BIOM25: Metagenomics practical

05 Feb 2017

Scratchpad for session:

https://docs.google.com/document/d/1DY8efRRM2MO7N2DuFTKN-QEmwOm9JuZF_UZKAFme9RU/edit?usp=sharing

Normal human microbiome

The MetaHIT project studied healthy volunteers, as well as people with diabetes and inflammatory bowel disease to characterise their microbiomes:

https://www.ebi.ac.uk/metagenomics/projects/ERP000108

Have a read of how the study was designed:

http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html

Q: Take 10 samples at random and look at their taxonomic distribution. Tabulate the top 3 phyla present and their relative abundances.

E. coli outbreak

Our paper describing the outbreak:

http://www.nejm.org/doi/full/10.1056/NEJMoa1107643

Our paper describing use of whole-genome shotgun metagenomics to diagnose the outbreak:

http://jama.jamanetwork.com/article.aspx?articleid=1677374

The data website:

https://www.ebi.ac.uk/metagenomics/projects/ERP001956

Q. Pick some samples at random. For example sample, look at the taxonomic distributions.

Q. Do any samples look abnormal, compared to the ‘normal’ microbiome?

Q. Are any toxins present? Which ones? What is the significance of this toxin and how might it cause disease?

Antibiotic resistance

Here is a report from one of the outbreak metagenomes using a different analysis pipeline:

https://app.onecodex.com/analysis/public/94b2f5f421a841be

Q. What antibiotic resistance genes are present? (Hint: check the AMR report)

Q. What antibiotics might the outbreak strain be resistant to?

Q. How could we prove that the outbreak strain is resistant to these antibiotics?

Non-human environment

Now, choose a non-human environment to study, and to present to the group:

Soil: https://www.ebi.ac.uk/metagenomics/projects/doSearch?search=Search&biome=SOIL

Water: https://www.ebi.ac.uk/metagenomics/projects/doSearch?search=Search&biome=MARINE

Animal: https://www.ebi.ac.uk/metagenomics/projects/doSearch?search=Search&biome=NON_HUMAN_HOST

Artificial: https://www.ebi.ac.uk/metagenomics/projects/doSearch?search=Search&biome=ENGINEERED

Q. What did the study set out to find?

Q. How did they sample their environment? How many samples did they look at?

Q. How does this environment compare taxonomically with the human gut? Is it more or less diverse? Are the set of organisms present similar or different?

Q. How does this environment compare functionally with the human gut? Can you explain these findings in the context of the environment?