There's also the "American Gut" project on IndieGogo:
http://www.indiegogo.com/americangutThey're a little more expensive ($99 for a one-sample kit), but it's run by Rob Knight, who I consider to be the foremost authority on human microbiome analysis in the world.
Either one sounds really exciting, but it'll be the amount of sequencing per sample, the quality of the analysis, and the number of samples in the study that will make all the difference.
Patrik