Microbiota dysbiosis in inflammatory bowel diseases: in silico investigation of the oxygen hypothesis

BMC Systems Biology

Table 1 Nominal parameter values for the multispecies biofilm model

Symbol	Parameter	Value	Units	Source
L	Biofilm thickness	40	μm	[44]
D _X	Biomass diffusion coefficients	1x10 ⁻¹⁰	cm²/s	[41]
k _X	Biomass mass transfer coefficients	1x10 ⁻⁷	cm/s	[41]
X _b	Biomass bulk concentrations	0	g/L	[41]
D _N	Carbohydrate diffusion coefficients	2x10 ⁻⁶	cm²/s	[43]
	Amino acid diffusion coefficients	2x10 ⁻⁶	cm²/s	[43]
	Oxygen diffusion coefficient	8x10 ⁻⁶	cm²/s	[43]
k _N	Nutrient mass transfer coefficients	2x10 ⁻⁴	cm/s	[41]
	Amino acid mass transfer coefficients	2x10 ⁻⁴	cm/s	[41]
	Oxygen mass transfer coefficient	2x10 ⁻²	cm/s	Specified
O _b	Oxygen bulk concentration	0	mM	Specified
D _P	Byproduct diffusion coefficients	2x10 ⁻⁶	cm²/s	[43]
k _P	Byproduct mass transfer coefficients	5x10 ⁻⁶	cm/s	[41]
	Butyrate mass transfer coefficient	5x10 ⁻⁵	cm/s	Tuned
	Propionate mass transfer coefficient	1x10 ⁻⁵	cm/s	Tuned
P _b	Byproduct bulk concentrations	0	mM	[41]
v _max	Carbohydrate maximum uptake rates	10	mmol/gDW/h	[45]
	Amino acid maximum uptake rates	1	mmol/gDW/h	[45]
	Oxygen maximum uptake rate	20	mmol/gDW/h	[45]
	Byproduct maximum uptake rates	10	mmol/gDW/h	[41]
K _m	Carbohydrate Michaelis-Menten constants	0.5	mM	[45]
	Amino acids Michaelis-Menten constants	0.1	mM	[45]
	Oxygen Michaelis-Menten constant	0.003	mM	[45]
	Byproduct Michaelis-Menten constants	0.5	mM	[41]
ATPM	B. thetaiotaomicron ATP maintenance	8.43	mmol/gDW/h	[35]
	F. prausnitzii ATP maintenance	4.75	mmol/gDW/h	Tuned
	E. coli ATP maintenance	5.5	mmol/gDW/h	Tuned

ISSN: 1752-0509