1. Introduction to metagenomics Agnieszka S. Juncker Center for Biological Sequence Analysis Technical University of Denmark

2. Outline Metagenomics The human gut

3. From genomics to metagenomics Genomics E. coli, Science, 1997Human, Nature/Science, 2001 Metagenomics Saragasso sea, Science, 2004Human gut, Nature, 2010

4. What is Metagenomics? Metagenomics From Wikipedia, the free encyclopedia Metagenomics (also Environmental Genomics, Ecogenomics or Community Genomics) is the study of genomes recovered from environmental samples as opposed to from clonal cultures. Metagenomics ( Environmental Genomics, Ecogenomics or Community Genomics) is the study of genetic material recovered directly from environmental samples. Metagenomics is application of modern genomic techniques to the study of communities of microbial organisms directly in their natural environments, bypassing the need for isolation and lab cultivation of individual species Chen & Pachter, 2005

5. B) 99% of microbial species cannot currently be cultivated A) Most microbial activities are carried out by complex communities of microorganisms... Culturing: a few hundreds species per gram 16S sequencing: few thousands per gram A hand full of soil... About Metagenomics

6. Why Metagenomics? Discovery of: novel natural products new antibiotica new molecules with new functions new enzymes and bioactive molecules what is a genome/species diversity of life interplay between human and microbes how do microbial communities work and how stable are they holistic view on biology

7. Environments

8. Sample preparation Design of study and sampling (sample size, timing, replicates) Avoid contamination Pre-treatment, e.g. filtering

9. DNA extraction from sample Lysation and DNA extraction, many methods availble, different biases

10. Thomas Sicheritz-PonténCenter for Biological Sequence AnalysisTechnical University of DenmarkThomas Sicheritz-PonténCenter for Biological Sequence AnalysisTechnical University of Denmark Metagenomics approaches Sequence-basedFunctional (computational)(experimental)

11. Thomas Sicheritz-PonténCenter for Biological Sequence AnalysisTechnical University of DenmarkThomas Sicheritz-PonténCenter for Biological Sequence AnalysisTechnical University of Denmark Sequence-based metagenomics Sampling DNA extraction PCR+sequencing of 16S rDNA Phylogeny analysis Sequencing Assembly Gene finding and annotation Comparison 16S rDNA sequencingWhole-genome sequencing

12. Metagenomics data analysis Taxonomy annotationFunctional annotation

13. Metagenomics data analysis – wrap up Sequence reads Assembly (contigs) Gene prediction Count matrix calculation (in case of many samples) Taxonomy annotation (BLAST, LCA) Functional annotation (COG, KEGG, GO) Main statistical analysis

14. Project examples <

15. The human microbiome 15

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17. Human intestines

18. Metagenomics of the human gut

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22. Functions of the human gut microbiome

24. Inflammatory Bowel Diseases (IBD) In medicine, inflammatory bowel disease (IBD) is a group of inflammatory conditions of the colon and small intestine. The major types of IBD are Crohn's disease and ulcerative colitis. The incidence of Crohn's disease has been ascertained from population studies in Norway and the United States and is similar at 6 to 7.1:100,000. Crohn's disease The incidence of ulcerative colitis in North America is 10–12 cases per 100,000 per year, with a peak incidence of ulcerative colitis occurring between the ages of 15 and 25. Ulcerative colitis

25. Metagenomic Species Richness

26. Acknowledgements Marcelo Bertalan Søren Brunak Thomas Sicheritz Pontén Pia Friis Lene Blicher H. Bjørn Nielsen Damian Plichta Laurent Gautier Falk Hildebrand (from Jeroen’s group)