{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T20:36:43Z","timestamp":1768595803142,"version":"3.49.0"},"reference-count":73,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2020,9,21]],"date-time":"2020-09-21T00:00:00Z","timestamp":1600646400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004663","name":"Ministry of Science and Technology, Taiwan","doi-asserted-by":"publisher","award":["108-2320-B-080-001"],"award-info":[{"award-number":["108-2320-B-080-001"]}],"id":[{"id":"10.13039\/501100004663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ministry of Economic Affairs, Taiwan","award":["109-EC-17-A-22-0525"],"award-info":[{"award-number":["109-EC-17-A-22-0525"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Lactobacillus acidophilus is one of the most commonly used industrial products worldwide. Since its probiotic efficacy is strain-specific, the identification of probiotics at both the species and strain levels is necessary. However, neither phenotypic nor conventional genotypic methods have enabled the effective differentiation of L. acidophilus strains. In this study, a whole-genome sequence-based analysis was carried out to establish high-resolution strain typing of 41 L. acidophilus strains (including commercial isolates and reference strains) using the cano-wgMLST_BacCompare analytics platform; consequently, a strain-specific discrimination method for the probiotic strain LA1063 was developed. Using a core-genome multilocus sequence-typing (cgMLST) scheme based on 1390 highly conserved genes, 41 strains could be assigned to 34 sequence types. Subsequently, we screened a set of 92 loci with a discriminatory power equal to that of the 1390 loci cgMLST scheme. A strain-specific polymerase chain reaction combined with a multiplex minisequencing method was developed based on four (phoU, secY, tilS, and uvrA_1) out of 21 loci, which could be discriminated between LA1063 and other L. acidophilus strains using the cgMLST data. We confirmed that the strain-specific single-nucleotide polymorphisms method could be used to quickly and accurately identify the L. acidophilus probiotic strain LA1063 in commercial products.<\/jats:p>","DOI":"10.3390\/microorganisms8091445","type":"journal-article","created":{"date-parts":[[2020,9,21]],"date-time":"2020-09-21T08:18:01Z","timestamp":1600676281000},"page":"1445","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Development of a High-Resolution Single-Nucleotide Polymorphism Strain-Typing Assay Using Whole Genome-Based Analyses for the Lactobacillus acidophilus Probiotic Strain"],"prefix":"10.3390","volume":"8","author":[{"given":"Chien-Hsun","family":"Huang","sequence":"first","affiliation":[{"name":"Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5844-8428","authenticated-orcid":false,"given":"Chih-Chieh","family":"Chen","sequence":"additional","affiliation":[{"name":"Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan"},{"name":"Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan"}]},{"given":"Shih-Hau","family":"Chiu","sequence":"additional","affiliation":[{"name":"Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan"}]},{"given":"Jong-Shian","family":"Liou","sequence":"additional","affiliation":[{"name":"Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan"}]},{"given":"Yu-Chun","family":"Lin","sequence":"additional","affiliation":[{"name":"Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8766-8342","authenticated-orcid":false,"given":"Jin-Seng","family":"Lin","sequence":"additional","affiliation":[{"name":"Culture Collection &amp; Research Institute, Synbio Tech Inc., Kaohsiung 82151, Taiwan"}]},{"given":"Lina","family":"Huang","sequence":"additional","affiliation":[{"name":"Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9482-1448","authenticated-orcid":false,"given":"Koichi","family":"Watanabe","sequence":"additional","affiliation":[{"name":"Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan"},{"name":"Culture Collection &amp; Research Institute, Synbio Tech Inc., Kaohsiung 82151, Taiwan"},{"name":"Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, No. 50, Ln. 155, Sec. 3, Keelung Rd., Taipei 10673, Taiwan"}]}],"member":"1968","published-online":{"date-parts":[[2020,9,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1099\/00207713-42-3-487","article-title":"Taxonomic study of the Lactobacillus acidophilus group, with recognition of Lactobacillus gallinarum sp. nov. and Lactobacillus johnsonii sp. nov. and synonymy of Lactobacillus acidophilus group A3 (Johnson et al. 1980) with the type strain of Lactobacillus amylovorus (Nakamura 1981)","volume":"42","author":"Fujisawa","year":"1992","journal-title":"Int. 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