MFG: Microbial Functional Group (MFG) dataframes
In HelenKettle/microPop: Modelling Microbial Populations

Description Usage Format Details

This is a generic description of the dataframes describing the pathways and parameters of each microbial functional group. Each resource (substrate, metabolic product or biomass (if microbial production is included in the chemical stoichiometry)) has a column. The first column can be used for describing the units of each parameter. This is optional and just for clarity - it is not used within microPop (note, the units column must be labelled 'units' and it can not contain NAs). The row names and their details are given below:

Rtype Describes the type of resource. Can be S (substitutable substrate), Se (essential substrate), Sb (boosting substrate), Sm (microbial substrate), Sw (water as a substrate), P (product), Pb (biomass product) or X (not used)
halfSat Half-saturation constant for Monod Equation growth. Units must match the units of the resources. Resources that aren't used for growth will have entry NA.
yield This is the biomass yield i.e. mass of microbes/mass of substrate consumed. Note this is NOT a mol/mol yield! Resources that aren't used for growth will have entry NA.
maxGrowthRate Maximum growth rate of the group. Units are per unit time where time has the same units as those used for the microPopModel input arguments 'times'. Resources that aren't used for growth must have entry NA.
stoichiom The chemical stoichiometry in moles of each resource (note that this may also include biomass (see Xsu)).
keyResource If the stoichiometry is specified and all resources are essential then stoichiom will be used to determine rates of production and uptake and now 'yield' is the biomass produced per gram of the key resource specified here.
pHcorners Specified using 4 values in the first 4 columns. The pH limitation on growth is described by a trapezium. For increasing pH values the limitation goes from 0,1,1,0 at the points specified by the pHcorners.
numPathways The number of metabolic pathways the group has. If this is greater than 1 see details below for naming conventions.

MFG

A dataframe with the row names in the itemised list below and a column for units (optional) and for each resource required by the microbial group.

If there is more than one pathway the row names are as above but followed by .2 for second pathway, .3 for third pathway and so on. E.g. halfSat.2, yield.2

Note, when constructing new dataframes for new microbial functional groups (MFGs), the order of the rows does not matter but the names of the rows must be the same as those above. Also, the order of the resources columns does not matter (although if there is a 'units' column it must be the first column). The resources may be different for each MFG (e.g. See Bacteroides and Xsu).

When the user tells microPop which groups to use via the microbeNames input argument, the package will determine the names of all the resources and MFGs in the system and then check they are also in the system information files.

Note that the optional units column can not contain NAs. For entries without units put 'none'.

HelenKettle/microPop documentation built on May 18, 2019, 9:15 p.m.