Simple statistics help
 

Hello there,

I am currently working on a metagenomics project on the oral microbiome. I am new to metagenomics and not the best at statistics, so please bear with me:)

I have 3 conditions: a control, an antibiotic-treated, and another type of antibiotic-treated.

I was referred to Metaphlan2, which turned out to be great. Super grateful for the tool. Generated a nice heat map and got some nice preliminary results.

However, I am interested in only extracting bacterial species that have a differential relative abundance of some threshold across treatment groups. What is the easiest way to do this given the output metaphlan2 output (relative abundance)? Any help would be appreciated.

I start with indicator species analysis (indicspecies package in R). you'll need to correct the p-values for multiple comparisons, the package doesn't automatically do that.

From the same guys that created Metaphlan there's also a tool called LEfSe which you could use for this. It may be easier for you if you're new to this!