What Are The Similarities And/Or Differences Between 16S And 18S Metagenomic Approaches

Question

[Ketil]

Anybody have any experience with 18S amplicon sequencing (or other kinds of eukaryote metagenomics)? Most people seem to be 16S prokaryote projects - are there any particular challenges with eukaryotes I should be aware of? What kind of equipment (e.g. sequencer tech) is recommended, and how much would an experiment cost in lab time and reagents?

Answer 1

[Pawel Szczesny]

If you move outside of 16S you will find many other marker genes, which might suit you more than 18S. In terms of analysis, I don't have much experience with 18S because for metagenome samples with fungi (and often plants) which I am often analyzing ITS (internal transcribed spacer) is a much better marker. There are already databases available (such as ITSonDB), plus you can easily find lot's of papers already on the topic. I'm not doing experiments, I cannot answer that part of the question.

Also, keep an eye on Consortium for the Barcode of Life.

[Ketil]

Thanks for the response, I should have thought about ITS as well. That gives me something else to Google.