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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CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM
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