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Song Z, Ge Y, Yu X, Liu R, Liu C, Cheng K, Guo L, Yao S. Development of a single nucleotide polymorphism-based strain-identified method for Streptococcus thermophilus CICC 6038 and Lactobacillus delbrueckii ssp. bulgaricus CICC 6047 using pan-genomics analysis. J Dairy Sci 2024; 107:4248-4258. [PMID: 38246550 DOI: 10.3168/jds.2023-23655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024]
Abstract
The health benefits conferred by probiotics is specific to individual probiotic strains, highlighting the importance of identifying specific strains for research and production purposes. Streptococcus thermophilus CICC 6038 and Lactobacillus delbrueckii ssp. bulgaricus CICC 6047 are exceedingly valuable for commercial use with an excellent mixed-culture fermentation. To differentiate these 2 strains from other S. thermophilus and L. delbrueckii ssp. bulgaricus, a specific, sensitive, accurate, rapid, convenient, and cost-effective method is required. In this study, we conducted a pan-genome analysis of S. thermophilus and L. delbrueckii ssp. bulgaricus to identify species-specific core genes, along with strain-specific SNPs. These genes were used to develop suitable PCR primers, and the conformity of sequence length and unique SNPs was confirmed by sequencing for qualitative identification at the strain level. The results demonstrated that SNPs analysis of PCR products derived from these primers could distinguish CICC 6038 and CICC 6047 accurately and reproducibly from the other strains of S. thermophilus and L. delbrueckii ssp. bulgaricus, respectively. The strain-specific PCR method based on SNPs herein is universally applicable for probiotics identification. It offers valuable insights into identifying probiotics at the strain level that is fit-for-purpose in quality control and compliance assessment of commercial dairy products.
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Affiliation(s)
- Zhiquan Song
- China National Research Institute of Food and Fermentation Industries Co. Ltd., China Center of Industrial Culture Collection, Beijing, 100015, China
| | - Yuanyuan Ge
- China National Research Institute of Food and Fermentation Industries Co. Ltd., China Center of Industrial Culture Collection, Beijing, 100015, China; Beijing Forestry University, College of Biological Sciences and Biotechnology, Beijing, 100083, China
| | - Xuejian Yu
- China National Research Institute of Food and Fermentation Industries Co. Ltd., China Center of Industrial Culture Collection, Beijing, 100015, China
| | - Rui Liu
- China National Research Institute of Food and Fermentation Industries Co. Ltd., China Center of Industrial Culture Collection, Beijing, 100015, China
| | - Chong Liu
- China National Research Institute of Food and Fermentation Industries Co. Ltd., China Center of Industrial Culture Collection, Beijing, 100015, China
| | - Kun Cheng
- China National Research Institute of Food and Fermentation Industries Co. Ltd., China Center of Industrial Culture Collection, Beijing, 100015, China
| | - Lizheng Guo
- China National Research Institute of Food and Fermentation Industries Co. Ltd., China Center of Industrial Culture Collection, Beijing, 100015, China
| | - Su Yao
- China National Research Institute of Food and Fermentation Industries Co. Ltd., China Center of Industrial Culture Collection, Beijing, 100015, China.
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Dias RS, Kremer FS, da Costa de Avila LF. In silico prospection of Lactobacillus acidophilus strains with potential probiotic activity. Braz J Microbiol 2023; 54:2733-2743. [PMID: 37801223 PMCID: PMC10689588 DOI: 10.1007/s42770-023-01139-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/26/2023] [Indexed: 10/07/2023] Open
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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Affiliation(s)
- Rafaella Sinnott Dias
- 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.
| | - Frederico Schmitt Kremer
- Bioinformatics Laboratory, Technological Development Center, Federal University of Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Luciana Farias da Costa de Avila
- 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
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Kiousi DE, Karadedos DM, Sykoudi A, Repanas P, Kamarinou CS, Argyri AA, Galanis A. Development of a Multiplex PCR Assay for Efficient Detection of Two Potential Probiotic Strains Using Whole Genome-Based Primers. Microorganisms 2023; 11:2553. [PMID: 37894211 PMCID: PMC10609308 DOI: 10.3390/microorganisms11102553] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Probiotics are microorganisms that exert strain-specific health-promoting effects on the host. Τhey are employed in the production of functional dairy or non-dairy food products; still, their detection in these complex matrices is a challenging task. Several culture-dependent and culture-independent methods have been developed in this direction; however, they present low discrimination at the strain level. Here, we developed a multiplex PCR assay for the detection of two potential probiotic lactic acid bacteria (LAB) strains, Lactiplantibacillus plantarum L125 and Lp. pentosus L33, in monocultures and yogurt samples. Unique genomic regions were identified via comparative genomic analysis and were used to produce strain-specific primers. Then, primer sets were selected that produced distinct electrophoretic DNA banding patterns in multiplex PCR for each target strain. This method was further implemented for the detection of the two strains in yogurt samples, highlighting its biotechnological applicability. Moreover, it can be applied with appropriate modifications to detect any bacterial strain with available WGS.
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Affiliation(s)
- Despoina E. Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Dimitrios M. Karadedos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Anastasia Sykoudi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Panagiotis Repanas
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
| | - Christina S. Kamarinou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece;
| | - Anthoula A. Argyri
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, 14123 Lycovrissi, Greece;
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (D.M.K.); (A.S.); (P.R.); (C.S.K.)
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Ramireddy L, Tsen HY, Chiang YC, Hung CY, Wu SR, Young SL, Lin JS, Huang CH, Chiu SH, Chen CC, Chen CC. Molecular Identification and Selection of Probiotic Strains Able to Reduce the Serum TMAO Level in Mice Challenged with Choline. Foods 2021; 10:foods10122931. [PMID: 34945482 PMCID: PMC8700464 DOI: 10.3390/foods10122931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 02/07/2023] Open
Abstract
Trimethylamine oxide (TMAO) originates from trimethylamine (TMA), which is oxidized in the liver by hepatic flavin-containing monooxygenases (FMO3). TMA is produced by its dietary precursors such as choline, carnitine, and phosphatidylcholine by gut microbiota. TMAO attracts attention, identified as a novel and independent risk factor for promoting obesity, atherosclerosis and cardiovascular disease (CVD), chronic kidney disease (CKD), insulin tolerance, and colon cancer. Probiotics have been considered as live microorganisms, providing benefits to their host when they are given in sufficient quantities and administered continuously. The objective of this study is to suggest a method to select potential probiotic strains to reduce the serum concentration of TMAO in mice fed with choline. In this work, we chose three lactobacilli with strong adherence capability, and fed multistrain formula (MF) to the mice challenged with choline. On days 7, 14, and day 28, it was found that the MF-containing L. amylovorus LAM1345, Lpb. plantarum LP1145, and Lim. fermentum LF33 showed a significant reduction in serum TMAO and TMA levels. For the single strains, LP1145 reduced TMAO on days 14 and 28, and strain LAM1345 reduced TMAO significantly on days 7 and day 14. For strain LF1143 from strain LF33, it showed no significant effect on TMAO and TMA. Thus, MF showed the best effect, which may be due to the additive and synergetic effect and the contribution of strain LP1145 and LAM1345. Finally, for the LAM1345 and LP1145 strains, we used molecular identification and typing methods to assure that these two strains are unique strains. The methods used for LAM 1345 were leader peptidase A (lepA) gene analysis and phylogenetic analysis, while for strain LP 1145and other strains of Lpb. plantarum subsp. plantarum sequences were compared using the whole-genome multilocus sequence typing (wgMLST) method.
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Affiliation(s)
- Latha Ramireddy
- Department of Food Science and Technology, Hung Kuang University, No. 1018, Sec. 6, Taiwan Boulevard, Shalu District, Taichung 43302, Taiwan;
- Correspondence: (L.R.); (H.-Y.T.); Tel.: +886-4-26318652 (ext. 5085) (H.-Y.T.); Fax: 886-4-26527731 (H.-Y.T.)
| | - Hau-Yang Tsen
- Department of Food Science and Technology, Hung Kuang University, No. 1018, Sec. 6, Taiwan Boulevard, Shalu District, Taichung 43302, Taiwan;
- Correspondence: (L.R.); (H.-Y.T.); Tel.: +886-4-26318652 (ext. 5085) (H.-Y.T.); Fax: 886-4-26527731 (H.-Y.T.)
| | - Yu-Chen Chiang
- Department of Food Nutrition and Biotechnology, Asia University, Taichung 41354, Taiwan;
| | - Chen-Ying Hung
- Department of Internal Medicine, Taipei Veterans General Hospital, Hsinchu Branch, Hsinchu 310, Taiwan;
| | - Shih-Rong Wu
- Department of Food Science and Technology, Hung Kuang University, No. 1018, Sec. 6, Taiwan Boulevard, Shalu District, Taichung 43302, Taiwan;
| | - San-Land Young
- Culture Collection and Research Institute, Synbio Tech Inc., Kaohsiung 82151, Taiwan; (S.-L.Y.); (J.-S.L.)
| | - Jin-Seng Lin
- Culture Collection and Research Institute, Synbio Tech Inc., Kaohsiung 82151, Taiwan; (S.-L.Y.); (J.-S.L.)
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (C.-H.H.); (S.-H.C.); (C.-C.C.)
| | - Shih-Hau Chiu
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (C.-H.H.); (S.-H.C.); (C.-C.C.)
| | - Chien-Chi Chen
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (C.-H.H.); (S.-H.C.); (C.-C.C.)
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan;
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