========== 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 (````). 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