If you follow this blog, you'll know that we have discussed a series of studies that indicate microbiomes are uniquely qualified for their host species, sometimes in ways that the phylogeny of the animal yields the same relationships as the "phylosymbiosis" pattern (guest blog post) in the microbial community. These discoveries are important because they emerge out of an initial paradigm in which studies within species have shown variation in the microbiome upon changes in diet or disease. But comparative biologists who think in ecological/evolutionary ways have started to illuminate the rules of microbiome assembly across different species.
It's now safe to say that in the last few years, we have gained a clear understanding that under controlled laboratory studies, the crosstalk between microbiomes and host genomes is undoubtedly intimate, clear, and specific. The gut microbial community is strongly shaped by host selection, perhaps even independently of a phylosymbiosis pattern from 16S data (Oh et al 2010, ISME). If we understand the molecular signals between this conversation, then we can better understand superorganisms (our genes + microbial symbionts) in evolutionary and applied ways.