A pet food composition, comprising: protein, carbohydrates, fat, fiber, and at least 12 distinct metabolites including at least 3 distinct metabolites for modulating each of phosphorus, alkaline phosphatase, aspartate aminotransferase, and gamma-glutamyltransferase in a companion animal; wherein the metabolite that modulates phosphorus is selected from the group consisting of homocysteine, erythritol, arabitol, betaine, N-acetylphenylalanine, 3-hydroxybutyrate (BHBA), citrulline, mannose, 2-oxindole-3-acetate, N-acetyltryptophan, glycerate, xylonate, threitol, 3-aminoisobutyrate, arachidonate (20:4n6), gamma-glutamylphenylalanine, phenylalanine, trigonelline (N'-methylnicotinate), allantoin, glutathione (oxidized (GSSG)), N-acetylserine, arabinose, and mixtures thereof; wherein the metabolite that modulates alkaline phosphatase is selected from the group consisting of lysine, gamma-glutamylphenylalanine, arabinose, phenylalanine, and mixtures thereof; wherein the metabolite that modulates aspartate aminotransferase is selected from the group consisting of 3-ureidopropionate, threitol, erythronate, gulono-1,4-lactone, C-glycosyltryptophan, urea, 2-hydroxyglutarate, butyrylcarnitine, dimethylglycine, pseudouridine, eicosapentaenoate (EPA; 20:5n3), uracil, 1-linoleoylglycerophosphoinositol, dihomo-linolenate (20:3n3 or n6), phosphate, and mixtures thereof; and wherein the metabolite that modulates gamma-glutamyltransferase is selected from the group consisting of 3-aminoisobutyrate, trigonelline (N'-methylnicotinate), N-acetylserine, taurochenodeoxycholate, erythritol, 15-methylpalmitate (isobar with 2-methylpalmitate), allantoin, taurocholate, threitol, 3-phosphoglycerate, betaine, arabitol, sebacate (decanedioate), stachydrine, citrulline, citrate, glycolate (hydroxyacetate), campesterol, and mixtures thereof, 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 phosphorus, alkaline phosphatase, aspartate aminotransferase, or gamma-glutamyltransferase in the companion animal upon administration of the pet food to the companion animal. protein, carbohydrates, fat, fiber, and at least 12 distinct metabolites including at least 3 distinct metabolites for modulating each of phosphorus, alkaline phosphatase, aspartate aminotransferase, and gamma-glutamyltransferase in a companion animal; wherein the metabolite that modulates phosphorus is selected from the group consisting of homocysteine, erythritol, arabitol, betaine, N-acetylphenylalanine, 3-hydroxybutyrate (BHBA), citrulline, mannose, 2-oxindole-3-acetate, N-acetyltryptophan, glycerate, xylonate, threitol, 3-aminoisobutyrate, arachidonate (20:4n6), gamma-glutamylphenylalanine, phenylalanine, trigonelline (N'-methylnicotinate), allantoin, glutathione (oxidized (GSSG)), N-acetylserine, arabinose, and mixtures thereof; wherein the metabolite that modulates alkaline phosphatase is selected from the group consisting of lysine, gamma-glutamylphenylalanine, arabinose, phenylalanine, and mixtures thereof; wherein the metabolite that modulates aspartate aminotransferase is selected from the group consisting of 3-ureidopropionate, threitol, erythronate, gulono-1,4-lactone, C-glycosyltryptophan, urea, 2-hydroxyglutarate, butyrylcarnitine, dimethylglycine, pseudouridine, eicosapentaenoate (EPA; 20:5n3), uracil, 1-linoleoylglycerophosphoinositol, dihomo-linolenate (20:3n3 or n6), phosphate, and mixtures thereof; and wherein the metabolite that modulates gamma-glutamyltransferase is selected from the group consisting of 3-aminoisobutyrate, trigonelline (N'-methylnicotinate), N-acetylserine, taurochenodeoxycholate, erythritol, 15-methylpalmitate (isobar with 2-methylpalmitate), allantoin, taurocholate, threitol, 3-phosphoglycerate, betaine, arabitol, sebacate (decanedioate), stachydrine, citrulline, citrate, glycolate (hydroxyacetate), campesterol, and mixtures thereof, 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 phosphorus, alkaline phosphatase, aspartate aminotransferase, or gamma-glutamyltransferase in the companion animal upon administration of the pet food to the companion animal.