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 vitamin D3, and 1,25 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, pseudouridine, myo-inositol, 1-methylguanosine, xylitol, pyroglutamine, and mixtures thereof; wherein the metabolite that modulates 25 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 2 vitamin D3 is selected from the group consisting of arachidonate (20:4n6), pantothenate (Vitamin B5), mannose, isobutyrylcarnitine, sphingomyelin, 3-hydroxybutyrate (BHBA), prolylhydroxyproline, glycerate, dihomolinolenate (20:3n3 or 3n6), adrenate (22:4n6), alpha-tocopherol, caproate (6:0), octanoylcarnitine, 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 vitamin D3, or 1,25 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 vitamin D3, and 1,25 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, pseudouridine, myo-inositol, 1-methylguanosine, xylitol, pyroglutamine, and mixtures thereof; wherein the metabolite that modulates 25 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 2 vitamin D3 is selected from the group consisting of arachidonate (20:4n6), pantothenate (Vitamin B5), mannose, isobutyrylcarnitine, sphingomyelin, 3-hydroxybutyrate (BHBA), prolylhydroxyproline, glycerate, dihomolinolenate (20:3n3 or 3n6), adrenate (22:4n6), alpha-tocopherol, caproate (6:0), octanoylcarnitine, 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 vitamin D3, or 1,25 2 vitamin D3 in the companion animal upon administration of the pet food to the companion animal.