Antibiotics

[tenguzame]

Greetings, Is there the possibility within BacArena to simulate antimicrobial production and resistance? It would be awesome to track these dynamics within a microbial consortium.

[jotech]

hi, hm I'm already thinking about this for some time. It is not an easy task bc the mechanism how antibiotics work are so diverse and often not metabolic. Do you have a special one in mind? Besides this, we have a simple predator-prey dynamics available:

library(BacArena)
data("Ec_core")

pred  <- Bac(Ec_core, type="predator")
prey  <- Bac(Ec_core, type="prey", predator="predator")
arena <- Arena(n=50, m=50)
arena <- addOrg(arena,prey,amount=50)
arena <- addOrg(arena,pred,amount=50)
arena <- addSubs(arena, smax=0.005, mediac="EX_glc(e)", unit="mM")
arena <- addSubs(arena, smax=1, mediac=c("EX_pi(e)", "EX_h2o(e)",
                                         "EX_o2(e)", "EX_nh4(e)"), unit="mM") 
sim   <- simEnv(arena, time=5)

With this, it may possible to model an antibiotics as a predator which can kill certain vulnerable species. What do you think?

[tenguzame]

Hi, Yes, I was already thinking about something like that, but I am afraid that it won't work in a complex system such as the one I'm studying. I can try to make it work, though: is your predator/prey mechanics customizable? What about "hacking" the metabolite database to add both the antibiotic and the molecular system to break it down, even in a very simplistic way? Antibiotics would lower the biomass of all the organisms in the system, unless they have a corresponding metabolite which lowers the concentration of the antibiotic on the cells surrounding the bacteria. Would it be feasible? Thanks!

Il 1 ott 2019 20:41, jo notifications@github.com ha scritto:

hi, hm I'm already thinking about this for some time. It is not an easy task bc the mechanism how antibiotics work are so diverse and often not metabolic. Do you have a special one in mind? Besides this, we have a simple predator-prey dynamics available:

library(BacArena) data("Ec_core")

pred <- Bac(Ec_core, type="predator") prey <- Bac(Ec_core, type="prey", predator="predator") arena <- Arena(n=50, m=50) arena <- addOrg(arena,prey,amount=50) arena <- addOrg(arena,pred,amount=50) arena <- addSubs(arena, smax=0.005, mediac="EX_glc(e)", unit="mM") arena <- addSubs(arena, smax=1, mediac=c("EX_pi(e)", "EX_h2o(e)", "EX_o2(e)", "EX_nh4(e)"), unit="mM") sim <- simEnv(arena, time=5)

With this, it may possible to model an antibiotics as a predator which can kill certain vulnerable species. What do you think?

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