Removing sequences of human origin from ASV table

[lewisNU (Lewis)]

Hi again guys,

I'm working on environmental air samples and would like to remove any taxa of human origin that could have been introduced during sampling. The plan is to remove all human associated bacteria and compare the diversity before doing so and after. I have ~2000 taxa assigned ASVs to screen.

Does anyone have any suggestions on the fastest way to go about this short of copying and pasting the ASVs into a database and seeing the top match?

Best wishes,
Lewis

[colinbrislawn (Colin J Brislawn)]

Hello Lewis,

Great question! Welcome to the Qiime forums.

EDIT: Be careful, removing real microbes introduces bias!!
I think this plugin will do the job. All you need is a list of microbes you think are human associated, and this plugin can remove them from your table.
https://docs.qiime2.org/2018.6/tutorials/filtering/?highlight=filtering#taxonomy-based-filtering-of-tables-and-sequences

I guess the other question is, how do you know what microbes are human associated, and also are never present in environmental air samples? Many microbes are generalists, so I would be equally worried about removing real microbes from my samples.

Do you have any reason to think your environmental air samples were contaminated by humans?

Colin