How health status and abundance of bacteria are related through PCA?

[tmy1018]

Hi,

I have a question about how health status and abundance of bacteria are correlated using PCA in this paper (A human gut microbial gene catalogue established by metagenomic sequencing):

http://www.nature.com/nature/journal/v464/n7285/fig_tab/nature08821_F4.html

I don't really understand how PCA was done, the authors doesn't seem to have too much detail on it. Can someone tell me more about how PCA was done in this diagram?

Thanks for your help!

[Richard Finney]

What's the question?

Note to those who did not click on the image: it shows that traditional Principle components analysis 2D plot show differing gut bacteria composition for Crohns, UC, and "healthy" patients.

A word of caution: correlation is not always causation. Crohn's patients do have different gut flora (bateria, arachaea (sp?), etc.). The patient may have some underlying different immune systems which results in a different gut flora ... or a different gut flora perhaps spearheaded by the introduction of an invasive species results in sickness.

[tmy1018]

What's the question?

Note to those who did not click on the image: it shows that traditional Principle components analysis 2D plot show differing gut bacteria composition for Crohns, UC, and "healthy" patients.

A word of caution: correlation is not always causation. Crohn's patients do have different gut flora (bateria, arachaea (sp?), etc.). The patient may have some underlying different immune systems which results in a different gut flora ... or a different gut flora perhaps spearheaded by the introduction of an invasive species results in sickness.

My question is that I don't really know how the authors used health status and abundance of species to do this PCA.