Preparing and importing custom diets and taxonomy files for q2-MICOM

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Hi Merhbod,

So cool to see you using MICOM. Sorry that the docs did not address those questions well. Growth media/environmental conditions was our recent focus area and some of the recent developments did not make it into the docs yet. The good news is that there are pretty simple solutions to all of them now :sweat_smile:

  1. This is a very common question we get. The VMH diets do need some processing to be unable with MICOM. Basically, the steps are:
  • convert units to mmol/gDW/h and adjust IDs
  • (for gut) dilute components usually absorbed in the small intestine
  • fill in components that are required for bacterial growth but absent in the growth medium
    This is now documented in the new MICOM media repository (GitHub - micom-dev/media: Environmental growth media for MICOM.) that provides notebooks that go from the raw data to the QIIME 2 artifacts. There is already one VMH diet that was converted and that might be a good starting point to convert the others. If you do so we would love to get a PR with the new medium :smiling_face_with_three_hearts:

  1. Yes good point. Initially, we just matched by names across those DBs which usually does not perform well with SILVA. For 16S we now recommend using a classifier based on the Refseq 16S sequences which give the best mapping in our experiments. Alex Carr from our lab built one for 515f-805r. If that is useful I'll happy to share it with you if you send me your E-mail to cdiener(a)isbscience.org. GTDB has been requested before and I am on that but still need to map all the AGORA strains from NCBI to GTDB for that. There is an issue tracking that. I originally hoped that AGORA 2 would come out before that but that seems to take a bit longer.

  2. Internally MICOM only uses per-sample media, so it's definitely possible. It's already implemented in the plugin even though it's not documented yet since the analyses are a bit more challenging. Here is a gist that creates a per-sample medium. just using that in qiime micom grow will apply the sample-specific media. If your media use different amounts of nutrients I would correct for that in downstream analyses. For instance, if one medium supplies twice as much nutrients it would lead to higher growth rates and fluxes in those samples.

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