Environmental growth media for MICOM 🌱 🌍 🍕

This repo contains recipes and artifacts for growth media with use in MICOM. Community contributions are very much welcome and invited 😄

How to add a new recipe/medium

If you don't have one already create a new Qiime 2 environment along with q2-micom. See here on how to do that. After activating the environment add Jupyter Lab as well:

conda install jupyter-lab

Make a fork of the repository (Fork button on the upper right) and clone it onto your own machine:

git clone USER/media

Create a new branch and start Jupyter Lab:

cd USER/media
git checkout -b my_medium_description
jupyter lab

Create a new Jupyter Notebook that contains the code and reasoning for creating the new medium. The notebook must produce a new Qiime 2 artifact medium in the "media" subfolder. See the AGORA notebook for an example. The name of the artifact should indicate the following:

1. the condition/context (western diet, nitrogen-limited, rich, etc.)
2. the environment (gut, soil, ocean, etc.)
3. The model database/ID system used to design the medium (AGORA, CARVEME, BIGG, etc.)

Run all steps in the notebook and save it. Then add a new entry in the Available media section using the following template:

---

*Short description of the medium*

[recipe](https://nbviewer.jupyter.org/github/micom-dev/media/blob/main/recipes/my_recipe.ipynb) |
[medium](https://github.com/micom-dev/media/raw/main/media/my_recipe.qza)

Longer description of the growth medium.

Finally create a pull request on this repository which will make your medium for addition into the repo.

Available media

Western diet medium for the human gut (AGORA)

recipe | medium

This is a growth medium representing the likely distribution of available nutrients in the lower intesting under an average European diet. The medium was taken from https://doi.org/10.1038/nbt.4212 and components commonly absorbed in the small intestine were diluted 1:10. The medium is adapted to the AGORA database 1.03.

---

Western diet medium for the human gut (CARVEME)

recipe | medium

This is a growth medium representing the likely distribution of available nutrients in the lower intesting under an average European diet. The medium was taken from https://doi.org/10.1038/nbt.4212 and components commonly absorbed in the small intestine were diluted 1:10. Only components that could be mapped to the CARVEME DB were kept and the medium was completed to allow growth for all 1.8K+ genera in the database. The medium is adapted to the CARVEME reconstructions using Refseq v84.

---

VMH diets

Diet	Recipe	Medium
Austrian average diet	Austrian average recipe	Austrian average medium
high fat/protein low carb diet	high fat low carb recipe	high fat low carb medium
high fiber diet	high fiber	high fiber medium
fermented foods diet (80% high fiber diet + 20% fermented foods)	fermented recipe	fermented medium
baby formula	formula recipe	formula medium

These are the completed VMH growth medium representing a variety of diets. Components commonly adsorbed in the small intestine were identified by matching reactions to metabolites adsorbed in the Recon3 human model.

Provided diets:

• Austrian average diet
• high fat/protein low carb diet
• high fiber diet
• fermented foods diet (80% high fiber diet + 20% fermented foods)
• baby formula

---

Breast milk-fed infant (AGORA)

recipe | medium

This is a completed medium based on a breast milk-only diet of an infant. Lactose is the major carbon source here. Medium was depleted for components absorbed by human cells and mucin/primary bile acids were added to the medium.

---

Single meal diets (AGORA)

Population	Region	Recipe	Medium
Hadza	Tanzania	Hadza meal recipe	Hadza meal medium
Me'Phaa	Mexico	Me'Phaa recipe	Me'Phaa medium
Chepang	Nepal	Chepang meal recipe	Chepang meal medium

Those are ~1000kcal single meal media for a set of indigenous populations across the globe. Each of them tends to include 4-5 representative food items detailed in the source mapping. Those are not necessarily representative for the diverse diets of the respective poopulation, but are usually more realistic than an average European diet. For a more in depth discussion please refer to the 2022 ISB Microbiome Series.