Multiplex variable number of tandem repeats for Oenococcus oeni and applications

Claisse, Olivier; Lonvaud‐Funel, Aline

doi:10.1016/j.fm.2013.08.012

Cited by 23 publications

(10 citation statements)

References 30 publications

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“…It was first used in 1993, and often afterwards, although it is difficult and time-consuming (Kelly et al 1993 ; Tenreiro et al 1994 ; Sato et al 2001 ; Guerrini et al 2003 ; López et al 2007 ; Larisika et al 2008 ; Gonzalez-Arenzana et al 2012a , b ; Zapparoli et al 2012 ; Wang et al 2015 ; Vigentini et al 2016 ). More simple and rapid methods based on the use of PCR were later developed and applied, such as Rapid Amplification of Polymorphic DNA (RAPD) (Zavaleta et al 1997 ; Zapparoli et al 2000 ; Reguant & Bordons 2003 ; Lechiancole et al 2006 ; Canas et al 2009 ; Capozzi et al 2010 ; Solieri et al 2010 ; Marques et al 2011 ), Amplified Fragment Length Polymorphism (AFLP) (Viti et al 1996 ; Sato et al 2000 ; Cappello et al 2008 ; Cappello et al 2010 ), or more recently Multiple Loci VNTR Analysis (MLVA), which targets genomic regions conserved among all strains but with different sizes as they contain a variable number of tandem repeats (VNTR) (Claisse & Lonvaud-Funel 2012 ; Claisse & Lonvaud-Funel 2014 ; Garofalo et al 2015 ; Cruz-Pio et al 2017 ; El Khoury et al 2017 ; Franquès et al 2017 ). The methods have revealed that there is a great diversity of strains in each region, several strains in each wine tank, and generally 2 to 6 major strains during MLF; that strains present in the vineyard at the surface of grapes contribute to MLF in wines produced from these grapes; that strains can persist in cellars for several years and thus contribute to MLF in wines produced during several consecutive vintages.…”

Section: O Oeni Strains Diversity: Methods and Applicationsmentioning

confidence: 99%

Distribution of Oenococcus oeni populations in natural habitats

Lorentzen

Lucas

2019

Appl Microbiol Biotechnol

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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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Section: O Oeni Strains Diversity: Methods and Applicationsmentioning

confidence: 99%

Distribution of Oenococcus oeni populations in natural habitats

Lorentzen

Lucas

2019

Appl Microbiol Biotechnol

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“…Bacterial colonies were genotyped by multilocus variable-number tandemrepeat analysis (MLVA) specific to O. oeni. The MLVA was performed as described by Claisse and Lonvaud-Funel (37). Briefly, for each colony two multiplex PCRs were performed using 2 or 3 pairs of labeled primers in order to amplify 5 regions of tandem repeats (TRs).…”

Section: Methodsmentioning

confidence: 99%

Biogeography of Oenococcus oeni Reveals Distinctive but Nonspecific Populations in Wine-Producing Regions

Khoury

Campbell-Sills

Salin

et al. 2017

Appl Environ Microbiol

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Understanding the mechanisms behind the typicity of regional wines inevitably brings attention to microorganisms associated with their production. Oenococcus oeni is the main bacterial species involved in wine and cider making. It develops after the yeast-driven alcoholic fermentation and performs the malolactic fermentation, which improves the taste and aromatic complexity of most wines. Here, we have evaluated the diversity and specificity of O. oeni strains in six regions. A total of 235 wines and ciders were collected during spontaneous malolactic fermentations and used to isolate 3,212 bacterial colonies. They were typed by multilocus variable analysis, which disclosed a total of 514 O. oeni strains. Their phylogenetic relationships were evaluated by a second typing method based on single nucleotide polymorphism (SNP) analysis. Taken together, the results indicate that each region holds a high diversity of strains that constitute a unique population. However, strains present in each region belong to diverse phylogenetic groups, and the same groups can be detected in different regions, indicating that strains are not genetically adapted to regions. In contrast, greater strain identity was seen for cider, white wine, or red wine of Burgundy, suggesting that genetic adaptation to these products occurred.IMPORTANCE This study reports the isolation, genotyping, and geographic distribution analysis of the largest collection of O. oeni strains performed to date. It reveals that there is very high diversity of strains in each region, the majority of them being detected in a single region. The study also reports the development of an SNP genotyping method that is useful for analyzing the distribution of O. oeni phylogroups. The results show that strains are not genetically adapted to regions but to specific types of wines. They reveal new phylogroups of strains, particularly two phylogroups associated with white wines and red wines of Burgundy. Taken together, the results shed light on the diversity and specificity of wild strains of O. oeni, which is crucial for understanding their real contribution to the unique properties of wines.

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“…The implantation of the S. cerevisiae strain was controlled at mid-alcoholic fermentation by InterDelta analysis (Legras and Karst, 2003). The implantation of O. oeni strain was controlled at mid-malolactic fermentation by PCR Variable Number of Tandem Repeat (VNTR) with TR1 (Claisse and Lonvaud-Funel, 2014).…”

Section: Monitoring Fermentative Kinetics and Implanting Yeasts And Bmentioning

confidence: 99%

Bio-Protection as an Alternative to Sulphites: Impact on Chemical and Microbial Characteristics of Red Wines

et al. 2020

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In wine, one method of limiting the addition of sulphites, a harmful and allergenic agent, is bio-protection. This practice consists of the early addition of microorganisms on grape must before fermentation. Non-Saccharomyces yeasts have been proposed as an interesting alternative to sulphite addition. However, scientific data proving the effectiveness of bio-protection remains sparse. This study provides the first analysis of the chemical and microbiological effects of a Metschnikowia pulcherrima strain inoculated at the beginning of the red winemaking process in three wineries as an alternative to sulphiting. Like sulphiting, bio-protection effectively limited the growth of spoilage microbiota and had no influence on the phenolic compounds protecting musts and wine from oxidation. The bio-protection had no effect on the volatile compounds and the sensory differences were dependent on the experimental sites. However, a non-targeted metabolomic analysis by FTICR-MS highlighted a bio-protection signature.

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Multiplex variable number of tandem repeats for Oenococcus oeni and applications

Cited by 23 publications

References 30 publications

Distribution of Oenococcus oeni populations in natural habitats

Distribution of Oenococcus oeni populations in natural habitats

Biogeography of Oenococcus oeni Reveals Distinctive but Nonspecific Populations in Wine-Producing Regions

Bio-Protection as an Alternative to Sulphites: Impact on Chemical and Microbial Characteristics of Red Wines

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