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Old 07-17-2018, 05:49 AM   #6
Genetic Librarian
Location: Europe

Join Date: May 2017
Posts: 31

If you use an amplicon approach (16S v3v4) you do not need any form of depletion, because you just amplify bacterial 16S sequences . The primers are specific, so that it does not matter how much of host RNA is present. The same reason why you do not get host reads in your 16S datasets from DNA.
Host depletion and bacterial enrichment is something you need for metatranscriptomes, not for 16S.
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