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Dikmen H, Goktas H, Demirbas F, Kayacan S, Ispirli H, Arici M, Turker M, Sagdic O, Dertli E. Multilocus sequence typing of L. bulgaricus and S. thermophilus strains from Turkish traditional yoghurts and characterisation of their techno-functional roles. Food Sci Biotechnol 2024; 33:625-635. [PMID: 38274192 PMCID: PMC10805743 DOI: 10.1007/s10068-023-01366-2] [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: 03/03/2023] [Revised: 05/16/2023] [Accepted: 06/06/2023] [Indexed: 01/27/2024] Open
Abstract
In this study, Streptococcus thermophilus and Lactobacillus bulgaricus strains from traditional Turkish yoghurts were isolated, identified by 16S rRNA sequencing and genotypically 14 S. thermophilus and 6 L. bulgaricus strains were obtained as distinct strains by MLST analysis. Lactic acid production levels of the L. bulgaricus strains were higher than S. thermophilus strains. HPLC analysis showed that EPS monosaccharide composition of the strains mainly consisted of glucose and galactose. In general, all strains were found to be susceptible for antibiotics, except some strains were resistance to gentamicin and kanamycin. Apart from two strains of S. thermophilus, all strains displayed strong auto-aggregation level greater than 95% at 24 h incubation. S. thermophilus strains showed higher cell surface hydrophobicity than L. bulgaricus strains. This study demonstrated the isolation, identification, genotypic discrimination and techno-functional features of wild type yoghurt starter cultures which can potentially find place in industrial applications. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-023-01366-2.
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Affiliation(s)
- Hilal Dikmen
- Food Engineering Department, Chemical and Metallurgical Faculty, Yildiz Technical University, Istanbul, Turkey
| | - Hamza Goktas
- Food Technology Programme, Vocational School, Istinye University, Topkapi Campus, Zeytinburnu, Istanbul, Turkey
| | - Fatmanur Demirbas
- Food Engineering Department, Chemical and Metallurgical Faculty, Yildiz Technical University, Istanbul, Turkey
| | - Selma Kayacan
- Food Engineering Department, Chemical and Metallurgical Faculty, Yildiz Technical University, Istanbul, Turkey
| | - Humeyra Ispirli
- Central Research Laboratory, Bayburt University, Bayburt, Turkey
| | - Muhammet Arici
- Food Engineering Department, Chemical and Metallurgical Faculty, Yildiz Technical University, Istanbul, Turkey
| | | | - Osman Sagdic
- Food Engineering Department, Chemical and Metallurgical Faculty, Yildiz Technical University, Istanbul, Turkey
| | - Enes Dertli
- Food Engineering Department, Chemical and Metallurgical Faculty, Yildiz Technical University, Istanbul, Turkey
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2
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Khan IUH, Chen W, Cloutier M, Lapen DR, Craiovan E, Wilkes G. Pathogenicity assessment of Arcobacter butzleri isolated from Canadian agricultural surface water. BMC Microbiol 2024; 24:17. [PMID: 38191309 PMCID: PMC10773081 DOI: 10.1186/s12866-023-03119-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/09/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Water is considered a source for the transmission of Arcobacter species to both humans and animals. This study was conducted to assess the prevalence, distribution, and pathogenicity of A. butzleri strains, which can potentially pose health risks to humans and animals. Cultures were isolated from surface waters of a mixed-use but predominately agricultural watershed in eastern Ontario, Canada. The detection of antimicrobial resistance (AMR) and virulence-associated genes (VAGs), as well as enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) assays were performed on 913 A. butzleri strains isolated from 11 agricultural sampling sites. RESULTS All strains were resistant to one or more antimicrobial agents, with a high rate of resistance to clindamycin (99%) and chloramphenicol (77%), followed by azithromycin (48%) and nalidixic acid (49%). However, isolates showed a significantly (p < 0.05) high rate of susceptibility to tetracycline (1%), gentamycin (2%), ciprofloxacin (4%), and erythromycin (5%). Of the eight VAGs tested, ciaB, mviN, tlyA, and pldA were detected at high frequency (> 85%) compared to irgA (25%), hecB (19%), hecA (15%), and cj1349 (12%) genes. Co-occurrence analysis showed A. butzleri strains resistant to clindamycin, chloramphenicol, nalidixic acid, and azithromycin were positive for ciaB, tlyA, mviN and pldA VAGs. ERIC-PCR fingerprint analysis revealed high genetic similarity among strains isolated from three sites, and the genotypes were significantly associated with AMR and VAGs results, which highlight their potential environmental ubiquity and potential as pathogenic. CONCLUSIONS The study results show that agricultural activities likely contribute to the contamination of A. butzleri in surface water. The findings underscore the importance of farm management practices in controlling the potential spread of A. butzleri and its associated health risks to humans and animals through contaminated water.
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Affiliation(s)
- Izhar U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada.
| | - Wen Chen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Michel Cloutier
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - David R Lapen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Emilia Craiovan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Graham Wilkes
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
- Natural Resources Canada, Ottawa, ON, Canada
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3
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MLST analysis of genetic diversity of Bacillus coagulans strains to evaluate effects on constipation model. FOOD SCIENCE AND HUMAN WELLNESS 2022. [DOI: 10.1016/j.fshw.2022.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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4
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Chen J, Lv H, Zhang Z, Zhang H, Zhang B, Wang X, Liu Y, Zhang M, Pang H, Qin G, Wang L, Tan Z. Multilocus Sequence Typing of Leuconostoc mesenteroides Strains From the Qinghai-Tibet Plateau. Front Microbiol 2021; 12:614286. [PMID: 33584616 PMCID: PMC7874059 DOI: 10.3389/fmicb.2021.614286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/05/2021] [Indexed: 12/21/2022] Open
Abstract
Leuconostoc mesenteroides strains were a type of epiphytic bacterium widely used in fermented foods and products in the biochemical and pharmaceutical industries but data on its presence in foods from Qinghai-Tibet Plateau in China was scarce. In this study, molecular analysis based on multilocus sequence typing (MLST) with eight housekeeping genes (pyrG, groeL, rpoB, recA, uvrC, murC, carB, and pheS) was carried out on 45 L. mesenteroides strains isolated from different plants and dairy products from Qinghai-Tibet Plateau in China. The objective of this study was to perform genetic diversity analysis and explore the relationship between strains and isolate samples or separate regions. A total of 25 sequence types (STs) were identified with a diversity of up to 55.6%, which were grouped into one clonal complexes (CCs), 3 doublets and 17 singletons by eBURST. The results of minimum spanning tree and clustering analysis indicated these L. mesenteroides strains from the Qinghai-Tibet Plateau were relatively weakly related to the isolated region. However, there was a close relationship between the genotypes of L. mesenteroides strains and the type of the isolated sample, which was consistent with the results of API 50CH. The MLST scheme presented in this study provides a shareable and comparable sequence database and enhances our knowledge of the population diversity of L. mesenteroides strains which will be further used for the selection of industrial strains.
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Affiliation(s)
- Jun Chen
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Ion-Beam Bioengineering, School of Physics, Zhengzhou University, Zhengzhou, China
| | - Haoxin Lv
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
| | - Zhixia Zhang
- Henan Key Laboratory of Ion-Beam Bioengineering, School of Physics, Zhengzhou University, Zhengzhou, China
| | - Hua Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.,School of Food and Biological Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Bei Zhang
- Department of Chemical and Environmental Engineering, Jiaozuo University, Jiaozuo, China
| | - Xing Wang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Yuan Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Miao Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Huili Pang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Guangyong Qin
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Lei Wang
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Zhongfang Tan
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
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5
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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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6
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Sharma A, Lee S, Park YS. Molecular typing tools for identifying and characterizing lactic acid bacteria: a review. Food Sci Biotechnol 2020; 29:1301-1318. [PMID: 32995049 PMCID: PMC7492335 DOI: 10.1007/s10068-020-00802-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 02/08/2023] Open
Abstract
Identification and classification of beneficial microbes is of the highest significance in food science and related industries. Conventional phenotypic approaches pose many challenges, and they may misidentify a target, limiting their use. Genotyping tools show comparatively better prospects, and they are widely used for distinguishing microorganisms. The techniques already employed in genotyping of lactic acid bacteria (LAB) are slightly different from one another, and each tool has its own advantages and disadvantages. This review paper compiles the comprehensive details of several fingerprinting tools that have been used for identifying and characterizing LAB at the species, sub-species, and strain levels. Notably, most of these approaches are based on restriction digestion, amplification using polymerase chain reaction, and sequencing. Nowadays, DNA sequencing technologies have made considerable progress in terms of cost, throughput, and methodology. A research journey to develop improved versions of generally applicable and economically viable tools for fingerprinting analysis is ongoing globally.
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Affiliation(s)
- Anshul Sharma
- Department of Food and Nutrition, Gachon University, Seongnam, 13120 Republic of Korea.,Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229 India
| | - Sulhee Lee
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365 Republic of Korea
| | - Young-Seo Park
- Department of Food Science and Biotechnology, Gachon University, Seongnam, 13120 Republic of Korea
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7
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Prete R, Long SL, Joyce SA, Corsetti A. Genotypic and phenotypic characterization of food-associated Lactobacillus plantarum isolates for potential probiotic activities. FEMS Microbiol Lett 2020; 367:5835222. [DOI: 10.1093/femsle/fnaa076] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/07/2020] [Indexed: 11/12/2022] Open
Abstract
ABSTRACT
Lactic acid bacterium, Lactobacillus plantarum, has been applied, for centuries, for food and drink fermentations. Given the benefits associated with fermented products, Lb. plantarum strains have captured considerable industrial and scientific interest, so that they are included as fundamental components of functional foods. Indeed, some strains are marketed as probiotics. In the present study, food- and gut-associated Lb. plantarum isolates were genetically characterized by multilocus sequence typing (MLST) and phenotypically characterized for properties that could influence their probiotic potential. MLST and phylogenetic analysis stratified 22 Lb. plantarum isolates into six lineages. The isolates were further phenotypically characterized by an in vitro assay to assess their potential gut community influence via a limited number of assays including acidification activity, strain displacement activity and their intrinsic range of antibiotic resistance. Given growing recognition of the benefits of fermented foods, and the prevalence of Lb. plantarum in these applications, this study highlights analysis of a subset of preliminary important strain-specific features. These features are of interest to all stakeholders, to inform isolate comparison and selection for current functional food associations, and that can serve as a basis for future strain and food-microbe fermentation product development.
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Affiliation(s)
- Roberta Prete
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via Renato Balzarini 1, 64100 Teramo, Italy
- APC Microbiome Ireland, Biosciences Building, University College Cork, T12YT20 Cork , Ireland
| | - Sarah L Long
- APC Microbiome Ireland, Biosciences Building, University College Cork, T12YT20 Cork , Ireland
- School of Biochemistry and Cell Biology, Biosciences Building, University College Cork, T12YT20 Cork, Ireland
| | - Susan A Joyce
- APC Microbiome Ireland, Biosciences Building, University College Cork, T12YT20 Cork , Ireland
- School of Biochemistry and Cell Biology, Biosciences Building, University College Cork, T12YT20 Cork, Ireland
| | - Aldo Corsetti
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via Renato Balzarini 1, 64100 Teramo, Italy
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8
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Lorentzen MPG, Lucas PM. Distribution of Oenococcus oeni populations in natural habitats. Appl Microbiol Biotechnol 2019; 103:2937-2945. [PMID: 30788540 PMCID: PMC6447504 DOI: 10.1007/s00253-019-09689-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 12/02/2022]
Abstract
Oenococcus oeni is the lactic acid bacteria species most commonly encountered in wine, where it develops after the alcoholic fermentation and achieves the malolactic fermentation that is needed to improve the quality of most wines. O. oeni is abundant in the oenological environment as well as in apple cider and kombucha, whereas it is a minor species in the natural environment. Numerous studies have shown that there is a great diversity of strains in each wine region and in each product or type of wine. Recently, genomic studies have shed new light on the species diversity, population structure, and environmental distribution. They revealed that O. oeni has unique genomic features that have contributed to its fast evolution and adaptation to the enological environment. They have also unveiled the phylogenetic diversity and genomic properties of strains that develop in different regions or different products. This review explores the distribution of O. oeni and the diversity of strains in natural habitats.
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Affiliation(s)
- Marc P. G. Lorentzen
- Unité de recherche Oenologie, EA 4577, USC 1366 INRA, ISVV, Université de Bordeaux, F-33882 Villenave d’Ornon, France
| | - Patrick M. Lucas
- Unité de recherche Oenologie, EA 4577, USC 1366 INRA, ISVV, Université de Bordeaux, F-33882 Villenave d’Ornon, France
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9
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Evidence of the genetic diversity and clonal population structure of Oenococcus oeni strains isolated from different wine-making regions of China. J Microbiol 2018; 56:556-564. [PMID: 30047084 DOI: 10.1007/s12275-018-7568-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 05/23/2018] [Accepted: 05/28/2018] [Indexed: 01/19/2023]
Abstract
Studies of the genetic diversity and population structure of Oenococcus oeni (O. oeni) strains from China are lacking compared to other countries and regions. In this study, amplified fragment length polymorphism (AFLP) and multilocus sequence typing (MLST) methods were used to investigate the genetic diversity and regional evolutionary patterns of 38 O. oeni strains isolated from different wine-making regions in China. The results indicated that AFLP was markedly more efficient than MLST for typing O. oeni strains. AFLP distinguished 37 DNA patterns compared to 7 sequence types identified using MLST, corresponding to discriminatory indices of 0.999 and 0.602, respectively. The AFLP results revealed a high level of genetic diversity among the O. oeni strains from different regions of China, since two subpopulations and an intraspecific homology higher than 60% were observed. Phylogenetic analysis of the O. oeni strains using the MLST method also identified two major phylogroups, which were differentiated into two distinct clonal complexes by minimum spanning tree analysis. Neither intragenic nor intergenic recombination verified the existence of the clonal population structure of the O. oeni strains.
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10
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Romero J, Ilabaca C, Ruiz M, Jara C. Oenococcus oeni in Chilean Red Wines: Technological and Genomic Characterization. Front Microbiol 2018; 9:90. [PMID: 29491847 PMCID: PMC5817079 DOI: 10.3389/fmicb.2018.00090] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 01/15/2018] [Indexed: 12/26/2022] Open
Abstract
The presence and load of species of LAB at the end of the malolactic fermentation (MLF) were investigated in 16 wineries from the different Chilean valleys (Limarí, Casablanca, Maipo, Rapel, and Maule Valleys) during 2012 and 2013, using PCR-RFLP and qPCR. Oenococcus oeni was observed in 80% of the samples collected. Dominance of O. oeni was reflected in the bacterial load (O. oeni/total bacteria) measured by qPCR, corresponding to >85% in most of the samples. A total of 178 LAB isolates were identified after sequencing molecular markers, 95 of them corresponded to O. oeni. Further genetic analyses were performed using MLST (7 genes) including 10 commercial strains; the results indicated that commercial strains were grouped together, while autochthonous strains distributed among different genetic clusters. To pre-select some autochthonous O. oeni, these isolates were also characterized based on technological tests such as ethanol tolerance (12 and 15%), SO2 resistance (0 and 80 mg l−1), and pH (3.1 and 3.6) and malic acid transformation (1.5 and 4 g l−1). For comparison purposes, commercial strain VP41 was also tested. Based on their technological performance, only 3 isolates were selected for further examination (genome analysis) and they were able to reduce malic acid concentration, to grow at low pH 3.1, 15% ethanol and 80 mg l−1 SO2. The genome analyses of three selected isolates were examined and compared to PSU-1 and VP41 strains to study their potential contribution to the organoleptic properties of the final product. The presence and homology of genes potentially related to aromatic profile were compared among those strains. The results indicated high conservation of malolactic enzyme (>99%) and the absence of some genes related to odor such as phenolic acid decarboxylase, in autochthonous strains. Genomic analysis also revealed that these strains shared 470 genes with VP41 and PSU-1 and that autochthonous strains harbor an interesting number of unique genes (>21). Altogether these results reveal the presence of local strains distinguishable from commercial strains at the genetic/genomic level and also having genomic traits that enforce their potential use as starter cultures.
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Affiliation(s)
- Jaime Romero
- Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Carolina Ilabaca
- Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Departamento de Agroindustria y Enología, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | | | - Carla Jara
- Departamento de Agroindustria y Enología, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
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11
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Bottari B, Felis GE, Salvetti E, Castioni A, Campedelli I, Torriani S, Bernini V, Gatti M. Effective identification of Lactobacillus casei group species: genome-based selection of the gene mutL as the target of a novel multiplex PCR assay. MICROBIOLOGY-SGM 2017; 163:950-960. [PMID: 28721852 DOI: 10.1099/mic.0.000497] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lactobacillus casei,Lactobacillus paracasei and Lactobacillusrhamnosus form a closely related taxonomic group (the L. casei group) within the facultatively heterofermentative lactobacilli. Strains of these species have been used for a long time as probiotics in a wide range of products, and they represent the dominant species of nonstarter lactic acid bacteria in ripened cheeses, where they contribute to flavour development. The close genetic relationship among those species, as well as the similarity of biochemical properties of the strains, hinders the development of an adequate selective method to identify these bacteria. Despite this being a hot topic, as demonstrated by the large amount of literature about it, the results of different proposed identification methods are often ambiguous and unsatisfactory. The aim of this study was to develop a more robust species-specific identification assay for differentiating the species of the L. casei group. A taxonomy-driven comparative genomic analysis was carried out to select the potential target genes whose similarity could better reflect genome-wide diversity. The gene mutL appeared to be the most promising one and, therefore, a novel species-specific multiplex PCR assay was developed to rapidly and effectively distinguish L. casei, L. paracasei and L. rhamnosus strains. The analysis of a collection of 76 wild dairy isolates, previously identified as members of the L. casei group combining the results of multiple approaches, revealed that the novel designed primers, especially in combination with already existing ones, were able to improve the discrimination power at the species level and reveal previously undiscovered intraspecific biodiversity.
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Affiliation(s)
- Benedetta Bottari
- Department of Food and Drug Science, University of Parma, Viale delle Scienze 49/A, 43124 Parma, Italy.,Multidisciplinary Interdepartmental Dairy Center - MILC, University of Parma, Parma, Italy
| | - Giovanna E Felis
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Elisa Salvetti
- School of Microbiology and APC Microbiome Institute, University College Cork, Western Road, Cork, Ireland
| | - Anna Castioni
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.,Present address: Panificio Zorzi S.r.l., Loc. Brà 1, 37020 Brentino Belluno, Verona, Italy
| | - Ilenia Campedelli
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Sandra Torriani
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Valentina Bernini
- Department of Food and Drug Science, University of Parma, Viale delle Scienze 49/A, 43124 Parma, Italy
| | - Monica Gatti
- Department of Food and Drug Science, University of Parma, Viale delle Scienze 49/A, 43124 Parma, Italy.,Multidisciplinary Interdepartmental Dairy Center - MILC, University of Parma, Parma, Italy
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12
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Liu Z, Ge X, Yang Z, Zhang C, Zhao G, Chen E, Liu J, Zhang X, Li F. Genome-wide identification and characterization of SnRK2 gene family in cotton (Gossypium hirsutum L.). BMC Genet 2017; 18:54. [PMID: 28606097 PMCID: PMC5469022 DOI: 10.1186/s12863-017-0517-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/17/2017] [Indexed: 01/02/2023] Open
Abstract
Background Sucrose non-fermenting-1-related protein kinase 2 (SnRK2) is a plant-specific serine/threonine kinase family involved in the abscisic acid (ABA) signaling pathway and responds to osmotic stress. A genome-wide analysis of this protein family has been conducted previously in some plant species, but little is known about SnRK2 genes in upland cotton (Gossypium hirsutum L.). The recent release of the G. hirsutum genome sequence provides an opportunity to identify and characterize the SnRK2 kinase family in upland cotton. Results We identified 20 putative SnRK2 sequences in the G. hirsutum genome, designated as GhSnRK2.1 to GhSnRK2.20. All of the sequences encoded hydrophilic proteins. Phylogenetic analysis showed that the GhSnRK2 genes were classifiable into three groups. The chromosomal location and phylogenetic analysis of the cotton SnRK2 genes indicated that segmental duplication likely contributed to the diversification and evolution of the genes. The gene structure and motif composition of the cotton SnRK2 genes were analyzed. Nine exons were conserved in length among all members of the GhSnRK2 family. Although the C-terminus was divergent, seven conserved motifs were present. All GhSnRK2s genes showed expression patterns under abiotic stress based on transcriptome data. The expression profiles of five selected genes were verified in various tissues by quantitative real-time RT-PCR (qRT-PCR). Transcript levels of some family members were up-regulated in response to drought, salinity or ABA treatments, consistent with potential roles in response to abiotic stress. Conclusions This study is the first comprehensive analysis of SnRK2 genes in upland cotton. Our results provide the fundamental information for the functional dissection of GhSnRK2s and vital availability for the improvement of plant stress tolerance using GhSnRK2s. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0517-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhao Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Chaojun Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ge Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Eryong Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xueyan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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Sulaiman IM, Jacobs E, Simpson S, Kerdahi K. Multilocus Genetic Characterization of Lactobacillus fermentum Isolated from Ready-to-Eat Canned Food. J Food Prot 2017; 80:963-968. [PMID: 28467184 DOI: 10.4315/0362-028x.jfp-16-546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The primary mission of the U.S. Food and Drug Administration is to enforce the Food, Drug, and Cosmetic Act and regulate food, drug, and cosmetic products. Thus, this agency monitors the presence of pathogenic microorganisms in these products, including canned foods, as one of the regulatory action criteria and also ensures that these products are safe for human consumption. This study was carried out to investigate the effectiveness of pathogen control and integrity of ready-to-eat canned food containing Black Bean Corn Poblano Salsa. A total of nine unopened and recalled canned glass jars from the same lot were examined initially by conventional microbiologic protocols that involved a two-step enrichment, followed by streaking on selective agar plates, for the presence of gram-positive and gram-negative bacteria. Of the eight subsamples examined for each sample, all subsamples of one of the containers were found positive for the presence of slow-growing rod-shaped, gram-positive, facultative anaerobic bacteria. The recovered isolates were subsequently sequenced at rRNA and gyrB loci. Afterward, multilocus sequence typing (MLST) was performed characterizing 11 additional known MLST loci (clpX, dnaA, dnaK, groEL, murC, murE, pepX, pyrG, recA, rpoB, and uvrC). Analyses of the nucleotide sequences of rRNA, gyrB, and 11 MLST loci confirmed these gram-positive bacteria recovered from canned food to be Lactobacillus fermentum . Thus, the DNA sequencing of housekeeping MLST genes can provide species identification of L. fermentum and can be used in the canned food monitoring program of public health importance.
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Affiliation(s)
- Irshad M Sulaiman
- Southeast Regional Laboratory, U.S. Food and Drug Administration, 60 Eighth Street N.E., Atlanta, Georgia 30309, USA
| | - Emily Jacobs
- Southeast Regional Laboratory, U.S. Food and Drug Administration, 60 Eighth Street N.E., Atlanta, Georgia 30309, USA
| | - Steven Simpson
- Southeast Regional Laboratory, U.S. Food and Drug Administration, 60 Eighth Street N.E., Atlanta, Georgia 30309, USA
| | - Khalil Kerdahi
- Southeast Regional Laboratory, U.S. Food and Drug Administration, 60 Eighth Street N.E., Atlanta, Georgia 30309, USA
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Cruz-Pio LE, Poveda M, Alberto MR, Ferrer S, Pardo I. Exploring the biodiversity of two groups of Oenococcus oeni isolated from grape musts and wines: Are they equally diverse? Syst Appl Microbiol 2017; 40:1-10. [DOI: 10.1016/j.syapm.2016.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 11/04/2016] [Accepted: 11/05/2016] [Indexed: 11/27/2022]
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15
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Delorme C, Legravet N, Jamet E, Hoarau C, Alexandre B, El-Sharoud WM, Darwish MS, Renault P. Study of Streptococcus thermophilus population on a world-wide and historical collection by a new MLST scheme. Int J Food Microbiol 2016; 242:70-81. [PMID: 27894009 DOI: 10.1016/j.ijfoodmicro.2016.11.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 01/27/2023]
Abstract
We analyzed 178 Streptococcus thermophilus strains isolated from diverse products, from around the world, over a 60-year period with a new multilocus sequence typing (MLST) scheme. This collection included isolates from two traditional cheese-making sites with different starter-use practices, in sampling campaigns carried out over a three years period. The nucleotide diversity of the S. thermophilus population was limited, but 116 sequence types (ST) were identified. Phylogenetic analysis of the concatenated sequences of the six housekeeping genes revealed the existence of groups confirmed by eBURST analysis. Deeper analyses performed on 25 strains by CRISPR and whole-genome analysis showed that phylogenies obtained by MLST and whole-genome analysis were in agreement but differed from that inferred by CRISPR analysis. Strains isolated from traditional products could cluster in specific groups indicating their origin, but also be mixed in groups containing industrial starter strains. In the traditional cheese-making sites, we found that S. thermophilus persisted on dairy equipment, but that occasionally added starter strains may become dominant. It underlined the impact of starter use that may reshape S. thermophilus populations including in traditional products. This new MLST scheme thus provides a framework for analyses of S. thermophilus populations and the management of its biodiversity.
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Affiliation(s)
- Christine Delorme
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Nicolas Legravet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Emmanuel Jamet
- Actilait, 419, route des champs laitiers, F-74 800 La Roche sur Foron, France
| | - Caroline Hoarau
- Actilait, 419, route des champs laitiers, F-74 800 La Roche sur Foron, France
| | - Bolotin Alexandre
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Walid M El-Sharoud
- Food Safety and Microbial Physiology Laboratory, Dairy Department, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
| | - Mohamed S Darwish
- Food Safety and Microbial Physiology Laboratory, Dairy Department, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
| | - Pierre Renault
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Zhao G, Song Y, Wang C, Butt HI, Wang Q, Zhang C, Yang Z, Liu Z, Chen E, Zhang X, Li F. Genome-wide identification and functional analysis of the TIFY gene family in response to drought in cotton. Mol Genet Genomics 2016; 291:2173-2187. [PMID: 27640194 PMCID: PMC5080297 DOI: 10.1007/s00438-016-1248-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 09/02/2016] [Indexed: 11/26/2022]
Abstract
Jasmonates control many aspects of plant biological processes. They are important for regulating plant responses to various biotic and abiotic stresses, including drought, which is one of the most serious threats to sustainable agricultural production. However, little is known regarding how jasmonate ZIM-domain (JAZ) proteins mediate jasmonic acid signals to improve stress tolerance in cotton. This represents the first comprehensive comparative study of TIFY transcription factors in both diploid A, D and tetraploid AD cotton species. In this study, we identified 21 TIFY family members in the genome of Gossypium arboretum, 28 members from Gossypium raimondii and 50 TIFY genes in Gossypium hirsutum. The phylogenetic analyses indicated the TIFY gene family could be divided into the following four subfamilies: TIFY, PPD, ZML, and JAZ subfamilies. The cotton TIFY genes have expanded through tandem duplications and segmental duplications compared with other plant species. Gene expression profile revealed temporal and tissue specificities for TIFY genes under simulated drought conditions in Gossypium arboretum. The JAZ subfamily members were the most highly expressed genes, suggesting that they have a vital role in responses to drought stress. Over-expression of GaJAZ5 gene decreased water loss, stomatal openings, and the accumulation of H2O2 in Arabidopsis thaliana. Additionally, the results of drought tolerance assays suggested that this subfamily might be involved in increasing drought tolerance. Our study provides new data regarding the genome-wide analysis of TIFY gene families and their important roles in drought tolerance in cotton species. These data may form the basis of future studies regarding the relationship between drought and jasmonic acid.
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Affiliation(s)
- Ge Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yun Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Caixiang Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Hamama Islam Butt
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Qianhua Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Chaojun Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhao Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Eryong Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xueyan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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Vigentini I, Praz A, Domeneghetti D, Zenato S, Picozzi C, Barmaz A, Foschino R. Characterization of malolactic bacteria isolated from Aosta Valley wines and evidence of psychrotrophy in some strains. J Appl Microbiol 2016; 120:934-45. [PMID: 26820246 DOI: 10.1111/jam.13080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 11/23/2015] [Accepted: 01/04/2016] [Indexed: 11/27/2022]
Affiliation(s)
- I. Vigentini
- Department of Food, Environmental and Nutrition Sciences; Università degli studi di Milano; Milan Italy
| | - A. Praz
- Department of Food, Environmental and Nutrition Sciences; Università degli studi di Milano; Milan Italy
| | | | - S. Zenato
- Institut Agricole Régional of Aosta; Aosta Italy
| | - C. Picozzi
- Department of Food, Environmental and Nutrition Sciences; Università degli studi di Milano; Milan Italy
| | - A. Barmaz
- Institut Agricole Régional of Aosta; Aosta Italy
| | - R. Foschino
- Department of Food, Environmental and Nutrition Sciences; Università degli studi di Milano; Milan Italy
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Ashrafi R, Pulkkinen K, Sundberg LR, Pekkala N, Ketola T. A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates. BMC Microbiol 2015; 15:243. [PMID: 26518592 PMCID: PMC4628280 DOI: 10.1186/s12866-015-0576-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 10/16/2015] [Indexed: 12/02/2022] Open
Abstract
Background Columnaris disease caused by Flavobacterium columnare is a serious problem in aquaculture, annually causing large economic losses around the world. Despite considerable research, the molecular epidemiology of F. columnare remains poorly understood. Methods We investigated the population structure and spatiotemporal changes in the genetic diversity of F. columnare population in Finland by using a multilocus sequence typing (MLST) and analysis (MLSA) based on DNA sequence variation within six housekeeping genes. A total of 83 strains of F. columnare were collected from eight different areas located across the country between 2003 and 2012. Results Partial sequencing of six housekeeping genes (trpB, tuf, atpA, rpoD, gyrB and dnaK) revealed eight sequence types and a moderate level of genetic diversity (H = 0.460). Phylogenetic analysis of the concatenated protein-encoding gene sequence data (ca. 3,509 nucleotides) formed two lineages, which could be further divided into five clusters. All analysed F. columnare strains appeared to have a genetic origin distinct from that of another important fish pathogen form the genus Flavobacterium, F. psychrophilum. Although the value of the index of association between alleles, 0.292 (P < 0.001), supports some degree of clonality for this species in Finland, recombination has introduced molecular diversity to the population almost three times more than mutation. Conclusion The results suggest that Finnish F. columnare strains have an epidemic population structure followed by clonal expansion of successful genotypes. Our study with reproducible methodology and comparable results establishes a robust framework for the discrimination and phylogenetic analysis of F. columnare isolates, which will help to improve our understanding about geographic distribution and epidemiology of columnaris disease. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0576-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roghaieh Ashrafi
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyvaskyla, P.O. Box 35, Jyväskylän yliopisto, FI-40014, Finland.
| | - Katja Pulkkinen
- Department of Biological and Environmental Science, University of Jyvaskyla, P.O. Box 35, Jyväskylän yliopisto, FI-40014, Finland.
| | - Lotta-Riina Sundberg
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyvaskyla, P.O. Box 35, Jyväskylän yliopisto, FI-40014, Finland.
| | - Nina Pekkala
- Department of Biological and Environmental Science, University of Jyvaskyla, P.O. Box 35, Jyväskylän yliopisto, FI-40014, Finland.
| | - Tarmo Ketola
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyvaskyla, P.O. Box 35, Jyväskylän yliopisto, FI-40014, Finland.
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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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Genomic diversity of Oenococcus oeni populations from Castilla La Mancha and La Rioja Tempranillo red wines. Food Microbiol 2015; 49:82-94. [DOI: 10.1016/j.fm.2015.02.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/26/2015] [Accepted: 02/02/2015] [Indexed: 11/20/2022]
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Dan T, Liu W, Song Y, Xu H, Menghe B, Zhang H, Sun Z. The evolution and population structure of Lactobacillus fermentum from different naturally fermented products as determined by multilocus sequence typing (MLST). BMC Microbiol 2015; 15:107. [PMID: 25990318 PMCID: PMC4437502 DOI: 10.1186/s12866-015-0447-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/14/2015] [Indexed: 11/11/2022] Open
Abstract
Background Lactobacillus fermentum is economically important in the production and preservation of fermented foods. A repeatable and discriminative typing method was devised to characterize L. fermentum at the molecular level. The multilocus sequence typing (MLST) scheme developed was based on analysis of the internal sequence of 11 housekeeping gene fragments (clpX, dnaA, dnaK, groEL, murC, murE, pepX, pyrG, recA, rpoB, and uvrC). Results MLST analysis of 203 isolates of L. fermentum from Mongolia and seven provinces/ autonomous regions in China identified 57 sequence types (ST), 27 of which were represented by only a single isolate, indicating high genetic diversity. Phylogenetic analyses based on the sequence of the 11 housekeeping gene fragments indicated that the L. fermentum isolates analyzed belonged to two major groups. A standardized index of association (IAS) indicated a weak clonal population structure in L. fermentum. Split decomposition analysis indicated that recombination played an important role in generating the genetic diversity observed in L. fermentum. The results from the minimum spanning tree strongly suggested that evolution of L. fermentum STs was not correlated with geography or food-type. Conclusions The MLST scheme developed will be valuable for further studies on the evolution and population structure of L. fermentum isolates used in food products. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0447-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tong Dan
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Yuqin Song
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Haiyan Xu
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Bilige Menghe
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
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Garofalo C, El Khoury M, Lucas P, Bely M, Russo P, Spano G, Capozzi V. Autochthonous starter cultures and indigenous grape variety for regional wine production. J Appl Microbiol 2015; 118:1395-408. [DOI: 10.1111/jam.12789] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/24/2015] [Accepted: 03/02/2015] [Indexed: 11/30/2022]
Affiliation(s)
- C. Garofalo
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente; Università di Foggia; Foggia Italy
| | - M. El Khoury
- University of Bordeaux; ISVV; Villenave d'Ornon France
| | - P. Lucas
- University of Bordeaux; ISVV; Villenave d'Ornon France
| | - M. Bely
- University of Bordeaux; ISVV; Villenave d'Ornon France
| | - P. Russo
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente; Università di Foggia; Foggia Italy
| | - G. Spano
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente; Università di Foggia; Foggia Italy
| | - V. Capozzi
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente; Università di Foggia; Foggia Italy
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Petri A, Rabenstein A, Kuever J, König H. Application of MALDI-TOF-MS and nested SAPD-PCR for discrimination ofOenococcus oeniisolates at the strain level. ACTA ACUST UNITED AC 2015. [DOI: 10.1080/09571264.2015.1009015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Wang T, Li H, Wang H, Su J. Multilocus sequence typing and pulsed-field gel electrophoresis analysis of Oenococcus oeni from different wine-producing regions of China. Int J Food Microbiol 2015; 199:47-53. [PMID: 25625911 DOI: 10.1016/j.ijfoodmicro.2015.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 12/18/2014] [Accepted: 01/08/2015] [Indexed: 11/16/2022]
Abstract
The present study established a typing method with NotI-based pulsed-field gel electrophoresis (PFGE) and stress response gene schemed multilocus sequence typing (MLST) for 55 Oenococcus oeni strains isolated from six individual regions in China and two model strains PSU-1 (CP000411) and ATCC BAA-1163 (AAUV00000000). Seven stress response genes, cfa, clpL, clpP, ctsR, mleA, mleP and omrA, were selected for MLST testing, and positive selective pressure was detected for these genes. Furthermore, both methods separated the strains into two clusters. The PFGE clusters are correlated with the region, whereas the sequence types (STs) formed by the MLST confirm the two clusters identified by PFGE. In addition, the population structure was a mixture of evolutionary pathways, and the strains exhibited both clonal and panmictic characteristics.
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Affiliation(s)
- Tao Wang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hua Li
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Hua Wang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Su
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
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Fahimi N, Brandam C, Taillandier P. A mathematical model of the link between growth and L-malic acid consumption for five strains of Oenococcus oeni. World J Microbiol Biotechnol 2014; 30:3163-72. [PMID: 25248866 DOI: 10.1007/s11274-014-1743-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 09/15/2014] [Indexed: 11/24/2022]
Abstract
In winemaking, after the alcoholic fermentation of red wines and some white wines, L-malic acid must be converted into L-lactic acid to reduce the acidity. This malolactic fermentation (MLF) is usually carried out by the lactic acid bacteria Oenococcus oeni. Depending on the level of process control, selected O. oeni is inoculated or the natural microbiota of the cellar is used. This study considers the link between growth and MLF for five strains of O. oeni species. The kinetics of growth and L-malic acid consumption were followed in modified MRS medium (20 °C, pH 3.5, and 10 % ethanol) in anaerobic conditions. A large variability was found among the strains for both their growth and their consumption of L-malic acid. There was no direct link between biomass productivities and consumption of L-malic acid among strains but there was a link of proportionality between the specific growth of a strain and its specific consumption of L-malic acid. Experiments with and without malic acid clearly demonstrated that malic acid consumption improved the growth of strains. This link was quantified by a mathematical model comparing the intrinsic malic acid consumption capacity of the strains.
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Affiliation(s)
- N Fahimi
- Laboratoire de Génie Chimique, Université de Toulouse, INPT, UPS, 4, Allée Emile Monso, BP 83234, 31432, Toulouse Cedex 4, France,
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Cappello MS, De Domenico S, Logrieco A, Zapparoli G. Bio-molecular characterisation of indigenous Oenococcus oeni strains from Negroamaro wine. Food Microbiol 2014; 42:142-8. [PMID: 24929730 DOI: 10.1016/j.fm.2014.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 01/03/2014] [Accepted: 02/11/2014] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | - Giacomo Zapparoli
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
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Implications of new research and technologies for malolactic fermentation in wine. Appl Microbiol Biotechnol 2014; 98:8111-32. [PMID: 25142694 DOI: 10.1007/s00253-014-5976-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/18/2014] [Accepted: 07/21/2014] [Indexed: 01/11/2023]
Abstract
The initial conversion of grape must to wine is an alcoholic fermentation (AF) largely carried out by one or more strains of yeast, typically Saccharomyces cerevisiae. After the AF, a secondary or malolactic fermentation (MLF) which is carried out by lactic acid bacteria (LAB) is often undertaken. The MLF involves the bioconversion of malic acid to lactic acid and carbon dioxide. The ability to metabolise L-malic acid is strain specific, and both individual Oenococcus oeni strains and other LAB strains vary in their ability to efficiently carry out MLF. Aside from impacts on acidity, LAB can also metabolise other precursors present in wine during fermentation and, therefore, alter the chemical composition of the wine resulting in an increased complexity of wine aroma and flavour. Recent research has focused on three main areas: enzymatic changes during MLF, safety of the final product and mechanisms of stress resistance. This review summarises the latest research and technological advances in the rapidly evolving study of MLF and investigates the directions that future research may take.
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Dan T, Liu W, Sun Z, Lv Q, Xu H, Song Y, Zhang H. A novel multi-locus sequence typing (MLST) protocol for Leuconostoc lactis isolates from traditional dairy products in China and Mongolia. BMC Microbiol 2014; 14:150. [PMID: 24912963 PMCID: PMC4063691 DOI: 10.1186/1471-2180-14-150] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 06/04/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Economically, Leuconostoc lactis is one of the most important species in the genus Leuconostoc. It plays an important role in the food industry including the production of dextrans and bacteriocins. Currently, traditional molecular typing approaches for characterisation of this species at the isolate level are either unavailable or are not sufficiently reliable for practical use. Multilocus sequence typing (MLST) is a robust and reliable method for characterising bacterial and fungal species at the molecular level. In this study, a novel MLST protocol was developed for 50 L. lactis isolates from Mongolia and China. RESULTS Sequences from eight targeted genes (groEL, carB, recA, pheS, murC, pyrG, rpoB and uvrC) were obtained. Sequence analysis indicated 20 different sequence types (STs), with 13 of them being represented by a single isolate. Phylogenetic analysis based on the sequences of eight MLST loci indicated that the isolates belonged to two major groups, A (34 isolates) and B (16 isolates). Linkage disequilibrium analyses indicated that recombination occurred at a low frequency in L. lactis, indicating a clonal population structure. Split-decomposition analysis indicated that intraspecies recombination played a role in generating genotypic diversity amongst isolates. CONCLUSIONS Our results indicated that MLST is a valuable tool for typing L. lactis isolates that can be used for further monitoring of evolutionary changes and population genetics.
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Affiliation(s)
| | | | | | | | | | | | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P, R, China, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, P, R, China.
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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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Wine. Food Microbiol 2014. [DOI: 10.1128/9781555818463.ch37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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González-Arenzana L, Santamaría P, López R, López-Alfaro I. Oenococcus oeni strain typification by combination of Multilocus Sequence Typing and Pulsed Field Gel Electrophoresis analysis. Food Microbiol 2014; 38:295-302. [DOI: 10.1016/j.fm.2013.07.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 07/26/2013] [Accepted: 07/30/2013] [Indexed: 10/26/2022]
Affiliation(s)
- Lucía González-Arenzana
- ICVV, Instituto de Ciencias de la Vid y del Vino (Gobierno de La Rioja, Universidad de La Rioja and CSIC), C/Madre de Dios 51, 26006 Logroño, La Rioja, Spain
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Cafaro C, Bonomo MG, Rossano R, Larocca M, Salzano G. Efficient recovery of whole cell proteins in Oenococcus oeni—a comparison of different extraction protocols for high-throughput malolactic starter applications. Folia Microbiol (Praha) 2014; 59:399-408. [DOI: 10.1007/s12223-014-0312-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 02/20/2014] [Indexed: 10/25/2022]
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Jin G, Wang H, Zhang C, Li C, Du L, Grbin PR, Li H. Characterization and amino acid metabolism performances of indigenous Oenococcus oeni isolated from Chinese wines. Eur Food Res Technol 2013. [DOI: 10.1007/s00217-013-2112-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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34
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Claisse O, Lonvaud-Funel A. Multiplex variable number of tandem repeats for Oenococcus oeni and applications. Food Microbiol 2013; 38:80-6. [PMID: 24290630 DOI: 10.1016/j.fm.2013.08.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 07/30/2013] [Accepted: 08/19/2013] [Indexed: 10/26/2022]
Abstract
Oenococcus oeni is responsible for the malolactic fermentation of wine. Genomic diversity has already been established in this species. In addition, winemakers usually report varying starter-culture efficiency. It is essential to monitor indigenous and selected strains in order to understand strain survival and development during the winemaking process. A previous article described a variable number of tandem repeats (VNTR) scheme, based on five polymorphic loci of the genome. VNTR typing of O. oeni was highly discriminating, faster, and more reliable than the PFGE or MLST methods. The objective of this study was to set up a faster protocol by multiplexing, taking advantage of the high performance of multicolor capillary electrophoresis. The primers were labeled with multiple fluorescent dyes. PCR conditions were adapted by multiplexing amplifications in two separate PCR mixtures for the five loci, both at the same annealing temperature. The resulting assay proved to be robust, accurate, fast and easy to perform. Thanks to this new protocol, all O. oeni strains used in the study were typed using the five tandem repeats (TR). As expected, the primers for the five TR loci were specific to O. oeni. The method was improved to analyze isolated and mixed colonies, as well as bacteria harvested from wine using fast technology for analysis of nucleic acids (FTA(®)) technology. Finally, predictive models were constructed, to predict phylogenetic relationships and associate bacterial strain resistance to freeze-drying with fragment length analysis (FLA) profiles and genotypic and phenotypic characters.
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Affiliation(s)
- Olivier Claisse
- Université Bordeaux, ISVV, EA 4577, UR Oenologie, F-33140 Villenave d'Ornon, France; INRA, ISVV, USC 1366, UR Œnologie, F-33140 Villenave d'Ornon, France.
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Rhizobium pongamiae sp. nov. from root nodules of Pongamia pinnata. BIOMED RESEARCH INTERNATIONAL 2013; 2013:165198. [PMID: 24078904 PMCID: PMC3783817 DOI: 10.1155/2013/165198] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 06/06/2013] [Indexed: 11/17/2022]
Abstract
Pongamia pinnata has an added advantage of N2-fixing ability and tolerance to stress conditions as compared with other biodiesel crops. It harbours “rhizobia” as an endophytic bacterial community on its root nodules. A gram-negative, nonmotile, fast-growing, rod-shaped, bacterial strain VKLR-01T was isolated from root nodules of Pongamia that grew optimal at 28°C, pH 7.0 in presence of 2% NaCl. Isolate VKLR-01 exhibits higher tolerance to the prevailing adverse conditions, for example, salt stress, elevated temperatures and alkalinity. Strain VKLR-01T has the major cellular fatty acid as C18:1
ω7c (65.92%). Strain VKLR-01T was found to be a nitrogen fixer using the acetylene reduction assay and PCR detection of a nifH gene. On the basis of phenotypic, phylogenetic distinctiveness and molecular data (16S rRNA, recA, and atpD gene sequences, G + C content, DNA-DNA hybridization etc.), strain VKLR-01T = (MTCC 10513T = MSCL 1015T) is considered to represent a novel species of the genus Rhizobium for which the name Rhizobium pongamiae sp. nov. is proposed. Rhizobium pongamiae may possess specific traits that can be transferred to other rhizobia through biotechnological tools and can be directly used as inoculants for reclamation of wasteland; hence, they are very important from both economic and environmental prospects.
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36
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Potential and limitations of MALDI-TOF MS for discrimination within the species Leuconostoc mesenteroides and Leuconostoc pseudomesenteroides. J Verbrauch Lebensm 2013. [DOI: 10.1007/s00003-013-0826-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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37
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Turchi B, Van Tassell M, Lee A, Nuvoloni R, Cerri D, Miller M. Short communication: Phenotypic and genetic diversity of wild Lactococcus lactis isolated from traditional Pecorino cheeses of Tuscany. J Dairy Sci 2013; 96:3558-63. [DOI: 10.3168/jds.2012-6518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 02/13/2013] [Indexed: 11/19/2022]
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38
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Genetic diversity of dairy Geotrichum candidum strains revealed by multilocus sequence typing. Appl Microbiol Biotechnol 2013; 97:5907-20. [PMID: 23467823 DOI: 10.1007/s00253-013-4776-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 12/07/2012] [Accepted: 12/12/2012] [Indexed: 01/20/2023]
Abstract
The introduction of multilocus sequence typing (MLST) for strain characterization provided the first sequence-based approach for genotyping many fungi, leading to reproducible, reliable, and exchangeable data. A MLST scheme based on the analysis of six housekeeping genes was developed for genotyping Geotrichum candidum. The scheme was first developed using 18 isolates for which the complete sequences of the alanyl-tRNA synthetase (ALA1), pyruvate kinase (CDC19), acetyl-coA acetyltransferase (ERG10), glutaminyl-tRNA synthase (GLN4), phosphoglucoisomerase (PGI1), and phosphoglucomutase (PGM2) housekeeping genes were determined. Multiple sequence alignments of these genes were used to define a set of loci showing, as closely as possible, the same phylogenetic resolution level as complete gene sequences. This scheme was subsequently validated with 22 additional isolates from dairy and non-dairy sources. Overall, 58 polymorphic sites were indexed among 3,009 nucleotides analyzed. Depending on the loci, four to eight alleles were detected, generating 17 different sequence types, of which ten were represented by a single strain. MLST analysis suggested a predominantly clonal population for the 40 G. candidum isolates. Phylogenetic analysis of the concatenated sequences revealed a distantly related group of four isolates. Interestingly, this group diverged with respect to internal transcribed spacers 1 (ITS1), 5.8S, and ITS2 analysis. The reproducibility of the MLST approach was compared to random amplification of microsatellites by PCR (RAM-PCR), a gel profiling method previously proposed for G. candidum strain typing. Our results found MLST differentiation to be more efficient than RAM-PCR, and MLST also offered a non-ambiguous, unique language, permitting data exchange and evolutionary inference.
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39
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Martino ME, Maifreni M, Marino M, Bartolomeoli I, Carraro L, Fasolato L, Cardazzo B. Genotypic and phenotypic diversity of Pediococcus pentosaceus strains isolated from food matrices and characterisation of the penocin operon. Antonie van Leeuwenhoek 2013; 103:1149-63. [DOI: 10.1007/s10482-013-9897-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 02/20/2013] [Indexed: 11/30/2022]
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40
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Claisse O, Lonvaud-Funel A. Development of a multilocus variable number of tandem repeat typing method for Oenococcus oeni. Food Microbiol 2012; 30:340-7. [DOI: 10.1016/j.fm.2012.01.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 01/03/2012] [Accepted: 01/03/2012] [Indexed: 11/24/2022]
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41
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Suzzi G. From wild strain to domesticated strain: the philosophy of microbial diversity in foods. Front Microbiol 2011; 2:169. [PMID: 21887153 PMCID: PMC3157009 DOI: 10.3389/fmicb.2011.00169] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 07/26/2011] [Indexed: 11/16/2022] Open
Affiliation(s)
- Giovanna Suzzi
- Food Science Department, University of Teramo Teramo, Italy
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42
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Detection and identification of microorganisms in wine: a review of molecular techniques. J Ind Microbiol Biotechnol 2011; 38:1619-34. [DOI: 10.1007/s10295-011-1020-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 07/20/2011] [Indexed: 10/17/2022]
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43
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Quantitative expression analysis of mleP gene and two genes involved in the ABC transport system in Oenococcus oeni during rehydration. Appl Microbiol Biotechnol 2011; 91:1601-9. [DOI: 10.1007/s00253-011-3498-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 07/08/2011] [Accepted: 07/18/2011] [Indexed: 11/27/2022]
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Abstract
Strains of Lactobacillus salivarius are increasingly employed as probiotic agents for humans or animals. Despite the diversity of environmental sources from which they have been isolated, the genomic diversity of L. salivarius has been poorly characterized, and the implications of this diversity for strain selection have not been examined. To tackle this, we applied comparative genomic hybridization (CGH) and multilocus sequence typing (MLST) to 33 strains derived from humans, animals, or food. The CGH, based on total genome content, including small plasmids, identified 18 major regions of genomic variation, or hot spots for variation. Three major divisions were thus identified, with only a subset of the human isolates constituting an ecologically discernible group. Omission of the small plasmids from the CGH or analysis by MLST provided broadly concordant fine divisions and separated human-derived and animal-derived strains more clearly. The two gene clusters for exopolysaccharide (EPS) biosynthesis corresponded to regions of significant genomic diversity. The CGH-based groupings of these regions did not correlate with levels of production of bound or released EPS. Furthermore, EPS production was significantly modulated by available carbohydrate. In addition to proving difficult to predict from the gene content, EPS production levels correlated inversely with production of biofilms, a trait considered desirable in probiotic commensals. L. salivarius displays a high level of genomic diversity, and while selection of L. salivarius strains for probiotic use can be informed by CGH or MLST, it also requires pragmatic experimental validation of desired phenotypic traits.
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45
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Evidence of distinct populations and specific subpopulations within the species Oenococcus oeni. Appl Environ Microbiol 2010; 76:7754-64. [PMID: 20935119 DOI: 10.1128/aem.01544-10] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Among the lactic acid bacteria (LAB) present in the oenological microbial ecosystem, Oenococcus oeni, an acidophilic lactic acid bacterium, is essential during winemaking. It outclasses all other bacterial species during malolactic fermentation (MLF). Oenological performances, such as malic acid degradation rate and sensorial impact, vary significantly according to the strain. The genetic diversity of the O. oeni species was evaluated using a multilocus sequence typing (MLST) scheme. Seven housekeeping genes were sequenced for a collection of 258 strains that had been isolated all over the world (particularly Burgundy, Champagne, and Aquitaine, France, Chile, South Africa, and Italy) and in several wine types (red wines, white wines, and champagne) and cider. The allelic diversity was high, with an average of 20.7 alleles per locus, many of them being rare alleles. The collection comprised 127 sequence types, suggesting an important genotypic diversity. The neighbor-joining phylogenetic tree constructed from the concatenated sequence of the seven housekeeping genes showed two major phylogenetic groups, named A and B. One unique strain isolated from cider composed a third group, rooting the phylogenetic tree. However, all other strains isolated from cider were in group B. Eight phylogenetic subgroups were statistically differentiated and could be delineated by the analysis of only 32 mutations instead of the 600 mutations observed in the concatenated sequence of the seven housekeeping genes. Interestingly, in group A, several phylogenetic subgroups were composed mostly of strains coming from a precise geographic origin. Three subgroups were identified, composed of strains from Chile, South Africa, and eastern France.
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Picozzi C, Bonacina G, Vigentini I, Foschino R. Genetic diversity in Italian Lactobacillus sanfranciscensis strains assessed by multilocus sequence typing and pulsed-field gel electrophoresis analyses. Microbiology (Reading) 2010; 156:2035-2045. [DOI: 10.1099/mic.0.037341-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lactobacillus sanfranciscensis is a lactic acid bacterium that characterizes the sourdough environment. The genetic differences of 24 strains isolated in different years from sourdoughs, mostly collected in Italy, were examined and compared by PFGE and multilocus sequence typing (MLST). The MLST scheme, based on the analysis of six housekeeping genes (gdh, gyrA, mapA, nox, pgmA and pta) was developed for this study. PFGE with the restriction enzyme ApaI proved to have higher discriminatory power, since it revealed 22 different pulsotypes, while 19 sequence types were recognized through MLST analysis. Notably, restriction profiles generated from three isolates collected from the same firm but in three consecutive years clustered in a single pulsotype and showed the same sequence type, emphasizing the fact that the main factors affecting the dominance of a strain are correlated with processing conditions and the manufacturing environment rather than the geographical area. All results indicated a limited recombination among genes and the presence of a clonal population in L. sanfranciscensis. The MLST scheme proposed in this work can be considered a useful tool for characterization of isolates and for in-depth examination of the strain diversity and evolution of this species.
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Affiliation(s)
- Claudia Picozzi
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Gaia Bonacina
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Ileana Vigentini
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Roberto Foschino
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
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Torriani S, Felis GE, Fracchetti F. Selection criteria and tools for malolactic starters development: an update. ANN MICROBIOL 2010. [DOI: 10.1007/s13213-010-0072-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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48
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Solieri L, Genova F, De Paola M, Giudici P. Characterization and technological properties of Oenococcus oeni strains from wine spontaneous malolactic fermentations: a framework for selection of new starter cultures. J Appl Microbiol 2010; 108:285-98. [PMID: 19614854 DOI: 10.1111/j.1365-2672.2009.04428.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To characterize the genetic and phenotypic diversity of 135 lactic acid bacteria (LAB) strains isolated from Italian wines that undergone spontaneous malolactic fermentation (MLF) and propose a multiphasic selection of new Oenococcus oeni malolactic starters. METHODS AND RESULTS One hundred and thirty-five LAB strains were isolated from 12 different wines. On the basis of 16S amplified ribosomal DNA restriction analysis (ARDRA) with three restriction enzymes and 16S rRNA gene sequencing, 120 O. oeni strains were identified. M13-based RAPD analysis was employed to investigate the molecular diversity of O. oeni population. Technological properties of different O. oeni genotypes were evaluated in synthetic medium at increasing selective pressure, such as low pH (3.5, 3.2 and 3.0) and high ethanol values (10, 11 and 13% v/v). Finally, the malolactic activity of one selected strain was assessed in wine by malolactic trial in winery. CONCLUSIONS The research explores the genomic diversity of wine bacteria in Italian wines and characterizes their malolactic metabolism, providing an efficient strategy to select O. oeni strains with desirable malolactic performances and able to survive in conditions simulating the harsh wine environment. SIGNIFICANCE AND IMPACT OF THE STUDY This article contributes to a better understanding of microbial diversity of O. oeni population in Italian wines and reports a framework to select new potentially O. oeni starters from Italian wines during MLF.
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Affiliation(s)
- L Solieri
- Department of Agricultural and Food Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42100 Reggio Emilia, Italy.
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49
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Muñoz R, Gómez A, Robles V, Rodríguez P, Cebollero E, Tabera L, Carrascosa AV, Gonzalez R. Multilocus sequence typing of oenological Saccharomyces cerevisiae strains. Food Microbiol 2009; 26:841-6. [PMID: 19835769 DOI: 10.1016/j.fm.2009.05.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 05/18/2009] [Accepted: 05/21/2009] [Indexed: 10/20/2022]
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50
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Tanganurat W, Quinquis B, Leelawatcharamas V, Bolotin A. Genotypic and phenotypic characterization of Lactobacillus plantarum strains isolated from Thai fermented fruits and vegetables. J Basic Microbiol 2009; 49:377-85. [PMID: 19219901 DOI: 10.1002/jobm.200800185] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Ten Lactobacillus strains originally isolated from Thai fruits and vegetables fermentation were characterized by various phenotypic and genotypic methods. The phenotypic analysis using the method of carbohydrate fermentation patterns (API50CHL) revealed that the isolates belonged to the L. plantarum species. This was further confirmed by 16S rRNA gene sequencing. Multilocus sequence typing (MLST) revealed a strongly clonal population structure and a low genotypic diversity in this collection. However, the analyzed L. plantarum population demonstrated a higher level of diversification after API50CHL that reflects the role of available carbohydrate sources in bacterial evolution. Our results support the postulate that a combination of conventional biochemical and genotyping methods allows a thorough characterization and identification of isolates. We propose that genotypic characterization could be complemented by biochemical characterization to discriminate L. plantarum strains.
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Affiliation(s)
- Winee Tanganurat
- Department of Biotechnology, Kasetsart University, Bangkok, Thailand
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