Computational modeling of microbial communities applied to D. pigrum and S. aureus in the human nose

This repository introduces the codes applied to the nasal microbial community of the latest available curated GEMs of D. pigrum and S. aureus.

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A metabolic modeling community of organisms D. pigrum and S. aureus in a nasal medium. This implements functionality to analyze the interaction between these two species within a human nose using different approaches to construct a community.

Authors: Reihaneh Mostolizadeh, Manuel Glöckler

To run it as a package, refer to:

Repository: https://github.com/manuelgloeckler/ncmw

Full documentaion page: https://manuelgloeckler.github.io/ncmw/

► Getting started with this repository

Operating systems: MacOS, Windows, Linux.

All codes can be run separately in the jupyter notebook.

The package depends on third-party software that was successfully tested using Python (version 3.7 or later), COBRApy (version 0.19.0 or later), CPLEX (version 20.1.0). Alternativiely, other solvers for linear programing may be used as long as those are supported by COBRApy.

Overview

The repository has contained a folder named "Models," including models used in this work, a folder named "Media" including synthetic nasal medium (SNM3) used in this work and all other media created as a subset of SNM3, and all codes applied for the analysis in the related manuscript.

Model_Summary

DP_SA_summatymodel_1: gives an overview of both models used in this research
flux_distribution_SA: is an overview of flux distribution of S. aureus
flux_distribution_DP is an overview of flux distribution of D. pigrum
creat_compm_media the COMPM media was created

Similarity

jaccard_index: which computed the similarity between both species
uptake_sekeration_inverstigation: compare the similarity between both species from the perspective of uptake and secretion metabolites

Community

number_12 the analysis of the community based on the pooled approaches
number_13 the analysis of the community based on the integrated approaches while we have media SNM3, exchange, COMPM
number_14 the analysis of the community based on the shuttle approaches while we have media SNM3, exchange, COMPM (shuttle environment was considered as all 111 total exchange reactions)- linear combination of the objective function was implemented.
number_16 the analysis of the community based on the shuttle approaches while we have media SNM3, exchange, COMPM (shuttle environment was considered as all 111 total exchange reactions)- the convex combination of the objective function was implemented.
number_18 the analysis of the community based on the shuttle approaches while we have media SNM3, exchange, COMPM (shuttle environment was considered as all uptake and secreted metabolites)- linear combination of the objective function and convex combination were implemented.
numbers_20-21-22-23-24-25 computing the COOPM media in different scenarios and the analysis of the community in COOPM in all different conditions.
numbers_26-28 a brief analysis of different scenarios while the community was created as a package to be called.
optcom_comparison MICOM package by using otpcom objective function and the modification based on the nasal microbiom community.

☮ Licensing and distribution

The University of Tübingen, Germany

Name		Name	Last commit message	Last commit date
Latest commit History 35 Commits
Media		Media
Models		Models
DP_SA_summarymodel_1.ipynb		DP_SA_summarymodel_1.ipynb
README.md		README.md
community_model_21.ipynb		community_model_21.ipynb
community_model_22.ipynb		community_model_22.ipynb
community_model_23.ipynb		community_model_23.ipynb
community_model_24.ipynb		community_model_24.ipynb
community_model_25.ipynb		community_model_25.ipynb
community_model_COMPM_weights_16.ipynb		community_model_COMPM_weights_16.ipynb
community_model_Exchange_weights_16.ipynb		community_model_Exchange_weights_16.ipynb
community_model_Integrated_COMPM_13.ipynb		community_model_Integrated_COMPM_13.ipynb
community_model_Integrated_Exchange_13.ipynb		community_model_Integrated_Exchange_13.ipynb
community_model_Integrated_SNM_13.ipynb		community_model_Integrated_SNM_13.ipynb
community_model_SNM_weights_16.ipynb		community_model_SNM_weights_16.ipynb
community_model_approaches_26.ipynb		community_model_approaches_26.ipynb
community_model_pooled_12.ipynb		community_model_pooled_12.ipynb
community_model_shuttle_COMPM_14.ipynb		community_model_shuttle_COMPM_14.ipynb
community_model_shuttle_Exchange_14.ipynb		community_model_shuttle_Exchange_14.ipynb
community_model_shuttle_RM_14.ipynb		community_model_shuttle_RM_14.ipynb
community_model_shuttle_SNM_14.ipynb		community_model_shuttle_SNM_14.ipynb
community_model_shuttle_uptakeSecretion_COMPM_18.ipynb		community_model_shuttle_uptakeSecretion_COMPM_18.ipynb
community_model_shuttle_uptakeSecretion_Exchange_18.ipynb		community_model_shuttle_uptakeSecretion_Exchange_18.ipynb
community_model_shuttle_uptakeSecretion_SNM_18.ipynb		community_model_shuttle_uptakeSecretion_SNM_18.ipynb
community_model_shuttle_uptakes_RM_18.ipynb		community_model_shuttle_uptakes_RM_18.ipynb
community_models_prediction_interaction_table_28.ipynb		community_models_prediction_interaction_table_28.ipynb
community_models_table_28.ipynb		community_models_table_28.ipynb
creat_compm_media.ipynb		creat_compm_media.ipynb
flux_distribution_DP.ipynb		flux_distribution_DP.ipynb
flux_distribution_SA.ipynb		flux_distribution_SA.ipynb
jaccard_index.ipynb		jaccard_index.ipynb
optcom_comparison.ipynb		optcom_comparison.ipynb
optimization_20.ipynb		optimization_20.ipynb
uptake_sekeration_inverstigation.ipynb		uptake_sekeration_inverstigation.ipynb

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Computational modeling of microbial communities applied to D. pigrum and S. aureus in the human nose

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