What is the meaning of uncultured in taxonomy string?


I ran the dada2 pipeline in QIIME2 and assigned taxonomy using SILVA on 16S mouse fecal samples.

  1. what is the meaning of 'uncultured'?
  2. What is the difference between '__ 'and 'uncultured'?
  3. How should I deal with '___ 'and 'uncultured'?

Hello @JessyJay,

  1. Uncultured means that this bacterium hasn't been cultured. You can read about culturing here. Uncultured bacteria are generally less well understood because they haven't been isolated or propagated in the lab.

  2. The double underscore __ is used in these taxonomy strings to indicate that that the feature wasn't resolved to this taxonomic level in the database. This is different than g__uncultured or g__ which indicate that the feature was resolved to the genus level, but the matching organism in the database was not annotated/classified at this level.

  3. Hopefully these explanations give you an idea of how you should deal with them.

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