TABLE 1.

Functional analysis for gene and metabolic pathway prediction in infected and noninfected mice^a

Metabolic pathway	Gene	Associated bacterium	FDR	Effect size in infected BALB/c mice	P	q
Lipid metabolismb	Enoyl-CoA hydratase	Bacteroides thetaiotaomicron	5.743E–02	−4.6	0.000691712	0.005358871
	Tiglyl-CoA hydratase	Bacteroides thetaiotaomicron	5.359E–03	−4.64	0.000691712	0.005358871
	Long-chain fatty acid CoA ligase	Bacteroides thetaiotaomicron	1.835E–0	−3.09	0.003273173	0.018350702
	Acetyl-CoA carboxylase	Bacteroides thetaiotaomicron	1.463E–02	−3.39	0.002282365	0.014634670
	Acyl carrier malonyltransferase	Bacteroides thetaiotaomicron	1.110E–02	−3.76	0.001535573	0.011100064
	Beta ketoacyl acyl carrier protein	Parasutterella excrementihominis	1.182E–02	−3.6	0.001679678	0.011815909
	Long-chain fatty acid CoA ligase	Acetatifactur muris	2.075E–02	2.1	0.004208897	0.020745468
Amino acid metabolismc	Isoleucine tRNA ligase	Bacteroides thetaiotaomicron	1.419E–0	−3.43	0.002190388	0.014189590
	Leucine tRNA ligase	Bacteroides thetaiotaomicron	1.566E–02	−3.3	0.002510489	0.015657878
	Tryptophan tRNA ligase	Dubosiella newyorkensis	1.557E–02	−3.31	0.002489752	0.015570720
	Tryptophan synthase	Bacteroides thetaiotaomicron	9.214E–03	−4.01	0.001215979	0.009213813
		Faecalibaculum rodentium	1.951E–02	−2.9	0.003771024	0.019505084
	Branched-chain amino acid transaminase	Acutalibacter muris	1.950E–02	−2.96	0.003768102	0.019500525
	Chorismate synthase	Parasutterella excrementihominis	2.021E–02	−2.92	0.003967455	0.020212716
Nucleotide metabolism	Ribonucleoside diphosphate reductase	Parasutterella excrementihominis	6.064E–03	−4.48	0.000787853	0.006064403
	Hypoxanthine phosphoribosyltransferase	Faecalibaculum rodentium	6.568E–03	−4.39	0.000856150	0.006567651
	Purine nucleoside phosphorylase	Bacteroides thetaiotaomicron	9.383E–03	−3.98	0.001243739	0.009382987
Biosynthetic pathway to cobalamin	Precorrin 2 dehydrogenases	Faecalibaculum rodentium	2.315E–02	−2.73	0.005085668	0.023150662
Oxidative metabolism and CoA synthesis pathway	Succinate CoA ligase ADP forming	Bacteroides thetaiotaomicron	1.430E–02	−3.42	0.002212495	0.014301774
	Dephospho-CoA kinase	Dubosiella newyorkensis	1.779E–02	−3.14	0.003048271	0.017789402
Glycolysis and fermentation pathways	Pyruvate kinase	Bacteroides thetaiotaomicron	1.743E–02	−3.16	0.002959204	0.017426635
		Dubosiella newyorkensis	2.144E–02	−2.82	0.004491714	0.021443220

^aIdentification of genes and associated taxa was performed using the Humann3 tool, and statistical evaluation to determine statistically significant changes was performed with Maaslin2 from a multivariate mixed-effects model. The table shows the metabolic pathway, the genes involved in this pathway, the taxa associated with these genes, the false discovery rate (FDR), the effect size in infected mice, and the P and q statistical significance values. CoA, coenzyme A.

^bThat is, beta-oxidation and fatty acid synthesis and metabolism.

^cThat is, the synthesis of SCFAs (leucine, valine, and isoleucine), the synthesis of ornithine, the synthesis of arginine, and the synthesis of chorismate (a derivative of shikimic acid metabolism and precursor of aromatic amino acids such as phenylalanine, tryptophan, and tyrosine).