Per-sample media/diets in q2-micom¶

Under the hood micom and q2-micom do have support for sample-specific media. In fact, that is micom only knows sample-specific media. If a media is not sample-speciic it is internally copied for each sample in the data set. To get an understanding of how to create a per-sample medium for q2-micom let's first have a look at the actual format. Media/diets in micom are just DataFrames with at least the columns metabolite, reaction and flux.

import qiime2 as q2
import pandas as pd

arti = q2.Artifact.load("western_diet_gut.qza")
medium = arti.view(pd.DataFrame)
medium.head()

As you see you may also add additional columns to annotate your data. This is a global medium:

arti.type

MicomMedium[Global]

For a per sample medium you will need an additional column called sample_id. There should be a row for each metabolite that is consumed in each sample. So for instance let's assume we want to convert the current medium into sample-specific media for a normal and a diabetic sample that has higher glucose availability. For this we duplicate the medium, modify the glucose flux bound, add the sample IDs and concatenate the media.

diabetic = medium.copy()
diabetic.loc[diabetic.metabolite == "glc_m", "flux"] = 0.1
diabetic["sample_id"] = "diabetic"
medium["sample_id"] = "normal"

per_sample_medium = pd.concat([medium, diabetic])
per_sample_medium.head()

Not that the sample IDs have to correspond to your sample names used in your OTU table paased to qiime micom build.

Now we can save the medium as a per=sample q2-micom medium:

new_arti = q2.Artifact.import_data("MicomMedium[PerSample]", per_sample_medium)
new_arti.save("my_media.qza")

'my_media.qza'

And that's it 🎉 If you use this saved media with qiime micom grow it will automatically apply the correct medium for each sample.

	flux	dilution	metabolite	reaction
0	0.014899	0.1	fru_m	EX_fru_m
1	0.014899	0.1	glc_m	EX_glc_m
2	0.014899	0.1	gal_m	EX_gal_m
3	0.014899	0.1	man_m	EX_man_m
4	0.014899	0.1	mnl_m	EX_mnl_m