Thursday, November 29, 2012

Convoluted title, cool paper in #PLoSGenetics on relative of insect mutualists causing a human infection

Saw this tweet a few minutes ago:

The title of the paper took me a reread or two to understand.  But once I got what they were trying to say I was intrigued.  And so I went to the paper:  PLOS Genetics: A Novel Human-Infection-Derived Bacterium Provides Insights into the Evolutionary Origins of Mutualistic Insect–Bacterial Symbioses.  And it is loaded with interesting tidbits.  First, the first section of the results details the history of the infection in a 71 year old male and his recovery and the isolation and characterization of a new bacterial strain.  Phylogenetic analysis revealed this was a close relative of the Sodalis endosymbionts of insects.

And then comparative genomics revealed a bit more detail about the history of this strain, it's relatives, and some of the insect endosymbionts.  And plus, it allowed the authors to make some jazzy figures such as

And this and other comparative analyses revealed some interesting findings.  As summarize by the authors
Our results indicate that ancestral relatives of strain HS have served as progenitors for the independent descent of Sodalis-allied endosymbionts found in several insect hosts. Comparative analyses indicate that the gene inventories of the insect endosymbionts were independently derived from a common ancestral template through a combination of irreversible degenerative changes. Our results provide compelling support for the notion that mutualists evolve from pathogenic progenitors. They also elucidate the role of degenerative evolutionary processes in shaping the gene inventories of symbiotic bacteria at a very early stage in these mutualistic associations.
The paper is definitely worth a look.


  1. Are the genomic data available for the genomes analysed in the paper ....

    1. Aargh --- looks like some may not be available. Will write to PLoS

  2. This is a common occurrence (across all journals) but PLOS should enforce stricter checks during production to ensure the availability of sequence data.

    I have had to write to two groups this week to request data from PLOS Biology and PLOS ONE papers:

    Both have replied saying data is being submitted to SRA, but this should not be begin done after publication.

    1. WTF? How can PLoS not be stricter about data when it is supposed to be about openness?

    2. It's hard to enforce through reviewers alone with the current system.

      There neeeds to be (i) a specific check done by the editorial/production team (ii) specific boxes to be filled in by reviewers to ensure that data is deposited or (iii) threat of retraction if data are not made available.

      However it is engineered, PLOS should lead the way.

    3. I had the same problem this week with this PLoS One Paper:

  3. Wrote to the corresponding author


    I am writing to ask if you can point me to the genome data from your recent paper in PLoS Genetics on the human infection / Sodalis story. I am unable to find in the paper links to the raw reads or to the genome assemblies. Is that data available somewhere? If not, why not?


  4. Hello all,

    I am one of the authors on this paper and I wanted to let everyone know we are working on getting the draft genome assembly data available. We are in the process of formatting the data for submission to Genbank right now. Sorry about not getting the data available sooner.

    1. Thanks. If you have a chance please post details here when available.

    2. Hello everybody,
      Our group has posted the genomic data from the paper on our server. You can find the link to the data in the comments section of our paper on the PLoS Genetics site. Here is the link:


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