Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus

Abstract

The lactic acid bacterium Streptococcus thermophilus is widely used for the manufacture of yogurt and cheese. This dairy species of major economic importance is phylogenetically close to pathogenic streptococci, raising the possibility that it has a potential for virulence. Here we report the genome sequences of two yogurt strains of S. thermophilus. We found a striking level of gene decay (10% pseudogenes) in both microorganisms. Many genes involved in carbon utilization are nonfunctional, in line with the paucity of carbon sources in milk. Notably, most streptococcal virulence-related genes that are not involved in basic cellular processes are either inactivated or absent in the dairy streptococcus. Adaptation to the constant milk environment appears to have resulted in the stabilization of the genome structure. We conclude that S. thermophilus has evolved mainly through loss-of-function events that remarkably mirror the environment of the dairy niche resulting in a severely diminished pathogenic potential.

Figure 1. Lateral gene transfer between S. thermophilus and dairy bacteria.

(a) Schematic representation of a 17-kb mosaic region of lateral gene transfer encompassing DNA fragments with more than 90% DNA/DNA identity with Lactococcus lactis subsp. lactis (L.L. lactis, blue), Lactococcus lactis subsp. cremoris (L.L. cremoris, red; Joint Genome Institute, http://www.jgi.doe.gov) and Lactobacillus bulgaricus (green; Joint Genome Institute, http://www.jgi.doe.gov). Rectangular boxes in color correspond to exchanged DNA regions; species, DNA fragment size and percentage of DNA identity are indicated below. IS1191 are shown as black boxes. Extension '-tr' indicates genes inactive because of a truncation or one or more frameshifts, pepD, endopeptidase; tnp, transposase; hsdR, restriction endonuclease; hsdM, methylase; dacA, carboxypeptidase; IS, insertion sequences. (b) Adhesion of S. thermophilus CNRZ1066 and L. bulgaricus. The two organisms were cultivated together in liquid broth to mid-exponential phase; a glass slide was deposited in the culture for 1 h, withdrawn and rinsed five times with water and observed under an optical microscope. Inset, higher magnification.