Who are the microbes in your neighborhood? Quite a few are from Melainabacteria - a new phylum sister to Cyanobacteria

I just love this paper ... The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria | eLife from the labs of Ruth Ley and Jill Banfield (1st author is the co-first authors are Sara C. Di Rienzi and Itai Sharon).  It 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.  I could write much more about this.  But, I think the paper really speaks for itself.  And it is open access so anyone and everyone can check it out.  And you should.  It is wonderful.

Fig 2 from Di Rienzi et al.

UPDATED 10/9/2013 to correct that there were co-first authors

New paper from some in the Eisen lab: phylogeny driven sequencing of cyanobacteria

(Cross post from my lab blog)

Quick post here.  This paper came out a few months ago but it was not freely available so I did not write about it (it is in PNAS but was not published with the PNAS Open Option — not my choice – lead author did not choose that option and I was not really in the loop when that choice was made).

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. [Proc Natl Acad Sci U S A. 2013] – PubMed – NCBI.

Anyway – it is now in Pubmed Central and at least freely available so I felt OK posting about it now.  It is in a way a follow up to the “A phylogeny driven genomic encyclopedia of bacteria and archaea” paper (AKA GEBA) from 2009 with this paper a zooming in on the cyanobacteria.

Interesting 2011 pub on origin of multicellularity in cyanobacteria

Just a quick one here.  There is an (openaccess) publication I thought people might find interesting: The origin of multicellularity in cyanobacteria.  Schirrmeister BE, Antonelli A, Bagheri HC. BMC Evol Biol. 2011 Feb 14;11:45.

In particular it has some very nice figures on phylogeny of cyanobacteria and the evolution of phenotypes in the group.

Figure 1. Phylogenetic tree of 1,254 cyanobacterial species. 

Figure 4. Phylogenetic tree of a cyanobacterial subset. 

Some of the same authors also have a paper on the need for better phylogenetic sampling of genome data in the group:


Evolution of cyanobacterial morphotypes: Taxa required for improved phylogenomic approaches. Schirrmeister BE, Anisimova M, Antonelli A, Bagheri HC. Commun Integr Biol. 2011 Jul;4(4):424-7. Epub 2011 Jul 1.

Though I note, I am a bit annoyed and surprised they did not cite my "Phylogeny driven genomic encyclopedia" paper in this pub ...