In microbiome studies, 16S rRNA is often amplified and sequenced to look at bacterial composition. Is there an equivalent method or gene one can amplify and sequence to assess viral and or fungal composition in the same consortia?
not actively doing research in that area but this may give some idea for fungi: http://www.pnas.org/content/109/16/6241.short
However, the ITS also has some downsides. I guess there is currently no better marker for fungi and the research field is a work in progress.
Concerning viruses it may be even harder. Just consider that you also have ds and ss viruses including RNA viruses... this is really complex!
you could potentially consider doing metagenomics and "simply" sequence as deep as possible. This will also pick up fungi and some(!) viruses. But this is something that you definitely don't wanna do large scale for comparative purposes, at least not yet. Sequencing is getting cheaper and cheaper though.
Good luck, Alex
this might be interesting to you regarding virus sequencing
Viral tagging reveals discrete populations in Synechococcus viral genome sequence space
Li Deng, J. Cesar Ignacio-Espinoza, Ann C. Gregory, Bonnie T. Poulos, Joshua S. Weitz, Philip Hugenholtz & Matthew B. Sullivan
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- Biological Science
- Biota
- Eukaryota
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