Analys av gener och arter i metagenomikdata

Abstract

As new extreme high throughput DNA sequencing methods continue to develop the large amounts of information that they give rise to in terms of metagenomic data opens the way for completely novel approaches to the study of microbial ecosystems. In this project we have investigated how relationships and connections between microbial genes and species that carry them can be found based entirely on their appearance in two separate datasets accumulated from the same samples using metagenomic analysis. The dataset used in the study consists of abundance of genes and species derived from DNA isolated from microbial communities in biofilms formed in seawater treated with different concentrations of the antimicrobial agent triclosan. Genes and species that responded in the same way to changes in the concentration of triclosan were grouped together for further analysis. The method used for creating the different constellations consisted of a first step where genes and species were clustered based on their abundance in the samples. In the next step genes with strong correlations to each cluster of species and species with strong correlations to each cluster of genes were identified. These constellations based on species and genes were robust appearing not to vary with variations in the parameters of the analysis and not to be dependent on whether the clustering was based on associations of genes or vice versa. The constellations were also homogeneous with respect to species and gene functionality (the same genes clustering with the same species) which we interpret as meaning that the likelihood of a tangible connection between them being identified is high. Clearly, concrete conclusions regarding the species and the genes they carry cannot me made using the methods we present here, but several interesting patterns have emerged that would bare further scrutiny. For example, genes involved with the horizontal transfer of DNA between species do not appear to survive in triclosan whereas genes associated with the bacterial immune system were highly associated with bacteria that were able to establish themselves in the presence of triclosan. Few analyses have been done in which information about the species present in a studied niche or ecosystem and the genes that they collectively contain are combined and there is much new information to be derived from such studies. Statistical approaches to the analysis of species and their collective genome has the potential to give new insights into previously unknown associations and to develop hypotheses that can be further tested experimentally.