Evolutionary genomics of lactobacilli

Lactobacilli are an interesting group of bacteria found in a large variety of ecosystems, from the human gut to milk to plant surfaces and other environments. They are used in food fermentations and as health-promoting bacteria. It is not yet clear how lactobacilli are able to survive and thrive in these different environments. Did Lactobacillus strains adapt, each to a specific environment? Or are some strains "nomads", able to survive in many different environments? We will attempt to solve the adaptation question in two ways. First, we will study gene copynumber variation between Lactobacillus strains. The DNA of a bacterial strain can contain multiple copies of a single gene, and this copy-number can differ between strains. It was recently observed that copy-number variation in gut bacteria is often found in genes linked to environmental adaptation. As a second way to investigate environmental adaptation, we will reconstruct the evolutionary history of the Lactobacilli. Bacterial strains can evolve in multiple ways; two important types of evolutionary events are that they can acquire genes from other bacteria or genes can get lost. We will use the full DNA sequences of at least fifty strains per species to find out which genes were acquired and which ones were lost by which ancestors in the course of evolution. We can then see whether there is a connection between these gene gain and loss events and the environment in which these ancestors lived.

Keywords:LACTOBACILLUS, GENOME ANALYSIS

Disciplines:Microbiology, Systems biology, Laboratory medicine