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Chen L, Wang G, Teng M, Wang L, Yang F, Jin G, Du H, Xu Y. Non-gene-editing microbiome engineering of spontaneous food fermentation microbiota-Limitation control, design control, and integration. Compr Rev Food Sci Food Saf 2023; 22:1902-1932. [PMID: 36880579 DOI: 10.1111/1541-4337.13135] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 03/08/2023]
Abstract
Non-gene-editing microbiome engineering (NgeME) is the rational design and control of natural microbial consortia to perform desired functions. Traditional NgeME approaches use selected environmental variables to force natural microbial consortia to perform the desired functions. Spontaneous food fermentation, the oldest kind of traditional NgeME, transforms foods into various fermented products using natural microbial networks. In traditional NgeME, spontaneous food fermentation microbiotas (SFFMs) are typically formed and controlled manually by the establishment of limiting factors in small batches with little mechanization. However, limitation control generally leads to trade-offs between efficiency and the quality of fermentation. Modern NgeME approaches based on synthetic microbial ecology have been developed using designed microbial communities to explore assembly mechanisms and target functional enhancement of SFFMs. This has greatly improved our understanding of microbiota control, but such approaches still have shortcomings compared to traditional NgeME. Here, we comprehensively describe research on mechanisms and control strategies for SFFMs based on traditional and modern NgeME. We discuss the ecological and engineering principles of the two approaches to enhance the understanding of how best to control SFFM. We also review recent applied and theoretical research on modern NgeME and propose an integrated in vitro synthetic microbiota model to bridge gaps between limitation control and design control for SFFM.
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Affiliation(s)
- Liangqiang Chen
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Kweichow Moutai Distillery Co., Ltd., Zunyi, China
| | | | | | - Li Wang
- Kweichow Moutai Distillery Co., Ltd., Zunyi, China
| | - Fan Yang
- Kweichow Moutai Distillery Co., Ltd., Zunyi, China
| | - Guangyuan Jin
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hai Du
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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Barchi Y, Philippe C, Chaïb A, Oviedo-Hernandez F, Claisse O, Le Marrec C. Phage Encounters Recorded in CRISPR Arrays in the Genus Oenococcus. Viruses 2022; 15:15. [PMID: 36680056 PMCID: PMC9867325 DOI: 10.3390/v15010015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/10/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
The Oenococcus genus comprises four recognized species, and members have been found in different types of beverages, including wine, kefir, cider and kombucha. In this work, we implemented two complementary strategies to assess whether oenococcal hosts of different species and habitats were connected through their bacteriophages. First, we investigated the diversity of CRISPR-Cas systems using a genome-mining approach, and CRISPR-endowed strains were identified in three species. A census of the spacers from the four identified CRISPR-Cas loci showed that each spacer space was mostly dominated by species-specific sequences. Yet, we characterized a limited records of potentially recent and also ancient infections between O. kitaharae and O. sicerae and phages of O. oeni, suggesting that some related phages have interacted in diverse ways with their Oenococcus hosts over evolutionary time. Second, phage-host interaction analyses were performed experimentally with a diversified panel of phages and strains. None of the tested phages could infect strains across the species barrier. Yet, some infections occurred between phages and hosts from distinct beverages in the O. oeni species.
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Affiliation(s)
| | | | | | | | | | - Claire Le Marrec
- UMR Oenologie 1366, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33882 Villenave d’Ornon, France
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Chaïb A, Philippe C, Jaomanjaka F, Barchi Y, Oviedo-Hernandez F, Claisse O, Le Marrec C. Phage-host interactions as a driver of population dynamics during wine fermentation: Betting on underdogs. Int J Food Microbiol 2022; 383:109936. [PMID: 36179497 DOI: 10.1016/j.ijfoodmicro.2022.109936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 09/03/2022] [Accepted: 09/15/2022] [Indexed: 10/14/2022]
Abstract
Winemaking is a complex process in which numerous microorganisms, mainly yeasts and lactic acid bacteria (LAB), play important roles. After alcoholic fermentation (AF), most wines undergo malolactic fermentation (MLF) to improve their organoleptic properties and microbiological stability. Oenococcus oeni is mainly responsible for this crucial process where L-malic acid (MA) in wine converts to softer L-lactic acid. The bacterium is better adapted to the limiting conditions imposed by the wine matrix and performs MLF under regular winemaking conditions, especially in wines with a pH below 3.5. Traditionally, this process has been conducted by the natural microbiota present within the winery. However, the start, duration and qualitative impact of spontaneous MLF are unpredictable, which prompts winemakers to use pure starter cultures of selected bacteria to promote a more reliable, simple, fast and efficient fermentation. Yet, their use does not always ensure a problem-free fermentation. Spontaneous initiation of the process may prove very difficult or does not occur at all. Such difficulties arise from a combination of factors found in some wines upon the completion of AF (high ethanol concentration, low temperature and pH, low nutrient concentrations, presence of free and bound SO2). Alongside these well documented facts, research has also provided evidence that negative interactions between O. oeni and other biological entities such as yeasts may also impact MLF. Another insufficiently described, but highly significant factor inhibiting bacterial growth is connected to the presence of bacteriophages of O. oeni which are frequently associated to musts and wines. The purpose of this review is to summarize the current knowledge about the phage life cycles and possible impacts on the trajectory of the microbiota during winemaking.
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Affiliation(s)
- Amel Chaïb
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, Villenave d'Ornon, France
| | - Cécile Philippe
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, Villenave d'Ornon, France
| | - Féty Jaomanjaka
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, Villenave d'Ornon, France
| | - Yasma Barchi
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, Villenave d'Ornon, France
| | - Florencia Oviedo-Hernandez
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, Villenave d'Ornon, France
| | - Olivier Claisse
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, Villenave d'Ornon, France
| | - Claire Le Marrec
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, Villenave d'Ornon, France.
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Chaïb A, Claisse O, Delbarre E, Bosviel J, Le Marrec C. Assessment of the lysogenic status in the lactic acid bacterium O. oeni during the spontaneous malolactic fermentation of red wines. Food Microbiol 2022; 103:103947. [DOI: 10.1016/j.fm.2021.103947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/12/2021] [Accepted: 11/14/2021] [Indexed: 11/04/2022]
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Exploring the diversity of bacteriophage specific to Oenococcus oeni and Lactobacillus spp and their role in wine production. Appl Microbiol Biotechnol 2021; 105:8575-8592. [PMID: 34694447 DOI: 10.1007/s00253-021-11509-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 12/19/2022]
Abstract
The widespread existence of bacteriophage has been of great interest to the biological research community and ongoing investigations continue to explore their diversity and role. They have also attracted attention and in-depth research in connection to fermented food processing, in particular from the dairy and wine industries. Bacteriophage, mostly oenophage, may in fact be a 'double edged sword' for winemakers: whilst they have been implicated as a causal agent of difficulties with malolactic fermentation (although not proven), they are also beginning to be considered as alternatives to using sulphur dioxide to prevent wine spoilage. Investigation and characterisation of oenophage of Oenococcus oeni, the main species used in winemaking, are still limited compared to lactococcal bacteriophage of Lactococcus lactis and Lactiplantibacillus plantarum (formally Lactobacillus plantarum), the drivers of most fermented dairy products. Interestingly, these strains are also being used or considered for use in winemaking. In this review, the genetic diversity and life cycle of phage, together with the debate on the consequent impact of phage predation in wine, and potential control strategies are discussed. KEY POINTS: • Bacteriophage detected in wine are diverse. • Many lysogenic bacteriophage are found in wine bacteria. • Phage impact on winemaking can depend on the stage of the winemaking process. • Bacteriophage as potential antimicrobial agents against spoilage organisms.
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Claisse O, Chaïb A, Jaomanjaka F, Philippe C, Barchi Y, Lucas PM, Le Marrec C. Distribution of Prophages in the Oenococcus oeni Species. Microorganisms 2021; 9:856. [PMID: 33923461 PMCID: PMC8074189 DOI: 10.3390/microorganisms9040856] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/10/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Oenococcus oeni is the most exploited lactic acid bacterium in the wine industry and drives the malolactic fermentation of wines. Although prophage-like sequences have been identified in the species, many are not characterized, and a global view of their integration and distribution amongst strains is currently lacking. In this work, we analyzed the complete genomes of 231 strains for the occurrence of prophages, and analyzed their size and positions of insertion. Our data show the limited variation in the number of prophages in O. oeni genomes, and that six sites of insertion within the bacterial genome are being used for site-specific recombination. Prophage diversity patterns varied significantly for different host lineages, and environmental niches. Overall, the findings highlight the pervasive presence of prophages in the O. oeni species, their role as a major source of within-species bacterial diversity and drivers of horizontal gene transfer. Our data also have implications for enhanced understanding of the prophage recombination events which occurred during evolution of O. oeni, as well as the potential of prophages in influencing the fitness of these bacteria in their distinct niches.
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Affiliation(s)
| | | | | | | | | | | | - Claire Le Marrec
- Unité de Recherche Œnologie, Bordeaux INP, University of Bordeaux, INRAE, ISVV, F-33882 Bordeaux, France; (O.C.); (A.C.); (F.J.); (C.P.); (Y.B.); (P.M.L.)
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Philippe C, Chaïb A, Jaomanjaka F, Claisse O, Lucas PM, Samot J, Cambillau C, Le Marrec C. Characterization of the First Virulent Phage Infecting Oenococcus oeni, the Queen of the Cellars. Front Microbiol 2021; 11:596541. [PMID: 33519734 PMCID: PMC7838156 DOI: 10.3389/fmicb.2020.596541] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/14/2020] [Indexed: 01/16/2023] Open
Abstract
There has been little exploration of how phages contribute to the diversity of the bacterial community associated with winemaking and may impact fermentations and product quality. Prophages of Oenococcus oeni, the most common species of lactic acid bacteria (LAB) associated with malolactic fermentation of wine, have been described, but no data is available regarding phages of O. oeni with true virulent lifestyles. The current study reports on the incidence and characterization of the first group of virulent oenophages named Vinitor, isolated from the enological environment. Vinitor phages are morphologically very similar to siphoviruses infecting other LAB. Although widespread during winemaking, they are more abundant in musts than temperate oenophages. We obtained the complete genomic sequences of phages Vinitor162 and Vinitor27, isolated from white and red wines, respectively. The assembled genomes shared 97.6% nucleotide identity and belong to the same species. Coupled with phylogenetic analysis, our study revealed that the genomes of Vinitor phages are architecturally mosaics and represent unique combinations of modules amongst LAB infecting-phages. Our data also provide some clues to possible evolutionary connections between Vinitor and (pro)phages associated to epiphytic and insect-related bacteria.
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Affiliation(s)
- Cécile Philippe
- University of Bordeaux, ISVV, EA4577 Œnologie, Villenave d’Ornon, France
| | - Amel Chaïb
- University of Bordeaux, ISVV, EA4577 Œnologie, Villenave d’Ornon, France
| | - Fety Jaomanjaka
- University of Bordeaux, ISVV, EA4577 Œnologie, Villenave d’Ornon, France
| | - Olivier Claisse
- University of Bordeaux, ISVV, EA4577 Œnologie, Villenave d’Ornon, France
- INRA, ISVV, USC 1366 Oenologie, Villenave d’Ornon, France
| | - Patrick M. Lucas
- University of Bordeaux, ISVV, EA4577 Œnologie, Villenave d’Ornon, France
| | - Johan Samot
- University of Bordeaux, ISVV, EA4577 Œnologie, Villenave d’Ornon, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Marseille, France
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Marseille, France
| | - Claire Le Marrec
- University of Bordeaux, ISVV, EA4577 Œnologie, Villenave d’Ornon, France
- Bordeaux INP, ISVV, EA4577 Œnologie, Villenave d’Ornon, France
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Philippe C, Chaïb A, Jaomanjaka F, Cluzet S, Lagarde A, Ballestra P, Decendit A, Petrel M, Claisse O, Goulet A, Cambillau C, Le Marrec C. Wine Phenolic Compounds Differently Affect the Host-Killing Activity of Two Lytic Bacteriophages Infecting the Lactic Acid Bacterium Oenococcus oeni. Viruses 2020; 12:E1316. [PMID: 33213034 PMCID: PMC7698478 DOI: 10.3390/v12111316] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/15/2022] Open
Abstract
To provide insights into phage-host interactions during winemaking, we assessed whether phenolic compounds modulate the phage predation of Oenococcus oeni. Centrifugal partition chromatography was used to fractionate the phenolic compounds of a model red wine. The ability of lytic oenophage OE33PA to kill its host was reduced in the presence of two collected fractions in which we identified five compounds. Three, namely, quercetin, myricetin and p-coumaric acid, significantly reduced the phage predation of O. oeni when provided as individual pure molecules, as also did other structurally related compounds such as cinnamic acid. Their presence was correlated with a reduced adsorption rate of phage OE33PA on its host. Strikingly, none of the identified compounds affected the killing activity of the distantly related lytic phage Vinitor162. OE33PA and Vinitor162 were shown to exhibit different entry mechanisms to penetrate into bacterial cells. We propose that ligand-receptor interactions that mediate phage adsorption to the cell surface are diverse in O. oeni and are subject to differential interference by phenolic compounds. Their presence did not induce any modifications in the cell surface as visualized by TEM. Interestingly, docking analyses suggest that quercetin and cinnamic acid may interact with the tail of OE33PA and compete with host recognition.
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Affiliation(s)
- Cécile Philippe
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Amel Chaïb
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Fety Jaomanjaka
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Stéphanie Cluzet
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Aurélie Lagarde
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Patricia Ballestra
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Alain Decendit
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
| | - Mélina Petrel
- Bordeaux Imaging Center, UMS3420 CNRS-INSERM, University Bordeaux, F-33000 Bordeaux, France;
| | - Olivier Claisse
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
- INRAE, ISVV, USC 1366 Oenologie, F-33140 Villenave d’Ornon, France
| | - Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, F-13020 Marseille, France; (A.G.); (C.C.)
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, F-13020 Marseille, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, F-13020 Marseille, France; (A.G.); (C.C.)
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, F-13020 Marseille, France
| | - Claire Le Marrec
- EA4577-USC1366 INRAE, Unité de Recherche OEnologie, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin (ISVV), F-33140 Villenave d’Ornon, France; (C.P.); (A.C.); (F.J.); (S.C.); (A.L.); (P.B.); (A.D.); (O.C.)
- Bordeaux INP, ISVV, EA4577 OEnologie, F-33140 Villenave d’Ornon, France
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Ledormand P, Desmasures N, Dalmasso M. Phage community involvement in fermented beverages: an open door to technological advances? Crit Rev Food Sci Nutr 2020; 61:2911-2920. [PMID: 32649837 DOI: 10.1080/10408398.2020.1790497] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacteriophages (phages) are considered the most abundant biological entities on Earth. An increasing interest in understanding phage communities, also called viromes or phageomes, has arisen over the past decade especially thanks to the development and the accessibility of Next Generation Sequencing techniques. Despite the increasing amount of available metagenomic data on microbial communities in various habitats, viromes remain poorly described in the scientific literature particularly when it comes to fermented food and beverages such as wine and cider. In this review, a particular attention is paid to the current knowledge on phage communities, with a special focus on fermented food viromes and the methodological tools available to undertake their study. There is a striking lack of available data on the fermented foods and beverages viromes. As far as we know, and although a number of phages have been isolated from wine, no general study has to date been carried out to assess the diversity of viromes in fermented beverages and their possible interactions with microbiota throughout the fermentation process. With the aim of establishing connections between the currently used technologies to carry out the analysis of viromes, possible applications of current knowledge to fermented beverages are examined.
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Lysogeny in the Lactic Acid Bacterium Oenococcus oeni Is Responsible for Modified Colony Morphology on Red Grape Juice Agar. Appl Environ Microbiol 2019; 85:AEM.00997-19. [PMID: 31375489 DOI: 10.1128/aem.00997-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/24/2019] [Indexed: 11/20/2022] Open
Abstract
Oenococcus oeni is the lactic acid bacterium (LAB) that most commonly drives malolactic fermentation in wine. Although oenococcal prophages are highly prevalent, their implications on bacterial fitness have remained unexplored and more research is required in this field. An important step toward achieving this goal is the ability to produce isogenic pairs of strains that differ only by the lysogenic presence of a given prophage, allowing further comparisons of different phenotypic traits. A novel protocol for the rapid isolation of lysogens is presented. Bacteria were first picked from the center of turbid plaques produced by temperate oenophages on a sensitive nonlysogenic host. When streaked onto an agar medium containing red grape juice (RGJ), cells segregated into white and red colonies. PCR amplifications with phage-specific primers demonstrated that only lysogens underwent white-red morphotypic switching. The method proved successful for various oenophages irrespective of their genomic content and attachment site used for site-specific recombination in the bacterial chromosome. The color switch was also observed when a sensitive nonlysogenic strain was infected with an exogenously provided lytic phage, suggesting that intracolonial lysis triggers the change. Last, lysogens also produced red colonies on white grape juice agar supplemented with polyphenolic compounds. We posit that spontaneous prophage excision produces cell lysis events in lysogenic colonies growing on RGJ agar, which, in turn, foster interactions between lysed materials and polyphenolic compounds to yield colonies easily distinguishable by their red color. Furthermore, the technique was used successfully with other species of LAB.IMPORTANCE The presence of white and red colonies on red grape juice (RGJ) agar during enumeration of Oenococcus oeni in wine samples is frequently observed by stakeholders in the wine industry. Our study brings an explanation for this intriguing phenomenon and establishes a link between the white-red color switch and the lysogenic state of O. oeni It also provides a simple and inexpensive method to distinguish between lysogenic and nonlysogenic derivatives in O. oeni with a minimum of expended time and effort. Noteworthy, the protocol could be adapted to two other species of LAB, namely, Leuconostoc citreum and Lactobacillus plantarum It could be an effective tool to provide genetic, ecological, and functional insights into lysogeny and aid in improving biotechnological processes involving members of the lactic acid bacterium (LAB) family.
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Measures to improve wine malolactic fermentation. Appl Microbiol Biotechnol 2019; 103:2033-2051. [DOI: 10.1007/s00253-018-09608-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 12/27/2018] [Indexed: 01/06/2023]
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Hayes S, Vincentelli R, Mahony J, Nauta A, Ramond L, Lugli GA, Ventura M, van Sinderen D, Cambillau C. Functional carbohydrate binding modules identified in evolved dits from siphophages infecting various Gram-positive bacteria. Mol Microbiol 2018; 110:777-795. [DOI: 10.1111/mmi.14124] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/29/2018] [Accepted: 09/05/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Stephen Hayes
- School of Microbiology; University College Cork; Cork Ireland
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques; Aix-Marseille Université; Campus de Luminy Marseille France
- Architecture et Fonction des Macromolécules Biologiques; Centre National de la Recherche Scientifique (CNRS); Campus de Luminy Marseille France
| | - Jennifer Mahony
- School of Microbiology; University College Cork; Cork Ireland
| | - Arjen Nauta
- FrieslandCampina; Amersfoort The Netherlands
| | - Laurie Ramond
- Architecture et Fonction des Macromolécules Biologiques; Aix-Marseille Université; Campus de Luminy Marseille France
- Architecture et Fonction des Macromolécules Biologiques; Centre National de la Recherche Scientifique (CNRS); Campus de Luminy Marseille France
| | - Gabriele A. Lugli
- Laboratory of Probiogenomics, Department of Life Sciences; University of Parma; Parma Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences; University of Parma; Parma Italy
| | - Douwe van Sinderen
- School of Microbiology; University College Cork; Cork Ireland
- APC Microbiome Ireland, University College Cork; Cork Ireland
| | - Christian Cambillau
- School of Microbiology; University College Cork; Cork Ireland
- Architecture et Fonction des Macromolécules Biologiques; Aix-Marseille Université; Campus de Luminy Marseille France
- Architecture et Fonction des Macromolécules Biologiques; Centre National de la Recherche Scientifique (CNRS); Campus de Luminy Marseille France
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Complete Genome Sequence of Lytic Oenococcus oeni Bacteriophage OE33PA. Microbiol Resour Announc 2018; 7:MRA00818-18. [PMID: 30533896 PMCID: PMC6256464 DOI: 10.1128/mra.00818-18] [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: 06/17/2018] [Accepted: 07/24/2018] [Indexed: 11/20/2022] Open
Abstract
Oenococcus oeni is the most common species of lactic acid bacteria associated with malolactic fermentation in wine. Here, we report the genome sequence of the lytic phage OE33PA (vB_OeS_OE33PA). Oenococcus oeni is the most common species of lactic acid bacteria associated with malolactic fermentation in wine. Here, we report the genome sequence of the lytic phage OE33PA (vB_OeS_OE33PA). It has a morphotype similar to that of members of the Siphoviridae family, a linear 39,866-bp double-stranded genome with cohesive ends, and 57 predicted open reading frames.
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Philippe C, Krupovic M, Jaomanjaka F, Claisse O, Petrel M, le Marrec C. Bacteriophage GC1, a Novel Tectivirus Infecting Gluconobacter Cerinus, an Acetic Acid Bacterium Associated with Wine-Making. Viruses 2018; 10:v10010039. [PMID: 29337868 PMCID: PMC5795452 DOI: 10.3390/v10010039] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/05/2018] [Accepted: 01/12/2018] [Indexed: 12/22/2022] Open
Abstract
The Gluconobacter phage GC1 is a novel member of the Tectiviridae family isolated from a juice sample collected during dry white wine making. The bacteriophage infects Gluconobacter cerinus, an acetic acid bacterium which represents a spoilage microorganism during wine making, mainly because it is able to produce ethyl alcohol and transform it into acetic acid. Transmission electron microscopy revealed tail-less icosahedral particles with a diameter of ~78 nm. The linear double-stranded DNA genome of GC1 (16,523 base pairs) contains terminal inverted repeats and carries 36 open reading frames, only a handful of which could be functionally annotated. These encode for the key proteins involved in DNA replication (protein-primed family B DNA polymerase) as well as in virion structure and assembly (major capsid protein, genome packaging ATPase (adenosine triphosphatase) and several minor capsid proteins). GC1 is the first tectivirus infecting an alphaproteobacterial host and is thus far the only temperate tectivirus of gram-negative bacteria. Based on distinctive sequence and life-style features, we propose that GC1 represents a new genus within the Tectiviridae, which we tentatively named “Gammatectivirus”. Furthermore, GC1 helps to bridge the gap in the sequence space between alphatectiviruses and betatectiviruses.
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Affiliation(s)
- Cécile Philippe
- Institut des Sciences de la Vigne et du Vin (ISVV), University Bordeaux, Equipe d'Accueil 4577, Unité de Recherche Oenologie, 33882 Villenave d'Ornon, France.
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, 75015 Paris, France.
| | - Fety Jaomanjaka
- Institut des Sciences de la Vigne et du Vin (ISVV), University Bordeaux, Equipe d'Accueil 4577, Unité de Recherche Oenologie, 33882 Villenave d'Ornon, France.
| | - Olivier Claisse
- Institut des Sciences de la Vigne et du Vin (ISVV), University Bordeaux, Equipe d'Accueil 4577, Unité de Recherche Oenologie, 33882 Villenave d'Ornon, France.
- Institut National de la Recherche Agronomique (INRA), ISVV, Unité Sous Contrat 1366 Oenologie, 33882 Villenave d'Ornon, France.
| | - Melina Petrel
- Bordeaux Imaging Center, University Bordeaux, Unité Mixte de Service 3420 CNRS-Unité de Service 4, Institut National de la Santé et de la Recherche Médicale, 33076 Bordeaux, France.
| | - Claire le Marrec
- Institut des Sciences de la Vigne et du Vin (ISVV), University Bordeaux, Equipe d'Accueil 4577, Unité de Recherche Oenologie, 33882 Villenave d'Ornon, France.
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