{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Growth media for the AGORA database\n", "\n", "AGORA is a database targeting the gut microbiota. As such we already supplied a growth medium based on an average western diet. We will start from this medium to illustrate how we can inspect the performance of growth medium in a model database and how to supplement a medium to allow fro growth for all models.\n", "\n", "The growth medium supllied here was created the following way:\n", "\n", "1. start with the growty medium reported in https://doi.org/10.1038/nbt.4212\n", "2. manually dilute all components absorbed in the small intestine (simple sugars, vitamins, amino acids, etc) 1:10 \n", "3. add in mucin\n", "4. deplete oxygen since the lower gut is mostly anaerobic\n", "\n", "We can take a look by reading it using micom." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | flux | \n", "dilution | \n", "metabolite | \n", "reaction | \n", "global_id | \n", "sample_id | \n", "
---|---|---|---|---|---|---|
reaction | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
EX_fru_m | \n", "0.014899 | \n", "0.100 | \n", "fru_m | \n", "EX_fru_m | \n", "EX_fru(e) | \n", "dummy | \n", "
EX_glc_m | \n", "0.014899 | \n", "0.100 | \n", "glc_m | \n", "EX_glc_m | \n", "EX_glc(e) | \n", "dummy | \n", "
EX_gal_m | \n", "0.014899 | \n", "0.100 | \n", "gal_m | \n", "EX_gal_m | \n", "EX_gal(e) | \n", "dummy | \n", "
EX_man_m | \n", "0.014899 | \n", "0.100 | \n", "man_m | \n", "EX_man_m | \n", "EX_man(e) | \n", "dummy | \n", "
EX_mnl_m | \n", "0.014899 | \n", "0.100 | \n", "mnl_m | \n", "EX_mnl_m | \n", "EX_mnl(e) | \n", "dummy | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
EX_glu_D_m | \n", "0.100000 | \n", "0.100 | \n", "glu_D_m | \n", "EX_glu_D_m | \n", "EX_glu_D(e) | \n", "dummy | \n", "
EX_gthrd_m | \n", "0.100000 | \n", "0.100 | \n", "gthrd_m | \n", "EX_gthrd_m | \n", "EX_gthrd(e) | \n", "dummy | \n", "
EX_h2_m | \n", "0.100000 | \n", "0.100 | \n", "h2_m | \n", "EX_h2_m | \n", "EX_h2(e) | \n", "dummy | \n", "
EX_no2_m | \n", "0.100000 | \n", "0.100 | \n", "no2_m | \n", "EX_no2_m | \n", "EX_no2(e) | \n", "dummy | \n", "
EX_o2_m | \n", "0.001000 | \n", "0.001 | \n", "o2_m | \n", "EX_o2_m | \n", "EX_o2(e) | \n", "dummy | \n", "
167 rows × 6 columns
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