m2m Inputs

Genomes or metabolic networks

If you have annotated genomes and no metabolic networks, you can reconstruct draft metabolic networks using m2m with the m2m workflow or the m2m recon commands. The genomes are expected to be in GenBank format (.gbk or .gbff) and the input is the directory containing subdirectories with the corresponding files. In addition, the name of the directory must match the name of the genbank file. Example:

input_folder
├── organism_1
│ └── organism_1.gbff
├── organism_2
│ └── organism_2.gbff
├── organism_3
│ └── organism_3.gbff
..
└── organism_n
  └── organism_n.gbff

If you already have metabolic networks, you can analyse them with the command m2m metacom that will perform the whole workflow except for the metabolic reconstruction part. The metabolic networks must be in SBML format. The input is a folder containing multiples SBML files. Example:

input_folder
├── organism_1.sbml
├── organism_2.sbml
├── organism_3.sbml
..
└── organism_n.sbml

Seeds

Seeds are a set of metabolites that define the nutritional conditions of the community. These metabolites can be components of the growth medium or co-factors of complex cycles (known as currency metabolites). Seeds must be in SBML format.

For example, this is a list of common currency metabolites (from Kim et al. 2015):

* proton
* water
* oxygen molecule
* NADP+
* NADPH
* ATP
* diphosphate
* carbon dioxide
* phosphate
* ADP
* coA
* UDP
* NAD+
* NADH
* AMP
* ammonia
* hydrogen peroxide
* oxidized electron acceptor
* reduced electron acceptor
* 3-5-ADP
* GDP
* carbon monoxide
* GTP
* FAD

The seed metabolites can be found in the literature. They can be also found from metabolic databases, for example metaboltites from nutrition in the VMH or growth media from MetaCyc (in this latter case, one should used the metabolites in the Constituents column).

Once a list of metabolites has been designed, these metabolites must be converted to a list of IDs of the metabolic database corresponding to your metabolic networks. For example, in the VMH seeds ethanol is etoh. In the MetaCyc database, the ID of ethanol is ETOH. Then the ID must be checked with the ID in the SBML files of the metabolic networks. In this example ETOH is associated to M_ETOH_c in the SBML file in the species field (<species id="M_ETOH_c" name="ETOH" compartment="c"/>). The M_ corresponds to metabolite (another possibility for this prefix is the R_ for reaction). And _c corresponds to the cytosol compartment.

Targets (Optional)

Targets are a set of metabolites whose producibility by the community will be checked and for which minimal communities will be computed. It is possible to give targets as a SBML file to Metage2Metabo with any of the commands m2m cscope, m2m mincom and m2m metacom. Adding targets will replace the metabolites from the cooperation potential (the addedvalue) as a metabolic objective whether these metabolites are producible either by individual organisms (with iscope), by the community (with cscope) and compute minimal communities producing these metabolites (with mincom).

The same conversion method than the one for the seeds is needed to create a useful targets file. In addition, one can customise the set of predefined targets from the cooperation potential by modifying the file community_analysis/targets.sbml and setting this file as targets with the -t argument.

Bibliography

Kim, T., Dreher, K., Nilo-Poyanco, R., Lee, I., Fiehn, O., Lange, B. M., Nikolau, B. J., Sumner, L., Welti, R., Wurtele, E. S., & Rhee, S. Y. (2015). Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis using a genome-scale metabolic network. Plant physiology, 167(4), 1685–1698. https://doi.org/10.1104/pp.114.252361