Table 4. Metabolic pathways that were significantly associated with ADG at 26 days of age

	Super pathway	Pathway	logFC	logCPM	LR	p-value	FDR
1	Aromatic compound degradation	Catechol degradation I (meta-cleavage pathway)	15.28376	8.613798	19.28901	1.12E-05	0.00437
2	Aromatic compound degradation	Catechol degradation to 2-hydroxypentadienoate II	12.99083	6.437917	15.3016	9.16E-05	0.0148
3	Aromatic compound degradation	Catechol degradation II (meta-cleavage pathway)	12.94294	6.817753	14.8872	0.000114	0.0148
4	Fatty acid and lipid biosynthesis	Super pathway of lipopolysaccharide biosynthesis	28.38013	2.42697	13.50893	0.000237	0.02309
5	Aromatic compound degradation	Toluene degradation II (aerobic) (via 4-methylcatechol)	10.58863	8.813538	12.74445	0.000357	0.023322
6	Aromatic compound degradation	Toluene degradation I (aerobic) (via o-cresol)	10.58859	8.813538	12.73057	0.00036	0.023322
7	Sugar acid metabolism	D-Galactarate degradation I	8.848847	4.542388	11.51003	0.000692	0.031156
8	Antibiotic resistance	Polymyxin resistance	15.29624	3.859829	11.46961	0.000707	0.031156
9	Sugar acid metabolism	Super pathway of D-glucarate and D-Galactarate degradation	8.848833	4.542388	11.43476	0.000721	0.031156
10	Nucleoside and nucleotide biosynthesis	Super pathway of pyrimidine nucleobases salvage	–0.46889	13.07049	10.52772	0.001176	0.045745
11	Sugar acid metabolism	D-glucarate degradation I	8.936948	4.805885	10.33191	0.001307	0.046238
12	Amine and polyamine degradation	Allantoin degradation IV (anaerobic)	12.94646	6.715548	9.796436	0.001749	0.051378

ADG, average daily gain; logFC, log fold-change; logCPM, log counts per million; LR, likelihood ratio; FDR, false discovery rate (adjusted p-value).