Hostmicrobeinteraction

AGORAEssentialMetabolites

This file contains a list of metabolites required by the AGORA microbial reconstructions to grow.

adjust

These constrains are specific to the host-microbiome interaction modeling performed for the publication.

analyzeHMmodel(modelHM, Diet, Results, ResultsSol, setStandard, RxnMin, RxnMax, LPSolver)

Perform host-microbiome optimisation for a set of defined model reactions

This function performs host-microbiome optimisation for a set of defined model reactions. Note that the fecal secretion rate for the microbiome community biomass reaction is constrained to lb = 0.4 and ub = 1.

USAGE:

[Results, ResultsSol, ResultsStats] = analyzeHMmodel (modelHM, Diet, Results, ResultsSol, setStandard, RxnMin, RxnMax, LPSolver)

INPUTS:

• modelHM – Host-microbiome model structure, with fields:

  • .sex - ‘male’ or ‘female’

  • .rxns - reaction identifiers

  • .c - objective coefficients

  • .lb - lower bounds

  • .ub - upper bounds

• Diet – Diet option: ‘EUAverageDiet’ (default), ‘HighFiberDiet’, ‘HighProteinDiet’, ‘UnhealthyDiet’, or ‘VegetarianDiet’

• Results – List of result names of FBA simulations (optional; new results are appended when provided)

• ResultsSol – Array of FBA solution vectors matching Results (optional; new results are appended when provided)

• setStandard – Apply the standard constraints (default 1)

• RxnMin – Reaction(s) in modelHM to be minimised

• RxnMax – Reaction(s) in modelHM to be maximised

• LPSolver – LP solver to use (‘tomlab_cplex’ or ‘ILOGcomplex’ default)

OUTPUTS:

• Results – List of result names of FBA simulations using modelHM

• ResultsSol – Array of FBA solution vectors corresponding to Results

• ResultsStats – List of solver status for each FBA solution

define solver

calculateCorrelations

This script creates microbiome models for HMP individuals using the Microbiome Modeling Toolbox

Almut Heinken

path where to save results

combineHarveyMicrotiota(modelH, modelM, couplingConstraint)

Combine a whole-body (Harvey/Harvetta) model with a microbial community model

This function combines a whole-body metabolic model (Harvey/Harvetta) and a microbial community model into a single host-microbiome model.

USAGE:

modelHM = combineHarveyMicrotiota (modelH, modelM, couplingConstraint)

INPUTS:

• modelH – Whole-body metabolic model structure, with fields:

  • .S - stoichiometric matrix

  • .C - coupling-constraint matrix

  • .A - combined constraint matrix (built from .S and .C if absent)

  • .b - right-hand side for the metabolite constraints

  • .d - right-hand side for the coupling constraints

  • .csense - metabolite constraint senses (E, L, G)

  • .dsense - coupling-constraint senses

  • .mets - metabolite identifiers

  • .ctrs - constraint identifiers

  • .rxns - reaction identifiers

• modelM – Microbiota model structure, with fields:

  • .S - stoichiometric matrix

  • .C - coupling-constraint matrix

  • .A - combined constraint matrix (built from .S and .C if absent)

  • .b - right-hand side for the metabolite constraints

  • .d - right-hand side for the coupling constraints

  • .csense - metabolite constraint senses (E, L, G)

  • .dsense - coupling-constraint senses

  • .mets - metabolite identifiers

  • .ctrs - constraint identifiers

  • .rxns - reaction identifiers

  • .rev - reversibility indicator per reaction

  • .lb - lower bounds

• couplingConstraint – Coupling constraint for the microbiome model (default 20000, as used in the whole-body metabolic model)

OUTPUT:

modelHM – Combined model structure holding both the whole-body model and the microbiota in one matrix, with fields:

• .A - combined constraint matrix

• .S - combined stoichiometric matrix

• .mets - combined metabolite identifiers

• .rxns - combined reaction identifiers

• .csense - constraint senses

• .subSystems - subsystem annotations

• .Microbiota - indicator vector: 1 for microbiota reactions, 0 for host reactions

setSimulationConstraints(model)

Set the remaining simulation constraints identified during debugging

This function sets the remaining simulation constraints identified during debugging. It needs to be applied to GF and MyWB models that were created with GF before Dec 2017.

USAGE:

[model] = setSimulationConstraints (model)

INPUT:

model – Whole-body metabolic model, with fields:

• .rxns - reaction identifiers

OUTPUT:

model – Model with updated simulation constraints