TABLE 1

RERs of genes involved in the bifid shunt and metabolite production, (A)XOS degradation, and stress and cellular responses in Bifidobacterium longum NCC2705 at different time points during growth in MCB supplemented with (A)XOS in coculture with Eubacterium rectale ATCC 33656

Metabolic pathwayGene, proteina3 h6 h9 h24 h
RERbPcRERPRERPRERP
Bifid shunt and metabolite productionBL0274, ribulokinase5.5490.011−2.5000.004−2.004<0.0011.2090.288
xylB, xylulokinase1.8970.0185.0980.00314.770<0.001−1.3460.055
BL0959, bifunctional xylulose-5-phosphate/fructose-6-phosphate phosphoketolase−2.8250.016−1.6000.167−1.8590.0011.1090.635
ldh1, lactate dehydrogenase1.9450.017−1.3250.0553.185<0.001−1.011d0.951
ldh2, lactate dehydrogenase1.1700.627−1.1510.5842.615<0.001−3.817<0.001
ackA, acetate kinase1.4890.209−1.0740.6292.913<0.0011.6760.034
adh2, bifunctional acetaldehyde-CoA/alcohol dehydrogenase7.498<0.001−1.3640.3591.851<0.001−1.7990.021
(A)XOS degradationBL1543, extracellular α-arabinofuranosidase6.1770.003−7.752<0.0012.7370.008−1.675d0.017
BL1544, extracellular α-arabinofuranosidase3.7940.006−12.048<0.0012.909<0.001−1.538d0.043
BL0181, intracellular α-arabinofuranosidase−1.3850.2391.0930.7331.3520.0361.0830.554
abfA1, intracellular α-arabinofuranosidase−1.9650.0061.768d0.001−2.882d<0.0011.246d0.111
abfA2, intracellular α-arabinofuranosidase8.7080.006−1.9840.081−1.4750.103−1.307d0.334
abfA3, intracellular α-arabinofuranosidase2.2840.0041.8090.062−1.4100.103−2.070d0.006
BL1138, intracellular α-arabinofuranosidase1.3580.349−1.1440.606−2.618<0.001−4.505d<0.001
Stress and cellular responsesgroEL, chaperonin GroEL−1.1310.4991.1060.623−2.058<0.001−2.4940.001
dnaK, chaperone DnaK3.265<0.0011.544<0.0011.0340.8111.7060.019
BL0618, Dps family protein1.3160.574−1.0700.717−2.0580.015−2.088<0.001
ftsZ, cell division protein1.2090.4821.1440.3731.1640.216−2.257<0.001
atpA, FoF1 ATP synthase, subunit α−1.2560.3952.444<0.0011.2460.056−2.3470.001
tuf, elongation factor Tu−1.6640.174−3.367<0.001−1.2470.4241.0090.968
  • a Gene functions are described in Table S3 in the supplemental material.

  • b Monoculture fermentation with B. longum NCC2705 in MCB with (A)XOS was used as a control. RERs depicted in bold showed a significant difference between the co- and monoculture fermentations (P < 0.050).

  • c Statistical significance was determined using REST 2009 software on the basis of a pairwise fixed reallocation randomization test with 2,000 permutations.

  • d RERs could not be interpreted, as the CT values obtained were above the CT cutoff value.