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The Metagenomics Group at CBS

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

Catalog of previous student projects.


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.


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

The following projects are suggestions to bachelor, master or Ph.D student projects.
(This is not a definitive list so if you have an idea of a project you would like to work on, please contact group leader Thomas Sicheritz-Pontén )
  • 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



If you are interested in learning more about the group or our work, please contact group leader Thomas Sicheritz-Pontén.

Selected publications


Nature coverA human gut microbial gene catalogue established by metagenomic sequencing Nature. 2010 Mar 4;464(7285):59-65.
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J; MetaHIT Consortium, Bork P, Ehrlich SD, Wang J.




SaqqaqAncient human genome sequence of an extinct Palaeo-Eskimo Nature. 2010 Feb 11;463(7282):757-62.
Morten Rasmussen, Yingrui Li, Stinus Lindgreen, Jakob Skou Pedersen, Anders Albrechtsen, Ida Moltke, Mait Metspalu, Ene Metspalu, Toomas Kivisild, Ramneek Gupta, Marcelo Bertalan, Kasper Nielsen, M. Thomas P. Gilbert, Yong Wang, Maanasa Raghavan, Paula F. Campos, Hanne Munkholm Kamp, Andrew S. Wilson, Andrew Gledhill, Silvana Tridico, Michael Bunce, Eline D. Lorenzen, Jonas Binladen, Xiaosen Guo, Jing Zhao, Xiuqing Zhang, Hao Zhang, Zhuo Li, Minfeng Chen, Ludovic Orlando, Karsten Kristiansen, Mads Bak, Niels Tommerup, Christian Bendixen, Tracey L. Pierre, Bjarne Grønnow, Morten Meldgaard, Claus Andreasen, Sardana A. Fedorova, Ludmila P. Osipova, Thomas F. G. Higham, Christopher Bronk Ramsey, Thomas v. O. Hansen, Finn C. Nielsen, Michael H. Crawford, Søren Brunak, Thomas Sicheritz-Pontén, Richard Villems, Rasmus Nielsen, Anders Krogh, Jun Wang & Eske Willerslev

Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis, Science. 2007 Jan 12;315(5809):207-12. Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UC, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, Van de Peer Y, Miranda-Saavedra D, Barton GJ, Westrop GD, Muller S, Dessi D, Fiori PL, Ren Q, Paulsen I, Zhang H, Bastida-Corcuera FD, Simoes-Barbosa A, Brown MT, Hayes RD, Mukherjee M, Okumura CY, Schneider R, Smith AJ, Vanacova S, Villalvazo M, Haas BJ, Pertea M, Feldblyum TV, Utterback TR, Shu CL, Osoegawa K, de Jong PJ, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik SB, Logsdon JM Jr, Henze K, Gupta A, Wang CC, Dunne RL, Upcroft JA, Upcroft P, White O, Salzberg SL, Tang P, Chiu CH, Lee YS, Embley TM, Coombs GH, Mottram JC, Tachezy J, Fraser-Liggett CM, Johnson PJ





The genome of the protist parasite Entamoeba histolytica, Nature. 2005 Feb 24;433(7028):865-8. Loftus B, Anderson I, Davies R, Alsmark UC, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ, Nozaki T, Suh B, Pop M, Duchene M, Ackers J, Tannich E, Leippe M, Hofer M, Bruchhaus I, Willhoeft U, Bhattacharya A, Chillingworth T, Churcher C, Hance Z, Harris B, Harris D, Jagels K, Moule S, Mungall K, Ormond D, Squares R, Whitehead S, Quail MA, Rabbinowitsch E, Norbertczak H, Price C, Wang Z, Guillen N, Gilchrist C, Stroup SE, Bhattacharya S, Lohia A, Foster PG, Sicheritz-Ponten T, Weber C, Singh U, Mukherjee C, El-Sayed NM, Petri WA Jr, Clark CG, Embley TM, Barrell B, Fraser CM, Hall N




Structure and Content of the Entamoeba histolytica Genome, Advances in Parasitology Volume 65, 2007, Pages 51-190. C.G. Clark, U.C.M. Alsmark, M. Tazreiter, Y. Saito, Nakano, V. Ali, S. Marion, C. Weber, C. Mukherjee, I. Bruchhaus, E. Tannich, M. Leippe, T. Sicheritz-Ponten, P.G. Foster, J. Samuelson, C.J. Noël, R.P. Hirt, T.M. Embley, C.A. Gilchrist, B.J. Mann, U. Singh, J.P. Ackers, S. Bhattacharya, A. Bhattacharya, A. Lohia, N. Guillén, M. Duchêne, T. Nozaki and N. Hall


Trichomonas vaginalis surface proteins: a view from the genome, Trends in Parasitology (in print), Hirt R.P., Noel C.J., Sicheritz-Ponten, T, Tachezy J and Fiori P.-L



Full list of CBS publications