On 2013 Oct 22, Jonathan Eisen commented:

This paper represents a landmark study in something that has intrigued many microbial diversity / human microbiome researchers for many years. Early in the history of sequencing rRNA genes from human microbiome samples, researchers discovered something a bit weird - quite a few sequences were coming from what appeared to be close relatives of Cyanobacteria. This was weird because all known Cyanobacteria were thought to be photosynthetic and - well - there is not too much light in the human gut. Now - one possible explanation for this was that these sequences were coming from photosynthetic bacteria but these bacteria were not residents of the human gut but came via consumable items (i.e., food and drink). Perhaps they were actually from chloroplasts of something in the diet (after all - chloroplasts are derived versions of cyanobacteria). This idea was discussed at many meetings I attended. But there was no evidence for this. Another possibility was that there was in fact some light in the human gut - leaking through from the outside or being produced from the inside. And perhaps this was enough to do a little photosynthesis. Sound crazy? Well, not so crazy after reports of photosynthesis in the deep sea. A third possibility was that these sequences were coming from residents of the human gut that were related to (or even within) cyanobacteria but were not photosynthetic. More detail on possible explanations are in this new paper and in some of the material cited therein. Anyway - Ruth Ley has been discussing these unusual sequences for years and now in this paper her group and the group of Jill Banfield at Berkeley (along with some others) has used metagenomics and detailed assembly and phylogenetic analysis to reveal many new insights into these sequences.

(this comment is based on a blog post I wrote about the paper: http://phylogenomics.blogspot.com/2013/10/who-are-microbes-in-your-neighborhood.html)

On 2013 Oct 22, Jonathan Eisen commented:

This paper represents a landmark study in something that has intrigued many microbial diversity / human microbiome researchers for many years. Early in the history of sequencing rRNA genes from human microbiome samples, researchers discovered something a bit weird - quite a few sequences were coming from what appeared to be close relatives of Cyanobacteria. This was weird because all known Cyanobacteria were thought to be photosynthetic and - well - there is not too much light in the human gut. Now - one possible explanation for this was that these sequences were coming from photosynthetic bacteria but these bacteria were not residents of the human gut but came via consumable items (i.e., food and drink). Perhaps they were actually from chloroplasts of something in the diet (after all - chloroplasts are derived versions of cyanobacteria). This idea was discussed at many meetings I attended. But there was no evidence for this. Another possibility was that there was in fact some light in the human gut - leaking through from the outside or being produced from the inside. And perhaps this was enough to do a little photosynthesis. Sound crazy? Well, not so crazy after reports of photosynthesis in the deep sea. A third possibility was that these sequences were coming from residents of the human gut that were related to (or even within) cyanobacteria but were not photosynthetic. More detail on possible explanations are in this new paper and in some of the material cited therein. Anyway - Ruth Ley has been discussing these unusual sequences for years and now in this paper her group and the group of Jill Banfield at Berkeley (along with some others) has used metagenomics and detailed assembly and phylogenetic analysis to reveal many new insights into these sequences.

(this comment is based on a blog post I wrote about the paper: http://phylogenomics.blogspot.com/2013/10/who-are-microbes-in-your-neighborhood.html)