Genomic DNA Fingerprinting of Oenococcus oeni Strains by Pulsed-Field Gel Electrophoresis and Randomly Amplified Polymorphic DNA-PCR

Zapparoli, Giacomo; Reguant, Cristina; Bordons, Albert; Torriani, Sandra; Dellaglio, Franco

doi:10.1007/s002840010069

Cited by 91 publications

(58 citation statements)

References 16 publications

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“…to discern regional differences in strains. An outcome of this analysis is the general view that O. oeni is a genetically homogenous species (Zapparoli et al 2000).…”

Section: Oenococcus Oeni Psu-1 (Atcc Baa-331) (Contributed By David Mmentioning

confidence: 99%

Discovering lactic acid bacteria by genomics

Klaenhammer

Altermann

Arigoni

et al. 2002

Lactic Acid Bacteria: Genetics, Metabolism and Applications

134

145

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This review summarizes a collection of lactic acid bacteria that are now undergoing genomic sequencing and analysis. Summaries are presented on twenty different species, with each overview discussing the organisms fundamental and practical significance, environmental habitat, and its role in fermentation, bioprocessing, or probiotics. For those projects where genome sequence data were available by March 2002, summaries include 30 a listing of key statistics and interesting genomic features. These efforts will revolutionize our molecular view of Gram-positive bacteria, as up to 15 genomes from the low GC content lactic acid bacteria are expected to be available in the public domain by the end of 2003. Our collective view of the lactic acid bacteria will be fundamentally changed as we rediscover the relationships and capabilities of these organisms through genomics.

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“…to discern regional differences in strains. An outcome of this analysis is the general view that O. oeni is a genetically homogenous species (Zapparoli et al 2000).…”

Section: Oenococcus Oeni Psu-1 (Atcc Baa-331) (Contributed By David Mmentioning

confidence: 99%

Discovering lactic acid bacteria by genomics

Klaenhammer

Altermann

Arigoni

et al. 2002

Lactic Acid Bacteria: Genetics, Metabolism and Applications

134

145

View full text Add to dashboard Cite

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“…Oenococcus oeni has been described as a relatively homogeneous species, and a variety of molecular approaches failed to clearly differentiate strains on a molecular level (23,39,45,48,49). Discrimination was accomplished only recently, using fine techniques, such as differential display PCR, restriction endonuclease analysis-pulsed-field gel electrophoresis (18,22,50), and multilocus sequence typing (7,8).…”

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confidence: 99%

Oenococcus oeni Genome Plasticity Is Associated with Fitness

Bon

Delaherche

Bilhere

et al. 2009

Appl Environ Microbiol

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Oenococcus oeni strains are well-known for their considerable phenotypic variations in terms of tolerance to harsh wine conditions and malolactic activity. Genomic subtractive hybridization (SH) between two isolates with differing enological potentials was used to elucidate the genetic bases of this intraspecies diversity and identify novel genes involved in adaptation to wine. SH revealed 182 tester-specific fragments corresponding to 126 open reading frames (ORFs). A large proportion of the chromosome-related ORFs resembled genes involved in carbohydrate transport and metabolism, cell wall/membrane/envelope biogenesis, and replication, recombination, and repair. Six regions of genomic plasticity were identified, and their analysis suggested that both limited recombination and insertion/deletion events contributed to the vast genomic diversity observed in O. oeni. The association of selected sequences with adaptation to wine was further assessed by screening a large collection of strains using PCR. No sequences were found to be specific to highly performing (HP) strains alone. However, there was a statistically significant positive association between HP strains and the presence of eight gene sequences located on regions 2, 4, and 5. Gene expression patterns were significantly modified in HP strains, following exposure to one or more of the common stresses in wines. Regions 2 and 5 showed no traces of mobile elements and had normal GC content. In contrast, region 4 had the typical hallmarks of horizontal transfer, suggesting that the strategy of acquiring genes from other bacteria enhances the fitness of O. oeni strains.

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“…Despite the exhaustive phenetic and molecular studies that have been performed on O. oeni, little is known about its population genetics. Studies carried out by using different molecular techniques such as chromosomal DNA-DNA hybridizations (7), 16S and 23S rRNA sequence analysis (39), and 16S-23S rRNA gene (rDNA) intergenic spacer region (ISR) sequencing (30,46) and also by DNA fingerprinting (29,44), pulsed-field gel electrophoresis (26), and randomly amplified polymorphic DNA (RAPD) analysis (45) suggest that this species is homogeneous. However, metabolic or physiological criteria, such as lactate dehydrogenases (17), carbohydrate fermentation (18), and cellular fatty acid patterns (42), have shown considerable diversity among strains of O. oeni.…”

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confidence: 99%

Allelic Diversity and Population Structure inOenococcus oenias Determined from Sequence Analysis of Housekeeping Genes

Rivas

Marcobal

Múñoz

2004

Appl Environ Microbiol

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Oenococcus oeni is the organism of choice for promoting malolactic fermentation in wine. The population biology of O. oeni is poorly understood and remains unclear. For a better understanding of the mode of genetic variation within this species, we investigated by using multilocus sequence typing (MLST) with the gyrB, pgm, ddl, recP, and mleA genes the genetic diversity and genetic relationships among 18 O. oeni strains isolated in various years from wines of the United States, France, Germany, Spain, and Italy. These strains have also been characterized by ribotyping and restriction fragment length polymorphism (RFLP) analysis of the PCRamplified 16S-23S rRNA gene intergenic spacer region (ISR). Ribotyping grouped the strains into two groups; however, the RFLP analysis of the ISRs showed no differences in the strains analyzed. In contrast, MLST in oenococci had a good discriminatory ability, and we have found a higher genetic diversity than indicated by ribotyping analysis. All sequence types were represented by a single strain, and all the strains could be distinguished from each other because they had unique combinations of alleles. Strains assumed to be identical showed the same sequence type. Phylogenetic analyses indicated a panmictic population structure in O. oeni. Sequences were analyzed for evidence of recombination by split decomposition analysis and analysis of clustered polymorphisms. All results indicated that recombination plays a major role in creating the genetic heterogeneity of O. oeni. A low standardized index of association value indicated that the O. oeni genes analyzed are close to linkage equilibrium. This study constitutes the first step in the development of an MLST method for O. oeni and the first example of the application of MLST to a nonpathogenic food production bacteria.Oenococcus oeni, formerly Leuconostoc oenos (7), is the species of lactic acid bacteria (LAB) most frequently associated with malolactic fermentation (MLF) in wine. MLF, which occurs after alcoholic fermentation during wine making, is induced by the growth of LAB. Normally, spontaneous MLF takes place when LAB develop in wine after alcoholic fermentation. However, when fermentation by indigenous bacteria is relied upon, the fitness of the bacteria present to carry out MLF may be highly variable, and consequently their winemaking properties are unpredictable. In order to exercise greater control over wine-making processes, common winemaking practices therefore involve inoculation of wine with either commercially prepared strains or in-house winery strains of malolactic bacteria (4). Therefore, the differentiation of O. oeni strains at the strain level becomes a major concern, since their adaptation to wine and influence on organoleptic quality are strain specific (2). Moreover, manufacturers of malolactic starters need accurate control of their products, and winemakers have to be able to recognize the inoculated strains during vinification. The need for positive identification of different isolates is also acknowled...

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Genomic DNA Fingerprinting of Oenococcus oeni Strains by Pulsed-Field Gel Electrophoresis and Randomly Amplified Polymorphic DNA-PCR

Cited by 91 publications

References 16 publications

Discovering lactic acid bacteria by genomics

Discovering lactic acid bacteria by genomics

Oenococcus oeni Genome Plasticity Is Associated with Fitness

Allelic Diversity and Population Structure inOenococcus oenias Determined from Sequence Analysis of Housekeeping Genes

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