A pet food composition, comprising: protein, carbohydrates, fat, fiber, and at least 6 distinct metabolites including at least 2 distinct metabolites for modulating each one of bone mineral content, 25(OH) vitamin D3, and 1,25(OH) 2 vitamin D3 in a companion animal; wherein the metabolite that modulates bone mineral content is selected from the group consisting of creatinine, gamma-glutamylleucine, ethanolamine, histidine, 4-acetylphenyl sulfate, phosphoethanolamine (PE), pseudouridine, myo-inositol, 1-methylguanosine, xylitol, pyroglutamine, and mixtures thereof; wherein the metabolite that modulates 25(OH) vitamin D3 is selected from the group consisting of arachidonate (20:4n6), pantothenate (Vitamin B5), mannose, anserine, cytidine, prolylhydroxyproline, arabonate, 3-hydroxybutyrate (BHBA), docosapentaenoate (DPA; 22:5n3), adrenate (22:4n6), N-acetylalanine, dihomolinoleate (20:2n6), stearate (18:0), palmitate (16:0), arabitol, taurolithocholate, glutamate, 17-methylstearate, docosapentaenoate (n6 DPA; 22:5n6), sphingomyelin, glycerate, oleate (18:1n9), and mixtures thereof; wherein the metabolite that modulates 1,25(OH) 2 vitamin D3 is selected from the group consisting of arachidonate (20:4n6), pantothenate (Vitamin B5), mannose, isobutyrylcarnitine (C4), sphingomyelin, 3-hydroxybutyrate (BHBA), prolylhydroxyproline, glycerate, dihomolinolenate (20:3n3 or 3n6), adrenate (22:4n6), alpha-tocopherol, caproate (6:0), octanoylcarnitine (C8), and mixtures thereof; and wherein the metabolites are present in amounts from 0.01 weight% to 10 weight% of the food composition; and wherein the pet food composition provides at least a 5% increase or at least a 5% decrease in the amount of at least one of bone mineral content, 25(OH) vitamin D3, or 1,25(OH)2 vitamin D3 in the companion animal upon administration of the pet food to the companion animal. protein, carbohydrates, fat, fiber, and at least 6 distinct metabolites including at least 2 distinct metabolites for modulating each one of bone mineral content, 25(OH) vitamin D3, and 1,25(OH) 2 vitamin D3 in a companion animal; wherein the metabolite that modulates bone mineral content is selected from the group consisting of creatinine, gamma-glutamylleucine, ethanolamine, histidine, 4-acetylphenyl sulfate, phosphoethanolamine (PE), pseudouridine, myo-inositol, 1-methylguanosine, xylitol, pyroglutamine, and mixtures thereof; wherein the metabolite that modulates 25(OH) vitamin D3 is selected from the group consisting of arachidonate (20:4n6), pantothenate (Vitamin B5), mannose, anserine, cytidine, prolylhydroxyproline, arabonate, 3-hydroxybutyrate (BHBA), docosapentaenoate (DPA; 22:5n3), adrenate (22:4n6), N-acetylalanine, dihomolinoleate (20:2n6), stearate (18:0), palmitate (16:0), arabitol, taurolithocholate, glutamate, 17-methylstearate, docosapentaenoate (n6 DPA; 22:5n6), sphingomyelin, glycerate, oleate (18:1n9), and mixtures thereof; wherein the metabolite that modulates 1,25(OH) 2 vitamin D3 is selected from the group consisting of arachidonate (20:4n6), pantothenate (Vitamin B5), mannose, isobutyrylcarnitine (C4), sphingomyelin, 3-hydroxybutyrate (BHBA), prolylhydroxyproline, glycerate, dihomolinolenate (20:3n3 or 3n6), adrenate (22:4n6), alpha-tocopherol, caproate (6:0), octanoylcarnitine (C8), and mixtures thereof; and wherein the metabolites are present in amounts from 0.01 weight% to 10 weight% of the food composition; and wherein the pet food composition provides at least a 5% increase or at least a 5% decrease in the amount of at least one of bone mineral content, 25(OH) vitamin D3, or 1,25(OH)2 vitamin D3 in the companion animal upon administration of the pet food to the companion animal. <EOS>