McMurGut 1.1 (MCMG754) - Metabolic environment and model catalog of the murine gut

The McMurGut pipeline to create your individual model catalog and diet file to simulate the mouse microbiome

Manuscript status: $${\color{green}bioRxiv}$$
https://doi.org/10.1101/2024.09.13.612865

Next step: $${\color{orange}Peer-reviewed}$$ $${\color{orange}submission}$$

McMurGut pipeline:

1) Retreiving murine genomes from our samples

• Perform 16S rRNA gene amplicon sequencing on mouse feces, followed by Qiime2 taxonomy analysis (https://github.com/qiime2) to receive taxonomy file and abundance table.
• Alternatively, perform whole genome sequencing of mouse feces, followed by applying Kraken2(https://github.com/DerrickWood/kraken2)/Bracken(https://github.com/jenniferlu717/Bracken) to receive Bracken output. Transform it to mpa-like style via kreport2mpa.py (https://github.com/jenniferlu717/KrakenTools). Modify it to taxonomy file and abundance table via kr2_to_Micom_vGH01.ipynb.
• Remove non_taxonomic entries from taxonomy file.
• Search genome catalogs such as MGBC, CMMG, UHGG and NCBI for (if available) 3 reference genomes for each species present in each genus
• Collect the genomes and compressed to .fna.gz format. CMMG genomes may be transformed from .gff.gz into .fna.gz via GFFintoFASTAvGH01.ipynb.

2) Creating metabolic models via gapseq

Use gapseq 1.2 for metabolic reconstruction and gapfilling of the genomes (https://github.com/jotech/gapseq)
>gapseq doall

McMurGut 1.1: Version: 1.2; Sequence DB md5sum: 17e92c9 (2023-12-12, Bacteria) (04.2024) for 753/754 genomes. Version: 1.2 ccd1144, 2022, used for 1/754 genomes: GCA_022179725.1_ASM2217972v1_genomic.

Collect .XML-files.
Create a manifest file containing all XML files.

3) Combining to McMurGut 1.1

Use Qiime2's export tool to combine XML models into a single model catalog, on all taxonomy levels.

McMurGut 1.1 model catalog MCMG754: 754 models.XML, creating...
MCMG754_species.qza
MCMG754_genus.qza
MCMG754_family.qza
MCMG754_order.qza

4) Creating diet file based on McMurGut

A skeleton medium was created, based on...

• ssniff chow composition chart
• theoretical mouse gut components, such as water, mucin, urea, murine bile acids
• Micom's complete_db_medium (Micom 0.35.0 in Qiime2-amplicon-2024.2), with target doubling time of 0.1 (every ~7h), maximum flux input of 10 mmol/hour, aiming to enable growth of genera in McMurGut 1.1. 132 of 134 genera were growing (check_db_medium). See create_medium_vGH01.ipynb.
  Oxygen and toxic substances, which were automatically added in a first completion step, were excluded in a second run ("cpd00007", "cpd00007", "cpd00055", "cpd00071", "cpd00025", "cpd00239", "cpd00075", "cpd00116", "cpd00150").

McMurGut 1.1 diet medium file: ssniff_MCMG754_v02_diet.qza

5) Calculate coverage of McMurgut and your sample taxonomy of interest

Collapse taxonomy from taxonomy file to genus level (Collapse_csvs_vGH01.ipynb)

6) Using McMurGut in Micom

(https://github.com/micom-dev)

Prepare taxonomy/abundance file for Micom

merge_tas_tfb_micom_vGH01.ipynb

Run Micom

micom_run2_vGH01.ipynb
Integrate MCMG754_genus.qza and ssniff_MCMG754_v02_diet.qza in Micom simulation (0.35.0).

Run Flux*abundance per genus

search_flux_species_vGH01.ipynb