In Silico Prediction of Horizontal Gene Transfer Events in Lactobacillus bulgaricus and Streptococcus thermophilus Reveals Protocooperation in Yogurt Manufacturing

Abstract

Lactobacillus bulgaricus and Streptococcus thermophilus, used in yogurt starter cultures, are well known for their stability and protocooperation during their coexistence in milk. In this study, we show that a close interaction between the two species also takes place at the genetic level. We performed an in silico analysis, combining gene composition and gene transfer mechanism-associated features, and predicted horizontally transferred genes in both L. bulgaricus and S. thermophilus. Putative horizontal gene transfer (HGT) events that have occurred between the two bacterial species include the transfer of exopolysaccharide (EPS) biosynthesis genes, transferred from S. thermophilus to L. bulgaricus, and the gene cluster cbs-cblB(cglB)-cysE for the metabolism of sulfur-containing amino acids, transferred from L. bulgaricus or Lactobacillus helveticus to S. thermophilus. The HGT event for the cbs-cblB(cglB)-cysE gene cluster was analyzed in detail, with respect to both evolutionary and functional aspects. It can be concluded that during the coexistence of both yogurt starter species in a milk environment, agonistic coevolution at the genetic level has probably been involved in the optimization of their combined growth and interactions. Lactobacillus delbrueckii subsp. bulgaricus (Lactobacillus bulgaricus)and Streptococcus thermophilus have been used in starter cultures for yogurt manufacturing for thousands of years. Both species are known to stably coexist in a milk environment and interact beneficially. This so-called protocooperation, previously defined as biochemical mutualism, involves the exchange of metabolites and/or stimulatory factors (38). Examples of biochemical protocooperation between L. bulgaricus and S. thermophilus include the action of cell wall-bound proteases, produced by L. bulgaricus strains, and formate, required for growth of L. bulgaricus and supplied by S. thermophilus (6, 7). An overview of the interactions between the two yogurt bacteria, including the exchange of CO 2 , pyruvate, folate, etc., can be found in a recently published review by Sieuwerts et al. (43). Putative genetic mechanisms underlying protocooperation, however, so far have not been studied in detail.The genomes of two L. bulgaricus strains and three S. thermophilus strains, all used in yogurt manufacturing, have been fully sequenced (3,32,33,34,39,44,46). The available genomic information could provide new insights into the genetic aspects of protocooperation between L. bulgaricus and S.

New Insights into Various Production Characteristics of Streptococcus thermophilus Strains

“…In the process of evolution, some carbohydrate metabolism genes, virulence genes and other genes gradually degrade and disappear in the stable milk environment [6,25,26,27]. The virulence genes in other streptococci are either non-functional or completely absent in S. thermophilus [6,25,26,27]. S. thermophilus contains genes for glycolytic pathway, the non-oxidative branch of the pentose phosphate pathway, and pyruvate metabolism.…”

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

“…protocooperative species L. bulgaricus and S. thermophilus (Li et al, 2013;Liu et al, 2009). Sequencing of Penicillium species isolated from the cheesemaking environment identified HGT of large genomic islands between these key fungal inhabitants of cheese (Cheeseman et al, 2014;Ropars et al, 2015;Gibbons and Rinker, 2015).…”

Exopolysaccharides Produced from <i>Lactobacillus delbrueckii</i> subsp. <i>bulgaricus</i>

“…The EPS synthesis genes of L. bulgaricus are encoded on chromosome DNA and transmitted horizontally from S. thermophilus during utilization as starters of fermented milk with S. thermophilus strains [33]. In this study, however, some eps genes have been shown with a complete genome analysis, and there is only one paper that discusses the eps cluster on L. bulgaricus [34].…”