Examining Committee  
Dr. Iris Joye, Chair  
Dr. Gisele LaPointe, Advisor  
Dr. Arthur Hill, Advisory Committee Member   
Dr. Lawrence Goodridge, Department Member  
  
TITLE: CHARACTERIZING BACTERIAL DIVERSITY IN UNDEFINED DAIRY STARTER CULTURES USED FOR CHEDDAR CHEESE PRODUCTION  
  
ABSTRACT:   
Mesophilic mixed cultures commonly used in Cheddar cheese production contain strains of bacteria with a limited number of species, usually a mix of Lactococcus lactis subspecies cremoris  and  subspecies  lactis.  To  gain  insight  into  the  microbial  diversity  of  Cheddar cheese starter mixtures, the community dynamics and diversity within nine undefined starter mixes were determined by 16S amplicon sequencing shotgun metagenomics and L. lactis isolate whole genome sequencing. Each starter culture showed a distinctive major consensuses  sequence  based  on  183 Lactococcus  lactis  species-specific  markers.  The genomes of 97 isolates of L. lactis  subsp. cremoris were grouped into 7 clades and their functions were compared using RAST (Rapid Annotation using Subsystem Technology).  Reddy differential agar was used to differentiate isolates between lactococcal subtypes, and those isolates were further classified for proteolytic and acidification performance to correlate phenotype with genome sequences. Isolates were grouped into categories of cremoris  genotype  cremoris  phenotype  (‘true  cremoris’)  and  cremoris  genotype  lactis phenotype.  This  can  help  further  explain  the  cremoris/lactis  genotype  and  phenotype discrepancies of the Lactococcus lactis subspecies.