ArticleBMC microbiology2013
Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods.
Article in BMC microbiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 34 citations in OpenAlex.
- Hybrid genome assembly and phenotypic assays reveal carbohydrate metabolism diversity in Lacticaseibacillus strains.Applied microbiology and biotechnology · 2026Article
- High-throughput generation and comparison of genome-scale metabolic models reveal strain-specific metabolic diversity in 439mSystems · 2026Article
- The strain-dependent cytostatic activity of Lactococcus lactis on CRC cell lines is mediated through the release of arginine deiminase.Microbial cell factories · 2024Article
- From genotype to phenotype: computational approaches for inferring microbial traits relevant to the food industry.FEMS microbiology reviews · 2023Review
- Occurrence of phenotypic variation inBiotechnology reports (Amsterdam, Netherlands) · 2022Article
- Phenotype testing, genome analysis, and metabolic interactions of three lactic acid bacteria strains existing as a consortium in a naturally fermented milk.Frontiers in microbiology · 2022Article
- Eye-color and Type-2 diabetes phenotype prediction from genotype data using deep learning methods.BMC bioinformatics · 2021Article
- GIMICA: host genetic and immune factors shaping human microbiota.Nucleic acids research · 2021Article
- Machine learning predicts and provides insights into milk acidification rates of Lactococcus lactis.PloS one · 2021Article
- Identification of Nitrogen Fixation Genes inMicroorganisms · 2020Article
- Article
- Uncovering carbohydrate metabolism through a genotype-phenotype association study of 56 lactic acid bacteria genomes.Applied microbiology and biotechnology · 2019Article
- Comparative Genome Analysis ofFrontiers in microbiology · 2019Article
- MAGNAMWAR: an R package for genome-wide association studies of bacterial orthologs.Bioinformatics (Oxford, England) · 2018Article
- Cell Surface Properties ofFrontiers in microbiology · 2017Article
- Microbial bioinformatics for food safety and production.Briefings in bioinformatics · 2016Review
- Correlation of Lactobacillus rhamnosus Genotypes and Carbohydrate Utilization Signatures Determined by Phenotype Profiling.Applied and environmental microbiology · 2015Article
- Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii.BMC genomics · 2015Article
- Functional genomics of lactic acid bacteria: from food to health.Microbial cell factories · 2014Review
- Genotypic and phenotypic analysis of dairy Lactococcus lactis biodiversity in milk: volatile organic compounds as discriminating markers.Applied and environmental microbiology · 2013Article
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Authors and funding
5 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLactococcus lactis is used in dairy food fermentation and for the efficient production of industrially relevant enzymes. The genome content and different phenotypes have been determined for multiple L. lactis strains in order to understand intra-species genotype and phenotype diversity and annotate gene functions. In this study, we identified relations between gene presence and a collection of 207 phenotypes across 38 L. lactis strains of dairy and plant origin. Gene occurrence and phenotype data were used in an iterative gene selection procedure, based on the Random Forest algorithm, to identify genotype-phenotype relations.
resultsA total of 1388 gene-phenotype relations were found, of which some confirmed known gene-phenotype relations, such as the importance of arabinose utilization genes only for strains of plant origin. We also identified a gene cluster related to growth on melibiose, a plant disaccharide; this cluster is present only in melibiose-positive strains and can be used as a genetic marker in trait improvement. Additionally, several novel gene-phenotype relations were uncovered, for instance, genes related to arsenite resistance or arginine metabolism.
conclusionsOur results indicate that genotype-phenotype matching by integrating large data sets provides the possibility to identify gene-phenotype relations, possibly improve gene function annotation and identified relations can be used for screening bacterial culture collections for desired phenotypes. In addition to all gene-phenotype relations, we also provide coherent phenotype data for 38 Lactococcus strains assessed in 207 different phenotyping experiments, which to our knowledge is the largest to date for the Lactococcus lactis species.
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