request, mega medium

[mmpust]

Dear developers, we would like to do cross-feeding simulations for bacteria growing in Mega Medium. I am unsure how to convert this information into a format that can be used with gapseq. Could you clarify how I can determine the flux rates and cpd-ids?
Thank you!

# Component	Amount (in 500 ml)
Milli-Q water (dH2O)	410 ml
1 M Potassium phophate buffer, pH 7.2	50 ml
TYG salts solution	20 ml
Tween 80	1 ml of 25% (v/v)
SCFA supplement	1.4 ml
0.8% (w/v) CaCl2	500 ul
FeSO4 7H20	500 ul of 0.4 mg/ml
Resazurin	2 ml of 0.25 mg/ml
Trypticase Peptone (BBL)	5 g
Yeast Extract (Bacto)	2.5 g
Meat Extract	2.5 g
L-Cysteine hydrochloride	0.25 g
D-(+)-Glucose	1 g
D-(+)-Cellobiose	0.5 g
D-(+)-Maltose monohydrate	0.5 g
D-(-)-Fructose	0.5 g
Soluble Starch	0.25 g
Vitamin K + Hematin (1%)	5 ml
Trace mineral supplement	5 ml
Vitamin supplement	5 ml

[Fake-star]

I have the same problem! I want to simulate culturing lactobacilli under MARS medium conditions, but I don't know how I should fill in the specific medium components.

[jotech]

I'm afraid that is not such an easy task. For silicon medium generation in general, you can have a look at this publication https://doi.org/10.1371/journal.pone.0236890
Unfortunately, some compounds, such as yeast or meat extract, are hard to quantify.
meat and yeast extract was estimated for the AAM growth medium, which we used in this study https://doi.org/10.1038/s41396-021-01153-z (supplementary file: AAM_co.csv), but it's a mixed diet. It's a mixed medium, but maybe you can find some estimates here.