Differential gene expression in multispecies biofilm

Main area:Microbiology
Target group:Biology, Bioinformatics, Molecular Biomedicine
Educational level:Masters
Project description:

In most environments, bacteria are part of multispecies biofilms and the biofilm mode-of-growth is predominant among most bacterial species. In biofilms, bacteria are enclosed in a self-produced polymeric matrix and more protected from disinfectants and antimicrobial agents than their planktonic counterparts.

It has been observed that the protective effect of biofilms may be further enhanced in multispecies biofilms due to various interactions. The presence of some species provides a protective effect on other species and may shield them from inactivating compounds. Therefore, species incapable of biofilm formation by themselves may be present in multispecies biofilms, which is of particular interest – and concern – with respect to pathogenic bacteria. These observed changes are likely to be caused by changes in gene expression when bacteria are forming biofilms in mixed communities compared to single species biofilms. The genes that are regulated differentially are however not yet identified.

We have identified a model system composed of four soil isolates interacting synergistically with respect to biofilm formation, sequenced their genomes and transcriptomes under specific conditions. Two student projects are related to this study:
1) Differential gene expression in single and multispecies biofilms: Based on the transcriptomes of single and multi species biofilms, genes expressed differently under these two conditions will be identified. Primers specifically suitable for quantitative PCR, targeting these genes will be designed. This enables validation/exploration of differential gene expression under different conditions at different stages in biofilm development.
2) Metabolic networks The inter-specific interactions in biofilms may in some cases be caused by metabolic complementation. Such metabolic interactions/dependencies may be reflected in the genes encoding metabolic functions, and can be identified by constructing bioinformatic “metabolic networks”. Based on the genome sequences of the four species mentioned above, metabolic networks will be generated to possibly explain the observed synergistic effect in biofilm formation.

Students with special interest in biofilms and inter-species interactions, interested in working with the model biofilm on a different (self-defined?) project are also welcome to contact us at Section of Microbiology.

References: M. Burmølle, J. Webb, D. Rao, L. H. Hansen, S. J. Sørensen and S. Kjelleberg (2006). Enhanced biofilm formation and increased resistance to antimicrobial agents and bacterial invasion are caused by synergistic interactions in multispecies biofilms. Applied and Environmental Microbiology, 72: 3916-23.

Keywords:Cooperation, Biofilm, Gene expression, Transcriptomics
Project home page: https://www.bio.ku.dk/english/research/microbiology/
Supervisor(s):  Mette Burmølle