Lysogeny broth (LB)

LB is a complex medium that was developed in 1951[1]. The following in sillico definition is derived from Oh et al.[2] and the definition in CarveMe[3]. As Selenium is a component of Oh et al.[2]’s definition but not soluable in water[4] possible Selenium sources were determined and added to the definition based on the paper ‘The use of high-selenium yeast to raise selenium status: how does it measure up?’[5].

Table 7 LB composition

name	source
3-[(2R)-2,4-Dihydroxy-3,3-dimethylbutanamido]propanoate [Pantothenate]	Calcium pantothenate (Vitamin B5)
4,5-Bis(hydroxymethyl)-2-methylpyridin-3-ol [Pyridoxine]	Pyridoxine (Vitamin B6)
4-Formyl-3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-1-ium [Pyridoxal]	Pyridoxal (CarveMe)
5-(1,2-Dithiolan-3-yl)pentanoate [Lipoate]	Lipoate (CarveMe)
5-Adenylic acid [AMP]	AMP (CarveMe)
5-Guanylic acid [GMP]	GMP (CarveMe)
5-Uridylic acid [UMP]	UMP (CarveMe)
Adenosine	Adenosine
Ammonia	Ammonium (CarveMe)
Arsenite	Arsenic
Biotin	Biotin (Vitamin B8)
CMP	CMP (CarveMe)
Cadmium(II) cation [Cd2+]	Cadmium
Calcium(II) cation [Ca(2+)]	Calcium pantothenate (Vitamin B5), Calcium
Chloride [Cl(-)]	Chloride
Chorismate	Chorismate
Chromate	Chromate (CarveMe)
Cob(I)alamin	Cyanocobalamin (Vitamin B12)
Cob(II)alamin	Cyanocobalamin (Vitamin B12)
Cobalt(II) cation [Co(2+)]	Co2+ (CarveMe)
Copper(II) cation [Cu(2+)]	Cu2+ (CarveMe)
D-Glucose	Carbohydrates (Glucose)
Deoxyadenosine	Deoxyadenosine
Deoxycytidine	Deoxycytidine
Dioxygen [O2]	O2 (CarveMe)
Glycine	Glycine
Guanosine	Guanosine (CarveMe)
Hydrogen [H(+)]	H+ (CarveMe)
Hydrogen sulfide	Hydrogen sulfide (CarveMe)
Hypoxanthine	Hypoxanthine
Inosine	Inosine
Iron(II) cation [Fe(2+)]	Fe2+ (CarveMe)
Iron(III) cation [Fe(3+)]	Fe3+ (CarveMe)
L-Cystine	Cystine
L-Alanine	Alanine
L-Arginine	Arginine
L-Aspartate	Aspartic acid
L-Cysteine	L-Cysteine (CarveMe)
L-Glutamate	Glutamic acid
L-Histidine	Histidine
L-Isoleucine	Isoleucine
L-Leucine	Leucine
L-Lysine	Lysine
L-Methionine	Methionine
L-Phenylalanine	Phenylalanine
L-Proline	Proline
L-Serine	Serine
L-Threonine	Threonine
L-Tryptophan	Tryptophan
L-Tyrosine	Tyrosine
L-Valine	Valine
Lead(II) cation [Pb(2+)]	Lead
Magnesium(II) cation [Mg(2+)]	Magnesium
Manganese(II) cation [Mn(2+)]	Mn2+ (CarveMe)
Mercury(II) cation [Hg(2+)]	Mercury
N-(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}benzoyl)-L-glutamic acid [Folate]	Folic acid (Vitamin B9)
Nickel(II) cation [Ni(2+)]	Ni2+ (CarveMe)
Phosphate [PO4(3-)]	Phosphorus (phosphate)
Potassium(I) cation [K(+)]	Potassium
Protoheme	Protoheme (CarveMe)
Pyridine-3-carboxylate [Niacin]	Niacin (Vitamin PP)
Riboflavin	Riboflavin (Vitamin B2)
Selenite [SeO3 (2-)]	Selenium
Sodium(I) cation [Na(+)]	Sodium, Selenium
Sulfate [SO4(2-)]	Sulfate
Tetraoxidomolybdate(VI) [Molybdate]	Molybdate (CarveMe)
Thiamine	Thiamine (Vitamin B1)
Thymidine	Thymidine
Uracil	Uracil
Uridine	Uridine
Vitamin B12	Cyanocobalamin (Vitamin B12)
Water [H2O]	H2O (CarveMe)
Zinc(II) cation [Zn(2+)]	Zinc
L-Selenomethionine	Selenium
gamma-Glutamyl-Se-methylselenocysteine	Selenium
L-Adenosylselenohomocysteine	Selenium

[1]

G. Bertani. STUDIES ON LYSOGENESIS I. Journal of Bacteriology, 62(3):293–300, sep 1951.

[2] (1,2)

You-Kwan Oh, Bernhard O. Palsson, Sung M. Park, Christophe H. Schilling, and Radhakrishnan Mahadevan. Genome-scale reconstruction of metabolic network in bacillus subtilis based on high-throughput phenotyping and gene essentiality data*. Journal of Biological Chemistry, 282(39):28791–28799, 2007. URL: https://www.sciencedirect.com/science/article/pii/S0021925820586110, doi:https://doi.org/10.1074/jbc.M703759200.

[3]

Daniel Machado, Sergej Andrejev, Melanie Tramontano, and Kiran Raosaheb Patil. Fast automated reconstruction of genome-scale metabolic models for microbial species and communities. Nucleic acids research, 46(15):7542–7553, 2018.

[4]

World Health Organization. Selenium in drinking-water. 2003. URL: https://www.who.int/docs/default-source/wash-documents/wash-chemicals/selenium-2003-background-document.pdf?sfvrsn=624fa2c0_4 (visited on 2024-02-19).

[5]

Margaret P. Rayman. The use of high-selenium yeast to raise selenium status: how does it measure up? British Journal of Nutrition, 92(4):557–573, 2004. doi:10.1079/BJN20041251.