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Comparative Genome Analysis of Lactococcus lactis Indicates Niche Adaptation and Resolves Genotype/Phenotype
Michiel Wels1,2, Roland Siezen2,3,4, Sacha van Hijum1,2,3
1NIZO Food Research B.V., Ede, Netherlands.
Frontiers in Microbiology
|February 16, 2019
Summary
Lactococcus lactis strains were analyzed using machine learning to resolve taxonomic confusion. Dairy strains likely evolved from plant isolates, with cremoris strains adapted to dairy environments.
Area of Science:
- Microbiology
- Genomics
- Dairy Science
Background:
- Lactococcus lactis is crucial for dairy fermentation, impacting flavor and texture through metabolites.
- Taxonomic classification is complicated by strains with cremoris genotypes but lactis phenotypes.
Purpose of the Study:
- To analyze genomes of dairy and non-dairy Lactococcus lactis strains.
- To resolve genotype/phenotype discrepancies within L. lactis subspecies.
- To identify genes associated with niche adaptation and subspecies specificity.
Main Methods:
- Comparative genomics of 43 L. lactis strains (19 dairy, 24 non-dairy).
- Application of machine-learning algorithms to identify orthologous groups (OGs).
- Analysis of phenotypic properties and plasmid-encoded genes.
Main Results:
- Machine learning accurately categorized strains, resolving genotype/phenotype disparities.
- Evidence suggests dairy L. lactis evolved from plant-associated ancestors.
- cremoris phenotype strains exhibit eroded genomes, limiting them to dairy environments.
Conclusions:
- Genome comparisons reveal niche and subspecies-specific genes in L. lactis.
- Findings clarify evolutionary relationships and aid industrial starter culture selection.
- Understanding L. lactis genomics is key for optimizing dairy fermentation processes.
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