Dataset: Predicted microbial interactions

Name: Results of computer simulations of inter-microbial metabolic exchange.
Published: 2022-02-03
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.806874.1

Project:

Microbial ecosystems in silico, in the lab and in the field: understanding interactions between abundant marine bacterial taxa (HADFBA)

Principal Investigator:

Daniel Segre (Boston University, BU)

Co-Principal Investigator:

Daniel Sher (University of Haifa)

BCO-DMO Data Manager:

Mathew Biddle (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Karen Soenen (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-02-03

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Results of computer simulations of inter-microbial metabolic exchange.

Abstract:

Results of computer simulations of inter-microbial metabolic exchange. The Zipped directory contains scripts and computationally generated predictions of growth phenotypes of pairs of bacteria under different growth conditions.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2022-02-03	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.806874.1	2022-02-03

Description

The Zipped directory contains scripts and computationally generated predictions of growth phenotypes of pairs of bacteria under different growth conditions.

The results from all growth simulations (1,051,596 simulations of two organisms with two carbon sources, with and without oxygen) are contained in the MATLAB structure 'MData.' Results are also provided in CSV format in 'MData.csv.zip.'

MData contains the following fields:

- aer and anaer: Data structures containing the following results for the simulations with and without oxygen, respectively:

- allGrewAlone: Binary vectors denoting whether or not both organisms grew in the first iteration of the algorithm.

- allGrewCross: Binary vectors denoting whether or not both organisms grew in the last iteration of the algorithm (after cross-feeding).

- expansions: Numerical vector detailing the number of medium expansions that occured in each simulation

- secMetCountsAlone: Numerical vector containing the number of metabolites secreted at the first iteration of each simulation.

- secMetCountsCross: Numerical vector containing the number of metabolites secreted at the last iteration of each simulation.

- sharedMedium: Cell array detailing the minimal medium composition.

- sub: Sparse binary double matrix detailing phenotypic information for the first (subject) organism in each simulation. Rows are simulations, column identities are contained in MData.col (Data given as row, column, value pairs in CSV version).

- par: Sparse binary double matrix detailing phenotypic information for the second (partner) organism in each simulation. Rows are simulations, column identities are contained in MData.col (Data given as row, column, value pairs in CSV version).

- Motifs: Data structure with two fields:

- MotifsGen: Cell array detailing the general interaction type in each simulation (C: commensal, M: mutualistic, N: non-interacting).

- MotifsSp: Cell array detailing the specific interaction motifs in each simulation (detailed in main text).

- col: Data structure defining which columns in the 'sub' and 'par' matrices correspond to phenotypic information (Species: organisms, CSources: carbon sources, absMets: absorbed metabolites corresponding to MData.fullMetList, secMets: secreted metabolites corresponding to MData.fullMetList, O2: oxygen availability, growthAlone: whether the organism grew alone in minimal medium, growthCross: whether the organism grew after cross-feeding).

- fullMetList: Cell array of all extracellular metabolites in all organism models.

- speciesPairCombos: Cell array of organisms used in each of the simulations.

- CSource pair combos: Cell array of carbon sources used in each of the simulations.

The model code is available in as .zip file: https://datadocs.bco-dmo.org/data/302/HADFBA/806874/1/data/CostlessExchange-1.0.zip
These files are also available in the following GitHub repository: https://github.com/BCODMO/CostlessExchange/tree/v1.0

Data Processing Description

BCO-DMO Processing Notes:

Originally submitted GitHub repository https://github.com/segrelab/CostlessExchange forked to https://github.com/BCODMO/CostlessExchange and tagged with release v1.0 which corresponds with this dataset submission.

The original repository may have continued updates.

Data Files

File

Results of computer simulations of inter-microbial metabolic exchange
filename: CostlessExchange-1.0.zip

(ZIP Archive (ZIP), 93.37 MB)
MD5:933aa750bddd62f5bd89f9c9061fd65a

The results from all growth simulations (1,051,596 simulations of two organisms with two carbon sources, with and without oxygen) are contained in the MATLAB structure 'MData.' Results are also provided in CSV format in 'MData.csv.zip.'

MData contains the following fields:

	- aer and anaer: Data structures containing the following results for the simulations with and without oxygen, respectively:

		- allGrewAlone: Binary vectors denoting whether or not both organisms grew in the first iteration of the algorithm.

		- allGrewCross: Binary vectors denoting whether or not both organisms grew in the last iteration of the algorithm (after cross-feeding).

		- expansions: Numerical vector detailing the number of medium expansions that occured in each simulation

		- secMetCountsAlone: Numerical vector containing the number of metabolites secreted at the first iteration of each simulation.

		- secMetCountsCross: Numerical vector containing the number of metabolites secreted at the last iteration of each simulation.

		- sharedMedium: Cell array detailing the minimal medium composition.

		- sub: Sparse binary double matrix detailing phenotypic information for the first (subject) organism in each simulation. Rows are simulations, column identities are contained in MData.col (Data given as row, column, value pairs in CSV version).

		- par: Sparse binary double matrix detailing phenotypic information for the second (partner) organism in each simulation. Rows are simulations, column identities are contained in MData.col (Data given as row, column, value pairs in CSV version).

		- Motifs: Data structure with two fields:

			- MotifsGen: Cell array detailing the general interaction type in each simulation (C: commensal, M: mutualistic, N: non-interacting).

			- MotifsSp: Cell array detailing the specific interaction motifs in each simulation (detailed in main text).

	- col: Data structure defining which columns in the 'sub' and 'par' matrices correspond to phenotypic information (Species: organisms, CSources: carbon sources, absMets: absorbed metabolites corresponding to MData.fullMetList, secMets: secreted metabolites corresponding to MData.fullMetList, O2: oxygen availability, growthAlone: whether the organism grew alone in minimal medium, growthCross: whether the organism grew after cross-feeding).

	- fullMetList: Cell array of all extracellular metabolites in all organism models.

	- speciesPairCombos: Cell array of organisms used in each of the simulations.

	- CSource pair combos: Cell array of carbon sources used in each of the simulations.