Introduction to metagenomics
Agnieszka S. Juncker
Center for Biological Sequence AnalysisTechnical University of Denmark
Outline
• Metagenomics
• The human gut
From genomics to metagenomics
Genomics
E. coli, Science, 1997 Human, Nature/Science, 2001
Metagenomics
Saragasso sea, Science, 2004 Human gut, Nature, 2010
What is Metagenomics?
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
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
Why Metagenomics?
Discovery of:novel natural productsnew antibioticanew molecules with new functionsnew enzymes and bioactive molecules
what is a genome/speciesdiversity of life interplay between human and microbeshow do microbial communities work and how stable are they
holistic view on biology
Environments
Sample preparation
Design of study and sampling (sample size, timing, replicates)
Avoid contamination
Pre-treatment, e.g. filtering
DNA extraction from sample
Lysation and DNA extraction, many methods availble, different biases
Metagenomics approaches
Sequence-based Functional (computational) (experimental)
Sequence-based metagenomics
SamplingDNA extraction
PCR+sequencing of 16S rDNAPhylogeny analysis
Sequencing
Assembly
Gene findingand annotation
Comparison
Comparison
16S rDNA sequencing Whole-genome sequencing
Metagenomics data analysis
Taxonomy annotation Functional annotation
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
Project examples
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The human microbiome
15
16
Human intestines
Metagenomics of the human gut
19
Functions of the human gut microbiome
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
Metagenomic Species Richness
Acknowledgements
Marcelo Bertalan
Søren Brunak
ThomasSicheritz Pontén
Pia Friis Lene Blicher
H. Bjørn Nielsen
Damian Plichta
Laurent Gautier
Falk Hildebrand(from Jeroen’s group)