Gut bacteria metabolic diversity

Another paper exploring microbial diversity of the human gut has been released in PLoS Biology. It is open source so go read it for yourself! There is also a summary article on the data intended for a lay audience. The data presented in the paper is very interesting. They sequenced the genomes of two gut bacteria, Bacteroides vulgatus and Bacteroides distasonis, and contrasted their metabolic potential (the genes present in the genome) with the well studied species Bacteroides thetaiotaomicron. This comparison does provide some evidence that niche specialization plays a role in maintaining the diversity of the gut microbiota.

The importance of studying the gut microbiota is summed up nicely in the beginning of the author summary:

"Our microbial partners provide us with certain features that we have not had to evolve on our own. In this sense, we should consider ourselves to be a supraorganism whose genetic landscape includes both our own genome as well as the genomes of our resident microbes, and whose physiologic features are a synthesis of human and microbial metabolic traits."

I would have worded the first sentence differently as saying 'have not had to" sounds a bit too teleological to me.

I am also troubled by their use (later in the introduction) of the term "top-down selection" in reference to host driven selective forces that they argue are responsible for maintaining a high degree of functional redundancy in the gut community. I am not aware that the term top-down selection, as used by the broader ecology community, is considered a force for the maintenance of ecosystem stability.

The end of the paper lists a set open questions that it would be very nice to have answers to:

"Do we share an identifiable core “microbiome”? If there is such a core, how does the shell of diversity that surrounds the core influence our individual physiologic properties? How is the human microbiome evolving (within and between individuals) over varying time scales as a function of our changing diets, lifestyle, and biosphere? Finally, how should we define members of the microbiome when microbes possess pan-genomes (all genes present in any of the strains of a species) with varying degrees of “openness” to acquisition of genes from other microbes?"