Spotlight on the viral diversity of fermented vegetables using viral metagenomics
| dc.rights.license | open | en_US |
| dc.contributor.author | GENDRE, Julia | |
| hal.structure.identifier | Unité de Recherche Œnologie [Villenave d'Ornon] [OENO] | |
| dc.contributor.author | LE MARREC, Claire | |
| dc.contributor.author | CHAILLOU, Stéphane | |
| dc.contributor.author | LANDAUD, Sophie | |
| dc.contributor.author | DUGAT-BONY, Eric | |
| dc.date.accessioned | 2024-03-20T13:31:46Z | |
| dc.date.available | 2024-03-20T13:31:46Z | |
| dc.date.conference | 2023-11 | |
| dc.identifier.uri | https://oskar-bordeaux.fr/handle/20.500.12278/188881 | |
| dc.description.abstractEn | Fermented vegetables are traditionally made using natural microorganisms found in the raw ingredients. The bacterial and fungal communities of fermented vegetables are well known, which is not the case for phage communities. Previous studies have identified various phages infecting different bacteria in sauerkraut, revealing the complexity of phages in this ecosystem, and metagenomic analysis highlighted the predominance of uncharacterized phages. Our project aims to provide a comprehensive description of the viral communities in fermented plant-based foods (sauerkraut, fermented carrots, and fermented turnips) to better understand their role in these microbial ecosystems. The viral fraction was purified, quantified by epifluorescence microscopy and determined through a viral metagenomics approach involving nucleic acid extraction, DNA and RNA amplification and high throughput sequencing. A bioinformatics pipeline was established to process raw reads into viral operational taxonomic units (vOTUs). Representative sequences from each vOTU were analyzed to predict viral contigs and host. Based on epifluorescence microscopy, we estimated the concentration of viruses at 5 x 107 particles/g of sample. Viral metagenomics analysis identified viral contigs with sequence homology to known phages, including those infecting Lactobacillus brevis, a common species in fermented vegetables. Some contigs were predicted to be viral, albeit without strong homology to known viruses, but with a bacterial host prediction, mainly belonging to lactic acid bacteria typically found in vegetable fermentation. In conclusion, this study offers insights into the composition of viral communities in different fermented vegetables, focusing on extracellular viral particles. The findings suggest that several phages target the dominant lactic acid bacteria involved in the fermentation process, potentially influencing bacterial successions in the ecosystem. Understanding the ecological roles of these phages is crucial for controlling their activity and ensuring the quality of the fermentation process. | |
| dc.language.iso | EN | en_US |
| dc.rights | Attribution 3.0 United States | * |
| dc.rights.uri | http://creativecommons.org/licenses/by/3.0/us/ | * |
| dc.subject.en | Bacteriophage | |
| dc.subject.en | Epifluorescence microscopy | |
| dc.subject.en | Fermented vegetable | |
| dc.subject.en | Virome | |
| dc.title.en | Spotlight on the viral diversity of fermented vegetables using viral metagenomics | |
| dc.type | Poster | en_US |
| dc.subject.hal | Sciences du Vivant [q-bio]/Biologie végétale | en_US |
| bordeaux.hal.laboratories | Oenologie - UMR 1366 | en_US |
| bordeaux.institution | Université de Bordeaux | en_US |
| bordeaux.institution | Bordeaux INP | en_US |
| bordeaux.institution | INRAE | en_US |
| bordeaux.conference.title | PHAGES in LYON 2023 | en_US |
| bordeaux.country | fr | en_US |
| bordeaux.conference.city | Lyon | en_US |
| hal.invited | oui | en_US |
| hal.popular | non | en_US |
| hal.audience | Internationale | en_US |
| hal.export | false | |
| dc.rights.cc | CC BY | en_US |
| bordeaux.COinS | ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.au=GENDRE,%20Julia&LE%20MARREC,%20Claire&CHAILLOU,%20St%C3%A9phane&LANDAUD,%20Sophie&DUGAT-BONY,%20Eric&rft.genre=unknown |
