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

<

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)