Organisms will not utilize substrates

[wtscott31]

Hi all,

I have been experiencing a peculiar problem with my genome-scale reconstructions being unable to take up any substrates/metabolites or excrete any products/metabolites. I provide a mineral medium plus glucose, yet nothing seems to work to get my model microorganisms to use the supplied metabolites. Therefore, the microbes die after a few iterations. Has anyone else experienced this using BacArena? How can I solve this issue?

[maringos]

Hi,

may I ask for providing us with a minimal example? Are you sure that the exchange reactions and not the names of the metabolites are used in the addSubs function?

Best,
Yorgos

[mixiaoluo88]

Hi, I've been in a simmilar situation.

I want to simulate the metabolic model of multiple strains to determine how competitive these bacteria are.

here is my script, with the substance used LB medium. (I put the file in the attachment):
LB_medium.txt

simulateMultiGrowth <- function(modelPaths,allmodels, simulationTime, n, m, substances){
  library(BacArena)
  library(sybil)
  SYBIL_SETTINGS("SOLVER","cplexAPI") 

  arena <- Arena(n=n, m=m)

  for (models in allmodels) {
    sbml_model <- readRDS(file.path(modelPaths,models))  
    bac <- Bac(sbml_model)   
    arena <- addOrg(arena, bac, amount=5) 
  }
  
  # add substances
  for (sub in substances) {
    arena <- addSubs(arena, smax=1, mediac=paste0('EX_',sub,'_e0'), unit="mM")
  }
  # addSubs(arena, smax=100, mediac=c("EX_pi(e)", "EX_h2o(e)", "EX_o2(e)", "EX_nh4(e)"), unit="mM")

  # start sim
  eval <- simEnv(arena, time=simulationTime)
 
  growthPlot <- plotCurves2(eval, legendpos="right")
  # plot 
  pdf('spatial_time_curve.pdf')
  par(mfrow=c(2,2))
  evalArena(eval, show_legend = TRUE, time=seq(1,10,2))
  dev.off()

  png(paste(bac@type, "GrowthCurve.png", sep="_"), width=800, height=600)
  print(growthPlot)
  dev.off()

  return(list(results,plots=c("GrowthCurve.png", "SubstrateConsumption.png")))
}

No matter how many times I run it, the results always tell me:
Rplots.pdf

[1] "All organisms died!"
[1] "All substances have variance of zero."
$rect
$rect$w
[1] 2.824062

$rect$h
[1] 1.75814

$rect$left
[1] 8.575938

$rect$top
[1] 3.37907


$text
$text$x
 [1] 9.127188 9.127188 9.127188 9.127188 9.127188 9.127188 9.127188 9.127188
 [9] 9.127188 9.127188 9.127188

$text$y
 [1] 3.232558 3.086047 2.939535 2.793023 2.646512 2.500000 2.353488 2.206977
 [9] 2.060465 1.913953 1.767442

I look forward to hearing from you，
hongyang lvy

[onix1988]

Hello everyone,
I’ve encountered the same issue. I generated metabolic models in ModelSeed, but when I run the simulation, the microorganisms die. Does anyone have any suggestions? Have those who faced this issue managed to solve it?
Thank you very much for your help!