[Coral-List] Coral Microbial Genomics Initiative

[Carolin Frank]

Dear coral reef colleagues,

We are writing to ask for input on beneficial coral-associated  
microbes and the availability of isolates from the community of coral  
microbiologists.

As you know, there is increasing evidence that coral-associated  
bacteria benefit corals through biogeochemical cycling and protection  
against pathogens. So far, genome sequencing of isolates has been  
underused as a means to learn more about the beneficial contributions  
of bacteria to coral health and holobiont ecosystem functioning.

If you are a coral microbiologist and have novel bacterial or archaeal  
isolates from healthy corals, we would like specific feedback on  
whether you would be willing to participate in a collaborative  
proposal to the Joint Genome Institute (JGI) Community Sequencing  
Program.  We feel that this has to be a community at large effort to  
have a significant impact on coral reef science. Professor Eugene  
Rosenberg and others have committed to the initial effort.

The aim of the proposal will be to 1) understand more about the  
function of phylogenetically-diverse nonpathogenic bacteria in the  
holobiont and 2) to create a reference set of genomes for improved  
annotation and analysis of coral microbial metagenomes. If funded, the  
genome sequences would be available for annotation and analysis  
through JGI’s Integrated Microbial Genomes (IMG) system, a community  
resource for analysis and annotation.

If you are interested in joining our collaborative effort to sequence  
isolates from the coral holobiont, please send information regarding  
your isolates to coralprokaryotes at gmail.com. We can only submit a  
total of 10 strains for this first proposal, but we also hope to build  
a community database as a resource for future collaborative proposals  
for genome sequencing (i.e. in 2011).

We feel that a community-driven effort will go a lot farther than  
individual projects, and therefore envision collaboration at all  
stages, from annotation and analysis to manuscript writing and  
publication. If funded, these initial 10 genomes will be a starting  
point that will allow us to centralize information via IMG, and will  
be helpful to many more people than just those that participate  
initially.  For maximum community access, we plan to set up an online  
searchable database as the information comes in.

If you are interested in joining this effort, please provide the  
following information regarding proposed strains for genome sequencing:

1. Isolation location and coral species ID
2. Strain characterization (e.g. 16S rRNA top blast hit, biochemical  
characterization)
3. Ecological characterization (e.g. environmental distribution,  
dynamics, etc)
4. Relevant publications
5. Contact information
6. Permission to include the above information in a database of coral  
associated-isolates (Yes or No)?

You can find out more about our initial team at the websites listed  
below.

Carolin Frank (http://granada.ucmerced.edu/~cfrank/Home.html)
Mónica Medina (http://www.medinalab.org/)
Janelle Thompson (http://thompsonlab.mit.edu)

Best,

Carolin Frank