Analyzing bacterial interaction and cross-feeding patterns with BacArena

0-crossfeeding.R

#
# The sihumi example data set consists of a simulation of 8 gut microbes growing on a western diet for 8 hours.
# Here, we use it to study microbial interactions
#


library(BacArena)

data("sihumi_test")

plotGrowthCurve(sihumi_test)[[2]]

# check for most changing substance concentrations
getVarSubs(sihumi_test)
subs <- names(head(getVarSubs(sihumi_test),30))
plotSubCurve(sihumi_test, mediac=subs)[[1]]

# what are bacteria doing with these substances? 
plotSpecActivity(sihumi_test, subs=subs)[[2]]

# find crossfeeding interactions
findFeeding3(sihumi_test, mets = subs, time=6)

1-abundance.png

2-substances.png

3-activity.png

4-crossfeeding.png