Making micom genus metabolites models

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1

Hi, I'm trying to build a mouse microbiome model using micom-q2.
But the AGORA file that micom tutorial provided don't have some genus included in my mouse metagenome sequences data.
So I want to make a genus metabolites model, and there's some questions.

  1. What's the genus model? I mean, there's a lot of species in one genus classification. What species is included in the genus metabolite model? The whole? or The choose one?

  2. Then, how can make a genus model? I have the original AGORA files(GitHub - VirtualMetabolicHuman/AGORA: The aim of this repository is to maintain, refine, and expand the AGORA collection of genome-scale metabolic reconstructions for human gut microbes through the use of issues. Please note that pull requests will be automatically closed.) classified species level.

  1. If I have to merge the species files for one genus metabolite model, the reactions and metabolites from different species are all included? or selected?
  2. If I have to select the reactions or metabolites, what criteria do you choose?
  3. What's the tool that I can use for the merge?

Please let me know the way to make the genus metabolites models.
I'll be waiting for the reply. Thanks!

4

Hello @Hansol-cloud,

Welcome to the forums! :wave:

These are great questions, and the bet the lead author of MICOM would have great answers!

Paging @cdiener :postal_horn: :badger:

5

Hi,

Happy to see you are considering MICOM for your work. You are definitely right. AGORA was built from strains of strains commonly found in the human gut and will probably be suboptimal for a mouse gut. Unfortunately, we don’t provide a curated model database specific to the mouse gut. However, we provide a database based on the CARVEME automatic reconstructions of all genomes in Refseq and that should cover the most common genera in the mouse gut better.

If you want to build your own model database the best strategy is to use the commands included in the q2-micom plugin.

Okay, and here the answers to the questions:

  1. A genus model in MICOM is a pan-genus model, so it includes the union of all metabolic reactions of the strains for that genus. The biomass composition will be the average of all strains.

  2. All strains in AGORA are already covered by the model database from the tutorial. Genera that don’t appear there are not covered by AGORA.

  3. Yep, see (1). All reactions from the species will be included.

  4. Nope, don’t need to select anything.

  5. The tool is MICOM :wink: MICOM can merge models either via the database builder as mentioned above or ad-hoc when using the single model API in Python (not available in q2-micom). Though we recommend to always build the model database first because it is much faster and more reproducible.

1 Like
6

Thank you Christian!

I saw that CARVEME database link, but I couldn't download any file.
It took a very long time (5h), and even it was stopped on the way.
I'll try to make own database.

7

Oh, I retried to download CARVEME_genus file and it was work!

8

Yeah Zenodo hosts in Europe (hosted by CERN actually) and sometimes that can be slow when downloading from other continents. Glad it worked though! There is a human gut diet specification adapted for the CARVEME model database at GitHub - micom-dev/media: Environmental growth media for MICOM. in case that will be helpful.