Molecular approaches to uncover phage-lactic acid bacteria interactions in a model community simulating fermented beverages

Ledormand, Pierre; Desmasures, Nathalie; Bernay, Benoı̂t; Goux, Didier; Rué, Oliver; Midoux, Cédric; Monnet, Christophe; Dalmasso, Marion

doi:10.1016/j.fm.2022.104069

Cited by 7 publications

(7 citation statements)

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“…Two lytic phages targeting O. oeni (OE33PA and Vinitor162) and one lytic phage targeting Gluconobacter cerinus (GC1) have been recently described in wine [18,37,38]. Moreover, in a previous work, 120 samples (cider, apple must, crushed apples) were screened for phages targeting 160 potential strains from genera found in cider, and only one lytic siphophage UCMA 21115 was isolated [23]. This result strengthens the hypothesis that cider is a poor reservoir of free lytic phages.…”

Section: Discussionsupporting

confidence: 70%

“…Phageome DNA extraction methods adapted from other matrices [2,11] were first tested on cider samples spiked with phage UCMA 21115 [23], at concentrations ranging from 10 4 to 10 9 PFU/mL. In some cases, the pH of the samples was adjusted to 5.5 (Table 2-III-VII), as it corresponded to a pH value suitable for phage DNA extraction from cider in preliminary experiments (data not shown).…”

Section: Validation Of the Extraction Methods After Collection Of Pha...mentioning

confidence: 99%

“…To collect and extract total phage DNA from cider, different approaches were tested and are summarised in Table 2. First, phageome DNA extraction was tested on cider samples spiked with phage UCMA 21115, previously isolated from cider [23] and originating from the UCMA collection (Université de Caen Microbiologie Alimentaire, Caen, France), in order to validate the method used. Concentrations of phage UCMA 21115 ranging from 10 4 to 10 9 PFU/mL were used (Table 2-I, II and III).…”

Section: Cider Sample Collection For Phageome and Prophage Investigationmentioning

confidence: 99%

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Investigation of the Phageome and Prophages in French Cider, a Fermented Beverage

et al. 2022

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Phageomes are known to play a key role in the functioning of their associated microbial communities. The phageomes of fermented foods have not been studied thoroughly in fermented foods yet, and even less in fermented beverages. Two approaches were employed to investigate the presence of phages in cider, a fermented beverage made from apple, during a fermentation process of two cider tanks, one from an industrial producer and one from a hand-crafted producer. The phageome (free lytic phages) was explored in cider samples with several methodological developments for total phage DNA extraction, along with single phage isolation. Concentration methods, such as tangential flow filtration, flocculation and classical phage concentration methods, were employed and tested to extract free phage particles from cider. This part of the work revealed a very low occurrence of free lytic phage particles in cider. In parallel, a prophage investigation during the fermentation process was also performed using a metagenomic approach on the total bacterial genomic DNA. Prophages in bacterial metagenomes in the two cider tanks seemed also to occur in low abundance, as a total of 1174 putative prophages were identified in the two tanks overtime, and only two complete prophages were revealed. Prophage occurrence was greater at the industrial producer than at the hand-crafted producer, and different dynamics of prophage trends were also observed during fermentation. This is the first report dealing with the investigation of the phageome and of prophages throughout a fermentation process of a fermented beverage.

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Section: Discussionsupporting

confidence: 70%

Section: Validation Of the Extraction Methods After Collection Of Pha...mentioning

confidence: 99%

Section: Cider Sample Collection For Phageome and Prophage Investigationmentioning

confidence: 99%

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Investigation of the Phageome and Prophages in French Cider, a Fermented Beverage

et al. 2022

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“…Four microbial strains, Liquorilactobacillus mali UCMA 16447, Leuconostoc mesenteroides CIM 3004, Oenococcus oeni UCMA 19297 and Saccharomyces uvarum UCMA 10446, were used in this study to create a model microbial community. Phage UCMA 21115 targeting L. mali UCMA 16447 was used because it was the first lytic siphophage isolated from cider [ 27 ]. The lytic phage PLE001 targeting Ln.…”

Section: Methodsmentioning

confidence: 99%

“…and Lactobacillus sensu lato, performing the malolactic fermentation. Even if phage occurrence in cider seems to be low, their role still needs to be taken into consideration in this complex matrix [ 26 , 27 ]. The aim of the current study was to investigate the role played by phages on the behavior of a model microbial community inspired by cider.…”

Section: Introductionmentioning

confidence: 99%

Phages Shape Microbial Dynamics and Metabolism of a Model Community Mimicking Cider, a Fermented Beverage

Ledormand

Desmasures

Schlusselhuber

et al. 2022

Viruses

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Model microbial communities are often studied to better understand interactions and fluxes during fermentation processes. However, models that take into account the potential impact of bacteriophages (phages), which are recognized as drivers of microbial communities, are scarce, especially in fermented foods. This study aimed at investigating the behavior of a cider model microbial community, which was subjected to disturbance in the presence or absence of phages and at two different temperatures (25 °C and 15 °C). The model microbial community was composed of three lactic acid bacteria (LAB) strains belonging to the species Liquorilactobacillus mali, Leuconostoc mesenteroides and Oenococcus oeni, and of a Saccharomyces uvarum yeast strain. Two phages were selected, targeting L. mali and Ln. mesenteroides strains. In order to follow the behavior of the microbial community model, the phages and microbial strains were enumerated at several time points, and the metabolic signatures (sugar consumption, production of organic acids and volatile organic compounds) of the model microbial community were monitored. At 25 °C, the community with phages (P) was significantly closer to the control condition (C) than to the condition without phages (D). Microbial levels were similar between conditions C and P, which were characterized by high concentrations of compounds such as 2-phenylethanol, ethyl octanoate and isoamyl alcohol, and more globally by a more complex metabolic signature than that of condition D. In condition D, L. mali and Ln. mesenteroides were dominant while S. uvarum and O. oeni were less present, and this condition was characterized by a high concentration of ethyl lactate. At 15 °C, condition P differed from conditions C and D, as Ln. mesenteroides was not detected while the other strains all reached approximately the same levels. The metabolic range of condition P was less important than for conditions C and D. The current study showed that the influence of phages on the model microbial community dynamics and metabolisms after a disturbance phenomenon was temperature-dependent.

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The bacteriome-coupled phage communities continuously contract and shift to orchestrate the traditional rice vinegar fermentation

Ma,

Qian,

et al. 2024

Food Research International

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Molecular approaches to uncover phage-lactic acid bacteria interactions in a model community simulating fermented beverages

Cited by 7 publications

References 48 publications

Investigation of the Phageome and Prophages in French Cider, a Fermented Beverage

Investigation of the Phageome and Prophages in French Cider, a Fermented Beverage

Phages Shape Microbial Dynamics and Metabolism of a Model Community Mimicking Cider, a Fermented Beverage

The bacteriome-coupled phage communities continuously contract and shift to orchestrate the traditional rice vinegar fermentation

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