0.28. 9.45E-01. -1.16. 4.03E-02. L2-63_01124 adhE_2 Aldehyde-alcohol dehydrogenase. -0.4. 5.81E- ... L2-63_01219 ntpD_1 V-type sodium pump subunit D. 0 .... 5.70E-15. RUMGNA_00585 2-isopropylmalate synthase. -1.45. 1.18E-04. 0.19 ... RUMGNA_00789 Hypothetical protein. -1.21. 7.53E-02. 0.55. 3.61E-01. 1.76.
Table S1: Primers used to quantify bacteria by qPCR Primer name UniF UniR Rflbr730F Clep866mR 16SRgF 16RgR
Sequence
Target (16S Amplicon Reference rRNA gene of:) size All bacteria 147-148nt (Fuller et al., 2007) cluster IV 157nt (Ramirez-Farias Ruminococcus et al., 2009) spp. Ruminococcus 57nt (Joossens et al., gnavus 2011)
GTGSTGCAYGGYYGTCGTCA ACGTCRTCCMCNCCTTCCTC GGCGGCYTRCTGGGCTTT CCAGGTGGATWACTTATTGTG TTAA TGGCGGCGTGCTTAACA TCCGAAGAAATCCGTCAAGGT
Fuller, Z., Louis, P., Mihajlovski, A., Rungapamestry, V., Ratcliffe, B., and Duncan, A.J. (2007). Influence of cabbage processing methods and prebiotic manipulation of colonic microflora on glucosinolate breakdown in man. Br J Nutr 98(2), 364-372. doi: 10.1017/S0007114507709091. Joossens, M., Huys, G., Cnockaert, M., De Preter, V., Verbeke, K., Rutgeerts, P., et al. (2011). Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives. Gut 60(5), 631-637. doi: 10.1136/gut.2010.223263. Ramirez-Farias, C., Slezak, K., Fuller, Z., Duncan, A., Holtrop, G., and Louis, P. (2009). Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii. Br J Nutr 101(4), 541-550. doi: 10.1017/S0007114508019880.
Table S2: Sequences used as reference for genome mining Target protein PduQ PduC PduD PduE Lactaldehyde reductase PduP acryloyl-CoA reductase methylmalonyl-CoA carboxytransferase FucU FucI FucK L-fuculose-1-phosphate aldolase
Sequence used as reference: Accession number Organism NP_460997.1 Salmonella enterica subsp. NP_460985.1 enterica serovar NP_460986.1 Typhimurium str. LT2 NP_460987.1 Ruminococcus lactaris EDY33573.1 ATCC 29176 SCY17815.1 Blautia sp. SF-50 GAX63847.1 Clostridioides difficile ACJ24327.1
Clostridium symbiosum
NP_417284.1 NP_417282.1 NP_417283.2
Escherichia coli str. K-12 substr. MG1655
NP_417280.1
no no no no yes yes yes yes
NCBI reference sequence? yes yes yes yes
Table S3: List of differentially expressed R. bromii genes Gene name:
Annotation
Rb_SS vs Rb+Rg_SS*
Rb_RS vs Rb+Rg_RS*
Rb_SS vs Rb_RS*
Rb+Rg_SS vs Rb+Rg_RS*
Log2FC**
padj
Log2FC
padj
Log2FC
padj
Log2FC
padj
L2-63_00114 gltB Ferredoxin-dependent glutamate synthase 1
1.41
1.26E-02
1.55
1.69E-03
0.11
9.79E-01
0.26
7.00E-01
L2-63_00390 serine/threonine protein kinase
-0.18
8.41E-01
-2.3
3.31E-10
1.02
2.59E-01
-1.1
2.06E-02
L2-63_00637 trpE Anthranilate synthase component 1
-3.22
1.42E-26
-3.09
7.42E-24
-0.36
8.47E-01
-0.23
6.29E-01
L2-63_00638 trpG Anthranilate synthase component II
-3
3.16E-23
-2.94
9.62E-22
-0.29
9.19E-01
-0.23
6.33E-01
L2-63_00639 trpD2 Anthranilate phosphoribosyltransferase 2
-3.12
1.42E-26
-2.78
8.61E-21
-0.43
7.52E-01
-0.09
8.50E-01
L2-63_00640 trpC Indole-3-glycerol phosphate synthase
-3.09
1.72E-24
-2.7
2.49E-18
-0.42
7.89E-01
-0.03
9.58E-01
L2-63_00641 trpB_2 Tryptophan synthase beta chain
-3.22
7.35E-28
-2.43
1.44E-15
-0.56
6.54E-01
0.23
6.31E-01
L2-63_00642 trpA Tryptophan synthase alpha chain
-3.23
2.06E-28
-2.37
4.53E-15
-0.53
6.61E-01
0.34
4.39E-01
L2-63_00643 cobB NAD-dependent deacetylase
-3.3
2.71E-29
-2.22
2.98E-13
-0.64
6.03E-01
0.44
3.06E-01
L2-63_00722 metH B12-dependent methionine synthase
-0.16
8.15E-01
1.53
4.71E-07
-0.56
6.43E-01
1.13
1.06E-03
L2-63_00870 ydjE Inner membrane metabolite transport protein
0.29
7.65E-01
-1.66
9.62E-04
0.78
6.54E-01
-1.17
4.12E-02
L2-63_00871 gutB Sorbitol dehydrogenase
0.12
9.19E-01
-1.91
6.39E-05
0.76
6.54E-01
-1.26
2.53E-02
L2-63_00872 gatY D-tagatose-1,6-bisphosphate aldolase subunit
0.14
8.92E-01
-2.24
4.97E-07
0.82
6.43E-01
-1.56
3.06E-03
L2-63_00873 ydjH Uncharacterized sugar kinase
0.14
8.94E-01
-2.27
3.73E-07
0.74
6.54E-01
-1.66
1.06E-03
L2-63_00874 yhdN General stress protein 69
0.05
9.66E-01
-2.54
4.92E-09
0.77
6.54E-01
-1.82
2.52E-04
L2-63_00875 glcR_2 HTH-type transcriptional repressor
-0.19
7.68E-01
-1.69
3.54E-08
0.25
9.33E-01
-1.25
2.82E-04
L2-63_00876 gltP Glutamate-aspartate carrier protein
-0.02
9.91E-01
-1.61
2.57E-05
0.58
6.69E-01
-1.02
2.70E-02
L2-63_00933 fus_1 Elongation factor G
-0.62
3.87E-01
-2.06
8.71E-06
0.28
9.45E-01
-1.16
4.03E-02
L2-63_01124 adhE_2 Aldehyde-alcohol dehydrogenase
-0.4
5.81E-01
-2.33
4.92E-09
0.06
9.84E-01
-1.88
2.44E-05
L2-63_01219 ntpD_1 V-type sodium pump subunit D
0
9.99E-01
-1.61
3.79E-06
-0.13
9.69E-01
-1.74
3.25E-06
L2-63_01220 ntpB_1 V-type sodium pump subunit B
-0.01
9.92E-01
-1.68
1.19E-06
-0.15
9.60E-01
-1.82
1.29E-06
L2-63_01221 ntpA V-type sodium ATPase catalytic subunit A
0.05
9.62E-01
-1.66
1.80E-05
-0.14
9.69E-01
-1.85
4.03E-06
L2-63_01222 ntpG V-type sodium pump subunit G
-0.02
9.90E-01
-1.68
3.17E-05
0.05
9.84E-01
-1.62
2.19E-04
L2-63_01223 ntpC V-type sodium pump subunit C
0.2
8.15E-01
-1.57
6.39E-05
0.03
9.98E-01
-1.74
2.44E-05
L2-63_01224 V-type ATP synthase subunit E
0.13
8.83E-01
-1.59
3.17E-05
0.08
9.81E-01
-1.63
6.15E-05
L2-63_01225 ntpK Sodium ATPase proteolipid component
0.16
8.60E-01
-1.49
2.76E-04
0.03
9.98E-01
-1.61
1.85E-04
L2-63_01277 metK S-adenosylmethionine synthase
1.16
1.93E-02
2.65
5.01E-13
-0.64
6.61E-01
0.86
7.68E-02
L2-63_01983 metE 5-methyltetrahydropteroyltriglutamate
0.01
9.96E-01
1.62
4.19E-07
-0.34
8.65E-01
1.27
3.25E-04
*Condition A vs Condition B: genes with an up-regulated transcription in Condition A (Log2FC>1.5 and padj
