Reader Comments
Post a new comment on this article
Post Your Discussion Comment
Please follow our guidelines for comments and review our competing interests policy. Comments that do not conform to our guidelines will be promptly removed and the user account disabled. The following must be avoided:
- Remarks that could be interpreted as allegations of misconduct
- Unsupported assertions or statements
- Inflammatory or insulting language
Thank You!
Thank you for taking the time to flag this posting; we review flagged postings on a regular basis.
closeA good first metagenomic study of an important ecosystem
Posted by jeisen on 25 Sep 2007 at 05:10 GMT
Overall I like the paper for two reasons.
First there is some interesting science in here, which is not the case for all genomics or metagenomics papers. In particular I find the comparison to the ALOHA depth series metagenomic data to be most interesting. For example, they found that the deep Mediterranean communities' metagenome appears to be most similar to the metagenome of communities from closer to the surface in the ALOHA series. This suggests to the authors that temperature may be more related to microbial genomic diversity than depth (the ALOHA temperature profile drops off more quickly than the Mediterranean profile). I am not sure they are right in this but it is the right type of analysis to do --- just as in "normal" genomic sequencing, the power of metagenomics is going to come from comparative studies.
My second reason for liking the paper is they make appropriate caveats for many of the analyses. Such caveats are needed because we are in the infancy of metagenomics and the analysis required is quite complex and nobody is really sure exactly what to do or how to do it. In addition, the data sets we would like to compare to are not there yet ( e.g., they point out my own pet peeve - that the phylogenetic sampling of genomes of cultured organisms is very biased).