Table 2.

Selected KEGG pathways (KEGG orthology level 3) in cecal samples being differently enriched in CON- and TGS-fed pigs

KEGG pathway	Meana	log2 fold change	SEb	p value	q value‡
00633 Nitrotoluene degradation [PATH:ko00633]	389	1.982	0.375	< 0.001	< 0.001
00983 Drug metabolism - other enzymes [PATH:ko00983]	1046	1.772	0.353	< 0.001	< 0.001
00940 Phenylpropanoid biosynthesis [PATH:ko00940]	9129	1.613	0.213	< 0.001	< 0.001
02060 Phosphotransferase system (PTS) [PATH:ko02060]	6289	1.040	0.217	< 0.001	< 0.001
00130 Ubiquinone and other terpenoid-quinone biosynthesis [PATH:ko00130]	3982	0.969	0.224	< 0.001	< 0.001
00040 Pentose and glucuronate interconversions [PATH:ko00040]	14,629	0.803	0.191	< 0.001	< 0.001
04141 Protein processing in endoplasmic reticulum [PATH:ko04141]	803	0.789	0.193	< 0.001	< 0.001
00052 Galactose metabolism [PATH:ko00052]	20,395	0.739	0.125	< 0.001	< 0.001
00051 Fructose and mannose metabolism [PATH:ko00051]	17,994	0.673	0.126	< 0.001	< 0.001
00730 Thiamine metabolism [PATH:ko00730]	9877	0.607	0.125	< 0.001	< 0.001
02010 ABC transporters [PATH:ko02010]	49,093	−0.413	0.075	< 0.001	< 0.001
03013 RNA transport [PATH:ko03013]	1493	−0.453	0.112	< 0.001	< 0.001
04122 Sulfur relay system [PATH:ko04122]	5609	−0.976	0.197	< 0.001	< 0.001
00360 Phenylalanine metabolism [PATH:ko00360]	2011	−1.286	0.311	< 0.001	< 0.001
02040 Flagellar assembly [PATH:ko02040]	7812	−1.370	0.269	< 0.001	< 0.001
00380 Tryptophan metabolism [PATH:ko00380]	255	−1.651	0.294	< 0.001	< 0.001
00531 Glycosaminoglycan degradation [PATH:ko00531]	391	1.077	0.275	< 0.001	0.001
00860 Porphyrin and chlorophyll metabolism [PATH:ko00860]	7948	0.594	0.152	< 0.001	0.001
00680 Methane metabolism [PATH:ko00680]	4678	−0.375	0.096	< 0.001	0.001
00630 Glyoxylate and dicarboxylate metabolism [PATH:ko00630]	3354	−0.418	0.108	< 0.001	0.001
03070 Bacterial secretion system [PATH:ko03070]	24,985	−0.367	0.104	< 0.001	0.002
00500 Starch and sucrose metabolism [PATH:ko00500]	18,633	−0.245	0.075	0.001	0.006
04142 Lysosome [PATH:ko04142]	3227	0.593	0.187	0.002	0.007
00350 Tyrosine metabolism [PATH:ko00350]	2333	−0.932	0.294	0.002	0.007
00511 Other glycan degradation [PATH:ko00511]	2316	0.665	0.214	0.002	0.008
04151 PI3K-Akt signaling pathway [PATH:ko04151]	5164	−0.822	0.267	0.002	0.009
00590 Arachidonic acid metabolism [PATH:ko00590]	829	1.026	0.351	0.003	0.014
00300 Lysine biosynthesis [PATH:ko00300]	23,314	0.136	0.047	0.004	0.014
00510 N-Glycan biosynthesis [PATH:ko00510]	918	0.545	0.202	0.007	0.024
00564 Glycerophospholipid metabolism [PATH:ko00564]	5568	0.154	0.057	0.007	0.024
00010 Glycolysis / Gluconeogenesis [PATH:ko00010]	23,481	−0.160	0.059	0.007	0.024
00061 Fatty acid biosynthesis [PATH:ko00061]	13,010	−0.165	0.061	0.007	0.024
00330 Arginine and proline metabolism [PATH:ko00330]	26,554	0.284	0.106	0.007	0.025
00071 Fatty acid metabolism [PATH:ko00071]	133	−1.077	0.423	0.011	0.036
00900 Terpenoid backbone biosynthesis [PATH:ko00900]	12,834	0.216	0.086	0.012	0.037
00020 Citrate cycle (TCA cycle) [PATH:ko00020]	15,173	0.415	0.171	0.015	0.045
03020 RNA polymerase [PATH:ko03020]	29,030	−0.385	0.159	0.015	0.045
02030 Bacterial chemotaxis [PATH:ko02030]	8461	−0.680	0.278	0.015	0.045
03060 Protein export [PATH:ko03060]	1992	0.193	0.083	0.020	0.056
00520 Amino sugar and nucleotide sugar metabolism [PATH:ko00520]	18,729	0.147	0.064	0.022	0.062
00280 Valine leucine and isoleucine degradation [PATH:ko00280]	5486	−0.240	0.108	0.026	0.067
00785 Lipoic acid metabolism [PATH:ko00785]	167	−0.642	0.287	0.025	0.067
00030 Pentose phosphate pathway [PATH:ko00030]	12,994	−0.128	0.058	0.027	0.068
00750 Vitamin B6 metabolism [PATH:ko00750]	4284	0.280	0.131	0.033	0.077
00540 Lipopolysaccharide biosynthesis [PATH:ko00540]	10,816	0.615	0.292	0.035	0.081
00908 Zeatin biosynthesis [PATH:ko00908]	2398	0.174	0.085	0.040	0.091
04146 Peroxisome [PATH:ko04146]	6168	−0.179	0.088	0.041	0.091
00053 Ascorbate and aldarate metabolism [PATH:ko00053]	334	0.498	0.250	0.046	0.099
03018 RNA degradation [PATH:ko03018]	30,822	−0.183	0.092	0.046	0.099

^‡False discovery rate (Benjamini-Hochberg) corrected p value

^aNormalized reads (hit counts). Only the most abundant KEGG pathways (> 0.01% of all reads) that were altered by the dietary starch source are presented (n = 8 per diet)

^bStandard error of the log₂fold change