Table 2.

Selected transcripts upregulated in cells cultivated in different milk-based samples compared to B. breve 4L grown on MRS plus lactose

GeneFunctionFold change above controla (P value) for each milk source
HumanFormulaCowRice basedSoybean basedSynthetic medium
BIFBRE_02893Galactoside symporter2.15 (2.60E−05)2.25 (3.78E−05)1.77 (2.20E−04)1.99 (5.96E−05)1.73 (5.32E−03)2.01 (5.32E−03)
BIFBRE_02991α-Glucosidase1.80 (6.72E−01)1.46 (9.88E−01)1.76 (3.32E−03)1.82 (1.98E−01)2.03 (6.54E−02)5.62 (6.54E−02)
BIFBRE_04186Permease protein of ABC transporter system0.81 (1.12E−04)1.12 (2.05E−04)0.78 (4.73E−01)4.72 (6.66E−05)4.84 (3.48E−04)5.49 (3.48E−04)
BIFBRE_04185Permease protein of ABC transporter system0.50 (9.36E−02)0.79 (3.34E−01)0.44 (4.73E−01)4.96 (1.96E−06)3.69 (2.23E−06)3.07 (2.23E−06)
BIFBRE_04183Solute binding protein of ABC transporter system1.10 (3.97E−01)1.57 (2.59E−01)1.04 (1.86E−02)6.23 (3.51E−05)3.30 (2.50E−03)1.34 (2.50E−03)
BIFBRE_02906Iron binding ferritin-like antioxidant protein2.75 (6.98E−01)2.07 (7.99E−02)2.54 (3.32E−03)6.44 (3.65E−05)4.24 (6.58E−04)6.01 (6.58E−04)
BIFBRE_02907Hypothetical membrane-spanning protein3.12 (6.98E−01)2.20 (7.99E−02)2.61 (3.32E−03)3.77 (3.65E−05)2.43 (6.58E−04)2.83 (6.58E−04)
BIFBRE_02924Phosphoenolpyruvate carboxylase4.57 (5.71E−01)3.84 (4.21E−01)2.85 (4.73E−01)1.78 (2.14E−01)1.15 (4.88E−05)1.87 (4.88E−05)
BIFBRE_02934Conserved hypothetical protein2.72 (5.37E−01)3.12 (7.22E−01)2.83 (3.32E−03)3.03 (3.82E−01)6.86 (6.31E−03)4.47 (6.31E−03)
BIFBRE_02936Glycogen or amylose phosphorylase4.37 (1.09E−03)5.41 (5.52E−04)3.42 (3.32E−03)4.55 (5.03E−04)2.67 (2.30E−05)4.19 (2.30E−05)
BIFBRE_02980CrcB family protein2.35 (9.53E−03)2.68 (6.61E−01)4.58 (3.32E−03)4.99 (2.59E−01)2.88 (6.69E−01)2.84 (6.69E−01)
BIFBRE_02994FimA0.55 (6.96E−01)0.71 (1.65E−01)0.57 (1.86E−02)0.59 (1.84E−01)2.08 (4.20E−01)0.60 (4.20E−01)
BIFBRE_03022TadE/TadF protein3.57 (2.66E−03)3.72 (2.33E−02)3.14 (3.32E−03)4.53 (1.24E−03)6.23 (1.69E−02)4.11 (1.69E−02)
BIFBRE_03022TadE/TadF protein3.59 (3.37E−04)3.78 (1.34E−03)3.26 (6.61E−01)5.03 (3.32E−03)5.50 (2.16E−04)3.78 (2.17E−06)
BIFBRE_03114Dipeptidase A2.55 (5.81E−02)3.02 (3.37E−04)3.23 (1.85E−02)2.73 (2.09E−03)2.62 (1.02E−04)2.76 (3.00E−03)
BIFBRE_03115Glycosyltransferase2.04 (3.75E−03)1.30 (9.75E−03)2.55 (3.32E−03)2.00 (5.89E−04)2.15 (2.99E−02)2.20 (2.99E−02)
BIFBRE_03118Ammonium transporter10.16 (2.29E−03)24.16 (4.40E−03)21.60 (4.52E−04)9.05 (4.73E−02)6.01 (1.87E−02)7.94 (1.87E−02)
BIFBRE_03119Nitrogen regulatory protein P-II15.88 (2.17E−06)53.85 (5.91E−07)43.52 (4.73E−01)21.35 (2.22E−06)12.60 (8.52E−06)9.02 (8.52E−06)
BIFBRE_03154MFS transporter5.19 (5.33E−04)4.55 (1.85E−02)3.24 (3.32E−03)3.70 (5.81E−02)2.27 (2.65E−01)2.04 (2.65E−01)
BIFBRE_03155Hypothetical protein2.06 (5.33E−04)2.66 (1.85E−02)2.65 (3.32E−03)3.07 (5.81E−02)2.32 (2.65E−01)1.19 (2.65E−01)
BIFBRE_03188Chorismate mutase2.97 (2.16E−04)3.61 (8.29E−05)3.41 (1.02E−04)2.22 (1.34E−03)2.80 (3.37E−04)2.24 (1.31E−03)
BIFBRE_03293Nicotinate phosphoribosyltransferase2.52 (8.68E−03)4.00 (4.07E−02)2.35 (4.73E−01)3.76 (1.70E−01)4.49 (5.17E−01)4.49 (5.17E−01)
BIFBRE_03432Permease protein5.73 (2.09E−03)4.99 (3.00E−03)10.15 (4.73E−01)4.90 (1.31E−03)2.03 (1.16E−01)1.81 (1.16E−01)
BIFBRE_03338Hypothetical protein2.04 (1.55E−02)2.01 (7.84E−01)2.58 (3.32E−03)1.24 (5.58E−03)1.84 (2.39E−01)1.79 (2.39E−01)
BIFBRE_03340Conserved hypothetical protein2.92 (5.13E−03)2.77 (5.87E−03)3.05 (3.32E−03)2.50 (2.96E−01)6.83 (1.23E−02)2.29 (1.23E−02)
BIFBRE_03341Oligosaccharide repeat unit transporter2.61 (2.29E−03)0.69 (3.16E−03)2.50 (4.73E−01)0.80 (5.08E−03)0.98 (7.33E−05)1.05 (7.33E−05)
BIFBRE_03342Glycosyltransferase4.44 (2.91E−04)1.34 (5.00E−02)3.54 (3.32E−03)1.36 (2.03E−01)1.66 (9.24E−01)3.40 (9.24E−01)
BIFBRE_03386Galactose-1-phosphate uridylyltransferase2.36 (1.51E−02)0.93 (7.13E−01)2.30 (3.32E−03)1.22 (1.96E−03)0.98 (9.41E−03)0.90 (9.41E−03)
BIFBRE_03387Galactokinase2.05 (1.53E−03)0.72 (7.37E−01)2.03 (3.32E−03)0.57 (3.29E−01)0.56 (9.20E−01)1.37 (9.20E−01)
BIFBRE_03423Solute binding protein of ABC transporter system1.53 (1.36E−04)4.11 (2.76E−03)1.97 (1.86E−02)1.29 (7.20E−04)1.03 (1.57E−03)0.80 (1.57E−03)
BIFBRE_03427ATP binding protein of ABC transporter system1.82 (5.48E−02)3.83 (3.59E−03)2.39 (3.10E+04)1.82 (5.55E−01)1.41 (9.06E−01)1.63 (9.06E−01)
BIFBRE_03433Permease of ABC transporter for sugars2.83 (4.14E−04)2.58 (5.16E−04)4.16 (4.73E−01)3.23 (4.81E−04)1.69 (2.58E−04)0.93 (2.58E−04)
BIFBRE_03436Solute binding protein of ABC transporter system7.68 (4.14E−04)8.28 (5.16E−04)8.99 (1.86E−02)10.36 (4.81E−04)7.80 (2.58E−04)12.34 (2.58E−04)
BIFBRE_03440Solute binding protein of ABC transporter system for peptides9.81 (4.14E−04)6.78 (5.16E−04)5.94 (1.86E−02)2.65 (4.81E−04)2.74 (2.58E−04)2.59 (2.58E−04)
BIFBRE_03442Permease protein of ABC transporter system for peptides2.93 (4.14E−04)3.41 (5.16E−04)2.94 (4.73E−01)1.49 (4.81E−04)2.07 (2.58E−04)1.74 (2.58E−04)
BIFBRE_03443ATP binding protein of ABC transporter system for peptides4.45 (4.14E−04)1.92 (5.16E−04)3.76 (1.36E−07)1.40 (4.81E−04)1.27 (2.58E−04)1.40 (2.58E−04)
BIFBRE_03444ATP binding protein of ABC transporter system for peptides3.46 (4.14E−04)3.07 (5.16E−04)2.93 (9.09E−04)2.00 (4.81E−04)1.76 (2.58E−04)2.58 (2.58E−04)
BIFBRE_03493Solute binding protein of ABC transporter system0.47 (6.10E−01)0.46 (1.00E+00)0.70 (1.86E−02)4.62 (1.22E−01)3.59 (5.85E−01)4.09 (5.85E−01)
BIFBRE_03532CrcB family protein1.67 (8.33E−03)2.19 (1.45E−02)1.58 (3.32E−03)3.07 (6.82E−01)2.14 (1.39E−02)1.80 (1.39E−02)
BIFBRE_03611Glutamine synthetase9.05 (1.31E−01)22.81 (8.83E−01)12.46 (3.32E−03)5.42 (2.58E−02)3.04 (6.67E−01)1.47 (6.67E−01)
BIFBRE_03613Hypothetical membrane-spanning protein2.12 (9.95E−06)2.16 (2.29E−06)1.58 (3.32E−03)3.13 (3.97E−05)1.67 (6.75E−04)1.75 (6.75E−04)
BIFBRE_03625Glutamate N-acetyltransferase1.94 (1.74E−02)3.01 (3.26E−03)1.76 (3.32E−03)2.29 (9.68E−03)1.53 (2.89E−01)3.22 (2.89E−01)
BIFBRE_03626Acetylglutamate kinase1.53 (1.74E−02)2.14 (3.26E−03)1.29 (2.07E+04)1.17 (9.68E−03)1.28 (2.89E−01)1.91 (2.89E−01)
BIFBRE_036981,4-α-Glucan branching enzyme2.50 (2.76E−02)1.57 (7.64E−04)2.03 (3.90E+03)1.06 (1.81E−04)1.07 (5.03E−02)1.70 (5.03E−02)
BIFBRE_03829N-Acetylglucosamine-6-phosphate deacetylase1.51 (2.93E−04)1.24 (1.86E−04)1.64 (3.32E−03)2.58 (2.51E−01)1.78 (4.97E−03)2.41 (4.97E−03)
BIFBRE_03830Glucosamine-6-phosphate isomerase1.04 (2.93E−04)0.98 (1.86E−04)1.11 (3.32E−03)2.46 (2.51E−01)2.03 (4.97E−03)1.51 (4.97E−03)
BIFBRE_03833NagC-type transcriptional regulator0.86 (6.02E−01)1.09 (1.41E−01)1.06 (3.32E−03)2.84 (5.26E−03)2.12 (1.38E−03)0.97 (1.38E−03)
BIFBRE_03835Transporter, MFS superfamily1.24 (3.81E−03)2.20 (7.00E−01)0.99 (1.86E−02)5.13 (4.90E−02)3.46 (3.33E−02)1.21 (3.33E−02)
BIFBRE_03836Sulfatase family protein1.77 (1.05E−01)2.47 (1.67E−04)1.22 (1.86E−02)2.35 (2.06E−06)2.21 (1.10E−05)1.69 (1.10E−05)
BIFBRE_03889Chorismate synthase3.24 (3.16E−05)3.96 (1.51E−05)2.33 (2.61E−04)2.59 (1.07E−04)2.56 (1.59E−04)3.11 (3.48E−05)
BIFBRE_03895ATP binding protein of ABC transporter system2.45 (3.22E−04)0.83 (6.71E−02)0.99 (2.72E+041.50 (1.64E−03)0.75 (8.74E−03)0.83 (8.74E−03)
BIFBRE_03896ATP binding protein of ABC transporter system3.09 (5.68E−03)1.32 (4.81E−01)1.79 (3.697E−05)1.54 (1.35E−01)1.10 (2.96E−01)1.30 (2.96E−01)
BIFBRE_03897Oligopeptide transport ATP binding protein3.33 (5.68E−03)1.11 (4.81E−01)1.76 (4.73E−01)1.19 (1.35E−01)0.83 (2.96E−01)1.72 (2.96E−01)
BIFBRE_03898Cysteine desulfurase/selenocysteine lyase3.14 (5.68E−03)1.62 (4.81E−01)1.72 (3.32E−03)1.20 (1.35E−01)0.95 (2.96E−01)1.84 (2.96E−01)
BIFBRE_03899IscU protein2.97 (8.48E−05)1.09 (1.34E−02)1.65 (3.32E−03)1.20 (2.76E−01)0.95 (7.98E−01)1.30 (7.98E−01)
BIFBRE_03936Glycosyltransferase2.36 (2.21E−05)2.79 (2.65E−03)1.61 (3.32E−03)2.04 (2.45E−05)2.15 (5.90E−05)3.37 (5.90E−05)
BIFBRE_04161N-Acylglucosamine 2-epimerase family protein4.29 (1.49E−05)2.86 (3.78E−05)2.57 (3.32E−03)1.79 (1.51E−05)2.03 (7.67E−04)2.52 (7.67E−04)
BIFBRE_04167Sugar ABC transporter system, permease4.46 (8.39E−01)1.25 (8.11E−02)2.02 (1.86E−02)1.23 (2.70E−02)1.42 (8.96E−01)1.01 (8.96E−01)
BIFBRE_04168Solute binding protein of ABC transporter system3.04 (8.39E−01)1.40 (8.11E−02)1.94 (1.86E−02)1.12 (2.70E−02)1.84 (8.96E−01)1.14 (8.96E−01)
BIFBRE_04943Oligopeptide transport ATP binding protein1.56 (1.74E−04)2.01 (3.56E−05)2.08 (4.73E−01)1.08 (6.76E−05)0.78 (1.31E−04)0.77 (1.31E−04)
BIFBRE_04942Oligopeptide transport system permease protein2.07 (1.34E−01)1.80 (2.76E−02)1.53 (4.73E−01)0.94 (7.80E−01)0.76 (3.91E−01)0.66 (3.91E−01)
BIFBRE_04941Oligopeptide transport system permease protein2.73 (1.34E−01)3.11 (2.76E−02)1.76 (4.73E−01)1.19 (7.80E−01)0.73 (3.91E−01)0.44 (3.91E−01)
BIFBRE_04896N-Acetylglucosamine-6-phosphate deacetylase3.08 (3.85E−04)3.34 (2.35E−03)3.23 (3.32E−03)12.62 (2.51E−04)5.15 (1.08E−04)12.17 (1.08E−04)
BIFBRE_04895Glucosamine-6-phosphate isomerase1.79 (3.85E−04)3.00 (2.35E−03)1.74 (3.32E−03)10.85 (2.51E−04)3.91 (1.08E−04)5.57 (1.08E−04)
BIFBRE_04813Undecaprenol N-acetylglucosamine transferase1.79 (8.63E−02)2.11 (5.73E−01)2.37 (1.86E−02)1.57 (7.52E−01)1.66 (3.27E−02)1.43 (3.27E−02)
BIFBRE_04783Histidinol dehydrogenase2.72 (4.61E−04)3.23 (1.86E−04)2.82 (3.81E−04)3.27 (1.36E−04)2.65 (5.86E−04)2.07 (3.04E−03)
BIFBRE_04540Galactoside symporter2.80 (6.21E−04)2.65 (9.75E−03)3.23 (3.32E−03)0.33 (7.04E−04)0.91 (2.00E−03)0.41 (2.00E−03)
BIFBRE_04539β-Galactosidase2.04 (7.16E−05)2.02 (1.08E−04)2.42 (1.91E−04)0.32 (4.20E−05)0.32 (5.49E−01)0.35 (5.49E−01)
BIFBRE_04535Solute binding protein of ABC transporter system (lactose)1.73 (6.87E−04)2.58 (7.97E−04)0.93 (1.86E−02)6.83 (2.99E−05)6.57 (4.79E−05)6.07 (4.79E−05)
BIFBRE_04494Permease protein of ABC transporter system1.99 (9.37E−01)4.87 (2.67E−02)1.98 (4.73E−01)8.35 (4.93E−01)5.84 (3.48E−01)4.04 (3.48E−01)
BIFBRE_04493Solute binding protein of ABC transporter system2.84 (9.28E−02)5.61 (2.07E−03)3.25 (1.86E−02)13.13 (2.83E−04)13.13 (1.11E−03)16.83 (1.11E−03)
BIFBRE_04715Glutamate transport system permease protein GluC3.02 (9.37E−01)3.11 (2.35E−03)3.51 (3.32E−03)1.67 (6.76E−05)1.32 (3.91E−01)1.15 (3.27E−02)
BIFBRE_04716Permease protein of ABC transporter3.22 (3.85E−04)3.48 (1.86E−04)3.26 (1.86E−02)1.35 (2.51E−04)1.31 (1.08E−04)0.91 (3.27E−02)
BIFBRE_04187Hypothetical membrane-spanning protein1.03 (1.19E−03)1.54 (9.43E−04)1.09 (3.32E−03)4.51 (1.97E−02)2.52 (3.06E−01)1.16 (3.06E−01)
BIFBRE_04186Permease protein of ABC transporter system1.58 (8.40E−01)3.04 (1.04E−02)1.62 (4.73E−01)8.57 (4.53E−06)5.22 (1.29E−04)2.59 (1.29E−04)
BIFBRE_04185Permease protein of ABC transporter system0.87 (8.40E−01)6.19 (1.04E−02)1.03 (4.73E−01)30.27 (4.53E−06)10.63 (1.29E−04)2.29 (1.29E−04)
BIFBRE_04183Solute binding protein of ABC transporter system1.95 (7.68E−01)8.19 (1.60E−03)1.73 (1.86E−0223.85 (2.61E−05)13.82 (3.37E−04)8.00 (3.37E−04)
BIFBRE_02812α-Galactosidase1.81 (3.32E−03)2.23 (1.10E−03)2.12 (2.80E+03)1.89 (8.67E−04)4.02 (7.22E−04)2.01 (7.22E−04)
BIFBRE_04898Xaa-Pro aminopeptidase2.81 (3.81E−04)3.27 (1.19E−03)3.32 (3.85E−04)2.61 (2.35E−03)2.73 (2.35E−03)3.5 (9.28E−02)
BIFBRE_02830FimA2.09 (4.19E−01)1.82 (2.64E−01)1.84 (3.32E−03)2.21 (7.57E−04)1.80 (8.68E−05)2.19 (8.68E−05)
BIFBRE_02843ATP binding protein of ABC transporter system4.65 (3.54E−02)4.01 (1.71E−01)4.21 (4.50E+04)11.84 (6.80E−02)6.41 (5.67E−01)6.41 (5.67E−01)
BIFBRE_02846PTS, IIC component2.35 (3.54E−02)3.13 (1.71E−01)2.35 (4.73E−01)2.11 (6.80E−02)3.47 (5.67E−01)3.24 (5.67E−01)
  • a Values are the changes for each sample in comparison with the reference sample. The P values were calculated from replicate measurements of two different hybridization experiments.