TABLE 2

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

Metabolic pathwayGene, proteina3 h6 h9 h24 h
RERbPcRERPRERPRERP
Pentose phosphate pathway and metabolite productionEUBREC_0668, ribulokinase2.2980.0872.1550.0251.1790.417−3.425<0.001
EUBREC_2559, xylulokinase6.574<0.0011.5740.2321.9350.014−6.329<0.001
EUBREC_2460, transketolase domain protein16.138<0.0012.4260.0431.4440.255−7.692<0.001
EUBREC_1724, lactate dehydrogenase1.830<0.0011.5930.229−1.3760.160−2.0240.010
EUBREC_2331, lactate dehydrogenase4.653<0.001−1.8080.002−1.1260.497−4.831<0.001
EUBREC_ 1472, pyruvate:ferredoxin oxidoreductase3.594<0.0011.1650.5351.3000.115−1.852<0.001
EUBREC_0735, butyryl-CoA dehydrogenase belonging to the Bcd/Etf complex1.6520.1412.879<0.001−1.3950.253−2.2940.001
EUBREC_3075, butyryl-CoA:acetate CoA-transferase3.2340.0472.8770.0021.1130.435−5.5560.015
EUBREC_2390, ferredoxin hydrogenase2.6310.0021.0920.3611.5790.089−3.344<0.001
EUBREC_1646, ferredoxin belonging to the Rnf complex4.030<0.001−1.5020.017−2.0080.016−3.436<0.001
(A)XOS degradationEUBREC_1040, exo-oligoxylanase2.3810.016−1.9690.0151.2900.2091.7800.010
EUBREC_1042, bifunctional β-xylosidase/α-arabinofuranosidase1.5610.1623.865<0.0011.0270.867−11.494<0.001
EUBREC_1044, β-xylosidase2.1330.005−1.2180.344−1.1630.360−6.289<0.001
EUBREC_2454, α-arabinofuranosidase4.192<0.001−2.3260.007−1.1780.3702.3070.003
EUBREC_2578, α-arabinofuranosidase1.0620.809−2.2370.003−2.1740.002−2.2680.001
Stress and cellular responsesEUBREC_2270, chaperonin GroEL−1.5080.007−1.2560.2331.5330.027−3.040<0.001
EUBREC_0020, chaperone DnaK−1.5240.0754.765<0.0011.2920.281−1.9720.002
ftsZ, cell division protein2.075<0.0011.5330.050−1.1330.249−2.2220.027
atpA, FoF1 ATP synthase, α subunit−1.5670.1103.950<0.001−2.0960.014−1.5360.004
EUBREC_0383, elongation factor Tu1.8520.0211.971<0.001−1.0100.975−1.3790.062
  • a Gene functions are described in Table S4 in the supplemental material.

  • b Monoculture fermentations with E. rectale ATCC 33656 in mMCB 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.