Growth medium definition

Growth medium file format

A user gapfill medium can be defined in a 3-column comma-(csv) or tab-(tsv)-separated table.

  • 1st column “compounds”: Should list the compounds’ identifier

  • 2nd column “name”: List of compound names

  • 3rd column “maxFlux”: Defines the maximum uptake rate of the compound in mmol/gDW/hr

Example: M9-like medium (aerobic) with limited Glucose+Oxygen uptake and virtually unlimited salts/ions.

compounds,name,maxFlux
cpd00001,H2O,100
cpd00007,O2,10
cpd00009,Phosphate,100
cpd00027,D-Glucose,5
cpd00030,Mn2+,100
cpd00034,Zn2+,100
cpd00048,Sulfate,100
cpd00058,Cu2+,100
cpd00063,Ca2+,100
cpd00067,H+,100
cpd00099,Cl-,100
cpd00149,Co2+,100
cpd00205,K+,100
cpd00254,Mg,100
cpd00531,Hg2+,100
cpd00971,Na+,100
cpd01012,Cd2+,100
cpd01048,Arsenate,100
cpd10515,Fe2+,100
cpd10516,fe3,100
cpd11595,chromate,100
cpd00013,NH3,100

List of potential nutrients

A table with all nutrients (IDs and names), that can be part of a growth medium definition is stored in your gapseq installation (dat/nutrients.tsv) or accessed also directly on github.

A list of database-specific compounds, which might diverge from metabolite entries in other databases, is given in the database section.

Predicting a growth medium

Comming up with a suited growth medium for gapfilling and flux-balance-analysis can be difficult, especially for organisms that are not-yet well characterized in their growth requirements.

gapseq provides a module that can predict a growth medium based on the results generated by gapseq find and gapseq draft. The predicted growth medium can directly be used also as gapfilling medium in gapseq fill.

The medium prediction module requires two inputs: The pathway prediction table (generated by gapseq find) and the draft model (generated by gapseq draft). An example:

gapseq medium -m ecoli-draft.RDS -p ecoli-all-Pathways.tbl

Using the optional flag -c specific metabolites can be added/removed from the medium prediction. The syntax for the flag option is

-c "[CompoundID_1]:[maxFlux_1];[CompoundID_2]:[maxFlux_2]".

For example, to remove oxygen from the final medium you can use:

gapseq medium -m ecoli-draft.RDS -p ecoli-all-Pathways.tbl -c "cpd00007:0"

This option is for instance helpful to ensure an anaerobic environment.

To remove oxygen and add L-Lactate with 10 mmol/gDW/hr to the final medium you can use:

gapseq medium -m ecoli-draft.RDS -p ecoli-all-Pathways.tbl -c "cpd00007:0;cpd00159:10"