title: Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods.
abstract: BACKGROUND
  Lactococcus 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.
  
  
  RESULTS
  A 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.
  
  
  CONCLUSIONS
  Our 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.
authors.affiliation: Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, PO Box 9101, Nijmegen, The Netherlands.
authors.forename: Jumamurat R
authors.initials: JR
authors.lastname: Bayjanov
authors.forename: Marjo J C
authors.initials: MJ
authors.lastname: Starrenburg
authors.forename: Marijke R
authors.initials: MR
authors.lastname: van der Sijde
authors.forename: Roland J
authors.initials: RJ
authors.lastname: Siezen
authors.forename: Sacha A F T
authors.initials: SA
authors.lastname: van Hijum
mesh_terms: D018053:Arsenites / Q000378:metabolism; D050260:Carbohydrate Metabolism; D024881:Drug Resistance, Bacterial; D014644:Genetic Variation; D005838:Genotype; D007218:Industrial Microbiology; D013294:Lactococcus lactis / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D010641:Phenotype; D010944:Plants / Q000382:microbiology*
chemical_list: D018053:Arsenites