Investigating microbial diversity by analysis of distant variable regions of 16S rRNA using MiSeq paired end sequencing

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

Describing microbial community is necessary to answer fundamental questions in microbial ecology. Since the majority of microorganisms are nonculturable, culture-independent genomic analysis such as next generation sequencing are of great importance for describing microbial communities. However, sequencing of rRNA gene by MiSeq platform is limited with a maximum of 300 bp that can be sequenced.

The aim of this project is to amplify part of rRNA gene flanking at least two variable regions using universal primers, and then sequencing the distantvariable regions by paired-end sequencing that will not necessarily will cover the whole amplicon. In  silico PCR amplification of the different variable regions of the 16S rRNA gene will be done, then 200 bp of the 16S rRNA gene sequences from the reference databases will be cut starting from the forward and reverse primers and joined together to generate artificial databases covering different combinations of the variable regions. In silico, 16S rRNA gene amplicons will be generated, clustered at different levels and classified against the artificial databases of 16S rRNA gene covering the same variable regions to determine the best analysis parameters. The best two variable regions combinations will be selected to design primers that will be applied to complex biological samples to evaluate the developed method.

This project at Section of Microbiology depends on one master student with fair knowledge in molecular biology and experience in UNIX and programming (Perl, Python, R etc) is advantageous.

Søren J. Sørensen:

Supervisor(s):  Søren J. Sørensen