ArticleBMC genomics2019
Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Evaluation of SpecificMicroorganisms · 2025Article
- Comparative genomic analysis of 255Microbiology spectrum · 2025Article
- A reassessment of the infra-species diversity patterns in the wine-associatedFrontiers in microbiology · 2025Article
- Viability and Diversity of the Microbial Cultures Available in Retail Kombucha Beverages in the USA.Foods (Basel, Switzerland) · 2024Article
- A new cheese population inEvolutionary applications · 2023Article
- Phage Encounters Recorded in CRISPR Arrays in the GenusViruses · 2022Article
- Genomic Analysis of an Excellent Wine-Making StrainPolish journal of microbiology · 2022Article
- Analysis of Transcriptomic Response to SOMicrobiology spectrum · 2021Article
- Distribution of Prophages in theMicroorganisms · 2021Article
- Distribution of Oenococcus oeni populations in natural habitats.Applied microbiology and biotechnology · 2019Review
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8 authors.
Funding
Abstract
backgroundOenococcus 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.
resultsSequence-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.
conclusionsThe 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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