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venturelli1

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v1

x1 = xBH

v10

x10 = xCH

v11

x11 = xDP

v12

x12 = xER

v2

x2 = xCA

v3

x3 = xBU

v4

x4 = xPC

v5

x5 = xBO

v6

x6 = xBV

v7

x7 = xBT

v8

x8 = xEL

v9

x9 = xFP

Parameters

Global parameters

aBHBH*

aBHBO*

aBHBT*

aBHBU*

aBHBV*

aBHCA*

aBHCH*

aBHDP*

aBHEL*

aBHER*

aBHFP*

aBHPC*

aBOBH*

aBOBO*

aBOBT*

aBOBU*

aBOBV*

aBOCA*

aBOCH*

aBODP*

aBOEL*

aBOER*

aBOFP*

aBOPC*

aBTBH*

aBTBO*

aBTBT*

aBTBU*

aBTBV*

aBTCA*

aBTCH*

aBTDP*

aBTEL*

aBTER*

aBTFP*

aBTPC*

aBUBH*

aBUBO*

aBUBT*

aBUBU*

aBUBV*

aBUCA*

aBUCH*

aBUDP*

aBUEL*

aBUER*

aBUFP*

aBUPC*

aBVBH*

aBVBO*

aBVBT*

aBVBU*

aBVBV*

aBVCA*

aBVCH*

aBVDP*

aBVEL*

aBVER*

aBVFP*

aBVPC*

aCABH*

aCABO*

aCABT*

aCABU*

aCABV*

aCACA*

aCACH*

aCADP*

aCAEL*

aCAER*

aCAFP*

aCAPC*

aCHBH*

aCHBO*

aCHBT*

aCHBU*

aCHBV*

aCHCA*

aCHCH*

aCHDP*

aCHEL*

aCHER*

aCHFP*

aCHPC*

aDPBH*

aDPBO*

aDPBT*

aDPBU*

aDPBV*

aDPCA*

aDPCH*

aDPDP*

aDPEL*

aDPER*

aDPFP*

aDPPC*

aELBH*

aELBO*

aELBT*

aELBU*

aELBV*

aELCA*

aELCH*

aELDP*

aELEL*

aELER*

aELFP*

aELPC*

aERBH*

aERBO*

aERBT*

aERBU*

aERBV*

aERCA*

aERCH*

aERDP*

aEREL*

aERER*

aERFP*

aERPC*

aFPBH*

aFPBO*

aFPBT*

aFPBU*

aFPBV*

aFPCA*

aFPCH*

aFPDP*

aFPEL*

aFPER*

aFPFP*

aFPPC*

aPCBH*

aPCBO*

aPCBT*

aPCBU*

aPCBV*

aPCCA*

aPCCH*

aPCDP*

aPCEL*

aPCER*

aPCFP*

aPCPC*

uBH*

uBO*

uBT*

uBU*

uBV*

uCA*

uCH*

uDP*

uEL*

uER*

uFP*

uPC*

default*

Functions and Rules

Assignment rules

fBU = xBU / (xBH + xCA + xBU + xPC + xBO + xBV + xBT + xEL + xFP + xCH + xDP + xER)

fBH = xBH / (xBH + xCA + xBU + xPC + xBO + xBV + xBT + xEL + xFP + xCH + xDP + xER)

fBV = xBV / (xBH + xCA + xBU + xPC + xBO + xBV + xBT + xEL + xFP + xCH + xDP + xER)

fPC = xPC / (xBH + xCA + xBU + xPC + xBO + xBV + xBT + xEL + xFP + xCH + xDP + xER)

fER = xER / (xBH + xCA + xBU + xPC + xBO + xBV + xBT + xEL + xFP + xCH + xDP + xER)

fBO = xBO / (xBH + xCA + xBU + xPC + xBO + xBV + xBT + xEL + xFP + xCH + xDP + xER)

fCH = xCH / (xBH + xCA + xBU + xPC + xBO + xBV + xBT + xEL + xFP + xCH + xDP + xER)

fBT = xBT / (xBH + xCA + xBU + xPC + xBO + xBV + xBT + xEL + xFP + xCH + xDP + xER)

fEL = xEL / (xBH + xCA + xBU + xPC + xBO + xBV + xBT + xEL + xFP + xCH + xDP + xER)

fFP = xFP / (xBH + xCA + xBU + xPC + xBO + xBV + xBT + xEL + xFP + xCH + xDP + xER)

fDP = xDP / (xBH + xCA + xBU + xPC + xBO + xBV + xBT + xEL + xFP + xCH + xDP + xER)

fCA = xCA / (xBH + xCA + xBU + xPC + xBO + xBV + xBT + xEL + xFP + xCH + xDP + xER)

Function definitions

Events

event48

Trigger: gt(time, 48)

Delay: 0

Assignments:

xBO = 0.05 * xBO
xBV = 0.05 * xBV
xBT = 0.05 * xBT
xEL = 0.05 * xEL
xBH = 0.05 * xBH
xCA = 0.05 * xCA
xBU = 0.05 * xBU
xPC = 0.05 * xPC
xFP = 0.05 * xFP
xCH = 0.05 * xCH
xDP = 0.05 * xDP
xER = 0.05 * xER

event24

Trigger: gt(time, 24)

Delay: 0

Assignments:

xBH = 0.05 * xBH
xCA = 0.05 * xCA
xBU = 0.05 * xBU
xPC = 0.05 * xPC
xBO = 0.05 * xBO
xBV = 0.05 * xBV
xBT = 0.05 * xBT
xEL = 0.05 * xEL
xFP = 0.05 * xFP
xCH = 0.05 * xCH
xDP = 0.05 * xDP
xER = 0.05 * xER

Constraints

Note that constraints are not enforced in simulations. It remains the responsibility of the user to verify that simulation results satisfy these constraints.

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Show modifiers*

Show compartments*

Gravity*

Repulsion*

Pool threshold*

Species:

Reactions:

Middle-click: pin/unpin nodes
Shift-click: pool/unpool species
Right-click: context menu

Apply alternate model layout to overlapping elements in current model:

Model schema*

Parameter*

Start*

End*

Steps*

Species

Rates

Assignment rules

Deciphering microbial interactions in synthetic human gut microbiome communities.

Ophelia S Venturelli
Alex C Carr
Garth Fisher
Ryan H Hsu
Rebecca Lau
Benjamin P Bowen
Susan Hromada
Trent Northen
Adam P Arkin

Mol. Syst. Biol. 2018; 14 (6):

PubMed: 29930200
PubMed Central: PMC6011841
DOI: 10.15252/msb.20178157
ISSN: 1744-4292
URL: https://ncbi.nlm.nih.gov/pubmed/29930200

Abstract

The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-dimensional consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi-species community dynamics, as opposed to higher-order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological drivers and responsive recipient species were discovered in the network. Our model demonstrated that a prevalent positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop that balances disparities in monospecies fitness levels. We show that negative interactions could generate history-dependent responses of initial species proportions that frequently do not originate from bistability. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis of microbial interactions. In sum, these methods defined the ecological roles of major human-associated intestinal species and illuminated design principles of microbial communities.

No additional notes are available for this model.

JWS Online documentation

venturelli1

Reactions

v1

v10

v11

v12

v2

v3

v4

v5

v6

v7

v8

v9

Parameters

Fixed species

Initial values

Functions and Rules

Assignment rules

Function definitions

Events

event48

event24

Constraints

Deciphering microbial interactions in synthetic human gut microbiome communities.

Abstract