Genomics and metagenomics of bacterial antibiotic and metal resistance

Introduction
The purpose of this research project is to understand different genetic mechanisms behind bacterial antibiotic and metal resistance. Our current focus is on antibiotic resistant bacterial communities in the Baltic Sea includincg its catchment area . The project aims at a phylogenic characterization of resistant bacterial populations and an improved understading of antibiotic resistance as a dynamic ecological phenomenon. In addition to basic knowledge, the results contribute significantly to medical microbiology, fish farming management and environmental risk assessment. We are especially interested in Lateral gene transfer which is an important mechanism of bacterial adaptation to adverse environmental conditions by the acquisition of genes. Genes are transferred between bacteria of different species, even between distant phyla. The most commonly known example of lateral gene transfer is the formation of antibiotic resistant bacterial strains in hospitals. Many other genes are transferred as well, making lateral gene transfer an important agent in bacterial evolution.

Genomic and metagenomic approach
Microbial diversity in any environmental setting is stunning. Estimates vary from 10000 to 1000000 bacterial species in a gram of soil, depending on the study and the definition used for a bacterial species. Most environmental bacteria are recalcitrant to cultivation. They are highly adapted to their ecological niches and are dependent on complex symbiotic relationships that are impossible to replicate under laboratory conditions. Therefore any attempts to cultivate the full diversity of sediment bacteria are doomed to fail.

We have adopted a different strategy, applying PCR- and sequencing based methods on total DNA isolated from the environmental samples. This allows us to accurately characterize bacterial community shifts in response to antibiotic pollution and to draw conclusions on the time scale and dynamics of resistance gene evolution. Using modern sequencing technologies in combination with statistical and mathematical tools, the daunting diversity of environmental bacteria can reasonably be dealt with.