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)

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

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

INPUT modelHM model structure containing the host-microbiome model Diet Diet option: ‘EUAverageDiet’ (default) Results List of result names of FBA simulations using modelHM. The function provides the option to append the new results

to a previous list of results. If not provided, a new list of results will be returned.

ResultsSol Array of FBA solution vectors corresponding to the optimization problems in Results. The function provides the option to append the new results

to a previous list of results. If not provided, a new list of results will be returned.

setStandard default: 1 RxnMin Reaction(s) in modelHM to be minimized RxnMax Reaction(s) in modelHM to be maximized LPSolver Define LP solver to be used (‘tomlab_cplex’ or

‘ILOGcomplex’ (default))

OUTPUT Results List of result names of FBA simulations using modelHM. ResultsSol Array of FBA solution vectors corresponding to the optimization problems in Results. ResultsStats List of solver status for each FBA solution

Ines Thiele 2016-2019

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)

This function combines harvey and a microbial community model

function modelHM = combineHarveyMicrotiota(modelH, modelM, couplingConstraint)

INPUT modelH Whole-body metabolic model structure modelM Microbiota model structure couplingConstraint coupling constraint for microbiome model (default:

20000, as used in the whole-body metabolic model

OUTPUT modelHM Model structure containing both Whole-body metabolic model and microbiota in one

matrix

Ines Thiele May 2016 replace Ex_AA[u] with an artificial transport reaction [luM] – > [luLI] updated to new structure we use ([d],[fe],[u]) for microbes - Nov 2017 IT

setSimulationConstraints(model)

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

function [model] = setSimulationConstraints(model)

INPUT model model structure (whole body metabolic model)

OUTPUT model model structure with updated constraints as defined in this file

Ines Thiele Dec 2017