Group leader: Thomas Sicheritz-Pontén
Less than 1% of most microorganisms can be grown and studied in the lab. With the advent of low-cost high-through-put DNA sequencing technologies, it has become possible to explore the genetic material from entire microbial communities directly without the need of culturing the organisms under study. This emerging field, known as Metagenomics, utilizes a huge genetic reservoir of non-culturable organisms as a resource for biotechnological and medical products and processes.
The Metagenomics group at CBS is collecting different samples from all-over the world and developing new tools that will address many of the unique challenges of metagenomics data sets. The majority of our projects are based on at least one of following three simple question: Who is in there? What are they doing? How are they doing it? Our major focus is on metatranscriptomics of the human microbiome - correlating changes in the human microbiome with changes in human health - where we are involved in the EU project Metagenomics of the human intestinal tract (MetaHIT).
We have a close collaboration with the Molecular and Cellular Evolution of Microbial Eukaryotes group in Newcastle, studying the impact of lateral gene transfer (LGT) on prokaryotic genome evolution and eukaryotic parasites. To facilitate the modeling of metabolic and signaling pathways in both prokaryotic and eukaryotic organisms, we are developing a protein features based pipeline centered around the how-suite (how, howlin, GAHowlin, powlin etc.) and also new methods for the analysis of genomic and metagenomic data, mostly based machine learning methods. Some examples are meTaxa, a taxonomy predictor for next-generation sequencing reads; NetPhosK, a neural network based phoshorylation predictor and SPyPhy - automatic, large-scale reconstructions of phylogenetic relationships of complete genomes.
Read more at the CBS website