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Marole TA, Sibanda T, Buys EM. Assessing probiotic viability in mixed species yogurt using a novel propidium monoazide (PMAxx)-quantitative PCR method. Front Microbiol 2024; 15:1325268. [PMID: 38389538 PMCID: PMC10882272 DOI: 10.3389/fmicb.2024.1325268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
Viability is a prerequisite for any therapeutic benefits associated with the ingestion of probiotic bacteria. Current culture-based techniques are inadequate for the enumeration of probiotics in mixed-species food products. This study utilized a quantitative PCR (qPCR) method coupled with propidium monoazide (PMAxx), and novel species-specific tuf gene primers to selectively enumerate Lacticaseibacillus rhamnosus, Bifidobacterium spp., and yogurt starter cultures in mixed-species probiotic yogurt. The method was optimized for PMAxx concentration and specificity and evaluated for efficiency and applicability. PMAxx-qPCR showed high specificity to the target organisms in mixed-species yogurt, quantifying only viable cells. The linear dynamic ranges were established over five to seven orders of magnitude. The assay was reliable with an efficiency of 91-99%, R2 values > 0.99, and a good correlation to the plate count method (r = 0.882). The results of this study demonstrate the high selectivity, improved lead time, and reliability of PMAxx-qPCR over the culture-dependent method, making it a valuable tool for inline viability verification during processing and improving probiotic quality assurance for processors and consumers.
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Affiliation(s)
- Tlaleo A Marole
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
| | - Thulani Sibanda
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
| | - Elna M Buys
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
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2
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Kuri A, Iida H, Kawahara K. Comparative analysis of glyceroglycolipids from Lactiplantibacillus pentosus and other Lactiplantibacillus species. J GEN APPL MICROBIOL 2023; 69:135-141. [PMID: 36476588 DOI: 10.2323/jgam.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Cellular lipids of Lactiplantibacillus species were extracted and neutral glyceroglycolipids (GGLs) were purified, and analyzed by thin-layer chromatography (TLC). Four GGLs with known structures were detected in GGL preparation of L. plantarum, and the same GGL profiles of TLC were observed for all other strains of Lactiplantibacillus species examined, suggesting that the GGL profile could be one of the chemotaxonomic characters of the genus Lactiplantibacillus. On the other hand, the quantity of each GGL showed some variation among species, and L. pentosus was found to have higher proportion of disaccharide-type GGL, designated GGL-3 in this study, compared with other species including L. plantarum. The quantitative difference of GGL-3 found in this study could be regarded as the characteristics of L. pentosus. The carbohydrate structure of L. pentosus GGL-3 was precisely analyzed by 1H NMR and methylation analysis, and the structure was confirmed to be αGal-(1→2)-αGlc-diacylglycerol, with the carbohydrate structure identical to that of L. plantarum, although fatty acid composition of the two GGL-3 showed some difference.
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Affiliation(s)
- Ayako Kuri
- Graduate School of Engineering, Kanto Gakuin University
- Faculty of Food and Health Sciences, Showa Women's University
| | - Hirokazu Iida
- Graduate School of Engineering, Kanto Gakuin University
- Department of Biosciences, College of Science and Engineering, Kanto Gakuin University
| | - Kazuyoshi Kawahara
- Graduate School of Engineering, Kanto Gakuin University
- Department of Biosciences, College of Science and Engineering, Kanto Gakuin University
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3
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Apostolakos I, Paramithiotis S, Mataragas M. Comparative Genomic Analysis Reveals the Functional Traits and Safety Status of Lactic Acid Bacteria Retrieved from Artisanal Cheeses and Raw Sheep Milk. Foods 2023; 12:foods12030599. [PMID: 36766127 PMCID: PMC9914385 DOI: 10.3390/foods12030599] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/21/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Lactic acid bacteria (LAB) are valuable for the production of fermented dairy products. We investigated the functional traits of LAB isolated from artisanal cheeses and raw sheep milk, assessed their safety status, and explored the genetic processes underlying the fermentation of carbohydrates. Lactiplantibacillus plantarum had the largest and more functional genome compared to all other LAB, while most of its protein-encoding genes had unknown functions. A key finding of our analysis was the overall absence of acquired resistance genes (RGs), virulence genes (VGs), and prophages, denoting that all LAB isolates fulfill safety criteria and can be used as starter or adjunct cultures. In this regard, the identified mobile genetic elements found in LAB, rather than enabling the integration of RGs or VGs, they likely facilitate the uptake of genes involved in beneficial functions and in the adaptation of LAB in dairy matrices. Another important finding of our study was that bacteriocins and CAZymes were abundant in LAB though each species was associated with specific genes, which in turn had different activity spectrums and identified applications. Additionally, all isolates were able to metabolize glucose, lactose, maltose, and sucrose, but Lactiplantibacillus plantarum was strongly associated with the fermentation of rhamnose, mannose, cellobiose, and trehalose whereas Levilactobacillus brevis with the utilization of arabinose and xylose. Altogether these results suggest that to fully exploit the beneficial properties of LAB, a combination of strains as food additives may be necessary. Interestingly, biological processes involved in the metabolism of carbohydrates that are not of direct interest for the dairy industry may yield valuable metabolites or activate pathways associated with beneficial health effects. Our results provide useful information for the development of new probiotic artisanal cheeses and probiotic starter cultures.
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Affiliation(s)
- Ilias Apostolakos
- Department of Dairy Research, Institution of Technology of Agricultural Products, Hellenic Agricultural Organization “DIMITRA”, 3 Ethnikis Antistaseos St., 45221 Ioannina, Greece
| | - Spiros Paramithiotis
- Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
| | - Marios Mataragas
- Department of Dairy Research, Institution of Technology of Agricultural Products, Hellenic Agricultural Organization “DIMITRA”, 3 Ethnikis Antistaseos St., 45221 Ioannina, Greece
- Correspondence:
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Multiplex SYBR Green real-time PCR for Lactobacillus acidophilus group species targeting biomarker genes revealed by a pangenome approach. Microbiol Res 2022; 259:127013. [DOI: 10.1016/j.micres.2022.127013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 02/16/2022] [Accepted: 03/16/2022] [Indexed: 11/19/2022]
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Fan X, Li X, Zhang T, Xu J, Shi Z, Wu Z, Wu J, Pan D, Du L. A Novel qPCR Method for the Detection of Lactic Acid Bacteria in Fermented Milk. Foods 2021; 10:3066. [PMID: 34945617 PMCID: PMC8700909 DOI: 10.3390/foods10123066] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/05/2021] [Accepted: 12/07/2021] [Indexed: 12/04/2022] Open
Abstract
The number of live lactic acid bacteria (LAB) is an important quality indicator for yogurt, the quantitative testing of LAB has become an important task in the evaluation of product quality and function. By analyzing and comparing the performance of 16S rRNA gene and tuf gene used in absolute quantification, the tuf gene with copy number 1 was selected as the target gene of six LAB. By drawing a standard curve to achieve qualitative and quantitative detection of six strains of LAB, the detection range was found to be 1 × 103-1 × 108 copies/µL. The traditional plate colony count and Flow Cytometry (FCM) were compared with the method of qPCR, which was used in this experiment. Meanwhile, the confocal laser microscope combined with STYO 9 and propidium iodide dyes was used to determine that the content of viable bacteria in the yogurt was more than 90%, which proved that the detection result using qPCR method was closer to the true level of LAB in yogurt. Compared with the existing methods, the method in this study allowed the qualitative and quantitative detection of the six kinds of LAB in yogurt, and the distribution of live and dead bacteria in yogurt could be calculated.
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Affiliation(s)
- Xiankang Fan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (X.F.); (X.L.); (T.Z.); (J.X.); (Z.S.); (Z.W.); (L.D.)
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Xiefei Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (X.F.); (X.L.); (T.Z.); (J.X.); (Z.S.); (Z.W.); (L.D.)
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Tao Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (X.F.); (X.L.); (T.Z.); (J.X.); (Z.S.); (Z.W.); (L.D.)
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Jue Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (X.F.); (X.L.); (T.Z.); (J.X.); (Z.S.); (Z.W.); (L.D.)
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Zihang Shi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (X.F.); (X.L.); (T.Z.); (J.X.); (Z.S.); (Z.W.); (L.D.)
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Zhen Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (X.F.); (X.L.); (T.Z.); (J.X.); (Z.S.); (Z.W.); (L.D.)
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Jihuan Wu
- Ningbo Yifule Biotechnology Co., Ltd., Ningbo 315500, China;
| | - Daodong Pan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (X.F.); (X.L.); (T.Z.); (J.X.); (Z.S.); (Z.W.); (L.D.)
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Lihui Du
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (X.F.); (X.L.); (T.Z.); (J.X.); (Z.S.); (Z.W.); (L.D.)
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
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Huang CH, Chen CC, Lin YC, Chen CH, Lee AY, Liou JS, Gu CT, Huang L. The mutL Gene as a Genome-Wide Taxonomic Marker for High Resolution Discrimination of Lactiplantibacillus plantarum and Its Closely Related Taxa. Microorganisms 2021; 9:microorganisms9081570. [PMID: 34442649 PMCID: PMC8399863 DOI: 10.3390/microorganisms9081570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/30/2022] Open
Abstract
The current taxonomy of the Lactiplantibacillus plantarum group comprises of 17 closely related species that are indistinguishable from each other by using commonly used 16S rRNA gene sequencing. In this study, a whole-genome-based analysis was carried out for exploring the highly distinguished target genes whose interspecific sequence identity is significantly less than those of 16S rRNA or conventional housekeeping genes. In silico analyses of 774 core genes by the cano-wgMLST_BacCompare analytics platform indicated that csbB, morA, murI, mutL, ntpJ, rutB, trmK, ydaF, and yhhX genes were the most promising candidates. Subsequently, the mutL gene was selected, and the discrimination power was further evaluated using Sanger sequencing. Among the type strains, mutL exhibited a clearly superior sequence identity (61.6–85.6%; average: 66.6%) to the 16S rRNA gene (96.7–100%; average: 98.4%) and the conventional phylogenetic marker genes (e.g., dnaJ, dnaK, pheS, recA, and rpoA), respectively, which could be used to separat tested strains into various species clusters. Consequently, species-specific primers were developed for fast and accurate identification of L. pentosus, L. argentoratensis, L. plantarum, and L. paraplantarum. During this study, one strain (BCRC 06B0048, L. pentosus) exhibited not only relatively low mutL sequence identities (97.0%) but also a low digital DNA–DNA hybridization value (78.1%) with the type strain DSM 20314T, signifying that it exhibits potential for reclassification as a novel subspecies. Our data demonstrate that mutL can be a genome-wide target for identifying and classifying the L. plantarum group species and for differentiating novel taxa from known species.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
- Correspondence:
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan;
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Yu-Chun Lin
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan; (Y.-C.L.); (C.-H.C.)
| | - Chia-Hsuan Chen
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan; (Y.-C.L.); (C.-H.C.)
| | - Ai-Yun Lee
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
| | - Chun-Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China;
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan; (A.-Y.L.); (J.-S.L.); (L.H.)
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7
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Metataxonomic analysis of microbiota from Pakistani dromedary camelids milk and characterization of a newly isolated Lactobacillus fermentum strain with probiotic and bio-yogurt starter traits. Folia Microbiol (Praha) 2021; 66:411-428. [PMID: 33566278 DOI: 10.1007/s12223-021-00855-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/20/2021] [Indexed: 10/22/2022]
Abstract
This study was undertaken to investigate the starter and probiotic potential of lactic acid bacteria isolated from dromedarian camel's milk using both culture-dependent and -independent approaches and metataxonomic analysis. Strains of lactic acid bacteria recovered were examined in vitro for tolerance to gastric acidity, bile, and lysozyme. Bile salt hydrolysis, serum cholesterol-lowering, oxalate degradation, proteolytic activity, exopolysaccharide production, and cell surface characteristics necessary for colonizing intestinal mucosa were also evaluated. A single strain of the species, Lactobacillus fermentum named NPL280, was selected through multivariate analysis as it harbored potential probiotic advantages and fulfilled safety criteria. The strain assimilated cholesterol, degraded oxalate, produced exopolysaccharides, and proved to be a proficient alternate yogurt starter with good viability in stored bio-yogurt. A sensorial analysis of the prepared bio-yogurt was also found to be exemplary. We conclude that the indigenous L. fermentum strain NPL280 has the desired traits of a starter and adjunct probiotic culture for dairy products.
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8
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Pérez-Díaz IM, Johanningsmeier SD, Anekella K, Pagán-Medina CG, Méndez-Sandoval L, Arellano C, Price R, Daughtry KV, Borges M, Bream C, Connelly L, Dieck SE, Levi MT, McMurtrie EK, Smith RE, Theora JC, Wendland P, Gómez-Rodríguez F, Arroyo-López FN. Genotypic and phenotypic diversity among Lactobacillus plantarum and Lactobacillus pentosus isolated from industrial scale cucumber fermentations. Food Microbiol 2020; 94:103652. [PMID: 33279077 DOI: 10.1016/j.fm.2020.103652] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 08/17/2020] [Accepted: 09/30/2020] [Indexed: 11/16/2022]
Abstract
The Lactobacillus plantarum and Lactobacillus pentosus genotypes existing in industrial-scale cucumber fermentations were defined using rep-PCR-(GTG)5. The ability of each genotype to ferment cucumbers under various conditions was evaluated. Rep-PCR-(GTG)5 was the technique capable of illustrating the most intraspecies discrimination compared to the sequencing of housekeeping genes (recA, dnaK, pheS and rpoA), MLST and RAPD with primers LP1, OPL5, M14 and COC. Ten genotypic clusters were defined for the 199 L. pentosus tested and three for the 17 L. plantarum clones. The ability of the 216 clones genotyped and 37 additional cucumber fermentation isolates, of the same species, to rapidly decrease the pH of cucumber juice medium under various combinations of sodium chloride (0 or 6%), initial pH (4.0 or 5.2) and temperatures (15 or 30 °C) was determined using a fractional factorial screening design. A reduced fermentation ability was observed for the L. plantarum strains as compared to L. pentosus, except for clone 3.2.8, which had a ropy phenotype and aligned to genotypic cluster A. L. pentosus strains belonging to three genotypic clusters (B, D and J) were more efficient in cucumber juice fermentation as compared to most L. plantarum strains. This research identified three genetically diverse L. pentosus strains and one L. plantarum as candidates for starter cultures for commercial cucumber fermentations.
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Affiliation(s)
- Ilenys M Pérez-Díaz
- USDA-Agricultural Research Service, Food Science Research Unit, Raleigh, NC, USA.
| | | | - Kartheek Anekella
- North Carolina State University, Department of Food, Bioprocessing, and Nutrition Sciences, Raleigh, NC, USA
| | | | - Lesley Méndez-Sandoval
- North Carolina State University, Department of Food, Bioprocessing, and Nutrition Sciences, Raleigh, NC, USA
| | - Consuelo Arellano
- North Carolina State University, Department of Statistics, Raleigh, NC, USA
| | - Robert Price
- North Carolina State University, Department of Food, Bioprocessing, and Nutrition Sciences, Raleigh, NC, USA
| | - Katheryne V Daughtry
- North Carolina State University, Department of Food, Bioprocessing, and Nutrition Sciences, Raleigh, NC, USA
| | - Michelle Borges
- North Carolina State University, Department of Food, Bioprocessing, and Nutrition Sciences, Raleigh, NC, USA
| | - Chloe Bream
- North Carolina State University, Department of Food, Bioprocessing, and Nutrition Sciences, Raleigh, NC, USA
| | - Lauren Connelly
- North Carolina State University, Department of Food, Bioprocessing, and Nutrition Sciences, Raleigh, NC, USA
| | - Susan E Dieck
- North Carolina State University, Department of Food, Bioprocessing, and Nutrition Sciences, Raleigh, NC, USA
| | - Meredith T Levi
- North Carolina State University, Department of Food, Bioprocessing, and Nutrition Sciences, Raleigh, NC, USA
| | - Erin K McMurtrie
- North Carolina State University, Department of Food, Bioprocessing, and Nutrition Sciences, Raleigh, NC, USA; North Carolina State University, Department of Chemistry, Raleigh, NC, USA
| | - Rickey E Smith
- North Carolina State University, Department of Food, Bioprocessing, and Nutrition Sciences, Raleigh, NC, USA
| | - Jeannette C Theora
- North Carolina State University, Department of Food, Bioprocessing, and Nutrition Sciences, Raleigh, NC, USA; North Carolina State University, Department of Chemistry, Raleigh, NC, USA
| | - Paige Wendland
- North Carolina State University, Department of Food, Bioprocessing, and Nutrition Sciences, Raleigh, NC, USA
| | - Francisco Gómez-Rodríguez
- Department of Food Biotechnology, Instituto de la Grasa, (CSIC), Campo Universitario Pablo de Olavide, Seville, Spain
| | - Francisco Noé Arroyo-López
- Department of Food Biotechnology, Instituto de la Grasa, (CSIC), Campo Universitario Pablo de Olavide, Seville, Spain
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Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin Microbiol Rev 2020; 33:33/4/e00053-19. [PMID: 32907806 DOI: 10.1128/cmr.00053-19] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.
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Anekella K, Pérez-Díaz IM. Characterization of robust Lactobacillus plantarum and Lactobacillus pentosus starter cultures for environmentally friendly low-salt cucumber fermentations. J Food Sci 2020; 85:3487-3497. [PMID: 32893884 DOI: 10.1111/1750-3841.15416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 07/14/2020] [Accepted: 07/21/2020] [Indexed: 02/04/2023]
Abstract
Seven candidates for starter cultures for cucumber fermentations belonging to the Lactobacillus pentosus and Lactobacillus plantarum species were characterized based on physiological features desired for pickling. The isolates presented variable carbohydrate utilization profile on API® 50CHL test strips. The L. pentosus strains were unable to utilize d-xylose in MRS broth or the M medium. The lactobacilli were unable to produce histamine, tyramine, putrescine, and cadaverine in biogenic amine broth containing the necessary precursors. Production of d-lactic acid by the lactobacilli, detected enzymatically, was stimulated by growth in MRS broth as compared to cucumber juice medium (CJM). The lactobacilli utilized malic acid in the malate decarboxylase medium. Exopolyssacharide biosynthesis related genes were amplified from the lactobacilli. A sugar type-dependent-ropy phenotype was apparent for all the cultures tested in MRS and CJM. The genes associated with bacteriocin production were detected in the lactobacilli, but not the respective phenotypes. The antibiotic susceptibility profile of the lactobacilli mimics that of other L. plantarum starter cultures. It is concluded that the lactobacilli strains studied here are suitable starter cultures for cucumber fermentation. PRACTICAL APPLICATION: The availability of such starter cultures enables the implementation of low salt cucumber fermentations that can generate products with consistent biochemistry and microbiological profile.
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Affiliation(s)
- Kartheek Anekella
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Ilenys M Pérez-Díaz
- USDA-Agriculture Research Service-Food Science & Market Quality and Handling Research Unit, 322 Schaub Hall, Raleigh, 27695, USA
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11
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Multi fragment melting analysis system (MFMAS) for one-step identification of lactobacilli. J Microbiol Methods 2020; 177:106045. [PMID: 32890569 DOI: 10.1016/j.mimet.2020.106045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 11/23/2022]
Abstract
The accurate identification of lactobacilli is essential for the effective management of industrial practices associated with lactobacilli strains, such as the production of fermented foods or probiotic supplements. For this reason, in this study, we proposed the Multi Fragment Melting Analysis System (MFMAS)-lactobacilli based on high resolution melting (HRM) analysis of multiple DNA regions that have high interspecies heterogeneity for fast and reliable identification and characterization of lactobacilli. The MFMAS-lactobacilli is a new and customized version of the MFMAS, which was developed by our research group. MFMAS-lactobacilli is a combined system that consists of i) a ready-to-use plate, which is designed for multiple HRM analysis, and ii) a data analysis software, which is used to characterize lactobacilli species via incorporating machine learning techniques. Simultaneous HRM analysis of multiple DNA fragments yields a fingerprint for each tested strain and the identification is performed by comparing the fingerprints of unknown strains with those of known lactobacilli species registered in the MFMAS. In this study, a total of 254 isolates, which were recovered from fermented foods and probiotic supplements, were subjected to MFMAS analysis, and the results were confirmed by a combination of different molecular techniques. All of the analyzed isolates were exactly differentiated and accurately identified by applying the single-step procedure of MFMAS, and it was determined that all of the tested isolates belonged to 18 different lactobacilli species. The individual analysis of each target DNA region provided identification with an accuracy range from 59% to 90% for all tested isolates. However, when each target DNA region was analyzed simultaneously, perfect discrimination and 100% accurate identification were obtained even in closely related species. As a result, it was concluded that MFMAS-lactobacilli is a multi-purpose method that can be used to differentiate, classify, and identify lactobacilli species. Hence, our proposed system could be a potential alternative to overcome the inconsistencies and difficulties of the current methods.
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Dioso CM, Vital P, Arellano K, Park H, Todorov SD, Ji Y, Holzapfel W. Do Your Kids Get What You Paid for? Evaluation of Commercially Available Probiotic Products Intended for Children in the Republic of the Philippines and the Republic of Korea. Foods 2020; 9:E1229. [PMID: 32899215 PMCID: PMC7555838 DOI: 10.3390/foods9091229] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 12/18/2022] Open
Abstract
A wide range of probiotic products is available on the market and can be easily purchased over the counter and unlike pharmaceutical drugs, their commercial distribution is not strictly regulated. In this study, ten probiotic preparations commercially available for children's consumption in the Republic of the Philippines (PH) and the Republic of Korea (SK) have been investigated. The analyses included determination of viable counts and taxonomic identification of the bacterial species present in each formulation. The status of each product was assessed by comparing the results with information and claims provided on the label. In addition to their molecular identification, safety assessment of the isolated strains was conducted by testing for hemolysis, biogenic amine production and antibiotic resistance. One out of the ten products contained lower viable numbers of recovered microorganisms than claimed on the label. Enterococcus strains, although not mentioned on the label, were isolated from four products. Some of these isolates produced biogenic amines and were resistant to one or several antibiotics. Metagenomic analyses of two products revealed that one product did not contain most of the microorganisms declared in its specification. The study demonstrated that some commercial probiotic products for children did not match their label claims. Infants and young children belong to the most vulnerable members of society, and food supplements including probiotics destined for this consumer group require careful checking and strict regulation before commercial distribution.
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Affiliation(s)
- Clarizza May Dioso
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines;
- Advanced Green Energy and Environment Department, Handong Global University, Pohang, Gyungbuk 37554, Korea; (K.A.); (H.P.); (S.D.T.)
| | - Pierangeli Vital
- Natural Sciences Research Institute, University of the Philippines Diliman, Quezon City 1101, Philippines;
| | - Karina Arellano
- Advanced Green Energy and Environment Department, Handong Global University, Pohang, Gyungbuk 37554, Korea; (K.A.); (H.P.); (S.D.T.)
| | - Haryung Park
- Advanced Green Energy and Environment Department, Handong Global University, Pohang, Gyungbuk 37554, Korea; (K.A.); (H.P.); (S.D.T.)
- HEM Inc., Business Incubator, Handong Global University, Pohang, Gyungbuk 37554, Korea;
| | - Svetoslav Dimitrov Todorov
- Advanced Green Energy and Environment Department, Handong Global University, Pohang, Gyungbuk 37554, Korea; (K.A.); (H.P.); (S.D.T.)
| | - Yosep Ji
- HEM Inc., Business Incubator, Handong Global University, Pohang, Gyungbuk 37554, Korea;
| | - Wilhelm Holzapfel
- Advanced Green Energy and Environment Department, Handong Global University, Pohang, Gyungbuk 37554, Korea; (K.A.); (H.P.); (S.D.T.)
- HEM Inc., Business Incubator, Handong Global University, Pohang, Gyungbuk 37554, Korea;
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Nel S, Davis SB, Endo A, Dicks LMT. Phylogenetic analysis of Leuconostoc and Lactobacillus species isolated from sugarcane processing streams. Microbiologyopen 2020; 9:e1065. [PMID: 32496663 PMCID: PMC7424246 DOI: 10.1002/mbo3.1065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/17/2020] [Accepted: 05/11/2020] [Indexed: 11/17/2022] Open
Abstract
High levels of gums such as dextran, produced by Leuconostoc and Lactobacillus spp., have a severe impact on factory throughput and sugar quality. This study aimed to determine the phylogenetic relationships between gum‐producing Leuconostoc and Lactobacillus bacteria which were isolated from various locations in a sugarcane processing factory at times when low‐ and high‐dextran raw sugar, respectively, were produced. Phylogenetic analysis of 16S rRNA gene sequences grouped 81 isolates with the type strains of Leuconostoc mesenteroides (subspp. mesenteroides, dextranicum, and cremoris), Leuconostoc pseudomesenteroides, Leuconostoc lactis, and Leuconostoc citreum, respectively. Forty‐three isolates clustered with the type strain of Lactobacillus fermentum. The phylogenetic relatedness of the isolates was determined by sequencing and analysis of the housekeeping genes rpoA and dnaA for Leuconostoc spp. and the pheS and tuf genes for the Lactobacillus spp. The rpoA gene proved discriminatory for the phylogenetic resolution of all of the isolated Leuconostoc spp. and the dnaA housekeeping gene was shown to be effective for isolates clustering with the type strains of Leuc. mesenteroides and Leuc. citreum. None of the loci examined permitted differentiation at the subspecies level of Leuc. mesenteroides. Single‐locus analysis, as well as the concatenation of the pheS and tuf housekeeping gene sequences, yielded identical phylogenies for the Lactobacillus isolates corresponding to L. fermentum.
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Affiliation(s)
- Sanet Nel
- Sugar Milling Research Institute NPC, c/o University of KwaZulu-Natal, Durban, South Africa.,Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Stephen B Davis
- Sugar Milling Research Institute NPC, c/o University of KwaZulu-Natal, Durban, South Africa
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Hokkaido, Japan
| | - Leon M T Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
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Huang CH, Li SW, Huang L, Watanabe K. Identification and Classification for the Lactobacillus casei Group. Front Microbiol 2018; 9:1974. [PMID: 30186277 PMCID: PMC6113361 DOI: 10.3389/fmicb.2018.01974] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/06/2018] [Indexed: 12/14/2022] Open
Abstract
Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus are phenotypically and genotypically closely related, and together comprise the L. casei group. Although the strains of this group are commercially valuable as probiotics, the taxonomic status and nomenclature of the L. casei group have long been contentious because of the difficulties in identifying these three species by using the most frequently used genotypic methodology of 16S rRNA gene sequencing. Long used as the gold standard for species classification, DNA–DNA hybridization is laborious, requires expert skills, and is difficult to use routinely in laboratories. Currently, genome-based comparisons, including average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH), are commonly applied to bacterial taxonomy as alternatives to the gold standard method for the demarcating phylogenetic relationships. To establish quick and accurate methods for identifying strains in the L. casei group at the species and subspecies levels, we developed species- and subspecies-specific identification methods based on housekeeping gene sequences and whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectral pattern analysis. By phylogenetic analysis based on concatenated housekeeping gene sequences (dnaJ, dnaK, mutL, pheS, and yycH), 53 strains were separated into four clusters corresponding to the four species: L. casei, L. paracasei and L. rhamnosus, and Lactobacillus chiayiensis sp. nov. A multiplex minisequencing assay using single nucleotide polymorphism (SNP)-specific primers based on the dnaK gene sequences and species-specific primers based on the mutL gene sequences provided high resolution that enabled the strains at the species level to be identified as L. casei, L. paracasei, and L. rhamnosus. By MALDI-TOF MS analysis coupled with an internal database and ClinProTools software, species- and subspecies-level L. casei group strains were identified based on reliable scores and species- and subspecies-specific MS peaks. The L. paracasei strains were distinguished clearly at the subspecies level based on subspecies-specific MS peaks. This article describes the rapid and accurate methods used for identification and classification of strains in the L. casei group based on housekeeping gene sequences and MALDI-TOF MS analysis as well as the novel speciation of this group including L. chiayiensis sp. nov. and ‘Lactobacillus zeae’ by genome-based methods.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Shiao-Wen Li
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Koichi Watanabe
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan.,Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
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15
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Huang CH, Huang L. Rapid species- and subspecies-specific level classification and identification of Lactobacillus casei group members using MALDI Biotyper combined with ClinProTools. J Dairy Sci 2018; 101:979-991. [DOI: 10.3168/jds.2017-13642] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 09/30/2017] [Indexed: 12/16/2022]
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16
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Li C, Song J, Kwok LY, Wang J, Dong Y, Yu H, Hou Q, Zhang H, Chen Y. Influence of Lactobacillus plantarum on yogurt fermentation properties and subsequent changes during postfermentation storage. J Dairy Sci 2017; 100:2512-2525. [DOI: 10.3168/jds.2016-11864] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 12/20/2016] [Indexed: 12/13/2022]
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17
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Maji UJ, Mohanty S. Genotypic characterization of Lactic acid bacteria in gut microbiome of freshwater fish. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717020138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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18
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Song Y, Sun Z, Guo C, Wu Y, Liu W, Yu J, Menghe B, Yang R, Zhang H. Genetic diversity and population structure of Lactobacillus delbrueckii subspecies bulgaricus isolated from naturally fermented dairy foods. Sci Rep 2016; 6:22704. [PMID: 26940047 PMCID: PMC4778129 DOI: 10.1038/srep22704] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/18/2016] [Indexed: 11/30/2022] Open
Abstract
Lactobacillus delbrueckii subsp. bulgaricus is one of the most widely used starter culture strains in industrial fermented dairy manufacture. It is also common in naturally fermented dairy foods made using traditional methods. The subsp. bulgaricus strains found in naturally fermented foods may be useful for improving current industrial starter cultures; however, little is known regarding its genetic diversity and population structure. Here, a collection of 298 L. delbrueckii strains from naturally fermented products in Mongolia, Russia, and West China was analyzed by multi-locus sequence typing based on eight conserved genes. The 251 confirmed subsp. bulgaricus strains produced 106 unique sequence types, the majority of which were assigned to five clonal complexes (CCs). The geographical distribution of CCs was uneven, with CC1 dominated by Mongolian and Russian isolates, and CC2–CC5 isolates exclusively from Xinjiang, China. Population structure analysis suggested six lineages, L1–L6, with various homologous recombination rates. Although L2–L5 were mainly restricted within specific regions, strains belonging to L1 and L6 were observed in diverse regions, suggesting historical transmission events. These results greatly enhance our knowledge of the population diversity of subsp. bulgaricus strains, and suggest that strains from CC1 and L4 may be useful as starter strains in industrial fermentation.
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Affiliation(s)
- Yuqin Song
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Chenyi Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Jie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Bilige Menghe
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
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Xu H, Liu W, Zhang W, Yu J, Song Y, Menhe B, Zhang H, Sun Z. Use of multilocus sequence typing to infer genetic diversity and population structure of Lactobacillus plantarum isolates from different sources. BMC Microbiol 2015; 15:241. [PMID: 26511725 PMCID: PMC4625847 DOI: 10.1186/s12866-015-0584-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 10/23/2015] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Lactobacillus plantarum is a lactic acid bacterium (LAB) of considerable industrial interest since it has an important role in the production of fermented food. In the present study, the genetic diversity and population structure within 186 L. plantarum isolates was determined based on a novel MLST scheme employing eight housekeeping genes. These isolates had originated from different sources and geographic regions: 179 isolates were from our own culture collection and originated from China and Mongolia and seven isolates were type or reference isolates from other collections. RESULTS The results showed that 179 isolates and seven reference isolates could be assigned to 73 different sequence types (STs), forming ten clonal complexes (CCs) and 23 singletons. There were 158 polymorphic sites detected in total, and the nucleotide diversity per site varied from 0.00401 in clpX to 0.03220 in groEL. The minimum spanning tree analyses suggested that the evolution of L. plantarum isolates have little relationship with ecological sources have similar nucleotide diversity. Phylogenetic trees and structure indicated that there were six lineages in the L. plantarum isolates used in our study. Split-decomposition and ClonalFrame analysis indicated that recombination had occurred throughout the population of L. plantarum, but it occurred at a low frequency in these eight loci. CONCLUSION We deduced that L. plantarum isolates from the same ecological niches have similar genetic diversity and population structure. The MLST scheme presented in this study provides abundant sequence data for L. plantarum and enabled global comparisons of isolates associated with various environmental origins to be made. This will further advance our understanding of the microbial ecology of this industrially important LAB.
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Affiliation(s)
- Haiyan Xu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.
| | - Wenyi Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.
| | - Jie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.
| | - Yuqin Song
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.
| | - Bilige Menhe
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, China.
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Yu J, Sun Z, Liu W, Xi X, Song Y, Xu H, Lv Q, Bao Q, Menghe B, Sun T. Multilocus sequence typing of Streptococcus thermophilus from naturally fermented dairy foods in China and Mongolia. BMC Microbiol 2015; 15:236. [PMID: 26497818 PMCID: PMC4620635 DOI: 10.1186/s12866-015-0551-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 10/07/2015] [Indexed: 12/04/2022] Open
Abstract
Background Streptococcus thermophilus is a major dairy starter used for manufacturing of dairy products. In the present study, we developed a multilocus sequence typing (MLST) scheme for this important food bacterium. Sequences of 10 housekeeping genes (carB, clpX, dnaA, murC, murE, pepN, pepX, pyrG, recA, and rpoB) were obtained for 239 S. thermophilus strains, which were isolated from home-made fermented dairy foods in 18 different regions of Mongolia and China. Methods All 10 genes of S. thermophilus were sequenced, aligned, and defined sequence types (STs) using the BioNumerics Software. The nucleotide diversity was calculated by START v2.0. The population structure, phylogenetic relationships and the role of recombination were inferred using ClonalFrame v1.2, SplitsTree 4.0 and Structure v2.3. Results The 239 S. thermophilus isolates and 18 reference strains could be assigned into 119 different STs, which could be further separated into 16 clonal complexes (CCs) and 38 singletons. Among the 10 loci, a total of 132 polymorphic sites were detected. The standardized index of association (IAS = 0.0916), split-decomposition and ρ/θ (relative frequency of occurrence of recombination and mutation) and r/m value (relative impact of recombination and mutation in the diversification) confirms that recombination may have occurred, but it occurred at a low frequency in these 10 loci. Phylogenetic trees indicated that there were five lineages in the S. thermophilus isolates used in our study. MSTree and ClonalFrame tree analyses suggest that the evolution of S. thermophilus isolates have little relationship with geographic locality, but revealed no association with the types of fermented dairy product. Phylogenetic analysis of 36 whole genome strains (18 S. thermophilus, 2 S. vestibularis and 16 S. salivarius strains) indicated that our MLST scheme could clearly separate three closely related species within the salivarius group and is suitable for analyzing the population structure of the other two species in the salivarius group. Conclusions Our newly developed MLST scheme improved the understanding on the genetic diversity and population structure of the S. thermophilus, as well as provided useful information for further studies on the genotyping and evolutionary research for S. thermophilus strains with global diversity. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0551-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Xiaoxia Xi
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Yuqin Song
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Haiyan Xu
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Qiang Lv
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Qiuhua Bao
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Bilige Menghe
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Tiansong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
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Ilha EC, Scariot MC, Treml D, Pereira TP, Sant′Anna ES, Prudêncio ES, Arisi ACM. Comparison of real-time PCR assay and plate count for Lactobacillus paracasei enumeration in yoghurt. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1137-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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22
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Zhang W, Liu W, Song Y, Xu H, Menghe B, Zhang H, Sun Z. Multilocus sequence typing of a dairy-associated Leuconostoc mesenteroides population reveals clonal structure with intragenic homologous recombination. J Dairy Sci 2015; 98:2284-93. [DOI: 10.3168/jds.2014-9227] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 12/31/2014] [Indexed: 11/19/2022]
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Dolci P, De Filippis F, La Storia A, Ercolini D, Cocolin L. rRNA-based monitoring of the microbiota involved in Fontina PDO cheese production in relation to different stages of cow lactation. Int J Food Microbiol 2014; 185:127-35. [DOI: 10.1016/j.ijfoodmicro.2014.05.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 03/21/2014] [Accepted: 05/26/2014] [Indexed: 01/27/2023]
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Xu H, Sun Z, Liu W, Yu J, Song Y, Lv Q, Zhang J, Shao Y, Menghe B, Zhang H. Multilocus sequence typing of Lactococcus lactis from naturally fermented milk foods in ethnic minority areas of China. J Dairy Sci 2014; 97:2633-45. [DOI: 10.3168/jds.2013-7738] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 01/17/2014] [Indexed: 11/19/2022]
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Herbel S, Lauzat B, von Nickisch-Rosenegk M, Kuhn M, Murugaiyan J, Wieler L, Guenther S. Species-specific quantification of probiotic lactobacilli in yoghurt by quantitative real-time PCR. J Appl Microbiol 2013; 115:1402-10. [DOI: 10.1111/jam.12341] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 08/19/2013] [Accepted: 09/04/2013] [Indexed: 11/29/2022]
Affiliation(s)
- S.R. Herbel
- Institute of Microbiology and Epizootics; Freie Universität Berlin; Berlin Germany
- Department of Biology, Chemistry, Pharmacy; Freie Universität Berlin; Berlin Germany
| | - B. Lauzat
- Institute of Microbiology and Epizootics; Freie Universität Berlin; Berlin Germany
| | | | - M. Kuhn
- CONGEN Biotechnologie GmbH; Berlin Germany
| | - J. Murugaiyan
- Institute of Animal and Environmental Hygiene; Freie Universität Berlin; Berlin Germany
| | - L.H. Wieler
- Institute of Microbiology and Epizootics; Freie Universität Berlin; Berlin Germany
| | - S. Guenther
- Institute of Microbiology and Epizootics; Freie Universität Berlin; Berlin Germany
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Huang CH, Chang MT, Huang L, Chu WS. Utilization of elongation factor Tu gene (tuf) sequencing and species-specific PCR (SS-PCR) for the molecular identification of Acetobacter species complex. Mol Cell Probes 2013; 28:31-3. [PMID: 23969032 DOI: 10.1016/j.mcp.2013.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/26/2013] [Accepted: 07/30/2013] [Indexed: 10/26/2022]
Abstract
The aim of this study was to use tuf gene as a molecular target for species discrimination in the Acetobacter genus, as well as to develop species-specific PCR method for direct species identification of Acetobacter aceti. The results showed that most Acetobacter species could be clearly distinguished, and the average sequence similarity for the tuf gene (89.5%) among type strains was significantly lower than that of the 16S rRNA gene sequence (98.0%). A pair of species-specific primers were designed and used to specifically identify A. aceti, but none of the other Acetobacter strains. Our data indicate that the phylogenetic relationships of most strains in the Acetobacter genus can be resolved using tuf gene sequencing, and the novel species-specific primer pair could be used to rapidly and accurately identify the species of A. aceti by the PCR based assay.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Road, Hsinchu 30062, Taiwan, ROC
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