Web of Science ®Google Scholar
• Naghmouchi, K., Y. Belguesmia, F. Bendali, G. Spano, B. S. Seal, and D. Drider. 2020. Lactobacillus fermentum: A bacterial species with potential for food preservation and biomedical applications. Crit. Rev. Food Sci. Nutr. 60 (20):3387–3399. doi:10.1080/10408398.2019.1688250.
   PubMed Web of Science ®Google Scholar
• Nidhi, S., U. Anand, P. Oleksak, P. Tripathi, J. A. Lal, G. Thomas, K. Kuca, and V. Tripathi. 2021. Novel CRISPR-Cas systems: An updated review of the current achievements, applications, and future research perspectives. Int. J. Mol. Sci. 22 (7):3327. doi:10.3390/ijms22073327.
   PubMed Web of Science ®Google Scholar
• Park, M. R., M. Shin, D. Mun, S. Y. Jeong, D. Y. Jeong, M. Song, G. Ko, T. Unno, Y. Kim, and S. Oh. 2020. Probiotic Lactobacillus fermentum strain JDFM216 improves cognitive behavior and modulates immune response with gut microbiota. Sci. Rep. 10 (1):21701. doi:10.1038/s41598-020-77587-w.
   PubMed Web of Science ®Google Scholar
• Pei, Z., F. A. Sadiq, X. Han, J. Zhao, H. Zhang, R. P. Ross, W. Lu, W. Chen, and L. A. McCue. 2021. Comprehensive scanning of prophages in Lactobacillus: Distribution, diversity, antibiotic resistance genes, and linkages with CRISPR-Cas systems. mSystems 6 (3):e0121120. doi:10.1128/mSystems.01211-20.
   PubMed Web of Science ®Google Scholar
• Peng, X., A. Ed-Dra, and M. Yue. 2022. Whole genome sequencing for the risk assessment of probiotic lactic acid bacteria. Crit. Rev. Food Sci. Nutr. 1:1–19. doi:10.1080/10408398.2022.2156476.
   Google Scholar
• Pohanka, M. 2020. D-lactic acid as a metabolite: Toxicology, diagnosis, and detection. Biomed. Res. Int. 2020:3419034. doi:10.1155/2020/3419034.
   PubMed Web of Science ®Google Scholar
• Pradhan, D., R. H. Mallappa, and S. Grover. 2020. Comprehensive approaches for assessing the safety of probiotic bacteria. Food Control. 108:106872. doi:10.1016/j.foodcont.2019.106872.
   Web of Science ®Google Scholar
• Raethong, N., C. Santivarangkna, W. Visessanguan, P. Santiyanont, W. Mhuantong, and N. Chokesajjawatee. 2022. Whole-genome sequence analysis for evaluating the safety and probiotic potential of Lactiplantibacillus pentosus 9D3, a gamma-aminobutyric acid (GABA)-producing strain isolated from Thai pickled weed. Front. Microbiol. 13:969548. doi:10.3389/fmicb.2022.969548.
   PubMed Web of Science ®Google Scholar
• Roux, E., A. Nicolas, F. Valence, G. Siekaniec, V. Chuat, J. Nicolas, Y. Le Loir, and E. Guédon. 2022. The genomic basis of the Streptococcus thermophilus health-promoting properties. BMC Genom. 23 (1):210. doi:10.1186/s12864-022-08459-y.
   PubMed Web of Science ®Google Scholar
• Rozman, V., P. M. Lorbeg, T. Accetto, and B. B. Matijašić. 2020. Characterization of antimicrobial resistance in lactobacilli and bifidobacteria used as probiotics or starter cultures based on integration of phenotypic and in silico data. Int. J. Food Microbiol. 314:108388. doi:10.1016/j.ijfoodmicro.2019.108388.
   PubMed Web of Science ®Google Scholar
• Rudkin, J. K., R. M. McLoughlin, A. Preston, R. C. Massey, and J. B. Bliska. 2017. Bacterial toxins: Offensive, defensive, or something else altogether? PLoS Pathog. 13 (9):e1006452. doi:10.1371/journal.ppat.1006452.
   PubMed Web of Science ®Google Scholar
• Ruiz-Capillas, C., and A. M. Herrero. 2019. Impact of biogenic amines on food quality and safety. Foods 8 (2):62. doi:10.3390/foods8020062.
   PubMed Web of Science ®Google Scholar
• Russel, J., R. Pinilla-Redondo, D. Mayo-Muñoz, S. A. Shah, and S. J. Sørensen. 2020. CRISPRCasTyper: Automated identification, annotation, and classification of CRISPR-Cas loci. Crispr. J. 3 (6):462–469. doi:10.1089/crispr.2020.0059.
   PubMedGoogle Scholar
• Salvetti, E., L. Orrù, V. Capozzi, A. Martina, A. Lamontanara, D. Keller, H. Cash, G.E. Felis, L. Cattivelli, S. Torriani, et al. 2016. Integrate genome-based assessment of safety for probiotic strains: Bacillus coagulans GBI-30, 6086 as a case study. Appl. Microbiol. Biotechnol. 100 (10):4595–4605. doi:10.1007/s00253-016-7416-9.
   PubMed Web of Science ®Google Scholar
• Santiago-López, L., A. Hernández-Mendoza, V. Mata-Haro, B. Vallejo-Cordoba, and A. F. González-Córdova. 2018. Immune response induced by fermented milk with potential probiotic strains isolated from artisanal cocido cheese. Food Agric. Immunol. 29 (1):911–929. doi:10.1080/09540105.2018.1485632.
   Web of Science ®Google Scholar
• Schmid, J., V. Sieber, and B. Rehm. 2015. Bacterial exopolysaccharides: Biosynthesis pathways and engineering strategies. Front Microbiol. 6:496. doi:10.3389/fmicb.2015.00496.
   PubMed Web of Science ®Google Scholar
• Seemann, T. 2014. Prokka: Rapid prokaryotic genome annotation. Bioinformatics 30 (14):2068–2069. doi:10.1093/bioinformatics/btu153.
   PubMed Web of Science ®Google Scholar
• Sharifi-Rad, J., C. F. Rodrigues, Z. Stojanović-Radić, M. Dimitrijević, A. Aleksić, K. Neffe-Skocińska, D. Zielińska, D. Kołożyn-Krajewska, B. Salehi, S. MiltonPrabu, et al. 2020. Probiotics: Versatile bioactive components in promoting human health. Medicina 56 (9):433. doi:10.3390/medicina56090433.
   PubMed Web of Science ®Google Scholar
• Sharma, A. K., N. Dhasmana, N. Dubey, N. Kumar, A. Gangwal, M. Gupta, and Y. Singh. 2017. Bacterial virulence factors: Secreted for survival. Indian J. Microbiol. 57 (1):1–10. doi:10.1007/s12088-016-0625-1.
   PubMed Web of Science ®Google Scholar
• Siguier, P., J. Perochon, L. Lestrade, J. Mahillon, and M. Chandler. 2006. Isfinder: The reference centre for bacterial insertion sequences. Nucleic Acids Res. 34 (90001):D32–D36. doi:10.1093/nar/gkj014.
   PubMed Web of Science ®Google Scholar
• Singh, A., V. Vishwakarma, and B. Singhal. 2018. Metabiotics: The functional metabolic signatures of probiotics: Current state-of-art and future research priorities—Metabiotics: Probiotics effector molecules. Adv. Biosci. Biotechnol. 9 (4):147–189. doi:10.4236/abb.2018.94012.
   Google Scholar
• Skinnider, M. A., C. W. Johnston, M. Gunabalasingam, N. J. Merwin, A. M. Kieliszek, R. J. MacLellan, H. Li, M.R. Ranieri, A.L. Webster, M.P. Cao, et al. 2020. Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences. Nat. Commun. 11(1):6058. doi:10.1038/s41467-020-19986-1.
   PubMed Web of Science ®Google Scholar
• Sousa, M. A., G. R. Rama, C. F. Volken de Souza, and C. E. Granada. 2020. Acid lactic lactobacilli as a biotechnological toll to improve food quality and human health. Biotechnol. Prog. 36 (2):e2937. doi:10.1002/btpr.2937.
   PubMed Web of Science ®Google Scholar
• Stergiou, O. S., K. Tegopoulos, D. E. Kiousi, M. Tsifintaris, A. C. Papageorgiou, C. C. Tassou, N. Chorianopoulos, P. Kolovos, and A. Galanis. 2021. Whole-genome sequencing, phylogenetic and genomic analysis of Lactiplantibacillus pentosus L33, a potential probiotic strain isolated from fermented sausages. Front Microbiol. 12:746659. doi:10.3389/fmicb.2021.746659.
   PubMed Web of Science ®Google Scholar
• Suwannasom, N., I. Kao, A. Pruß, R. Georgieva, and H. Bäumler. 2021. Riboflavin: The health benefits of a forgotten natural vitamin. Int. J. Mol. Sci. 21 (3):950. doi:10.3390/ijms21030950.
   Web of Science ®Google Scholar
• Tarrah, A., S. Pakroo, W. J. F. Lemos Junior, A. F. Guerra, V. Corich, and A. Giacomini. 2020. Complete genome sequence and carbohydrates-active enzymes (CAZymes) analysis of Lactobacillus paracasei DTA72, a potential probiotic strain with strong capability to use inulin. Curr. Microbiol. 77 (10):2867–2875. doi:10.1007/s00284-020-02089-x.
   PubMed Web of Science ®Google Scholar
• Tatusova, T., M. DiCuccio, A. Badretdin, V. Chetvernin, E. P. Nawrocki, L. Zaslavsky, A. Lomsadze, K. D. Pruitt, M. Borodovsky, and J. Ostell. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44 (14):6614–6624. doi:10.1093/nar/gkw569.
   PubMed Web of Science ®Google Scholar
• Urban-Chmiel, R., A. Marek, D. Stępień-Pyśniak, K. Wieczorek, M. Dec, A. Nowaczek, and J. Osek. 2022. Antibiotic resistance in bacteria-A review. Antibiotics 11 (8):1079. doi:10.3390/antibiotics11081079.
   Google Scholar
• Valdez-Baez, J., F. M. R. da Costa, A. C. Pinto Gomide, R. Profeta, A. L. da Silva, T. D. J. Sousa, M. V. C. Viana, R. Bentes Kato, M. F. Americo, A. dos Santos Freitas, et al. 2022. Comparative genomics and in silico evaluation of genes related to the probiotic potential of Bifidobacterium breve 1101A. Bacteria 1:161–182. doi:10.3390/bacteria1030013.
   Google Scholar
• Valeriano, V. D. V., J. K. Oh, B. B. Bagon, H. Kim, and D.-K. Kang. 2019. Comparative genomic analysis of Lactobacillus mucosae LM1 identifies potential niche-specific genes and pathways for gastrointestinal adaptation. Genomics 111 (1):24–33. doi:10.1016/j.ygeno.2017.12.009.
   PubMed Web of Science ®Google Scholar
• van Heel, A. J., A. de Jong, C. Song, J. H. Viel, J. Kok, and O. P. Kuipers. 2018. BAGEL4: A user-friendly web server to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Res. 46 (W1):W278–W281. doi:10.1093/nar/gky383.
   PubMed Web of Science ®Google Scholar
• Vandecraen, J., M. Chandler, A. Aertsen, and R. van Houdt. 2017. The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit. Rev. Microbiol. 43 (6):709–730. doi:10.1080/1040841x.2017.1303661.
   PubMed Web of Science ®Google Scholar
• Vinayamohan, P. G., A. J. Pellissery, and K. Venkitanarayanan. 2022. Role of horizontal gene transfer in the dissemination of antimicrobial resistance in food animal production. Curr. Opin. Food Sci. 47:100882. doi:10.1016/j.cofs.2022.100882.
   Web of Science ®Google Scholar
• Vitetta, L., S. Coulson, M. Thomsen, T. Nguyen, and S. Hall. 2017. Probiotics, D-lactic acidosis, oxidative stress and strain specificity. Gut. Microbes. 8 (4):311–322. doi:10.1080/19490976.2017.1279379.
   PubMed Web of Science ®Google Scholar
• Wang, Y., Q. Liang, B. Lu, H. Shen, S. Liu, Y. Shi, S. Leptihn, H. Li, J. Wei, C. Liu, et al. 2021a. Whole-genome analysis of probiotic product isolates reveals the presence of genes related to antimicrobial resistance, virulence factors, and toxic metabolites, posing potential health risks. BMC Genom. 22(1):210. doi:10.1186/s12864-021-07539-9.
   PubMed Web of Science ®Google Scholar
• Wang, Y., J. Wu, M. Lv, Z. Shao, M. Hungwe, J. Wang, X. Bai, J. Xie, Y. Wang, and W. Geng. 2021b. Metabolism characteristics of lactic acid bacteria and the expanding applications in food industry. Front Bioeng. Biotechnol. 9:612285. doi:10.3389/fbioe.2021.612285.
   PubMed Web of Science ®Google Scholar
• Wattam, A. R., D. Abraham, O. Dalay, T. L. Disz, T. Driscoll, J. L. Gabbard, J. J. Gillespie, R. Gough, D. Hix, R. Kenyon, et al. 2014. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res. 42(D1):D581–D591. doi:10.1093/nar/gkt1099.
   PubMed Web of Science ®Google Scholar
• Wendel, U. 2022. Assessing viability and stress tolerance of probiotics‒A review. Front Microbiol. 12:818468. doi:10.3389/fmicb.2021.818468.
   PubMed Web of Science ®Google Scholar
• Wendling, C. C. 2023. Prophage mediated control of higher order interactions - insights from multi-level approaches. Curr. Opin. Syst. Biol. 35:100469. doi:10.1016/j.coisb.2023.100469.
   Google Scholar
• Wróblewska, J., M. Wróblewski, I. Hołyńska-Iwan, M. Modrzejewska, J. Nuszkiewicz, W. Wróblewska, and A. Woźniak. 2023. The role of glutathione in selected viral diseases. Antioxidants 12 (7):1325. doi:10.3390/antiox12071325.
   Web of Science ®Google Scholar
• Wu, Y., Z. Ye, P. Feng, R. Li, X. Chen, X. Tian, R. Han, A. Kakade, P. Liu, and X. Li. 2021. Limosilactobacillus fermentum JL-3 isolated from “Jiangshui” ameliorates hyperuricemia by degrading uric acid. Gut. Microbes 13 (1):e1897211. doi:10.1080/19490976.2021.1897211.
   PubMed Web of Science ®Google Scholar
• Xiao, Y., J. Zhao, H. Zhang, Q. Zhai, and W. Chen. 2021. Mining genome traits that determine the different gut colonization potential of Lactobacillus and Bifidobacterium species. Microb. Genom. 7 (6):000581. doi:10.1099/mgen.0.000581.
   PubMed Web of Science ®Google Scholar
• Xie, Z., H. Tang, and J. Hancock. 2017. Isescan: Automated identification of insertion sequence elements in prokaryotic genomes. Bioinformatics 33 (21):3340–3347. doi:10.1093/bioinformatics/btx433.
   PubMed Web of Science ®Google Scholar
• Yadav, R., P. K. Singh, and P. Shukla. 2018. Metabolic engineering for probiotics and their genome-wide expression profiling. Curr. Protein Pept. Sci. 19 (1):68–74. doi:10.2174/1389203718666161111130157.
   PubMed Web of Science ®Google Scholar
• Ye, K., P. Li, and Q. Gu. 2020. Complete genome sequence analysis of a strain Lactobacillus pentosus ZFM94 and its probiotic characteristics. Genomics 112 (5):3142–3149. doi:10.1016/j.ygeno.2020.05.015.
   PubMed Web of Science ®Google Scholar
• Yoon, S.-H., S. Ha, J. Lim, S. Kwon, and J. Chun. 2017. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie. Van Leeuwenhoek 110 (10):1281–1286. doi:10.1007/s10482-017-0844-4.
   PubMed Web of Science ®Google Scholar
• Yu, Y., M. Zong, L. Lao, J. Wen, D. Pan, and Z. Wu. 2022. Adhesion properties of cell surface proteins in Lactobacillus strains in the GIT environment. Food Funct. 13 (6):3098–3109. doi:10.1039/d1fo04328e.
   PubMed Web of Science ®Google Scholar
• Zhang, H., T. Yohe, L. Huang, S. Entwistle, P. Wu, Z. Yang, P. K. Busk, Y. Xu, and Y. Yin. 2018. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 46 (W1):W95–W101. doi:10.1093/nar/gky418.
   PubMed Web of Science ®Google Scholar
• Zhang, L., H. Ma, M. Fakhar-E-Alam Kulyar, H. Pan, K. Li, A. Li, Q. Mo, Y. Wang, H. Dong, Y. Bao, et al. 2022. Complete genome analysis of lactobacillus fermentum YLF016 and its probiotic characteristics. Microb. Pathog. 162:105212. doi:10.1016/j.micpath.2021.105212.
   PubMed Web of Science ®Google Scholar
• Zhao, Y., K. Hong, J. Zhao, H. Zhang, Q. Zhai, and W. Chen. 2019. Lactobacillus fermentum and its potential immunomodulatory properties. J. Funct. Foods 56:21–32. doi:10.1016/j.jff.2019.02.044.
   Web of Science ®Google Scholar
• Zheng, J., S. Wittouck, E. Salvetti, C. M. A. P. Franz, H. M. B. Harris, P. Mattarelli, P. W. O’Toole, B. Pot, P. Vandamme, J. Walter, et al. 2020. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int. J. Syst. Evol. Microbiol. 70(4):2782–2858. doi:10.1099/ijsem.0.004107.
   PubMed Web of Science ®Google Scholar
• Zhu, K., F. Tan, J. Mu, R. Yi, X. Zhou, and X. Zhao. 2019. Anti-obesity effects of Lactobacillus fermentum CQPC05 isolated from Sichuan pickle in high-fat diet-induced obese mice through PPAR-α signaling pathway. Microorganisms 7 (7):194. doi:10.3390/microorganisms7070194.
   PubMed Web of Science ®Google Scholar