syntrophy of a Clostridium and a Methanogen

_syntrophy.R

library(BacArena)

SYBIL_SETTINGS("SOLVER", "cplexAPI")
set.seed(115)

# C. beijerinckii:
# - publication https://doi.org/10.1007/s00253-008-1654-4 
# - model http://bigg.ucsd.edu/models/iAF692
# M. barkeri:
# - publication: https://doi.org/10.1186/1752-0509-5-130
# - model: https://static-content.springer.com/esm/art%3A10.1186%2F1752-0509-5-130/MediaObjects/12918_2011_738_MOESM3_ESM.XML

mb <- readRDS("m.barkeri_iAF692.RDS")
cb <- readRDS("c.beijerinckii_iCM926.RDS")

ex <- findExchReact(cb)
cb@react_id[ex@react_pos] <- gsub("ex_","EX_",cb@react_id[ex@react_pos])

arena <- BacArena::Arena()

# set maximal uptake
bac1 <- Bac(model=mb)
bac1@lbnd["EX_h2(e)"]   <- -41
bac1@lbnd["EX_meoh(e)"] <- -16
bac1@lbnd["EX_ac(e)"]   <- -8
bac1@lbnd["EX_pyr(e)"]  <- -5
bac2 <- Bac(model=cb)
bac2@lbnd["EX_ac(e)"] <- -3.41

arena <- BacArena::addOrg(arena, bac1, amount=50)
arena <- BacArena::addOrg(arena, bac2, amount=50)

# minimal medium
min_barkeri <- c("EX_4abz(e)", "EX_cobalt2(e)", "EX_nac(e)", "EX_h2o(e)", "EX_h(e)",  "EX_nh4(e)", "EX_ni2(e)", "EX_pi(e)", "EX_so3(e)", "EX_cys_L(e)")
min_beijerinckii <- c("EX_h2o(e)", "EX_nh4(e)", "EX_h(e)", "EX_pi(e)", "EX_4abz(e)", "EX_so4(e)")
arena <- BacArena::addSubs(arena, mediac=min_beijerinckii, smax=1, unit="mM")
arena <- BacArena::addSubs(arena, mediac=min_barkeri, smax=1, unit="mM")
arena <- BacArena::addSubs(arena, mediac="EX_glc_D(e)", smax=0.1, unit="mM")
arena <- BacArena::addSubs(arena, mediac="EX_h2(e)", smax=0.05, unit="mM")
arena <- BacArena::addSubs(arena, mediac="EX_co2(e)", smax=0.05, unit="mM")

sim=BacArena::simEnv(arena, time=24, sec_obj="mtf")

plotGrowthCurve(sim)[[1]]
subs = c("EX_ac(e)", "EX_glc_D(e)", "EX_ch4(e)", "EX_h2(e)", "EX_co2(e)")
plotSubCurve(sim, mediac=subs)[[1]]
plotSubUsage(sim, subs=subs)[[2]]
findFeeding(sim)

c.beijerinckii_iCM926.RDS

crossfeed.pdf

growth.pdf

m.barkeri_iAF692.RDS

substances.pdf

usage.pdf

refers euba/BacArena#177