Defined Gut Microbiota Medium (dGMM)

The defined Gut Microbiota Medium (dGMM) is composed of all compounds described in ‘Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies’[1]. The dGMM was used under anaerobic conditions in the paper and, thus, does not contain any oxygen. However, a gas mix containing carbon dioxide, nitrogen and hydrogen was added to the anaerobic chamber. Hence, all three gases were added to the following definition.

Table 6 dGMM composition

name	source
3-[(2R)-2,4-Dihydroxy-3,3-dimethylbutanamido]propanoate [Pantothenate]	Calcium Pantothenate
4,5-Bis(hydroxymethyl)-2-methylpyridin-3-ol [Pyridoxine]	Pyridoxine HCl
4-Aminobenzoic acid	p-Aminobenzoic acid
5-(1,2-Dithiolan-3-yl)pentanoate [Lipoate]	Lipoic acid
Acetate [Acetic acid]	Acetic acid
Biotin	Biotin
Butyrate	Butyric acid
Calcium(II) cation [Ca(2+)]	CaCl2 (anhydrous), Calcium Pantothenate
Carbon dioxide [CO2]	Carbon dioxide (From gas mix)
Hydrogencarbonate	NaHCO3
Cellobiose	Cellobiose
Chloride [Cl(-)]	NiCl2.6H2O, CaCl2 (anhydrous), NaCl, Thiamine HCl, Pyridoxine HCl
Cob(I)alamin	Vitamin B12
Cob(II)alamin	Vitamin B12
Cobalt(II) cation [Co(2+)]	Co(NO3)2.6H2O
Copper(II) cation [Cu(2+)]	CuSO4 (anhydrous)
D-Fructose	Fructose
D-Glucose	D-Glucose
HemeD	Hematin
Hydrogen [H(+)]	Thiamine HCl, Pyridoxine HCl, KH2PO4
Iron(II) cation [Fe(2+)]	FeSO4.7H2O
Iron(III) cation [Fe(3+)]	FeSO4.7H2O
Isovalerate	Isovaleric acid
L-Cysteine	L-Cysteine
L-Histidine	L-Histidine
Magnesium(II) cation [Mg(2+)]	MgSO4*7H2O
Maltose	Maltose
Manganese(II) cation [Mn(2+)]	MnSO4*H2O
Menadione [Vitamin K]	Vitamin K (menadione)
N-(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}benzoyl)-L-glutamic acid [Folate]	Folic acid
Nickel(II) cation [Ni(2+)]	NiCl2.6H2O
Nitrate [NO3(-)]	Co(NO3)2.6H2O
Nitrogen	Nitrogen (From gas mix)
Phosphate [PO4(3-)]	KH2PO4
Potassium(I) cation [K(+)]	AlK(SO4)2 (anhydrous), KH2PO4
Propionate	Propionic acid
Pyridine-3-carboxylate [Niacin]	Niacin
Riboflavin	Riboflavin
Selenite [SeO3 (2-)]	Na2SeO3 (anhydrous)
Sodium(I) cation [Na(+)]	Na2SeO3 (anhydrous), Na2WO4.2H2O, NaCl, NaHCO3, Na2MoO4.2H2O
Sulfate [SO4(2-)]	FeSO4.7H2O, ZnSO4*7H2O, AlK(SO4)2 (anhydrous), CuSO4 (anhydrous), MnSO4*H2O, MgSO4*7H2O
Tetraoxidomolybdate(VI) [Molybdate]	Na2MoO4.2H2O
Thiamine	Thiamine HCl
Tungstate	Na2WO4.2H2O
Vitamin B12	Vitamin B12
Water [H2O]	FeSO4.7H2O, ZnSO4*7H2O, Co(NO3)2.6H2O, Na2WO4.2H2O, NiCl2.6H2O, MgSO4*7H2O, Na2MoO4.2H2O
Zinc(II) cation [Zn(2+)]	ZnSO4*7H2O
Dihydrogen [H2]	Hydrogen (From gas mix)
Aluminium(III) cation [Al(3+)]	AlK(SO4)2 (anhydrous)

[1]

Melanie Tramontano, Sergej Andrejev, Mihaela Pruteanu, Martina Klünemann, Michael Kuhn, Marco Galardini, Paula Jouhten, Aleksej Zelezniak, Georg Zeller, Peer Bork, Athanasios Typas, and Kiran Raosaheb Patil. Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies. Nature Microbiology, 3(4):514–522, Apr 2018. URL: https://doi.org/10.1038/s41564-018-0123-9, doi:10.1038/s41564-018-0123-9.