interpretation of Lefse results

Commands in mothur
1

Hi, I was wondering if anyone in the mothur community has found a way to functionally annotate the results from a Lefse analysis: I am comparing bacterial communities in two host species. I am identifying significantly different taxa using Lefse. At this point, I would like to functionally annotate my results to identify what kind of bacteria differ in abundance, not according to taxonomy but according to biological properties; for instance, are anaerobes overrepresented among the taxa found by Lefse or spore forming spp, etc. It’s analogous to what DAVID does with transcriptome data:
http://david.abcc.ncifcrf.gov/gene2gene.jsp.

thanks,

Giovanni

2

Infering function from 16S genes is at best an estimation, so I’d take any results you get with a grain of salt. That being said, look into the picrust functionality recently added to mothur:

http://www.mothur.org/wiki/Make.biom

Once you have a biom file compatible with picrust, you can load it into their site: http://huttenhower.sph.harvard.edu/galaxy/root?tool_id=PICRUSt_normalize