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Liu L, Peng S, Song W, Zhao H, Li H, Wang H. Genomic Analysis of an Excellent Wine-Making Strain Oenococcus oeni SD-2a. Pol J Microbiol 2022; 71:279-292. [PMID: 35716166 PMCID: PMC9252139 DOI: 10.33073/pjm-2022-026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/14/2022] [Indexed: 12/27/2022] Open
Abstract
Oenococcus oeni is an important microorganism in wine-making-related engineering, and it improves wine quality and stability through malolactic fermentation. Although the genomes of more than 200 O. oeni strains have been sequenced, only a few include completed genome maps. Here, the genome sequence of O. oeni SD-2a, isolated from Shandong, China, has been determined. It is a fully assembled genome sequence of this strain. The complete genome is 1,989,703 bp with a G+C content of 37.8% without a plasmid. The genome includes almost all the essential genes involved in central metabolic pathways and the stress genes reported in other O. oeni strains. Some natural competence-related genes, like comEA, comEC, comFA, comG operon, and comFC, suggest that O. oeni SD-2a may have natural transformation potential. A comparative genomics analysis revealed 730 gene clusters in O. oeni SD-2a homologous to those in four other lactic acid bacteria species (O. oeni PSU-1, O. oeni CRBO-11381, Lactiplantibacillus plantarum UNQLp11, and Pediococcus pentosaceus KCCM40703). A collinearity analysis showed poor collinearity between O. oeni SD-2a and O. oeni PSU-1, indicating great differences in their evolutionary histories. The results provide general knowledge of O. oeni SD-2a and lay the foundation for specific gene function analyses. ![]()
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Affiliation(s)
- Longxiang Liu
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Shuai Peng
- College of food science and engineering, Gansu Agricultural University, Lanzhou, China
| | - Weiyu Song
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Hongyu Zhao
- College of Enology, Northwest A&F University, Yangling, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, China
| | - Hua Li
- College of Enology, Northwest A&F University, Yangling, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, China
| | - Hua Wang
- College of Enology, Northwest A&F University, Yangling, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, China
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2
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Rivas GA, Valdés La Hens D, Delfederico L, Olguin N, Bravo-Ferrada BM, Tymczyszyn EE, Semorile L, Brizuela NS. Molecular tools for the analysis of the microbiota involved in malolactic fermentation: from microbial diversity to selection of lactic acid bacteria of enological interest. World J Microbiol Biotechnol 2022; 38:19. [PMID: 34989896 DOI: 10.1007/s11274-021-03205-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/08/2021] [Indexed: 01/19/2023]
Abstract
Winemaking is a complex process involving two successive fermentations: alcoholic fermentation, by yeasts, and malolactic fermentation (MLF), by lactic acid bacteria (LAB). During MLF, LAB can contribute positively to wine flavor through decarboxylation of malic acid with acidity reduction and other numerous enzymatic reactions. However, some microorganisms can have a negative impact on the quality of the wine through processes such as biogenic amine production. For these reasons, monitoring the bacterial community profiles during MLF can predict and control the quality of the final product. In addition, the selection of LAB from a wine-producing area is necessary for the formulation of native malolactic starter cultures well adapted to local winemaking practices and able to enhance the regional wine typicality. In this sense, molecular biology techniques are fundamental tools to decipher the native microbiome involved in MLF and to select bacterial strains with potential to function as starter cultures, given their enological and technological characteristics. In this context, this work reviews the different molecular tools (both culture-dependent and -independent) that can be applied to the study of MLF, either in bacterial isolates or in the microbial community of wine, and of its dynamics during the process.
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Affiliation(s)
- Gabriel Alejandro Rivas
- Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Laboratorio de Microbiología Molecular, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal, B1876BXD, Buenos Aires, Argentina
| | - Danay Valdés La Hens
- Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Laboratorio de Microbiología Molecular, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal, B1876BXD, Buenos Aires, Argentina
| | - Lucrecia Delfederico
- Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Laboratorio de Microbiología Molecular, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal, B1876BXD, Buenos Aires, Argentina
| | - Nair Olguin
- Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Laboratorio de Microbiología Molecular, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal, B1876BXD, Buenos Aires, Argentina
| | - Bárbara Mercedes Bravo-Ferrada
- Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Laboratorio de Microbiología Molecular, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal, B1876BXD, Buenos Aires, Argentina
| | - Emma Elizabeth Tymczyszyn
- Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Laboratorio de Microbiología Molecular, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal, B1876BXD, Buenos Aires, Argentina
| | - Liliana Semorile
- Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Laboratorio de Microbiología Molecular, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal, B1876BXD, Buenos Aires, Argentina
| | - Natalia Soledad Brizuela
- Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada (IMBA), Laboratorio de Microbiología Molecular, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal, B1876BXD, Buenos Aires, Argentina.
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3
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Biodiversity of Oenological Lactic Acid Bacteria: Species- and Strain-Dependent Plus/Minus Effects on Wine Quality and Safety. FERMENTATION 2021. [DOI: 10.3390/fermentation7010024] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Winemaking depends on several elaborate biochemical processes that see as protagonist either yeasts or lactic acid bacteria (LAB) of oenological interest. In particular, LAB have a fundamental role in determining the quality chemical and aromatic properties of wine. They are essential not only for malic acid conversion, but also for producing several desired by-products due to their important enzymatic activities that can release volatile aromatic compounds during malolactic fermentation (e.g., esters, carbonyl compounds, thiols, monoterpenes). In addition, LAB in oenology can act as bioprotectors and reduce the content of undesired compounds. On the other hand, LAB can affect wine consumers’ health, as they can produce harmful compounds such as biogenic amines and ethyl carbamate under certain conditions during fermentation. Several of these positive and negative properties are species- and strain-dependent characteristics. This review focuses on these aspects, summarising the current state of knowledge on LAB’s oenological diversity, and highlighting their influence on the final product’s quality and safety. All our reported information is of high interest in searching new candidate strains to design starter cultures, microbial resources for traditional/typical products, and green solutions in winemaking. Due to the continuous interest in LAB as oenological bioresources, we also underline the importance of inoculation timing. The considerable variability among LAB species/strains associated with spontaneous consortia and the continuous advances in the characterisation of new species/strains of interest for applications in the wine sector suggest that the exploitation of biodiversity belonging to this heterogeneous group of bacteria is still rising.
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4
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Characterization of natural Oenococcus oeni strains for Montepulciano d’Abruzzo organic wine production. Eur Food Res Technol 2020. [DOI: 10.1007/s00217-020-03466-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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5
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Impact of co-inoculation of Saccharomyces cerevisiae, Hanseniaspora uvarum and Oenococcus oeni autochthonous strains in controlled multi starter grape must fermentations. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.04.045] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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6
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Lorentzen MP, Campbell-Sills H, Jorgensen TS, Nielsen TK, Coton M, Coton E, Hansen L, Lucas PM. Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains. BMC Genomics 2019; 20:330. [PMID: 31046679 PMCID: PMC6498615 DOI: 10.1186/s12864-019-5692-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 04/12/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Oenococcus oeni is a lactic acid bacteria species adapted to the low pH, ethanol-rich environments of wine and cider fermentation, where it performs the crucial role of malolactic fermentation. It has a small genome and has lost the mutS-mutL DNA mismatch repair genes, making it a hypermutable and highly specialized species. Two main lineages of strains, named groups A and B, have been described to date, as well as other subgroups correlated to different types of wines or regions. A third group "C" has also been hypothesized based on sequence analysis, but it remains controversial. In this study we have elucidated the species population structure by sequencing 14 genomes of new strains isolated from cider and kombucha and performing comparative genomics analyses. RESULTS Sequence-based phylogenetic trees confirmed a population structure of 4 clades: The previously identified A and B, a third group "C" consisting of the new cider strains and a small subgroup of wine strains previously attributed to group B, and a fourth group "D" exclusively represented by kombucha strains. A pair of complete genomes from group C and D were compared to the circularized O. oeni PSU-1 strain reference genome and no genomic rearrangements were found. Phylogenetic trees, K-means clustering and pangenome gene clusters evidenced the existence of smaller, specialized subgroups of strains. Using the pangenome, genomic differences in stress resistance and biosynthetic pathways were found to uniquely distinguish the C and D clades. CONCLUSIONS The obtained results, including the additional cider and kombucha strains, firmly established the O. oeni population structure. Group C does not appear as fully domesticated as group A to wine, but showed several unique patterns which may be due to ongoing specialization to the cider environment. Group D was shown to be the most divergent member of O. oeni to date, appearing as the closest to a pre-domestication state of the species.
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Affiliation(s)
- Marc P Lorentzen
- University of Bordeaux, ISVV, Unit Oenology, F-33882, Villenave d'Ornon, France.
| | - Hugo Campbell-Sills
- University of Bordeaux, ISVV, Unit Oenology, F-33882, Villenave d'Ornon, France.,Lallemand SAS, 19 Rue des Briquetiers, 31702, Blagnac, France
| | - Tue S Jorgensen
- Department of Environmental Science, Environmental Microbial Genomics Group, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Tue K Nielsen
- Department of Environmental Science, Environmental Microbial Genomics Group, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Monika Coton
- Université de Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, EA 3882. ESIAB, Technopole Brest-Iroise, 29280, Plouzané, France
| | - Emmanuel Coton
- Université de Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, EA 3882. ESIAB, Technopole Brest-Iroise, 29280, Plouzané, France
| | - Lars Hansen
- Department of Environmental Science, Environmental Microbial Genomics Group, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Patrick M Lucas
- University of Bordeaux, ISVV, Unit Oenology, F-33882, Villenave d'Ornon, France
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7
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Genome Sequence of Oenococcus oeni UNQOe19, the First Fully Assembled Genome Sequence of a Patagonian Psychrotrophic Oenological Strain. Microbiol Resour Announc 2018; 7:MRA00889-18. [PMID: 30533887 PMCID: PMC6256454 DOI: 10.1128/mra.00889-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 07/13/2018] [Indexed: 11/20/2022] Open
Abstract
Oenococcus oeni UNQOe19 is a native strain isolated from a Patagonian pinot noir wine undergoing spontaneous malolactic fermentation. Here, we present the 1.83-Mb genome sequence of O. oeni UNQOe19, the first fully assembled genome sequence of a psychrotrophic strain from an Argentinean wine. Oenococcus oeni UNQOe19 is a native strain isolated from a Patagonian pinot noir wine undergoing spontaneous malolactic fermentation. Here, we present the 1.83-Mb genome sequence of O. oeni UNQOe19, the first fully assembled genome sequence of a psychrotrophic strain from an Argentinean wine.
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Contreras A, Ribbeck M, Gutiérrez GD, Cañon PM, Mendoza SN, Agosin E. Mapping the Physiological Response of Oenococcus oeni to Ethanol Stress Using an Extended Genome-Scale Metabolic Model. Front Microbiol 2018; 9:291. [PMID: 29545779 PMCID: PMC5838312 DOI: 10.3389/fmicb.2018.00291] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 02/07/2018] [Indexed: 11/13/2022] Open
Abstract
The effect of ethanol on the metabolism of Oenococcus oeni, the bacterium responsible for the malolactic fermentation (MLF) of wine, is still scarcely understood. Here, we characterized the global metabolic response in O. oeni PSU-1 to increasing ethanol contents, ranging from 0 to 12% (v/v). We first optimized a wine-like, defined culture medium, MaxOeno, to allow sufficient bacterial growth to be able to quantitate different metabolites in batch cultures of O. oeni. Then, taking advantage of the recently reconstructed genome-scale metabolic model iSM454 for O. oeni PSU-1 and the resulting experimental data, we determined the redistribution of intracellular metabolic fluxes, under the different ethanol conditions. Four growth phases were clearly identified during the batch cultivation of O. oeni PSU-1 strain, according to the temporal consumption of malic and citric acids, sugar and amino acids uptake, and biosynthesis rates of metabolic products - biomass, erythritol, mannitol and acetic acid, among others. We showed that, under increasing ethanol conditions, O. oeni favors anabolic reactions related with cell maintenance, as the requirements of NAD(P)+ and ATP increased with ethanol content. Specifically, cultures containing 9 and 12% ethanol required 10 and 17 times more NGAM (non-growth associated maintenance ATP) during phase I, respectively, than cultures without ethanol. MLF and citric acid consumption are vital at high ethanol concentrations, as they are the main source for proton extrusion, allowing higher ATP production by F0F1-ATPase, the main route of ATP synthesis under these conditions. Mannitol and erythritol synthesis are the main sources of NAD(P)+, countervailing for 51-57% of its usage, as predicted by the model. Finally, cysteine shows the fastest specific consumption rate among the amino acids, confirming its key role for bacterial survival under ethanol stress. As a whole, this study provides a global insight into how ethanol content exerts a differential physiological response in O. oeni PSU-1 strain. It will help to design better strategies of nutrient addition to achieve a successful MLF of wine.
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Affiliation(s)
- Angela Contreras
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Magdalena Ribbeck
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Guillermo D Gutiérrez
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo M Cañon
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sebastián N Mendoza
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation, Universidad de Chile, Santiago, Chile
| | - Eduardo Agosin
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
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9
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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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10
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11
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Sternes PR, Costello PJ, Chambers PJ, Bartowsky EJ, Borneman AR. Whole transcriptome RNAseq analysis of Oenococcus oeni reveals distinct intra-specific expression patterns during malolactic fermentation, including genes involved in diacetyl metabolism. Int J Food Microbiol 2017; 257:216-224. [DOI: 10.1016/j.ijfoodmicro.2017.06.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 06/06/2017] [Accepted: 06/25/2017] [Indexed: 12/23/2022]
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12
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Darsonval M, Alexandre H, Grandvalet C. Genetically engineered Oenococcus oeni strains to highlight the impact of estA2 and estA7 esterase genes on wine ester profile. Food Microbiol 2016; 60:21-8. [DOI: 10.1016/j.fm.2016.06.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 06/10/2016] [Accepted: 06/15/2016] [Indexed: 11/25/2022]
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13
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Protective role of glutathione addition against wine-related stress in Oenococcus oeni. Food Res Int 2016; 90:8-15. [DOI: 10.1016/j.foodres.2016.10.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/30/2016] [Accepted: 10/05/2016] [Indexed: 11/22/2022]
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14
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Sternes PR, Borneman AR. Consensus pan-genome assembly of the specialised wine bacterium Oenococcus oeni. BMC Genomics 2016; 17:308. [PMID: 27118061 PMCID: PMC4847254 DOI: 10.1186/s12864-016-2604-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 03/28/2016] [Indexed: 11/15/2022] Open
Abstract
Background Oenococcus oeni is a lactic acid bacterium that is specialised for growth in the ecological niche of wine, where it is noted for its ability to perform the secondary, malolactic fermentation that is often required for many types of wine. Expanding the understanding of strain-dependent genetic variations in its small and streamlined genome is important for realising its full potential in industrial fermentation processes. Results Whole genome comparison was performed on 191 strains of O. oeni; from this rich source of genomic information consensus pan-genome assemblies of the invariant (core) and variable (flexible) regions of this organism were established. Genetic variation in amino acid biosynthesis and sugar transport and utilisation was found to be common between strains. Furthermore, we characterised previously-unreported intra-specific genetic variations in the natural competence of this microbe. Conclusion By assembling a consensus pan-genome from a large number of strains, this study provides a tool for researchers to readily compare protein-coding genes across strains and infer functional relationships between genes in conserved syntenic regions. This establishes a foundation for further genetic, and thus phenotypic, research of this industrially-important species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2604-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peter R Sternes
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, South Australia, 5064, Australia
| | - Anthony R Borneman
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, South Australia, 5064, Australia.
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15
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Russo P, Capozzi V, Spano G, Corbo MR, Sinigaglia M, Bevilacqua A. Metabolites of Microbial Origin with an Impact on Health: Ochratoxin A and Biogenic Amines. Front Microbiol 2016; 7:482. [PMID: 27092133 PMCID: PMC4824791 DOI: 10.3389/fmicb.2016.00482] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/22/2016] [Indexed: 11/13/2022] Open
Abstract
Safety and quality are significant challenges for food; namely, safety represents a big threat all over the world and is one of the most important goal to be achieved in both Western Society and Developing Countries. Wine safety mainly relies upon some metabolites and many of them are of microbial origin. The main goal of this review is a focus on two kinds of compounds (biogenic amines and mycotoxins, mainly Ochratoxin A) for their deleterious effects on health. For each class of compounds, we will focus on two different traits: (a) synthesis of the compounds in wine, with a brief description of the most important microorganisms and factors leading this phenomenon; (b) prevention and/or correction strategies and new trends. In addition, there is a focus on a recent predictive tool able to predict toxin contamination of grape, in order to perform some prevention approaches and achieve safe wine.
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Affiliation(s)
| | | | | | | | | | - Antonio Bevilacqua
- Department of the Science of Agriculture, Food and Environment, University of FoggiaFoggia, Italy
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16
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Capozzi V, Garofalo C, Chiriatti MA, Grieco F, Spano G. Microbial terroir and food innovation: The case of yeast biodiversity in wine. Microbiol Res 2015; 181:75-83. [DOI: 10.1016/j.micres.2015.10.005] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 10/05/2015] [Accepted: 10/12/2015] [Indexed: 12/30/2022]
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17
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Campbell-Sills H, El Khoury M, Favier M, Romano A, Biasioli F, Spano G, Sherman DJ, Bouchez O, Coton E, Coton M, Okada S, Tanaka N, Dols-Lafargue M, Lucas PM. Phylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines. Genome Biol Evol 2015; 7:1506-18. [PMID: 25977455 PMCID: PMC4494047 DOI: 10.1093/gbe/evv084] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Oenococcus oeni is a lactic acid bacteria species encountered particularly in wine, where it achieves the malolactic fermentation. Molecular typing methods have previously revealed that the species is made of several genetic groups of strains, some being specific to certain types of wines, ciders or regions. Here, we describe 36 recently released O. oeni genomes and the phylogenomic analysis of these 36 plus 14 previously reported genomes. We also report three genome sequences of the sister species Oenococcus kitaharae that were used for phylogenomic reconstructions. Phylogenomic and population structure analyses performed revealed that the 50 O. oeni genomes delineate two major groups of 12 and 37 strains, respectively, named A and B, plus a putative group C, consisting of a single strain. A study on the orthologs and single nucleotide polymorphism contents of the genetic groups revealed that the domestication of some strains to products such as cider, wine, or champagne, is reflected at the genetic level. While group A strains proved to be predominant in wine and to form subgroups adapted to specific types of wine such as champagne, group B strains were found in wine and cider. The strain from putative group C was isolated from cider and genetically closer to group B strains. The results suggest that ancestral O. oeni strains were adapted to low-ethanol containing environments such as overripe fruits, and that they were domesticated to cider and wine, with group A strains being naturally selected in a process of further domestication to specific wines such as champagne.
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Affiliation(s)
- Hugo Campbell-Sills
- Univ. Bordeaux, ISVV, EA 4577 Œnologie, Villenave d'Ornon, France Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | | | - Marion Favier
- BioLaffort, Research Subsidiary of the Laffort group, Bordeaux, France
| | - Andrea Romano
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Franco Biasioli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Giuseppe Spano
- Department of Agriculture, Food and Environment Sciences, University of Foggia, Foggia, Italy
| | - David J Sherman
- INRIA, Univ. Bordeaux, Project team MAGNOME, Talence, France CNRS, Univ. Bordeaux, UMR 5800 LaBRI, Talence, France
| | - Olivier Bouchez
- INRA, UMR444, laboratoire de Génétique Cellulaire, Castanet-Tolosan, France GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, France
| | - Emmanuel Coton
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Monika Coton
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Sanae Okada
- NODAI Culture Collection Center, Tokyo University of Agriculture, Japan
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, Japan
| | - Marguerite Dols-Lafargue
- Univ. Bordeaux, ISVV, EA 4577 Œnologie, Villenave d'Ornon, France Bordeaux INP, ISVV, EA 4577 Œnologie, Villenave d'ornon, France
| | - Patrick M Lucas
- Univ. Bordeaux, ISVV, EA 4577 Œnologie, Villenave d'Ornon, France
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Non-Saccharomyces biodiversity in wine and the ‘microbial terroir’: a survey on Nero di Troia wine from the Apulian region, Italy. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1090-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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19
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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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Draft Genome Sequence of Lactobacillus plantarum Lp90 Isolated from Wine. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00097-15. [PMID: 25767234 PMCID: PMC4357756 DOI: 10.1128/genomea.00097-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Here, we describe the draft genome sequence and annotation of Lactobacillus plantarum strain Lp90, the first sequenced genome of a L. plantarum strain isolated from wine. This strain has a noticeable ropy phenotype and showed potential probiotic properties. The genome consists of 3,324,076 bp (33 contigs) and contains 3,155 protein coding genes, 34 pseudogenes, and 84 RNA genes.
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