454 Prerequsites In Metagenomics

Question

[Vishnu Priya]

If we plan for a metagenomic functional analysis of a marine samples what are we supposed to do before doing Whole Genome sequencing? I wish to find the metabolic potential of the sample so do we actually need to do 16s RNA amplification?

Answer 1

[Michael]

In my understanding, 16s-rDNA (if you were sequencing RNA instead (meta-transcriptome), you do not need to amplify the 16s either because >90% of your sample will consist of ribosomal RNA) amplification by PCR is for taxonomic composition analysis only. If you want an overview of the metabolic potential of the community as a whole, including unknown or unexpected genes, I would not recommend it, because you will get only 16s by design. If you want to see what genes, pathways, GO-terms, subsystems are part of the ecosystem, I would use unbiased sequences. I think this approach is called (whole) metagenome shotgun sequencing.

Some references are in this question.

A good and open introduction: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000667

You would optimally do both, sequence 16s amplicons and whole metagenome shotgun, both of which are covered in the ploscomp review.

[Vishnu Priya]

Thanks for the reply.. Can you suggest and reference papers to understand and distinguish the methods better?

[Vishnu Priya]

Thanks for the reply.. Can you suggest any reference papers to understand and distinguish the methods better?