= Changes in the gut microbiome: Analyzing Whole Genome Shotgun data =

== Supervisors ==

Floris Imhann
Marc Jan Bonder
Arnau Vich Vila

== Introduction ==

The microbiome is one of the hot topics in science right now. The human body contains 10 time more bacterial cells than human cells. Moreover, it is estimated that these bacteria together have 150 times more unique genes than the human genome. The microbiome is therefore called an additional organ, that has very large impact on human health and disease. [[BR]][[BR]]
Our group currently studies the gut microbiome in bowel diseases like Crohn's Disease, Ulcerative Colitis and Irritable Bowel Syndrome in which we see microbial shifts appear. We look at how the microbiome influences the lipid metabolism and we are analyzing how diet and medication changes the microbiome in the gut. [[BR]][[BR]]
After identifying bacteria using Next Generation Sequencing of one gene called 16S rRNA, our group started using a more complex technique called Whole Genome Shotgun Sequencing (WGS). With WGS all genes in a sample are sequenced. Using bioinformatics tools, the sequences can be used to identify which bacterial species are present.

== Project 8 - De novo assembly of microbiome data to detect host (human) DNA == 

This 6-week assignment consists of:
1. A short literature study to understand the microbiome: papers are provided
2. Comparison of bacterial taxonomy of WGS and 16S rRNA microbiome data 
3. Finding an a tool for de novo assymbly of bacterial genomes
4. Look for human sequence reads in Whole Genome Shotgun data from the gut microbiome.

== Literature ==

1. The Human Microbiome Project, Nature 2012
2. Explanation of Metaphlan, Nature Methods 2012, Analysis tool for WGS data
3. Explanation of QIIIME, Nature Methods, Analysis tool for 16S rRNA data
4. Example of a WGS study in patients with Liver Cirrhosis