Just got pointed to this very interesting paper by one of the authors: Genome-wide mapping of gene–microbiota interactions in susceptibility to autoimmune skin blistering : Nature Communications : Nature Publishing Group. I really really love this new approach of doing QTL experiments where the quantitative trait being measured is the relative abundance of various microbes. The first paper of this kind I know of that did such a QTL analysis was Benson et al. 2010 in PNAS in mouse. There have been a few others using this approach (e.g., Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits) and I am sure we will see many many more. Basically this approach allows one to identify genes / polymorphisms / regions of the genome in a host that influence the relative abundance of specific microbes. And such information will be critical in understanding the interactions of microbial communities with hosts.
Jonathan Eisen's Lab 