Metage2Metabo (M2M)

Metage2metabo is a Python3 tool to perform graph-based metabolic analysis starting from annotated genomes (reference genomes or metagenome-assembled genomes). It uses Pathway Tools in a automatic and parallel way to reconstruct metabolic networks for a large number of genomes. The obtained metabolic networks are then analyzed individually and collectively in order to get the added value of metabolic cooperation in microbiota over individual metabolism, and to identify and screen interesting organisms among all.

M2M can be used as a whole workflow (m2m workflow, m2m metacom) or steps can be performed individually (m2m recon, m2m iscope, m2m cscope, m2m addedvalue, m2m mincom, m2m seeds).

This project is licensed under the GNU Lesser General Public License - see the LICENSE.md file for details.

General information about the modelling

M2M has two main dependencies for modelling metabolic networks: MeneTools and Miscoto. Accordingly metabolic models in M2M follow the producibility in metabolic networks as defined by the network expansion algorithm. Mainly, two rules are followed:

• a recursive rule: the products of a reactions are producible if all reactants of this reaction are themselves producible

• an initiation rule: producibility is initiated by the presence of nutrients, called seeds.

A metabolite that is producible from a set of nutrients is described as being “in the scope of the seeds”. The computation is made using logic solvers (Answer Set Programming). The present modelling ignores the stoichiometry of reactions (2A + B –> C is considered equivalent to A + B –> C), and is therefore suited to non-curated or draft metabolic networks, as the ones built using M2M with the PathoLogic software of Pathway Tools handled by Mpwt. Many works have relied on network expansion to study organisms (here, here or there) and communities (here, here, or here). It has been compared, combined to steady-state modelling (Flux Balance Analysis).

Documentation of M2M

• Requirements and Installation
  • Requirements
  • Installation with pip
  • Installation with Docker
  • Installation with Singularity (e.g. on a cluster)
• Commands
  • Outputs and logs
  • m2m Commands
• m2m Inputs
  • Genomes or metabolic networks
  • Seeds
  • Targets (Optional)
  • Bibliography
• m2m Tutorial
  • Outputs and logs
  • m2m recon
  • m2m iscope, cscope and addedvalue
  • m2m mincom
  • m2m metacom
  • m2m workflow and m2m test
  • Including a host in the picture
  • More information
• m2m Outputs
  • m2m_metadata.json
  • m2m_command.log
  • pgdb folder
  • sbml
  • padmet
  • recon_stats.tsv
  • indiv_scopes
  • community_analysis
  • producibility_targets.json
• Supplementary information
  • Scope criterion of graph-based producibility
• m2m’s API
  • Workflow
  • SBML Management
  • Utils
  • m2m_analysis
  • Main
• m2m_analysis
  • Requirements
  • Presentation
  • m2m Tutorial
  • m2m_analysis output files
  • More information
• Troubleshooting
  • m2m_analysis: “Can’t connect to X11 window server using…”
  • UnicodeDecodeError when running m2m_analysis with Singularity

Additional features

M2M relies on packages that can also be used independantly with more features and additional options:

• mpwt: command-line and multi-process solutions to run Pathway Tools. Suitable to multiple reconstruction, for example genomes of a microbiota

• menetools: individual metabolic capabilities analysis using graph-based producibility criteria

• miscoto: community selection and metabolic screening in large-scal microbiotas, with or without taking a host into account

Authors

Clémence Frioux and Arnaud Belcour, Univ Bordeaux, Inria, INRAE, Bordeaux, France, Univ Grenoble Alpes, Inria, Grenoble, France and Univ Rennes, Inria, CNRS, IRISA, Rennes, France.

Acknowledgement

People of Pathway Tools (SRI International) for their help integrating Pathway Tools with command line and multi process in the mpwt package, used in M2M.

Indices and tables

• Index

• Module Index

• Search Page