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So, generally people apply 97% similarity cut-off for species/OTUs in 16S based metagenomics. As far as I know, the 97% cut-off became standard practice with full 16S sequences. However, in 16S amplicon metagenomics we usually inspect just partial 16S sequences (~200-400 bp) from some variable region. In such cases, would it not make more sense to apply a higher cut-off value for clustering. I've noticed that with our data, increasing the cut-off from 97% to 99% increases OTU count some 5-10 fold. Our samples are from deep underground, so there's little literature to go on what would be a sensible species count for a given sample, but somehow I have a feeling that e.g. 500 OTUs is more realistic than 50 OTUs. Any thoughts?
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savetherhino.org -
What platform are you sequencing on? I would like to see other's responses to this... I am sequencing on Ion Torrent PGM and the difference between 94, 97 and 99% is significant. I believe even within species, sometimes you only have 97% identity, or less. I don't know if I agree with you about your sensible species count. It sounds like your environment (deep underground) would not be an ideal place for speciation to occur, or a diverse population to develop-- too little movement, very static environment. So I would think it would be unlikely that too many species would develop to fill such a small niche as you are looking at... but maybe I'm wrong.
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