{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T04:01:45Z","timestamp":1793160105440,"version":"4.5.0"},"reference-count":138,"publisher":"MDPI AG","issue":"19","license":[{"start":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T00:00:00Z","timestamp":1759968000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan","award":["AP19679863"],"award-info":[{"award-number":["AP19679863"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Foods"],"abstract":"<jats:p>In this study, we conducted a whole-genome analysis of the Lacticaseibacillus paracasei subsp. paracasei 2LB isolated from Kazakh traditional fermented milk (koumiss) to identify genes associated with the safety and probiotic potential of the strain. A comparative genomic analysis of the core and pan-genome of L. paracasei 2LB was performed. Functional annotation revealed the presence of genes putatively involved in metabolism, genetic information processing, and cellular processes. In terms of safety parameters, the stability of its genetic material, the absence of the ability to synthesize virulence factors, and genes responsible for antibiotic resistance were characterized. Also, in vitro studies of the L. paracasei 2LB strain showed resistance to stress factors and antimicrobial activity, and the presence of coding sequences encoding adhesion factors, bacteriocins, bile salts, pH, cold and heat shock, and osmotic stress was observed through genomic analysis. These results indicate that the L. paracasei 2LB strain is a potential probiotic candidate and demonstrate that whole-genome analysis is a useful method for assessing the quality and safety of probiotics.<\/jats:p>","DOI":"10.3390\/foods14193449","type":"journal-article","created":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T16:54:31Z","timestamp":1760028871000},"page":"3449","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Lacticaseibacillus paracasei subsp. paracasei 2LB: Identification of Genes to Assess the Safety and Probiotic Potential of the Strain"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6999-8807","authenticated-orcid":false,"given":"Gulyaim","family":"Abitayeva","sequence":"first","affiliation":[{"name":"Republican Collection of Microorganisms LLP, Astana 010000, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8437-3346","authenticated-orcid":false,"given":"Diana","family":"Kurmangali","sequence":"additional","affiliation":[{"name":"Republican Collection of Microorganisms LLP, Astana 010000, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-3220-588X","authenticated-orcid":false,"given":"Temirlan","family":"Baikonys","sequence":"additional","affiliation":[{"name":"Republican Collection of Microorganisms LLP, Astana 010000, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhandarbek","family":"Bekshin","sequence":"additional","affiliation":[{"name":"Republican Collection of Microorganisms LLP, Astana 010000, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,10,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e00070-23","DOI":"10.1128\/msphere.00070-23","article-title":"Akkermansia muciniphila and Lactobacillus plantarum Ameliorate Systemic Lupus Erythematosus by Possibly Regulating Immune Response and Remodeling Gut Microbiota","volume":"8","author":"Guo","year":"2023","journal-title":"mSphere"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/s12974-023-02808-8","article-title":"Lactobacillus paracasei L9 Affects Disease Progression in Experimental Autoimmune Neuritis by Regulating Intestinal Flora Structure and Arginine Metabolism","volume":"20","author":"Meng","year":"2023","journal-title":"J. Neuroinflammation"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1007\/s12602-022-09999-1","article-title":"Characterization and Identification of Probiotic Features in Lacticaseibacillus paracasei Using a Comparative Genomic Analysis Approach","volume":"14","author":"Garrido","year":"2022","journal-title":"Probiotics Antimicrob. Proteins"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1038\/s41420-023-01666-w","article-title":"The Role of Lactobacillus in Inflammatory Bowel Disease: From Actualities to Prospects","volume":"9","author":"Li","year":"2023","journal-title":"Cell Death Discov."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1007\/s12602-021-09895-0","article-title":"Screening and Identification of Probiotic Lactobacilli from the Infant Gut Microbiota to Alleviate Lead Toxicity","volume":"15","author":"Chen","year":"2023","journal-title":"Probiotics Antimicrob. Proteins"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1016\/j.ijbiomac.2022.10.124","article-title":"Effects of Genes Required for Exopolysaccharides Biosynthesis in Lacticaseibacillus paracasei S-NB on Cell Surface Characteristics and Probiotic Properties","volume":"224","author":"Xiao","year":"2023","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2782","DOI":"10.1099\/ijsem.0.004107","article-title":"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","volume":"70","author":"Zheng","year":"2020","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1186\/s12934-020-01464-4","article-title":"Vaginal Microbiota and the Potential of Lactobacillus Derivatives in Maintaining Vaginal Health","volume":"19","author":"Chee","year":"2020","journal-title":"Microb. Cell Factories"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Dehghani Champiri, I., Bamzadeh, Z., Rahimi, E., and Rouhi, L. (2023). Lacticaseibacillus paracasei LB12, a Potential Probiotic Isolated from Traditional Iranian Fermented Milk (Doogh). Curr. Microbiol., 80.","DOI":"10.1007\/s00284-023-03376-z"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1644","DOI":"10.1007\/s12602-021-09789-1","article-title":"Assessment of the Safety of Lactobacillus casei IMV B-7280 Probiotic Strain on a Mouse Model","volume":"13","author":"Lazarenko","year":"2021","journal-title":"Probiotics Antimicrob. Proteins"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Colautti, A., Arnoldi, M., Comi, G., and Iacumin, L. (2022). Antibiotic Resistance and Virulence Factors in Lactobacilli: Something to Carefully Consider. Food Microbiol., 103.","DOI":"10.1016\/j.fm.2021.103934"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Castro-Gonz\u00e1lez, J.M., Castro, P., Sandoval, H., and Castro-Sandoval, D. (2019). Probiotic Lactobacilli Precautions. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.00375"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Ghosh, S., Sarangi, A.N., Mukherjee, M., Bhowmick, S., and Tripathy, S. (2019). Reanalysis of Lactobacillus paracasei Lbs2 Strain and Large-Scale Comparative Genomics Places Many Strains into Their Correct Taxonomic Position. Microorganisms, 7.","DOI":"10.3390\/microorganisms7110487"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Poon, T., Juana, J., Noori, D., Jeansen, S., Pierucci-Lagha, A., and Musa-Veloso, K. (2020). Effects of a Fermented Dairy Drink Containing Lacticaseibacillus paracasei subsp. paracasei CNCM I-1518 (Lactobacillus casei CNCM I-1518) and the Standard Yogurt Cultures on the Incidence, Duration, and Severity of Common Infectious Diseases: A Systematic Review and Meta-Analysis of Randomized Controlled Trials. Nutrients, 12.","DOI":"10.3390\/nu12113443"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"184","DOI":"10.31989\/ffhd.v14i3.1336","article-title":"Effects of Lacticaseibacillus paracasei 327 Intake on the Intestinal Environment in Healthy Adult Japanese: A Randomized, Double-Blind, Placebo-Controlled, Parallel-Group Trial","volume":"14","author":"Mihara","year":"2024","journal-title":"Funct. Foods Health Dis."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Moiseenko, K.V., Glazunova, O.A., Savinova, O.S., Shabaev, A.V., and Fedorova, T.V. (2023). Changes in Composition of Some Bioactive Molecules upon Inclusion of Lacticaseibacillus paracasei Probiotic Strains into a Standard Yogurt Starter Culture. Foods, 12.","DOI":"10.3390\/foods12234238"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Karnwal, A., and Malik, T. (2023). Characterization and Selection of Probiotic Lactic Acid Bacteria from Different Dietary Sources for Development of Functional Foods. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1170725"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Talib, N., Mohamad, N.E., Yeap, S.K., Hussin, Y., Aziz, M.N.M., Masarudin, M.J., Sharifuddin, S.A., Hui, Y.W., Ho, C.L., and Alitheen, N.B. (2019). Alitheen Isolation and Characterization of Lactobacillus Spp. from Kefir Samples in Malaysia. Molecules, 24.","DOI":"10.3390\/molecules24142606"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1997","DOI":"10.1007\/s00203-020-01883-2","article-title":"Whole-Genome Sequence and Comparative Genome Analysis of Lactobacillus paracasei DTA93, a Promising Probiotic Lactic Acid Bacterium","volume":"202","author":"Tarrah","year":"2020","journal-title":"Arch. Microbiol."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Wang, J., Wang, T., Li, Y., Fan, Z., Lv, Z., Liu, L., Li, X., and Li, B. (2022). Comparative Genomic Analysis of Lacticaseibacillus paracasei SMN-LBK from Koumiss. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.1042117"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Barreto Pinilla, C.M., Guzman Escudero, F., Torres Silva E Alves, A., Spadoti, L.M., and Brandelli, A. (2023). Draft Genome Sequence and Comparative Genome Analysis Reveal Potential Functional Properties in Lacticaseibacillus paracasei ItalPN16. Curr. Microbiol., 80.","DOI":"10.1007\/s00284-023-03515-6"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.1099\/ijsem.0.000760","article-title":"OrthoANI: An Improved Algorithm and Software for Calculating Average Nucleotide Identity","volume":"66","author":"Lee","year":"2016","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: Rapid Prokaryotic Genome Annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"eggNOG 5.0: A Hierarchical, Functionally and Phylogenetically Annotated Orthology Resource Based on 5090 Organisms and 2502 Viruses","volume":"47","author":"Szklarczyk","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Chen, J., Wu, H., and Wang, N. (2024). KEGG Orthology Prediction of Bacterial Proteins Using Natural Language Processing. BMC Bioinform., 25.","DOI":"10.1186\/s12859-024-05766-x"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"W115","DOI":"10.1093\/nar\/gkad328","article-title":"dbCAN3: Automated Carbohydrate-Active Enzyme and Substrate Annotation","volume":"51","author":"Zheng","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"W278","DOI":"10.1093\/nar\/gky383","article-title":"BAGEL4: A User-Friendly Web Server to Thoroughly Mine RiPPs and Bacteriocins","volume":"46","author":"Song","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-Mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Brettin, T., Davis, J.J., Disz, T., Edwards, R.A., Gerdes, S., Olsen, G.J., Olson, R., Overbeek, R., Parrello, B., and Pusch, G.D. (2015). RASTtk: A Modular and Extensible Implementation of the RAST Algorithm for Building Custom Annotation Pipelines and Annotating Batches of Genomes. Sci. Rep., 5.","DOI":"10.1038\/srep08365"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1145\/2629691","article-title":"NCBI BLASTP on High-Performance Reconfigurable Computing Systems","volume":"7","author":"Mahram","year":"2015","journal-title":"ACM Trans. Reconfigurable Technol. Syst."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1128\/JCM.03617-13","article-title":"Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia Coli","volume":"52","author":"Joensen","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"D163","DOI":"10.1093\/nar\/gkae869","article-title":"oriTDB: A Database of the Origin-of-Transfer Regions of Bacterial Mobile Genetic Elements","volume":"53","author":"Liu","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for Predictions of Phenotypes from Genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Cosentino, S., Voldby Larsen, M., M\u00f8ller Aarestrup, F., and Lund, O. (2013). PathogenFinder\u2014Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data. PLoS ONE, 8.","DOI":"10.1371\/annotation\/b84e1af7-c127-45c3-be22-76abd977600f"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In Silico Detection and Typing of Plasmids Using PlasmidFinder and Plasmid Multilocus Sequence Typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"W443","DOI":"10.1093\/nar\/gkad382","article-title":"PHASTEST: Faster than PHASTER, Better than PHAST","volume":"51","author":"Wishart","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1038\/s41579-019-0299-x","article-title":"Evolutionary Classification of CRISPR\u2013Cas Systems: A Burst of Class 2 and Derived Variants","volume":"18","author":"Makarova","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"W484","DOI":"10.1093\/nar\/gkad326","article-title":"Proksee: In-Depth Characterization and Visualization of Bacterial Genomes","volume":"51","author":"Grant","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Binda, S., Hill, C., Johansen, E., Obis, D., Pot, B., Sanders, M.E., Tremblay, A., and Ouwehand, A.C. (2020). Criteria to Qualify Microorganisms as \u201cProbiotic\u201d in Foods and Dietary Supplements. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.01662"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"EFSA Panel on Biological Hazards (BIOHAZ), Allende, A., Alvarez-Ord\u00f3\u00f1ez, A., Bortolaia, V., Bover-Cid, S., De Cesare, A., Dohmen, W., Guillier, L., Jacxsens, L., and Nauta, M. (2025). Update of the List of Qualified Presumption of Safety (QPS) Recommended Microbiological Agents Intentionally Added to Food or Feed as Notified to EFSA 21: Suitability of Taxonomic Units Notified to EFSA until September 2024. EFSA J., 23, e9169.","DOI":"10.2903\/j.efsa.2025.9169"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1099\/ijsem.0.002516","article-title":"Proposed Minimal Standards for the Use of Genome Data for the Taxonomy of Prokaryotes","volume":"68","author":"Chun","year":"2018","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Hall, B.G., and Nisbet, J. (2023). Building Phylogenetic Trees from Genome Sequences with kSNP4. Mol. Biol. Evol., 40.","DOI":"10.1093\/molbev\/msad235"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Inglin, R.C., Meile, L., and Stevens, M.J.A. (2018). Clustering of Pan- and Core-Genome of Lactobacillus Provides Novel Evolutionary Insights for Differentiation. BMC Genom., 19.","DOI":"10.1186\/s12864-018-4601-5"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Mu, Y., Zhang, C., Li, T., Jin, F.-J., Sung, Y.-J., Oh, H.-M., Lee, H.-G., and Jin, L. (2022). Development and Applications of CRISPR\/Cas9-Based Genome Editing in Lactobacillus. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms232112852"},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Jarocki, P., Komo\u0144-Janczara, E., Podle\u015bny, M., Kholiavskyi, O., Pytka, M., and Kordowska-Wiater, M. (2019). Genomic and Proteomic Characterization of Bacteriophage BH1 Spontaneously Released from Probiotic Lactobacillus rhamnosus Pen. Viruses, 11.","DOI":"10.3390\/v11121163"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Kandasamy, S., Lee, K.-H., Yoo, J., Yun, J., Kang, H.B., Kim, J.E., Oh, M.-H., and Ham, J.-S. (2024). Whole Genome Sequencing of Lacticaseibacillus Casei KACC92338 Strain with Strong Antioxidant Activity, Reveals Genes and Gene Clusters of Probiotic and Antimicrobial Potential. Front. Microbiol., 15.","DOI":"10.3389\/fmicb.2024.1458221"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Zhang, W., Ji, H., Zhang, D., Liu, H., Wang, S., Wang, J., and Wang, Y. (2018). Complete Genome Sequencing of Lactobacillus plantarum ZLP001, a Potential Probiotic That Enhances Intestinal Epithelial Barrier Function and Defense Against Pathogens in Pigs. Front. Physiol., 9.","DOI":"10.3389\/fphys.2018.01689"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1007\/s00253-012-4149-2","article-title":"Characterization of Putative Class II Bacteriocins Identified from a Non-Bacteriocin-Producing Strain Lactobacillus casei ATCC 334","volume":"97","author":"Kuo","year":"2013","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"e33823","DOI":"10.1016\/j.heliyon.2024.e33823","article-title":"Probiogenomic Analysis of Lactiplantibacillus Plantarum SPS109: A Potential GABA-Producing and Cholesterol-Lowering Probiotic Strain","volume":"10","author":"Chintakovid","year":"2024","journal-title":"Heliyon"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"e202210883","DOI":"10.1002\/anie.202210883","article-title":"Sactipeptide Engineering by Probing the Substrate Tolerance of a Thioether-Bond-Forming Sactisynthase","volume":"61","author":"Ali","year":"2022","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Sornsenee, P., Surachat, K., Kang, D.-K., Mendoza, R., and Romyasamit, C. (2024). Probiotic Insights from the Genomic Exploration of Lacticaseibacillus paracasei Strains Isolated from Fermented Palm Sap. Foods, 13.","DOI":"10.3390\/foods13111773"},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Romyasamit, C., Surachat, K., Pattaranggoon, N.C., Suksabay, P., Permpoon, U., Nam, T.-G., and Sornsenee, P. (2025). Phenotypic and Genomic Insights into Schleiferilactobacillus harbinensis WU01, a Candidate Probiotic with Broad-Spectrum Antimicrobial Activity Against ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter) Pathogens. Foods, 14.","DOI":"10.3390\/foods14071161"},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Salini, F., Iacumin, L., Comi, G., and Dicks, L. (2023). Thermophilin 13: In Silico Analysis Provides New Insight in Genes Involved in Bacteriocin Production. Microorganisms, 11.","DOI":"10.3390\/microorganisms11030611"},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Santarelli, G., Sanguinetti, M., Delogu, G., and De Maio, F. (2025). Comparative Genomic Analysis of Bacteriocin Genes in Lactobacillus crispatus Strains. Sci. Rep., 15.","DOI":"10.1038\/s41598-025-08321-7"},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Moiseenko, K.V., Begunova, A.V., Savinova, O.S., Glazunova, O.A., Rozhkova, I.V., and Fedorova, T.V. (2023). Biochemical and Genomic Characterization of Two New Strains of Lacticaseibacillus paracasei Isolated from the Traditional Corn-Based Beverage of South Africa, Mahewu, and Their Comparison with Strains Isolated from Kefir Grains. Foods, 12.","DOI":"10.3390\/foods12010223"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1725","DOI":"10.1007\/s12602-024-10216-4","article-title":"Lacticaseibacillus paracasei AD22 Stress Response in Brined White Cheese Matrix: In Vitro Probiotic Profiles and Molecular Characterization","volume":"17","author":"Dishan","year":"2025","journal-title":"Probiotics Antimicrob. Proteins"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"288","DOI":"10.4014\/mbl.1803.03001","article-title":"Molecular Characterization of Some Antilisterial Bacteriocin Genes from Enterococcus faecium and Pediococcus pentosaceus","volume":"46","author":"Salim","year":"2018","journal-title":"Microbiol. Biotechnol. Lett."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Surachat, K., Sangket, U., Deachamag, P., and Chotigeat, W. (2017). In Silico Analysis of Protein Toxin and Bacteriocins from Lactobacillus paracasei SD1 Genome and Available Online Databases. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0183548"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"402","DOI":"10.38212\/2224-6614.3369","article-title":"Transcriptome Analysis of Lactobacillus rhamnosus GG Strain Treated with Prebiotic\u2014Bovine Lactoferrin under a Cold Environment","volume":"29","author":"Liu","year":"2021","journal-title":"J. Food Drug Anal."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"133","DOI":"10.2174\/0929866528666211118084519","article-title":"Microbial Cold Shock Proteins: Overview of Their Function and Mechanism of Action","volume":"29","author":"Zhang","year":"2022","journal-title":"Protein Pept. Lett."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Papadimitriou, K., Alegr\u00eda, \u00c1., Bron, P.A., de Angelis, M., Gobbetti, M., Kleerebezem, M., Lemos, J.A., Linares, D.M., Ross, P., and Stanton, C. (2011). Responses of Lactic Acid Bacteria to Cold Stress. Stress Responses of Lactic Acid Bacteria, Springer.","DOI":"10.1007\/978-0-387-92771-8_21"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"802","DOI":"10.1111\/jam.15251","article-title":"Lactobacillus, Bifidobacterium and Lactococcus Response to Environmental Stress: Mechanisms and Application of Cross-protection to Improve Resistance against Freeze-drying","volume":"132","author":"Gao","year":"2022","journal-title":"J. Appl. Microbiol."},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Kim, M.-S., Min, B., Kim, I., Kwon, Y.-J., Park, S.-Y., Kim, B.-Y., Kim, B.-K., and Park, S.S. (2021). Complete Genome Sequencing and Comparative Genomic Analysis of Streptococcus thermophilus CKDB027, a Promising Probiotic Bacterial Strain. Food Suppl. Biomater. Health, 1.","DOI":"10.52361\/fsbh.2021.1.e28"},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Duru, I.C., Ylinen, A., Belanov, S., Pulido, A.A., Paulin, L., and Auvinen, P. (2021). Transcriptomic Time-Series Analysis of Cold- and Heat-Shock Response in Psychrotrophic Lactic Acid Bacteria. BMC Genom., 22.","DOI":"10.1186\/s12864-020-07338-8"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"6900","DOI":"10.1128\/JB.01673-12","article-title":"CspR, a Cold Shock RNA-Binding Protein Involved in the Long-Term Survival and the Virulence of Enterococcus Faecalis","volume":"194","author":"Michaux","year":"2012","journal-title":"J. Bacteriol."},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Michaux, C., and Giard, J.-C. (2016). New Insight into Cold Shock Proteins: RNA-binding Proteins Involved in Stress Response and Virulence. Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria, Wiley.","DOI":"10.1002\/9781119004813.ch85"},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Adu, K.T., Wilson, R., Nichols, D.S., Baker, A.L., Bowman, J.P., and Britz, M.L. (2018). Proteomic Analysis of Lactobacillus casei GCRL163 Cell-Free Extracts Reveals a SecB Homolog and Other Biomarkers of Prolonged Heat Stress. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0206317"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"1206","DOI":"10.1099\/mic.0.055657-0","article-title":"Proteomic and Transcriptomic Analysis of the Response to Bile Stress of Lactobacillus casei BL23","volume":"158","year":"2012","journal-title":"Microbiology"},{"key":"ref_69","first-page":"146","article-title":"Transcriptomic Analysis of Probiotic Oxidative Stress Resistance in Anti-Inflammatory Pathways","volume":"11","author":"Heydari","year":"2025","journal-title":"J. Genet. Resour."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"3012","DOI":"10.1099\/ijsem.0.004121","article-title":"Lactobacillus garii Sp. Nov., Isolated from a Fermented Cassava Product","volume":"70","author":"Diaz","year":"2020","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"2368","DOI":"10.1073\/pnas.0506914103","article-title":"Functional Dissection of YabA, a Negative Regulator of DNA Replication Initiation in Bacillus subtilis","volume":"103","author":"Velten","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1266\/ggs.83.111","article-title":"The Functional Analysis of YabA, Which Interacts with DnaA and Regulates Initiation of Chromosome Replication in Bacillus subtils","volume":"83","author":"Cho","year":"2008","journal-title":"Genes Genet. Syst."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"13370","DOI":"10.1093\/nar\/gku1098","article-title":"The Conserved GTPase LepA Contributes Mainly to Translation Initiation in Escherichia Coli","volume":"42","author":"Balakrishnan","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"3199","DOI":"10.1073\/pnas.1012994108","article-title":"Elongation Factor 4 (EF4\/LepA) Accelerates Protein Synthesis at Increased Mg2+ Concentrations","volume":"108","author":"Pech","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"3755","DOI":"10.1099\/ijsem.0.003969","article-title":"Genome-Based Reclassification of Lactobacillus casei: Emended Classification and Description of the Species Lactobacillus zeae","volume":"70","author":"Huang","year":"2020","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Arena, M.P., Capozzi, V., Longo, A., Russo, P., Weidmann, S., Rieu, A., Guzzo, J., Spano, G., and Fiocco, D. (2019). The Phenotypic Analysis of Lactobacillus plantarum Shsp Mutants Reveals a Potential Role for Hsp1 in Cryotolerance. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.00838"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1007\/s10529-020-03041-6","article-title":"Knock out of sHSP Genes Determines Some Modifications in the Probiotic Attitude of Lactiplantibacillus Plantarum","volume":"43","author":"Longo","year":"2021","journal-title":"Biotechnol. Lett."},{"key":"ref_78","doi-asserted-by":"crossref","unstructured":"Douillard, F.P., Mora, D., Eijlander, R.T., Wels, M., and De Vos, W.M. (2018). The PLoS ONE Editors Correction: Comparative Genomic Analysis of the Multispecies Probiotic-Marketed Product VSL#3. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0203548"},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Cheng, Z., Chen, J., Zhang, Y., Li, X., Zhang, N., Liu, F., and Jiao, Y. (2024). In Vitro Hypoglycemic Activities of Lactobacilli and Bifidobacterium Strains from Healthy Children\u2019s Sources and Their Effect on Stimulating GLP-1 Secretion in STC-1 Cells. Foods, 13.","DOI":"10.3390\/foods13040519"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"1473","DOI":"10.1111\/j.1365-2672.2011.05160.x","article-title":"Response of Lactobacillus casei BL23 to Phenolic Compounds: Response to Phenolic Compounds","volume":"111","author":"Landete","year":"2011","journal-title":"J. Appl. Microbiol."},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Backert, S., Bernegger, S., Sk\u00f3rko-Glonek, J., and Wessler, S. (2018). Extracellular HtrA Serine Proteases: An Emerging New Strategy in Bacterial Pathogenesis. Cell. Microbiol., 20.","DOI":"10.1111\/cmi.12845"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/j.micres.2011.07.001","article-title":"Inactivation of the ftsH Gene of Lactobacillus plantarum WCFS1: Effects on Growth, Stress Tolerance, Cell Surface Properties and Biofilm Formation","volume":"167","author":"Bove","year":"2012","journal-title":"Microbiol. Res."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"334","DOI":"10.4014\/mbl.1804.04001","article-title":"Genome Profiling for Health Promoting and Disease Preventing Traits Unraveled Probiotic Potential of Bacillus Clausii B106","volume":"46","author":"Kapse","year":"2018","journal-title":"Microbiol. Biotechnol. Lett."},{"key":"ref_84","doi-asserted-by":"crossref","unstructured":"Marrec, C.L. (2011). Responses of Lactic Acid Bacteria to Osmotic Stress. Stress Responses of Lactic Acid Bacteria, Springer.","DOI":"10.1007\/978-0-387-92771-8_4"},{"key":"ref_85","doi-asserted-by":"crossref","unstructured":"Mollova, D., Gozmanova, M., Apostolova, E., Yahubyan, G., Iliev, I., and Baev, V. (2023). Illuminating the Genomic Landscape of Lactiplantibacillus Plantarum PU3\u2014A Novel Probiotic Strain Isolated from Human Breast Milk, Explored through Nanopore Sequencing. Microorganisms, 11.","DOI":"10.3390\/microorganisms11102440"},{"key":"ref_86","doi-asserted-by":"crossref","unstructured":"Fan, X., Bao, T., Yi, H., Zhang, Z., Zhang, K., Liu, X., Lin, X., Zhang, Z., and Feng, Z. (2021). Ribosome Profiling and RNA Sequencing Reveal Genome-Wide Cellular Translation and Transcription Regulation Under Osmotic Stress in Lactobacillus rhamnosus ATCC 53103. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.781454"},{"key":"ref_87","doi-asserted-by":"crossref","unstructured":"Sevillano, E., Lafuente, I., Pe\u00f1a, N., Cintas, L.M., Mu\u00f1oz-Atienza, E., Hern\u00e1ndez, P.E., and Borrero, J. (2023). Evaluation of Safety and Probiotic Traits from a Comprehensive Genome-Based In Silico Analysis of Ligilactobacillus salivarius P1CEA3, Isolated from Pigs and Producer of Nisin S. Foods, 13.","DOI":"10.3390\/foods13010107"},{"key":"ref_88","doi-asserted-by":"crossref","unstructured":"Yogeswara, I.B.A., Pramesi, P.C., and Rahayu, E.S. (2023). Whole-Genome Sequence of Lactiplantibacillus plantarum Mut-3, Isolated from Indonesian Fermented Soybean (Tempeh). Microbiol. Resour. Announc., 12.","DOI":"10.1128\/mra.00513-22"},{"key":"ref_89","doi-asserted-by":"crossref","unstructured":"Sa\u0142a\u0144ski, P., Kowalczyk, M., Bardowski, J.K., and Szczepankowska, A.K. (2022). Health-Promoting Nature of Lactococcus Lactis IBB109 and Lactococcus Lactis IBB417 Strains Exhibiting Proliferation Inhibition and Stimulation of Interleukin-18 Expression in Colorectal Cancer Cells. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.822912"},{"key":"ref_90","doi-asserted-by":"crossref","unstructured":"Ma, X., Wang, G., Zhai, Z., Zhou, P., and Hao, Y. (2018). Global Transcriptomic Analysis and Function Identification of Malolactic Enzyme Pathway of Lactobacillus paracasei L9 in Response to Bile Stress. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.01978"},{"key":"ref_91","doi-asserted-by":"crossref","unstructured":"Kusada, H., Arita, M., Tohno, M., and Tamaki, H. (2022). Bile Salt Hydrolase Degrades \u03b2-Lactam Antibiotics and Confers Antibiotic Resistance on Lactobacillus paragasseri. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.858263"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"5509","DOI":"10.1128\/AEM.01177-13","article-title":"Malic Enzyme and Malolactic Enzyme Pathways Are Functionally Linked but Independently Regulated in Lactobacillus casei BL23","volume":"79","author":"Landete","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_93","doi-asserted-by":"crossref","unstructured":"Horn, N., Wegmann, U., Dertli, E., Mulholland, F., Collins, S.R.A., Waldron, K.W., Bongaerts, R.J., Mayer, M.J., and Narbad, A. (2013). Spontaneous Mutation Reveals Influence of Exopolysaccharide on Lactobacillus johnsonii Surface Characteristics. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0059957"},{"key":"ref_94","doi-asserted-by":"crossref","unstructured":"Deo, D., Davray, D., and Kulkarni, R. (2019). A Diverse Repertoire of Exopolysaccharide Biosynthesis Gene Clusters in Lactobacillus Revealed by Comparative Analysis in 106 Sequenced Genomes. Microorganisms, 7.","DOI":"10.3390\/microorganisms7100444"},{"key":"ref_95","doi-asserted-by":"crossref","unstructured":"Zhao, X., Liang, Q., Song, X., and Zhang, Y. (2023). Whole Genome Sequence of Lactiplantibacillus Plantarum MC5 and Comparative Analysis of Eps Gene Clusters. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1146566"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.1111\/j.1365-2672.2009.04508.x","article-title":"Characterization of a Fibronectin-binding Protein from Lactobacillus casei BL23","volume":"108","author":"Monedero","year":"2010","journal-title":"J. Appl. Microbiol."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"4465","DOI":"10.1128\/AEM.02497-10","article-title":"Functional Characterization of a Mucus-Specific LPXTG Surface Adhesin from Probiotic Lactobacillus rhamnosus GG","volume":"77","author":"Satokari","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_98","doi-asserted-by":"crossref","unstructured":"Souza, R.F.S., Jardin, J., Cauty, C., Rault, L., Bouchard, D.S., Berm\u00fadez-Humar\u00e1n, L.G., Langella, P., Monedero, V., Seyffert, N., and Azevedo, V. (2017). Contribution of Sortase SrtA2 to Lactobacillus casei BL23 Inhibition of Staphylococcus aureus Internalization into Bovine Mammary Epithelial Cells. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0174060"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1016\/j.it.2013.01.005","article-title":"Regulation of Intestinal Homeostasis and Immunity with Probiotic Lactobacilli","volume":"34","author":"Wells","year":"2013","journal-title":"Trends Immunol."},{"key":"ref_100","doi-asserted-by":"crossref","unstructured":"Rossi, F., Amadoro, C., Pallotta, M.L., and Colavita, G. (2022). Variability of Genetic Characters Associated with Probiotic Functions in Lacticaseibacillus Species. Microorganisms, 10.","DOI":"10.20944\/preprints202204.0029.v1"},{"key":"ref_101","doi-asserted-by":"crossref","unstructured":"B\u00e4uerl, C., Abitayeva, G., Sosa-Carrillo, S., Mencher-Beltr\u00e1n, A., Navarro-Lle\u00f3, N., Coll-Marqu\u00e9s, J.M., Z\u00fa\u00f1iga-Cabrera, M., Shaikhin, S., and P\u00e9rez-Martinez, G. (2019). P40 and P75 Are Singular Functional Muramidases Present in the Lactobacillus casei\/paracasei\/rhamnosus Taxon. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.01420"},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1002\/jobm.201600575","article-title":"Pyruvate Dehydrogenase Subunit \u03b2 of Lactobacillus plantarum Is a Collagen Adhesin Involved in Biofilm Formation","volume":"57","author":"Salzillo","year":"2017","journal-title":"J. Basic Microbiol."},{"key":"ref_103","first-page":"713","article-title":"Decreased Mucosal Adhesion of Lactobacillus Species in Patients with Inflammatory Bowel Disease","volume":"13","author":"Najafi","year":"2022","journal-title":"Casp. J. Intern. Med."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"2445","DOI":"10.1128\/JB.01618-09","article-title":"Physiological and Transcriptional Response of Lactobacillus casei ATCC 334 to Acid Stress","volume":"192","author":"Broadbent","year":"2010","journal-title":"J. Bacteriol."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"1152","DOI":"10.1111\/jam.15292","article-title":"Genomic Analysis Revealed Conserved Acid Tolerance Mechanisms from Native Micro-organisms in Fermented Feed","volume":"132","author":"Mortera","year":"2022","journal-title":"J. Appl. Microbiol."},{"key":"ref_106","doi-asserted-by":"crossref","unstructured":"Najar, I.N., Sharma, P., Das, R., Mondal, K., Singh, A.K., Radha, A., Sharma, V., Sharma, S., Thakur, N., and Gandhi, S.G. (2024). Exploring Probiotic Potential: A Comparative Genomics and In Silico Assessment of Genes within the Genus Geobacillus. bioRxiv.","DOI":"10.1101\/2024.05.15.594408"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1016\/j.resmic.2010.03.012","article-title":"Expression of the atpD Gene in Probiotic Lactobacillus plantarum Strains under in Vitro Acidic Conditions Using RT-qPCR","volume":"161","author":"Duary","year":"2010","journal-title":"Res. Microbiol."},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1139\/gen-2014-0020","article-title":"Comparative Genome-Scale Analysis of Niche-Based Stress-Responsive Genes in Lactobacillus helveticus Strains","volume":"57","author":"Senan","year":"2014","journal-title":"Genome"},{"key":"ref_109","doi-asserted-by":"crossref","unstructured":"Kamarinou, C.S., Kiousi, D.E., Repanas, P., Argyri, A.A., Chorianopoulos, N.G., and Galanis, A. (2024). Dissecting the Genetic Basis of the Technological, Functional, and Safety Characteristics of Lacticaseibacillus paracasei SRX10. Microorganisms, 12.","DOI":"10.3390\/microorganisms12010093"},{"key":"ref_110","doi-asserted-by":"crossref","unstructured":"Zhang, W., Wang, J., Zhang, D., Liu, H., Wang, S., Wang, Y., and Ji, H. (2019). Complete Genome Sequencing and Comparative Genome Characterization of Lactobacillus johnsonii ZLJ010, a Potential Probiotic with Health-Promoting Properties. Front. Genet., 10.","DOI":"10.3389\/fgene.2019.00812"},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"1352","DOI":"10.1111\/febs.13228","article-title":"ClpL Is a Chaperone without Auxiliary Factors","volume":"282","author":"Park","year":"2015","journal-title":"FEBS J."},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.fm.2017.03.020","article-title":"Effects of Heat, Cold, Acid and Bile Salt Adaptations on the Stress Tolerance and Protein Expression of Kefir-Isolated Probiotic Lactobacillus kefiranofaciens M1","volume":"66","author":"Chen","year":"2017","journal-title":"Food Microbiol."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1128\/MMBR.00076-15","article-title":"Stress Physiology of Lactic Acid Bacteria","volume":"80","author":"Papadimitriou","year":"2016","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_114","doi-asserted-by":"crossref","unstructured":"Kiousi, D.E., Efstathiou, C., Tegopoulos, K., Mantzourani, I., Alexopoulos, A., Plessas, S., Kolovos, P., Koffa, M., and Galanis, A. (2022). Genomic Insight Into Lacticaseibacillus paracasei SP5, Reveals Genes and Gene Clusters of Probiotic Interest and Biotechnological Potential. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.922689"},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"pgac116","DOI":"10.1093\/pnasnexus\/pgac116","article-title":"Structural Basis of Unisite Catalysis of Bacterial F0F1-ATPase","volume":"1","author":"Nakano","year":"2022","journal-title":"PNAS Nexus"},{"key":"ref_116","doi-asserted-by":"crossref","unstructured":"Li, J., Zhang, L., Mu, G., and Tuo, Y. (2023). Interpretation of Safety and Potential Probiotic Properties of Lactiplantibacillus plantarum Y42 Based on Genome-Wide Sequencing. Food Biosci., 56.","DOI":"10.1016\/j.fbio.2023.103249"},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1159\/000322233","article-title":"Functional Analysis of the P40 and P75 Proteins from Lactobacillus casei BL23","volume":"19","author":"Yan","year":"2010","journal-title":"Microb. Physiol."},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"3219","DOI":"10.1007\/s00203-021-02318-2","article-title":"Cell Surface and Extracellular Proteins of Potentially Probiotic Lactobacillus reuteri as an Effective Mediator to Regulate Intestinal Epithelial Barrier Function","volume":"203","author":"Singh","year":"2021","journal-title":"Arch. Microbiol."},{"key":"ref_119","doi-asserted-by":"crossref","unstructured":"European Food Safety Authority (EFSA) (2024). EFSA Statement on the Requirements for Whole Genome Sequence Analysis of Microorganisms Intentionally Used in the Food Chain. EFSA J., 22, 1\u201314.","DOI":"10.2903\/j.efsa.2024.8912"},{"key":"ref_120","unstructured":"Joint FAO\/WHO Food Standards Programme, and Codex Committee on Nutrition and Foods for Special Dietary Uses (2024). Discussion Paper on Harmonized Probiotic Guidelines for Use in Foods and Food Supplements."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1128\/MMBR.00020-10","article-title":"Mobility of Plasmids","volume":"74","author":"Smillie","year":"2010","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"2385","DOI":"10.4014\/jmb.2406.06003","article-title":"Comparison of Plasmid Curing Efficiency across Five Lactic Acid Bacterial Species","volume":"34","author":"Park","year":"2024","journal-title":"J. Microbiol. Biotechnol."},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1139\/cjm-2018-0275","article-title":"Horizontal Transfer of Antibiotic Resistance Genes in Clinical Environments","volume":"65","author":"Lerminiaux","year":"2019","journal-title":"Can. J. Microbiol."},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1093\/gbe\/evv247","article-title":"Genomic and Functional Characterization of the Unusual pLOCK 0919 Plasmid Harboring the spaCBA Pili Cluster in Lactobacillus casei LOCK 0919","volume":"8","author":"Grynberg","year":"2016","journal-title":"Genome Biol. Evol."},{"key":"ref_125","doi-asserted-by":"crossref","unstructured":"Tolmasky, M.E., and Alonso, J.C. (2015). Mobilizable Rolling-Circle Replicating Plasmids from Gram-Positive Bacteria: A Low-Cost Conjugative Transfer. Plasmids, ASM Press.","DOI":"10.1128\/9781555818982"},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.plasmid.2010.08.002","article-title":"Characterization of the Cryptic Plasmid pTXW from Lactobacillus paracasei TXW","volume":"65","author":"Zhang","year":"2011","journal-title":"Plasmid"},{"key":"ref_127","doi-asserted-by":"crossref","unstructured":"Belloso Daza, M.V., Milani, G., Cortimiglia, C., Pietta, E., Bassi, D., and Cocconcelli, P.S. (2022). Genomic Insights of Enterococcus faecium UC7251, a Multi-Drug Resistant Strain from Ready-to-Eat Food, Highlight the Risk of Antimicrobial Resistance in the Food Chain. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.894241"},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1007\/s00294-023-01271-5","article-title":"O\u2019. Insights from Metagenome-Assembled Genomes on the Genetic Stability and Safety of over-the-Counter Probiotic Products","volume":"69","author":"Aziz","year":"2023","journal-title":"Curr. Genet."},{"key":"ref_129","doi-asserted-by":"crossref","first-page":"2839","DOI":"10.1007\/s00284-021-02554-1","article-title":"Conjugal Transfer of Antibiotic Resistances in Lactobacillus spp.","volume":"78","author":"Ojha","year":"2021","journal-title":"Curr. Microbiol."},{"key":"ref_130","doi-asserted-by":"crossref","unstructured":"Scardaci, R., Bietto, F., Racine, P.-J., Boukerb, A.M., Lesouhaitier, O., Feuilloley, M.G.J., Scutera, S., Musso, T., Connil, N., and Pessione, E. (2022). Norepinephrine and Serotonin Can Modulate the Behavior of the Probiotic Enterococcus faecium NCIMB10415 towards the Host: Is a Putative Surface Sensor Involved?. Microorganisms, 10.","DOI":"10.3390\/microorganisms10030487"},{"key":"ref_131","doi-asserted-by":"crossref","unstructured":"Kong, L., Su, M., Sang, J., Huang, S., Wang, M., Cai, Y., Xie, M., Wu, J., Wang, S., and Foster, S.J. (2022). The W-Acidic Motif of Histidine Kinase Walk Is Required for Signaling and Transcriptional Regulation in Streptococcus Mutans. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.820089"},{"key":"ref_132","doi-asserted-by":"crossref","unstructured":"Qiu, M., Chen, Y., Wang, L., Li, L., Zhang, X., Ma, Z., and Liu, J. (2025). Screening, Identification, and Whole-Genome Sequencing of Ferulic Acid Esterase-Producing Lactic Acid Bacteria from Sheep Rumen. Microorganisms, 13.","DOI":"10.3390\/microorganisms13061295"},{"key":"ref_133","doi-asserted-by":"crossref","unstructured":"Koonin, E.V., and Makarova, K.S. (2019). Origins and Evolution of CRISPR-Cas Systems. Philos. Trans. R. Soc. B Biol. Sci., 374.","DOI":"10.1098\/rstb.2018.0087"},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"13508","DOI":"10.1002\/anie.201504741","article-title":"CRISPR-Cas: From the Bacterial Adaptive Immune System to a Versatile Tool for Genome Engineering","volume":"54","author":"Kirchner","year":"2015","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1146\/annurev.micro.112408.134123","article-title":"CRISPR\/Cas System and Its Role in Phage-Bacteria Interactions","volume":"64","author":"Deveau","year":"2010","journal-title":"Annu. Rev. Microbiol."},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1016\/j.molcel.2016.01.030","article-title":"Adaptation in CRISPR-Cas Systems","volume":"61","author":"Sternberg","year":"2016","journal-title":"Mol. Cell"},{"key":"ref_137","first-page":"142","article-title":"Characteristics of probiotic strains for the development of preventive drinks","volume":"4","author":"Abitaeva","year":"2022","journal-title":"Microbiol. Virol."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1046\/j.1365-2672.2003.01915.x","article-title":"Adhesion and aggregation ability of probiotic strain Lactobacillus acidophilus M92","volume":"94","author":"Kos","year":"2003","journal-title":"J. Appl. Microbiol."}],"container-title":["Foods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2304-8158\/14\/19\/3449\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T10:33:43Z","timestamp":1760092423000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2304-8158\/14\/19\/3449"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,9]]},"references-count":138,"journal-issue":{"issue":"19","published-online":{"date-parts":[[2025,10]]}},"alternative-id":["foods14193449"],"URL":"https:\/\/doi.org\/10.3390\/foods14193449","relation":{},"ISSN":["2304-8158"],"issn-type":[{"value":"2304-8158","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,9]]}}}