The Metagenomics Group at CBS

Group leader: Thomas Sicheritz Pontén
Members: Agnieszka Sierakowska Juncker, Asli Ismihan Özen, Aviaja Zenia Edna Lyberth Hauptmann, Bent Petersen, Damian Rafal Plichta, Dhany Saputra, Henrik Bjørn Nielsen, Henrik Marcus Geertz-Hansen, Ida Bonde, Jacob Bælum, Josef Korbinian Vogt, Nikolaj Blom, Simon Rasmussen, Thomas Nordahl Petersen
Guest members: Jens Friis-Nielsen, Ramneek Gupta

Catalog of previous student projects.

About the group

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.
Together with Comparative Genomics Group, will are giving the course Prokaryotic Gene Discovery, Metagenomics and Pangenomics (10 ECT)

A non-exhaustive list of current projects: Genomics Center for Molecular Epidemiology (Google bacterium) Antique Systems Biology (First ancient human genome) Metagenomics of the Human Intestinal Tract:  MetaHIT A (spying) phylogenomic approach to genome evolution: SPyPhy Horizontal Gene Transfer studies in the evolution of parasitic eukaryotes Genome Sequencing of eukaryotic parasites DNA of the Polar Seas  (part of the Galathea3 expedition) Marine Biotechnology Novel enzymes of industrial relevance: Novenia Projects based on CBS flagships: How, Howlin and PFM development of How and Howlin development of How* based tools, GAHowlin, Powlin metTaxa, predicting taxonomy of metagenomic data Protein Feature Method (PFM) pipeline clustering of metagenomic data in PFM space prediction of chaperone-dependent proteins prediction of Lipid raft associated proteins prediction of subcelullar locations

A non-exhaustive list of samples we are working on: Deep sea bacteria from North and South poles Bacteria in snow from the North Pole Ice cores from the North Pole Microbes from the Ikait Columns in Greenland Human gut microbiome from obese and lean individuals Human gut microbiome from IBD patients Infantile Colicky microflora Ancient DNA

Student projects

• Metatranscriptomics analysis of gene expression
• Genome annotation of microbial genomes
• Identification and analysis of phylogenic markers from metagenomic data
• Hunting enzymes in metagenomic data
• 16S analysis of microbial DNA from the Galathea III expedition
• Gene synteny trees
• Phylogenomic studies of microbial genomes
• Neural network based predictors
• Lateral gene transfer screens
• Protein function predictors
• Supertrees
  

Selected publications