TITLE

COMPOSITIONS AND METHODS THAT MODULATE BACTERIA IN A COMPANION ANIMAL

CROSS REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to U.S. Provisional Application Serial No. 62/434,560 filed December 15, 2016, the disclosure of which is incorporated in its entirety herein by this reference.

BACKGROUND

[0002] Probiotics have been used to modulate the microflora in animals as well as confer various health benefits to the animal. Probiotics can be defined as live microorganisms that confer a health benefit to a host when administered in adequate amounts. It is theorized that probiotics may impart their beneficial health effects either by increasing the resistance to colonization of mucosal surfaces by pathogenic bacteria (colonization resistance) or by exerting a direct effect on gut associated lymphoid tissue (GALT) that promotes the production of immunomodulators.

[0003] Probiotics have been used to modulate the course of a variety of infectious diseases in human medicine. In contrast, few studies have been performed in veterinary medicine. The majority of veterinary studies have been in large animals where probiotics have been used to attempt to alter the shedding of fecal pathogens or to improve production parameters such as weight gain, feed conversion rate, and reduced mortality. While benefits can be conferred, the addition of probiotics can provide unintentionally consequences including digestive discomfort, over stimulation of the immune system, and gene transfer.

SUMMARY

[0004] The present disclosure relates generally to pet food compositions; methods of enhancing nutritional benefit of a pet food; and methods for modulating bacteria of at least one of Bifidobacterium, Lactobacillus, or Clostridium perfringens in a companion animal. Specifically, the present disclosure relates to metabolites for modulating at least one of Bifidobacterium, Lactobacillus, or Clostridium perfringens in a companion animal.

[0005] The present inventors have developed a predictive model of Bifidobacterium, Lactobacillus, and Clostridium perfiingens by identifying metabolite compounds which correlate to Bifidobacterium, Lactobacillus, or Clostridium perfringens. A very controlled study was employed to minimize other external factors by using multiple canines all fed the same diet. A validation model was then developed by feeding different levels of the identified compounds (via a dietary change) to a group of canines and measuring changes in the corresponding bacterium.

[0006] Accordingly, in a general embodiment, the present disclosure provides a pet food composition comprising: protein, carbohydrates, fat, fiber, and a metabolite for modulating at least one of Bifidobacterium, Lactobacillus, or Clostridium perfringens in a companion animal. In one embodiment, the pet food composition can provide at least a 5% increase or a 5% decrease in the amount of Bifidobacterium, Lactobacillus, or Clostridium perfringens present in the companion animal. In one aspect, the pet food can provide an increase. In another aspect, the pet food can comprise a decrease.

[0007] The present disclosure also provides methods of minimizing costs associated with production of a pet food; methods of enhancing nutritional benefit of a pet food; methods for modulating the amount of Bifidobacterium, Lactobacillus, or Clostridium perfringens in a companion animal; and methods of measuring a change in the amount of at least one of Bifidobacterium, Lactobacillus, or Clostridium perfringens in a companion animal.

[0008] An advantage of one or more embodiments provided by the present disclosure is to increase or decrease Bifidobacterium, Lactobacillus, or Clostridium perfringens in a companion animal by adjusting the diet of the animal to increase the amount of a compound which positively modulates the specific bacterium or to decrease the amount of a compound which negatively modulates the specific bacterium.

[0009] Additional features and advantages are described herein and will be apparent from the following Detailed Description.

DETAILED DESCRIPTION

[0010] Definitions

[0011] As used in this disclosure and the appended claims, the singular forms "a," "an" and "the" include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to "a composition" or "the composition" includes two or more compositions. The term "and/or" used in the context of "X and/or Y" should be interpreted as "X," or "Y," or "X and Y." Where used herein, the terms "example" and "such as," particularly when followed by a listing of terms, are merely exemplary and illustrative, and are not exclusive or comprehensive.

[0012] As used herein, "about" is understood to refer to numbers in a range of numerals, for example the range of -10% to +10% of the referenced number, within -5% to +5% of the referenced number, or in one aspect, within -1% to +1% of the referenced number, and in a specific aspect, within -0.1% to +0.1% of the referenced number. Furthermore, all numerical ranges herein should be understood to include all integers, whole or fractions, within the range. Moreover, these numerical ranges should be construed as providing support for a claim directed to any number or subset of numbers in that range. For example, a disclosure of from 1 to 10 should be construed as supporting a range of from 1 to 8, from 3 to 7, from 1 to 9, from 3.6 to 4.6, from 3.5 to 9.9, and so forth.

[0013] All percentages expressed herein are by weight of the total weight of the food composition unless expressed otherwise. When reference is made to the pH, values correspond to pH measured at 25 °C with standard equipment. An "amount" can be the total amount of the referenced component per serving of the composition or per distinct unit of the composition and/or can be the weight percentage of the referenced component by dry weight. Moreover, an "amount" includes zero; for example, the recitation of an amount of a compound does not necessarily mean that the compound is present, unless followed by a range that excludes zero.

[0014] The terms "food," "food product" and "food composition" mean a product or composition that is intended for ingestion by an animal, including a human, and provides at least one nutrient to the animal. Further in this regard, these terms mean that the product or composition is in a form ready for consumption and is not merely an intermediate from which a consumable product or composition is made, although other food compositions can be added in some embodiments. The term "pet food" means any food composition intended to be consumed by a pet. The term "pet" means any animal which could benefit from or enjoy the compositions provided by the present disclosure. For example, the pet can be an avian, bovine, canine, equine, feline, hircine, lupine, murine, ovine, or porcine animal, but the pet can be any suitable animal.

[0015] The term "companion animal" means a dog or a cat. In an embodiment, the compositions and methods disclosed herein involve a senior dog or a senior cat. Dogs are considered senior in the last 25% of their lives. The life span of a dog depends on its size and/or its breed, but for the present disclosure a senior dog is a dog that is at least 5 years of age (e.g., at least 6 years of age, at least 7 years of age, or at least 8 years of age). The life span of a cat also depends on its size and/or its breed, but for the present disclosure a senior cat is a cat that is at least 7 years of age (e.g., at least 8 years of age, at least 9 years of age, or at least 10 years of age).

[0016] As used herein, "comparable companion animal" refers to a healthy animal of the same gender, breed, and age as the companion animal.

[0017] As used herein, "metabolite" refers to a compound having biological activity in a companion animal that is an intermediate or product of metabolism, and includes precursors thereof. As used herein, "precursor" refers to any compound that metabolizes to a metabolite during metabolism in a companion animal. For example, if the specific metabolite is cysteine, "the metabolite" comprises a cysteine precursor (e.g., methionine).

[0018] The term "effective amount" means an amount of a compound of the present invention that (i) treats or prevents the particular disease, condition, or disorder, (ii) attenuates, ameliorates, or eliminates one or more symptoms of the particular disease, condition, or disorder, or (iii) prevents or delays the onset of one or more symptoms of the particular disease, condition, or disorder described herein. In one embodiment, the present metabolite or combination of metabolites can be present in an effective amount for modulating the amount of Bifidobacterium, Lactobacillus, or Clostridium perfringens in a companion animal.

[0019] The dosages expressed herein are in milligrams per kilogram of body weight per day (mg/kg day) unless expressed otherwise.

[0020] The term "long-term administration" means periods of repeated administration or consumption in excess of one month. Periods of longer than two, three, or four months can be used for certain embodiments. Also, more extended periods can be used that include longer than 5, 6, 7, 8, 9, or 10 months. Periods in excess of 11 months or 1 year can also be used. Longer term use extending over 1, 2, 3, or more years are included in the invention. For certain aging animals, the animal will continue consuming on a regular basis for the remainder of its life. This can also be referred to as consumption for "extended" periods.

[0021] The term "regular basis" or "regular administration" means at least monthly dosing with the compositions or consumption of the compositions, and in one aspect, means at least weekly dosing. More frequent dosing or consumption, such as twice or three times weekly, can be performed in certain embodiments. Still, in other embodiments, regimens can be used that comprise at least once daily consumption. The skilled artisan will appreciate that the blood level of a compound or certain metabolites of that compound or which result after the consumption of that compound, may be a useful tool for assessing or determining dosing frequency. For example, for determining feeding amounts for pet food compositions comprising a certain metabolite, the blood concentration of that metabolite, may provide useful information. A frequency, regardless of whether expressly exemplified herein, that allows maintenance of a desired blood level of the measured compound, such as a metabolite, within acceptable ranges can be useful herein. The skilled artisan will appreciate that feeding amounts will be a function of the composition that is being consumed or administered as well as the animal consuming the food, and some food compositions may require more or less frequent administration to maintain a desired blood level of the measured compound {e.g., a metabolite).

[0022] The relative terms "improve," "increase," "enhance," "decrease" and the like refer to the effects of the composition disclosed herein (a composition comprising a metabolites) relative to a composition having a lower amount or lacking such metabolites, but otherwise identical.

[0023] A "blended" composition merely has at least two components having at least one different characteristic relative to each other. In one aspect, moisture content and water activity can be different in the context of the present disclosure. In this regard, description of a composition as "blended" does not imply that the blended composition has been subjected to processing sometimes referenced as "blending," namely mixing components so that they are indistinguishable from each other, and, in one aspect, such processing is avoided when mixing one component with the other components to form a blended composition (e.g., mixing a dry component with a wet or semi-moist component). Further in this regard, in a blended composition each of the at least two components having at least one different characteristic relative to each other can retain their distinct identity and appearance.

[0024] "Wet food" means a pet food having a moisture content from about 50% to about 90%, and in one aspect, from about 70% to about 90%. "Dry food" means a pet food having a moisture content less than about 20%, and in one aspect, less than about 15%, and in a specific aspect, less than about 10%. "Semi-moist food" means a pet food having a moisture content from about 20% to about 50%, and in one aspect, from about 25% to about 35%.

[0025] "Kibbles" is used synonymously with "chunks" herein and both terms mean pieces of dry or semi- moist pet food which can have a pellet shape or any other shape and can be made by slicing a food composition into separate pieces. Non-limiting examples of kibbles include particulates; pellets; pieces of pet food, dehydrated meat, meat analog, vegetables, and combinations thereof; and pet snacks, such as meat or vegetable jerky, rawhide, and biscuits. A "meat analog" is a meat emulsion product that resembles pieces of natural meat in appearance, texture, and physical structure.

[0026] The term "dietary supplement" means a product that is intended to be ingested in addition to the normal animal diet. Dietary supplements may be in any form, e.g., solid, liquid, gel, tablets, capsules, powder, and the like. In one aspect, they can be provided in convenient dosage forms. In some embodiments, they can be provided in bulk consumer packages such as bulk powders, liquids, gels, or oils. In other embodiments, supplements can be provided in bulk quantities to be included in other food items such as snacks, treats, supplement bars, beverages and the like.

[0027] The compositions disclosed herein may lack any element that is not specifically disclosed herein. Thus, a disclosure of an embodiment using the term "comprising" includes a disclosure of embodiments "consisting essentially of and "consisting of the components identified. Similarly, the methods disclosed herein may lack any step that is not specifically disclosed herein. Thus, a disclosure of an embodiment using the term "comprising" includes a disclosure of embodiments "consisting essentially of and "consisting of the steps identified. Any embodiment disclosed herein can be combined with any other embodiment disclosed herein unless explicitly and directly stated otherwise.

[0028] The present discussion of embodiments, aspects, examples, etc. are independent in that they can apply to all methods and compositions. For example, a metabolite used in a pet food composition can also be used in the method of modulating or a method of minimizing costs associated with making such a pet food, and vice versa.

Embodiments

[0029] In an aspect of the present disclosure, a pet food composition can comprise protein, carbohydrates, fat, fiber, and a metabolite for modulating the amount of at least one of Bifidobacterium, Lactobacillus, or Clostridium perfringens in a companion animal, such as a senior dog or a senior cat. In one embodiment, the pet food composition can provide an increase in the amount of at least one of Bifidobacterium, Lactobacillus, or Clostridium perfringens in the companion animal.

[0030] In another aspect of the present disclosure, a method of modulating the amount of at least one of Bifidobacterium, Lactobacillus, or Clostridium perfringens in a companion animal is provided. The method can comprise administering to the companion animal a pet food composition comprising protein, carbohydrates, fat, fiber, and a metabolite for modulating the amount of at least one of Bifidobacterium, Lactobacillus, or

Clostridium perfringens in a companion animal in the companion animal. In one aspect, the companion animal can be a senior dog or a senior cat.

[0031] In still another aspect of the present disclosure, a method of measuring a change in the amount of at least one of Bifidobacterium, Lactobacillus, or Clostridium perfringens in a companion animal can comprise obtaining a serum sample of the companion animal, measuring concentrations of at least three distinct metabolites from the serum sample that modulate at least one of Bifidobacterium, Lactobacillus, or Clostridium perfringem, and determining that the Bifidobacterium, Lactobacillus, or Clostridium perfringens has changed if, after comparing the metabolite concentrations to average metabolite concentrations of each metabolite of comparable companion animals, the metabolite concentrations are different than the average metabolite concentrations.

[0032] Yet another aspect of the present disclosure is a method of minimizing costs associated with production of a pet food having a first formulation designed for consumption by a companion animal, such as a senior dog or a senior cat. A further aspect of the present disclosure is a method of enhancing nutritional benefit of a pet food having a first formulation designed for consumption by a companion animal, such as a senior dog or a senior cat. These methods comprise adjusting the first formulation of the pet food to be a second formulation. At least one of the first and second formulations comprises a metabolite for modulating the amount of Bifidobacterium, Lactobacillus, or Clostridium perfringens in a companion animal. The adjusting comprises changing an amount of the metabolite in the first formulation to a different amount in the second formulation.

[0033] "Minimizing" costs means that the costs associated with making the second formulation are less than the costs associated with making the first formulation, for example on a per serving basis, per unit weight, per unit volume, per total energy, and the like. "Enhanced" nutritional benefit means that the nutritional benefit of the second formulation is greater than the nutritional benefit of the first formulation.

[0034] As discussed herein, the pet food compositions and methods can contain a metabolite or multiple metabolites for modulating the amounts of various bacterium. In various aspects, the compositions and methods can contain 1, 2, 3, 4, 5, 6, 7, 8, 9, or even 10 metabolites for modulating the amount of any one of the bacterium, or multiple bacteria, or for each bacterium. As such, in one embodiment, the composition can comprise at least 6 metabolites, including metabolites for individually modulating the amount of each one of Bifidobacterium, Lactobacillus, and Clostridium perfringens in a companion animal. In another embodiment, the composition can comprise at least 9 metabolites, including at least 3 metabolites for individually modulating the amounts of each one of Bifidobacterium, Lactobacillus, and Clostridium perfringens in a companion animal. In still another embodiment, the composition can comprise at least 12 metabolites, including at least 4 metabolites for individually modulating the amounts of each one of Bifidobacterium, Lactobacillus, and

Clostridium perfringens in a companion animal. Additionally, in one embodiment, the composition can comprise at least four distinct metabolites that modulate the amounts of at least one of Bifidobacterium, Lactobacillus, or Clostridium perfringens. Further, in one embodiment, the composition can comprise at least five distinct metabolites that modulate at least one of Bifidobacterium, Lactobacillus, or Clostridium perfringens. Still, in another embodiment, the method can modulate at least two bacterium selected from the group consisting of Bifidobacterium, Lactobacillus, and Clostridium perfringens and where the composition comprises at least six distinct metabolites, three distinct metabolites for modulating each of the at least two bacterium. Yet, in another embodiment, the method can modulate Bifidobacterium, Lactobacillus, and Clostridium perfringens and where the composition comprises at least nine distinct metabolites, three distinct metabolites for modulating each of Bifidobacterium, Lactobacillus, and Clostridium perfringens. As previously noted, the metabolite and bacteria relationships can be used for both method and composition embodiments.

[0035] In some embodiments, the metabolite negatively modulates the specific bacterium, and the changing of the amount of the metabolite comprises decreasing the amount of the metabolite. In other embodiments, the metabolite negatively modulates the specific bacterium, and the changing of the amount of the metabolite comprises increasing the amount of the metabolite. In some embodiments, the metabolite positively modulates the specific bacterium, and the changing of the amount of the metabolite comprises increasing the amount of the metabolite. In other embodiments, the metabolite positively modulates the specific bacterium, and the changing of the amount of the metabolite comprises decreasing the amount of the metabolite. These are not mutually exclusive embodiments; a particular embodiment can comprise decreasing the amount of a metabolite that negatively modulates a first specific bacterium and increasing the amount of a metabolite that positively modulates a second specific bacterium, and the first and second specific bacteria can be the same or different specific bacteria (e.g., one or more of Bifidobacterium, Lactobacillus, or Clostridium perfringens).

[0036] Decreasing the amount of the metabolite can comprise decreasing the amount of the metabolite directly and/or decreasing the amount of an ingredient which comprises the metabolite. In some embodiments, decreasing the amount of the metabolite can comprise decreasing the amount of a precursor of the metabolite directly and/or decreasing the amount of an ingredient which comprises a precursor of the metabolite. For example, the second formulation can contain, relative to the first formulation, less of an ingredient having a high amount of the metabolite or precursor thereof (e.g., an ingredient having an amount of the metabolite or precursor thereof that is higher than in one or more of the other ingredients).

[0037] Increasing the amount of the metabolite can comprise increasing the amount of the metabolite directly and/or decreasing the amount of an ingredient which comprises the metabolite. In some embodiments, increasing the amount of the metabolite can comprise increasing the amount of a precursor of the metabolite directly and/or increasing the amount of an ingredient which comprises a precursor of the metabolite. For example, the second formulation can contain, relative to the first formulation, more of an ingredient having a high amount of the metabolite or precursor thereof (e.g., an ingredient having an amount of the metabolite or precursor thereof that is higher than in one or more of the other ingredients).

[0038] Generally, the methods and compositions described herein can provide an increase or a decrease in the amount of at least one of Bifidobacterium, Lactobacillus, or Clostridium perfringens in the companion animal. In some embodiment, the increase or decrease can be at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, or even 50%. In one aspect, the compositions and methods can provide an increase. In another aspect, the compositions and methods can provide a decrease. As such, the present modulation, and resulting increase or decrease, can provide one of the following health benefits: weight gain, increased feed conversion rate, reduced mortality, decreased digestive discomfort, relief from irritable bowel syndrome, relief from Crohn's disease, reduction in bacterial overgrowth, increase in food digestion, increase in lactose metabolism, decreased negative effects of antibiotics, healthy skin, decreased yeast infections, increased absorption of nutrients, or increased immune system.

[0039] In one embodiment, the increase or decrease can be for at least two of Bifidobacterium,

Lactobacillus, and Clostridium perfringens. In another embodiment, the increase or decrease can be for

Bifidobacterium, Lactobacillus, and Clostridium perfringens.

[0040] Ingredients comprising the metabolite (e.g., a precursor of the metabolite) and optionally amounts of the metabolite in the ingredient can be identified by analysis of the ingredient, for example using a separation technique, such as gas chromatography or liquid chromatography, and then mass spectrometry.

[0041] In each of these compositions and methods, the pet food composition can be a wet food, a semi- moist food or a dry food. In an embodiment, the pet food composition is one or more components of a blended composition. In some embodiments, the pet food composition is a kibble, and in some embodiments, the pet food composition is a meat analog. Additionally, in another embodiment, the present composition for modulating a bacterium can be a dietary supplement comprising the metabolites described herein. Further, a method of modulating a bacterium can include administering to the companion animal the dietary supplement.

[0042] Such pet food compositions can be administered to the companion animal in amounts ranging from about 3 g of pet food per 1 lb body weight to about 16 g of pet food per 1 lb body weight of the companion animaLAdditionally, the metabolites can be present in amounts from about 0.01 weight% to about 10 weight% of the food composition. In one aspect, the metabolites can be present in concentrations of about 0.01 to about 1,000 mg kg of food. In another aspect, the metabolites can be present in concentrations from about 1 IU to about 500,000 IU per kilogram of food. In one embodiment, the pet food composition can be administered to the companion animal in amounts sufficient to maintain the health and/or body weight of the animal. In one aspect, the administration can be regular administration.

[0043] As noted above and detailed later in this application, the present inventors identified metabolite compounds which correlate to Bifidobacterium, Lactobacillus, or Clostridium perfringens. Thus, the metabolite in the pet food composition can be one of these compounds. Nevertheless, the metabolite can be any metabolite for modulating the amount of at least one of Bifidobacterium, Lactobacillus, or Clostridium perfringens in a companion animal, even if the metabolite is not explicitly disclosed herein. For example, the metabolite can be a compound identified using the methods disclosed herein but not itself explicitly disclosed herein. Furthermore, the metabolite can be a compound identified using a method not disclosed herein if the compound is reliably correlated to at least one of Bifidobacterium, Lactobacillus, or Clostridium perfringens.

[0044] As a non-limiting example, the metabolite can modulate Bifidobacterium and can be selected from the group consisting of campesterol, 7-ketodeoxycholate, 3-(4-hydroxyphenyl)propionate, 3-dehydrocarnitine, 12-dehydrocholate, X - 17314, X - 15461, chenodeoxycholate, 3-dehydrocholate, cholate, 15-methylpalmitate (isobar with 2-methylpalmitate) and mixtures thereof. In one embodiment, the metabolite can modulate Bifidobacterium and can be selected from the group consisting of campesterol, 7-ketodeoxycholate, 3-(4- hydroxyphenyl)propionate, 3-dehydrocarnitine, 12-dehydrocholate, chenodeoxycholate, 3-dehydrocholate, cholate, 15-methylpalmitate (isobar with 2-methylpalmitate) and mixtures thereof.

[0045] As another non-limiting example, the metabolite can modulate Lactobacillus and can be selected from the group consisting of X— 15461, 3-phenylpropionate (hydrocinnamate), 3-(4-hydroxyphenyl)propionate, mannitol, campesterol, indoleacetate, 3-dehydrocarnitine, X— 11378 and mixtures thereof. In one embodiment, the metabolite can modulate Lactobacillus and can be selected from the group consisting of 3-phenylpropionate (hydrocinnamate), 3-(4-hydroxyphenyl)propionate, mannitol, campesterol, indoleacetate, 3-dehydrocarnitine, and mixtures thereof.

[0046] As yet another non-limiting example, the metabolite can modulate Clostridium perfringens and can be selected from the group consisting of dihomo-linoleate (20:2n6), arachidonate (20:4n6), adrenate (22:4n6), mannose, 3 -hydroxybutyrate (BHBA), trigonelline (N'-methylnicotinate), eicosenoate (20:ln9 or 11), docosapentaenoate (n3 DPA; 22:5n3), palmitoyl sphingomyelin, glycerate, linolenate [alpha or gamma; (18:3n3 or 6)], dihomo-linolenate (20:3n3 or n6), X - 11378, X - 17010, 7-alpha-hydroxycholesterol, stearate (18:0), palmitate (16:0), glycolate (hydroxyacetate), stachydrine, X - 12450, X - 09789, campesterol, pantothenate, linoleate (18:2n6), docosapentaenoate (n6 DPA; 22:5n6), X - 11412, X - 17185, phenylalanine and mixtures thereof. In one embodiment, the metabolite can modulate Clostridium perfringens and can be selected from the group consisting of dihomo-linoleate (20:2n6), arachidonate (20:4n6), adrenate (22:4n6), mannose, 3- hydroxybutyrate (BHBA), trigonelline (N'-methylnicotinate), eicosenoate (20: ln9 or 11), docosapentaenoate (n3 DPA; 22:5n3), palmitoyl sphingomyelin, glycerate, linolenate [alpha or gamma; (18:3n3 or 6)], dihomo- linolenate (20:3n3 or n6), 7-alpha-hydroxycholesterol, stearate (18:0), palmitate (16:0), glycolate

(hydroxyacetate), stachydrine, campesterol, pantothenate, linoleate (18:2n6), docosapentaenoate (n6 DPA; 22:5n6), phenylalanine and mixtures thereof.

[0047] In yet another aspect of the present disclosure, a method enhances nutritional benefit of a pet food having a first formulation designed for consumption by companion animals, and the method comprises administering the pet food having the first formulation to a first companion animal. The method further comprises measuring in a sample of body fluid from the companion animal (e.g., plasma) an amount of a surrogate marker comprising a metabolite that modulates at least one of Bifidobacterium, Lactobacillus, or Clostridium perfringens. The method further comprises adjusting the first formulation of the pet food to be a second formulation having a difference from the first formulation selected from the group consisting of (i) an ingredient is present in the second formulation and is absent in the first formulation, (ii) an ingredient is absent in the second formulation and is present in the first formulation, (iii) an ingredient is present in the first and second formulations but in a different amount, and (iv) combinations thereof. The adjusting is based at least partially on the amount of the surrogate marker measured in the previous step. [0048] The adjusting can comprise directly decreasing the amount of a metabolite negatively modulating a specific bacterium and/or decreasing the amount of an ingredient which comprises a metabolite negatively modulating a specific bacterium. In some embodiments, decreasing the amount of the metabolite can comprise decreasing the amount of a precursor of the metabolite directly and/or decreasing the amount of an ingredient which comprises a precursor of the metabolite. For example, the second formulation can contain, relative to the first formulation, less of an ingredient having a high amount of the metabolite or precursor thereof (e.g., an ingredient having an amount of the metabolite or precursor thereof that is higher than in one or more of the other ingredients).

[0049] The adjusting can comprise increasing the amount of the metabolite can comprise directly increasing the amount of a metabolite positively modulating a specific bacterium and/or increasing the amount of an ingredient which comprises a metabolite positively modulating a specific bacterium. In some embodiments, increasing the amount of the metabolite can comprise increasing the amount of a precursor of the metabolite directly and/or increasing the amount of an ingredient which comprises a precursor of the metabolite. For example, the second formulation can contain, relative to the first formulation, more of an ingredient having a high amount of the metabolite or precursor thereof (e.g., an ingredient having an amount of the metabolite or precursor thereof that is higher than in one or more of the other ingredients).

[0050] As noted above, ingredients comprising the metabolite (e.g., a precursor of the metabolite) and optionally amounts of the metabolite in the ingredient can be identified by analysis of the ingredient, for example using a separation technique, such as gas chromatography or liquid chromatography, and then mass spectrometry.

[0051] The method further comprises producing the pet food in the second formulation. In an embodiment, the method comprises administering the pet food having the second formulation to a second companion animal.

[0052] This method can be used to provide customized nutrition for a specific companion animal. For example, the first and second companion animal can be the same specific companion animal such that the animal who is administered the pet food having the first formulation has one or more of their specific bacteria modulated by the first formulation assessed. Then this same animal is provided with the resultant second formulation which this animal will more effectively modulate the specific bacterium. Consequently, a pet owner can compensate for their pet's changes in one or more of Bifidobacterium, Lactobacillus, or Clostridium perfringens.

[0053] Alternatively or additionally, this method can be used to provide customized nutrition for companion animals who share one or more of a gender, an approximate age, an approximate size (e.g., body weight, height, and/or length) or a breed. For example, the second companion animal can be a different specific animal than the first companion animal but has a characteristic selected from the group consisting of (i) about the same age as the first companion animal, (ii) about the same size as the first companion animal, (iii) the same breed as the first companion animal, (iv) the same gender as the first companion animal, and (iv) combinations thereof. Preferably, the second companion animal is one of a plurality of companion animals who each share the characteristic with the first companion animal. The method can comprise administering the pet food having the second formulation to the plurality of companion animals. In an embodiment, at least a portion of the plurality of companion animals is located remotely relative to the first companion animal.

[0054] The pet food compositions disclosed herein can be any food formulated for consumption by a pet such as a companion animal. In an embodiment, the pet food composition provides complete nutrition as defined by the Association of American Feed Control Officials (AAFCO) and which depends on the type of animal for which the composition is intended (e.g., dog or cat).

[0055] The pet food composition can comprise meat, such as emulsified meat. Examples of suitable meat include poultry, beef, pork, lamb and fish, especially those types of meats suitable for pets. The meat can include any additional parts of an animal including offal. Some or all of the meat can be provided as one or more meat meals, namely meat that has been dried and ground to form substantially uniform-sized particles and as defined by AAFCO. Additionally or alternatively, vegetable protein can be used, such as pea protein, corn protein (e.g., ground corn or corn gluten), wheat protein (e.g., ground wheat or wheat gluten), soy protein (e.g., soybean meal, soy concentrate, or soy isolate), rice protein (e.g., ground rice or rice gluten) and the like.

[0056] The pet food compositions disclosed herein can comprise vegetable oil, a flavorant, a colorant and water. Suitable vegetable oils include soybean oil, corn oil, cottonseed oil, sunflower oil, canola oil, peanut oil, safflower oil, and the like. Examples of suitable flavorants include yeast, tallow, rendered animal meals (e.g., poultry, beef, lamb, pork), flavor extracts or blends (e.g., grilled beef), animal digests, and the like. Suitable colorants include FD&C colors, such as blue no. 1, blue no. 2, green no. 3, red no. 3, red no. 40, yellow no. 5, yellow no. 6, and the like; natural colors, such as caramel coloring, annatto, chlorophyllin, cochineal, betanin, turmeric, saffron, paprika, lycopene, elderberry juice, pandan, butterfly pea and the like; titanium dioxide; and any suitable food colorant known to the skilled artisan.

[0057] The pet food compositions disclosed herein can optionally include additional ingredients, such as other grains and/or other starches additionally or alternatively to flour, amino acids, fibers, sugars, animal oils, aromas, other oils additionally or alternatively to vegetable oil, humectants, preservatives, polyols, salts, oral care ingredients, antioxidants, vitamins, minerals, probiotic microorganisms, bioactive molecules or combinations thereof.

[0058] Suitable starches include a grain such as corn, rice, wheat, barley, oats, soy and the like, and mixtures of these grains, and can be included at least partially in any flour. Suitable humectants include salt, sugars, propylene glycol and polyhydric glycols such as glycerin and sorbitol, and the like. Suitable oral care ingredients include alfalfa nutrient concentrate containing chlorophyll, sodium bicarbonate, phosphates (e.g., tricalcium phosphate, acid pyrophosphates, tetrasodium pyrophosphate, metaphosphates, and orthophosphates), peppermint, cloves, parsley, ginger and the like. Examples of suitable antioxidants include butylated hydroxyanisole ("BHA") and butylated hydroxytoluene ("BHT"), vitamin E (tocopherols), and the like.

[0059] Non-limiting examples of vitamins that can be used include Vitamins A, B-complex (such as B-l, B-2, B-6 and B-12), C, D, E and K, niacin and acid vitamins such as pantothenic acid and folic acid and biotin. Non-limiting examples of suitable minerals include calcium, iron, zinc, magnesium, iodine, copper, phosphorus, manganese, potassium, chromium, molybdenum, selenium, nickel, tin, silicon, vanadium, boron and the like.

[0060] Non-limiting examples of suitable preservatives include potassium sorbate, sorbic acid, sodium methyl para-hydroxybenzoate, calcium propionate, propionic acid, and combinations thereof.

[0061] Specific amounts for each additional ingredient in the pet food compositions disclosed herein will depend on a variety of factors such as the ingredient included in the first edible material and any second edible material; the species of animal; the animal's age, body weight, general health, sex, and diet; the animal's consumption rate; the purpose for which the food product is administered to the animal; and the like. Therefore, the components and their amounts may vary widely.

[0062] For example, the amount of any of the above-noted ingredients can be decreased or increased based on the estimated effect on the amount of one or more of Bifidobacterium, Lactobacillus, or Clostridium perfringens (e.g., an effect identified by one of the methods disclosed herein). In an embodiment, the amount of one or more of the above-noted ingredients can be increased if such ingredients comprise a metabolite that positively modulates one or more of Bifidobacterium, Lactobacillus, or Clostridium perfringens. Additionally or alternatively, the amount of one or more of the above-noted ingredients can be decreased if such ingredients comprise a metabolite that negatively modulates one or more of Bifidobacterium, Lactobacillus, or Clostridium perfringens.

[0063] As noted above, ingredients comprising the metabolite (e.g., a precursor of the metabolite) and optionally amounts of the metabolite in the ingredient can be identified by analysis of the ingredient, for example using a separation technique, such as gas chromatography or liquid chromatography, and then mass spectrometry.

EXAMPLES

[0064] The following non-limiting examples are illustrative of embodiments of the present disclosure.

Methods

[0065] Each of the examples was derived from the following study.

[0066] 83 Canines were all fed Diet A for 5 weeks, followed by a 1 week transition period and then 15 were fed Diet B for 5 weeks as shown in the Table 1 below. Plasma samples were taken after overnight fasting using EDTA vacutainer tubes during the fifth week of feeding of each diet. After centrifugation, plasma was aliquoted into cryovials and frozen at -80 °C. Fecal samples were used to determine levels of bacteria. Levels of Bifidobacterium, Lactobacillus, or Clostridium perfringens were determined based on published 16S sequences using quantitative PCR.

Table 1

[0067] Metabolomic analysis was carried out using the following methods by Metabolon Inc. Samples were extracted and split into equal parts for analysis on GC/MS and LC/MS MS platforms. Proprietary software was used to match ions to an in-house library of standards for metabolite identification and for metabolite quantitation by peak area integration by Metabolon Inc. Mass and retention index are provided in the following tables such that each metabolite can be uniquely identified and individually distinguished.

[0068] At the time of analysis, samples were thawed and extracts prepared to remove protein, dislodge small molecules bound to protein or physically trapped in the precipitated protein matrix, and recover a wide range of chemically diverse metabolites. A separate aliquot of each experimental plasma sample was taken then pooled for the creation of "Client Matrix" (CMTRX) samples. These CMTRX samples were injected throughout the platform run and served as technical replicates, allowing variability in the quantitation of all consistently detected biochemicals to be determined and overall process variability and platform performance to be monitored. Extracts of all experimental and CMTRX samples were split for analysis on the GC MS and LC/MS/MS platforms.

[0069] The CMTRX technical replicate samples were treated independently throughout the process as if they were client study samples. All process samples (CMTRX and Grab test mixtures of organic components used to assess GC column performance, process blanks, etc.) were spaced evenly among the injections for each day and all client samples were randomly distributed throughout each day's run. Data were collected over multiple platform run days and thus 'block normalized' by calculating the median values for each run-day block for each individual compound. This normalization minimizes any inter-day instrument gain or drift, but does not interfere with intra-day sample variability. Missing values (if any) were assumed to be below the level of detection for that biochemical with the instrumentation used and were imputed with the observed minimum for that particular biochemical. [0070] A number of internal standards were added to each experimental and process standard sample just prior to injection into the mass spectrometers. A measure of the platform variability (7%) was determined by calculating the median relative standard deviation (RSD) for these internal standards. Because these standards are added to the samples immediately prior to injection into the instrument, this value reflects instrument variation. In addition, the median relative standard deviation (RSD) for the biochemicals that were consistently measured in the CMTRX represents the total variability within the process for the actual experimental samples and the variability in quantitation of the endogenous metabolites within these samples (12%). Results for the CMTRX and internal standards indicated that the platform produced data that met process specifications.

[0071] 589 total metabolites were detected in plasma. This total corresponds to many biochemicals (401) that matched a named structure in the reference library (named compounds). The remaining biochemicals (188) represent distinct chemical entities (that is, they represent a single molecule of discrete molecular formula and structure), but they do not currently match a named biochemical in the reference library (unnamed unknown compounds).

Example 1 (Clostridium perfringens)

[0072] Metabolite correlations with Clostridium perfringens were determined based on plasma metabolomics (Table 2). This provided a predictive model of compounds which can influence Clostridium perfringens either positively or negatively. Feeding different levels of these compounds (diet B vs diet A; Table 3), and noting changes in Clostridium perfringens (Table 4), served as a validation model. The metabolite compositions of the two different diets were determined to identify relative levels of specific compounds. Those validated by the model are shown in Table 5.

Table 2. Metabolite correlations with Clostridium perfrinsens. Correlations with a P value < 0.01 are reported.

ID Correlation Correlation Retention Mass

P-Value Index

beta-hydroxyisovalerate 0.5389 1.24E-07 1043 117.1

X - 18559 0.5374 1.36E-07 1864.9 254.1 dihomo-linoleate (20:2n6) 0.535 1.58E-07 5722 307.3

X - 11949 0.5201 3.97E-07 3830 220.1 arachidonate (20:4n6) 0.5143 5.61E-07 5525 303.4

X - 12672 0.5116 6.56E-07 1797 256 adrenate (22:4n6) 0.5003 1.26E-06 5684 331.3 mannose 0.4832 3.22E-06 1753.5 203.9

3-hydroxybutyrate (BHBA) 0.4818 3.48E-06 1203.5 116.9

X - 11787 -0.4742 5.19E-06 1126 148.1 trigonelline (N'-methylnicotinate) -0.4657 8.03E-06 757 138.1 cysteine-glutathione disulfide -0.4638 8.85E-06 821 427.1 eicosenoate (20: ln9 or 11) 0.4606 1.04E-05 5955 309.4

4-vinylphenol sulfate -0.4476 1.96E-05 3323 199.1 docosapentaenoate (n3 DP A; 22:5n3) 0.4442 2.31E-05 5574 329.4

2-aminobutyrate 0.434 3.73E-05 758 104.1 alpha-tocopherol 0.4248 5.65E-05 2305.4 502.5

X - 16009 0.4173 7.85E-05 2191 222 palmitoyl sphingomyelin 0.4126 9.60E-05 2524 311.3 pipecolate 0.4083 0.0001 1120 130.1 glycerate 0.4085 0.0001 1360.7 189 cysteine -0.4069 0.0001 1560.1 218

X - 11549 0.4037 0.0001 5093 339.3 linolenate [alpha or gamma; (18:3n3 or 6)] 0.4006 0.0002 5450 277.3 di omo-linolenate (20:3n3 or n6) 0.3842 0.0003 5600 305.4 betaine 0.3832 0.0003 721 118.2

X - 11378 0.3853 0.0003 5325 445.4 hydroquinone sulfate 0.3861 0.0003 1383 189

1,5-anhydroglucitol (1,5-AG) -0.375 0.0004 1788.7 217

X - 11437 -0.3784 0.0004 2888 231 glutarylcarnitine (C5) 0.3684 0.0006 1565 276.1

X - 16015 -0.3577 0.0008 3788 268.1

X - 17010 0.3544 0.0009 3169.5 189

X - 16869 -0.3563 0.0009 5179.8 330.2

2-linoleoylglycerophosphoethanolamine -0.352 0.001 5650 476.4 stearoyl sphingomyelin 0.3464 0.0012 #N/A #N/A

X - 12435 0.3471 0.0012 3174 357.2

7-alpha-hydroxycholesterol 0.3444 0.0013 2300 456.2

1-oleoylglycerophosphoethanolamine -0.3425 0.0014 5928 478.3

X - 13543 -0.3423 0.0014 1096 484.1 stearate (18:0) 0.3414 0.0015 5886 283.4 palmitate (16:0) 0.3395 0.0016 5619 255.3

X - 13866 -0.3396 0.0016 2406 253.1

X - 12339 0.3371 0.0017 1055 174.1 glycolate (hydroxyacetate) 0.3376 0.0017 1119 177

X - 18570 -0.3381 0.0017 3243.1 207 arginine 0.3292 0.0022 728 173.2 threonate 0.3228 0.0027 1560.7 292.1 stachydrine -0.3222 0.0028 860 144.1 catechol sulfate -0.3191 0.0031 1928 188.9

X - 12450 0.3179 0.0032 5397 251.4

2-ethylhexanoate 0.3146 0.0036 1210.5 201.2

X - 09789 -0.3143 0.0036 2613 153.1

X - 18558 0.3128 0.0038 1676.8 380.1 campesterol -0.3088 0.0043 2353 343.4 pantothenate 0.3055 0.0047 2218 220.1 linoleate (18:2n6) 0.2992 0.0057 5533 279.3 docosapentaenoate (n6 DPA; 22:5n6) 0.2979 0.0059 5625 329.4

2-oleoylglycerophosphoethanolamine -0.2973 0.006 5848 478.3

X - 11412 0.2975 0.006 3836 204.2

X - 16120 0.2968 0.0061 1271.7 164.1

X - 17185 -0.2937 0.0067 3069.1 215.2

X - 17502 -0.2886 0.0078 5093.4 297.3

1-palmitoylglycerophosphoinositol 0.288 0.0079 #N/A #N/A

X - 18487 -0.2877 0.008 1269.6 273.1 phenylalanine -0.2869 0.0081 2056 166.1

1-linoleoylglycerophosphoethanolamine -0.2829 0.0091 5725 476.3

X - 11843 -0.2817 0.0094 2710 230.1

2-hydroxybutyrate (AHB) 0.28 0.0099 1169.4 130.9

Table 3. Compound levels present in diets A and B. Values represent scaled imputed values (data are scaled such that the median value measured across all samples was set to 1.0 and missing values ( ^" if any ^" ) were imputed with the observed minimum for that particular compound).

ID A B beta-hydroxyisovalerate 0.48 0.48

X - 18559 0.78 0.78 dihomo-linoleate (20:2n6) 0.33 4.06 X - 11949 0.28 0.28 arachidonate (20:4n6) 0.43 4.48

X - 12672 0.72 0.72 adrenate (22:4n6) 0.82 5.31 mannose 0.21 1.45

3-hydroxybutyrate (BHBA) 0.18 0.34

X - 11787 0.04 0.06 trigonelline (N'-methylnicotinate) 12.47 1.65 cysteine-glutathione disulfide 0.04 0.04 eicosenoate (20:ln9 or 11) 0.32 2.11

4-vinylphenol sulfate 0.02 0.02 docosapentaenoate (n3 DPA; 22:5n3) 0.14 4.84

2-aminobutyrate 1.58 0.83 alpha-tocopherol 0.01 0.03

X - 16009 0.2 0.2 palmitoyl sphingomyelin 0.03 0.2 pipecolate 7.41 1.56 glycerate 3.38 9.94 cysteine 0.21 0.24

X - 11549 0.13 0.13 linolenate [alpha or gamma; (18:3n3 or 6)] 0.83 1.66 dihomo-linolenate (20:3n3 or n6) 0.42 5.03 betaine 0.61 0.69

X - 11378 0.05 0.11 hydroquinone sulfate 0.03 0.03

1,5-anhydroglucitol (1,5-AG) 0.28 0.28

X - 11437 0.05 0.05 glutarylcarnitine (C5) 0.27 0.27

X - 16015 0.02 0.02

X - 17010 0.68 2.51

X - 16869 0.29 0.29

2-linoleoylglycerophosphoethanolamine 0.56 2.58 stearoyl sphingomyelin #N/A #N/A

X - 12435 0.36 0.36 7-alpha-hydroxycholesterol 0.74 4.91

1-oleoylglycerophosphoethanolamine 0.16 5.65

X - 13543 0.1 0.1 stearate (18:0) 0.33 1.26 palmitate (16:0) 0.4 0.88

X - 13866 0.26 0.26

X - 12339 0.96 0.5 glycolate (hydroxyacetate) 0.89 0.94

X - 18570 0.08 0.08 arginine 1 0.63 threonate 0.61 0.22 stachydrine 3.62 0.78 catechol sulfate 0.02 0.02

X - 12450 0.17 1.43

2-ethylhexanoate 0.06 0.02

X - 09789 5.54 0.2

X - 18558 0.55 0.47 campesterol 1.56 0.72 pantothenate 12.83 19.07 linoleate (18:2n6) 0.8 0.92 docosapentaenoate (n6 DPA; 22:5n6) 0.61 4.77

2-oleoylglycerophosphoethanolamine 0.43 6.03

X - 11412 0.13 0.21

X - 16120 0.45 0.45

X - 17185 0.12 0.06

X - 17502 0.42 1.15

1-palmitoylglycerophosphoinositol #N/A #N/A

X - 18487 0.26 0.26 phenylalanine 0.75 0.64

1-linoleoylglycerophosphoethanolamine 0.48 2.77

X - 11843 0.19 0.19

2-hydroxybutyrate (AHB) 0.28 0.1

Table 4. Clostridium perfrinsens in response to diet A and Diet B. Diet A Diet B Difference

Parameter Mean StdDev Mean StdDev Mean StdErr p- value

Clostridium 5.6 1.1 8.2 0.4 -2.6528 0.2948 0 perfringens

Table 5. Compounds validated by dietary change.

ID RI Mass dihomo-linoleate (20:2n6) 5722 307.3 arachidonate (20:4n6) 5525 303.4 adrenate (22:4n6) 5684 331.3

Mannose 1753.5 203.9

3-hydroxybutyrate (BHBA) 1203.5 116.9 trigonelline (N'-methylnicotinate) 757 138.1 eicosenoate (20:ln9 or 11) 5955 309.4 docosapentaenoate (n3 DPA; 22:5n3) 5574 329.4 palmitoyl sphingomyelin 2524 311.3

Glycerate 1360.7 189 linolenate [alpha or gamma; (18:3n3 or 6)] 5450 277.3 dihomo-linolenate (20:3n3 or n6) 5600 305.4

X - 11378 5325 445.4

X - 17010 3169.5 189

7-alpha-hydroxycholesterol 2300 456.2 stearate (18:0) 5886 283.4 palmitate (16:0) 5619 255.3 glycolate (hydroxyacetate) 1119 177 stachydrine 860 144.1

X - 12450 5397 251.4

X - 09789 2613 153.1 campesterol 2353 343.4 pantothenate 2218 220.1 linoleate (18:2n6) 5533 279.3 docosapentaenoate (n6 DPA; 22:5n6) 5625 329.4

X - 11412 3836 204.2 X - 17185 3069.1 215.2 phenylalanine 2056 166.1

Example 2 (Lactobacillus)

[0073] Metabolite correlations with Lactobacillus were determined based on plasma metabolomics (Table 6). This provided a predictive model of compounds which can influence Lactobacillus either positively or negatively. Feeding different levels of these compounds (diet B vs diet A; Table 7), and noting changes in Lactobacillus (Table 8), served as a validation model. The metabolite compositions of the two different diets were determined to identify relative levels of specific compounds. Those compounds validated by the model are shown in Table 9.

Table 6. Metabolite correlations with Lactobacillus. Correlations with a P value < 0.01 are reported.

ID Correlation Correlation Retention Mass

P-Value Index

X - 15461 0.5878 4.15E-09 2125 160.1 equol sulfate 0.5318 1.93E-07 3625 321.2

X - 12156 0.5251 2.92E-07 3238 233.1 indolepropionate 0.5218 3.59E-07 1925 202.1

3-phenylpropionate (hydrocinnamate) 0.4995 1.32E-06 2830 149.1

X - 11334 0.4939 1.80E-06 982 259.1

3-(4-hydroxyphenyl)propionate 0.4715 6.00E-06 1727.9 179.1 mannitol 0.4548 1.38E-05 1839 319.1 campesterol 0.4416 2.62E-05 2353 343.4 indoleacrylate 0.433 3.89E-05 2529 186.1 indoleacetate 0.4304 4.38E-05 3760 176.1 indoleacetylglutamine 0.4286 4.76E-05 2530 302.2

1-arachidonoylglycerophosphoethanolamine 0.4205 6.81E-05 5731 500.3

X - 12212 0.4198 7.03E-05 3607 229.1

X - 12236 0.4166 8.09E-05 1321 245.1

X - 17443 0.4068 0.0001 3102.3 271.2

1-oleoylglycerophosphoethanolamine 0.3838 0.0003 5928 478.3 catechol sulfate 0.3844 0.0003 1928 188.9

3-dehydrocarnitine 0.3706 0.0005 1020 160.2

X - 15636 0.3581 0.0008 3814 243.1 2-arachidonoylglycerophosphoethanolamine 0.3526 0.001 5674 500.3

X - 15728 0.352 0.001 3972 231.1

2-oleoylglycerophosphoethanolamine 0.3502 0.0011 5848 478.3 taurolithocholate 0.3485 0.0012 5328 482.4

3-(3-hydroxyphenyl)propionate 0.3471 0.0012 2000 165.1

1-linoleoylglycerophosphoethanolamine 0.3434 0.0014 5725 476.3

4-acetylphenol sulfate 0.3421 0.0014 2399 215

1 -palmitoylplasmenylethanolamine 0.3424 0.0014 6153 436.4

N4-acetylcytidine 0.3336 0.0019 2030 286.1

1-heptadecanoylglycerophosphoethanolamine 0.3315 0.0021 6029 466.3 succinylcarnitine 0.3286 0.0023 1401 262.1

X - 11378 -0.3281 0.0023 5325 445.4 octadecanedioate 0.3133 0.0037 5033 313.3

N-acetylornithine 0.3092 0.0042 875 175.2

X - 16015 0.3089 0.0043 3788 268.1

X - 12010 0.3065 0.0046 1707 203.1

N-acetyltryptophan -0.305 0.0048 2650 245.2 kynurenine 0.2977 0.006 1902 209.1

N-acetyltyrosine -0.2967 0.0061 1677 222.2 adenosine 5'-monophosphate (AMP) 0.2927 0.0069 #N/A #N/A

X - 11987 -0.2894 0.0076 1409 139.2

X - 16480 0.2872 0.0081 4685.5 309.3 benzoate 0.285 0.0086 1291.5 179

Table 7. Compound levels present in diets A and B. Values represent scaled imputed values fdata are scaled such that the median value measured across all samples was set to 1.0 and missing values ( ^" if any) were imputed with the observed minimum for that particular compound ^" ).

ID A B

X - 15461 0.97 0.35

equol sulfate 0.08 0.08

X - 12156 0.19 0.19

indolepropionate 0.07 0.07

3 -phenylpropionate (hydrocinnamate) 18.68 0.13 X - 11334 0.19 0.19

3-(4-hydroxyphenyl)propionate 14.94 0.38 mannitol 12.51 1.72 campesterol 1.56 0.72 indoleacrylate 0.06 0.06 indoleacetate 1.78 0.46 indoleacetylglutamine 0.52 0.52

1-arachidonoylglycerophosphoethanolamine 0.14 4.6

X - 12212 0.21 0.21

X - 12236 0.1 0.1

X - 17443 0.21 0.21

1-oleoylglycerophosphoethanolamine 0.16 5.65 catechol sulfate 0.02 0.02

3-dehydrocarnitine 0.54 0.34

X - 15636 0.2 0.2

2-arachidonoylglycerophosphoethanolamine 0.33 10.33

X - 15728 0.32 0.32

2-oleoylglycerophosphoethanolamine 0.43 6.03 taurolithocholate 0.45 2.42

3 -(3-hydroxyphenyl)propionate 0.1 0.1

1-linoleoylglycerophosphoethanolamine 0.48 2.77

4-acetylphenol sulfate 0.4 0.56

1 -palmitoylplasmenylethanolamine 0.21 3.23

N4-acetylcytidine 0.53 0.53

1-heptadecanoylglycerophosphoethanolamine 0.18 2.28 · succinylcarnitine 0.32 0.32

X - 11378 0.05 0.11 octadecanedioate 0.06 0.07

N-acet lornithine 0.41 0.21

X - 16015 0.02 0.02

X - 12010 0.5 0.5

N-acetyltryptophan 1 0.24 kynurenine 0.05 0.04

N-acetyltyrosine 0.82 0.32 adenosine 5 '-monophosphate (AMP) #N/A #N/A

X - 11987 0.14 0.14

X - 16480 0.06 0.06 benzoate 0.03 0.03

Table 8. Lactobacillus in response to diet A and Diet B.

Table 9. Compounds validated by dietary change.

Example 3 (Bifidobacteriuni)

[0074] Metabolite correlations with Bifidobacterium were determined based on plasma metabolomics (Table 10). This provided a predictive model of compounds which can influence Bifidobacterium either positively or negatively. Feeding different levels of these compounds (diet B vs diet A; Table 11), and noting changes in Bifidobacterium (Table 12), served as a validation model. The metabolite compositions of the two different diets were determined in order to identify relative levels of specific compounds. Those compounds validated by the model are shown in Table 13.

Table 10. Metabolite correlations with Bifidobacterium. Correlations with a P value < 0.01 are reported.

ID Correlation Correlation Retention Mass

P-Value Index indoleacrylate 0.5948 2.43E-09 2529 186.1 equol sulfate 0.5634 2.41E-08 3625 321.2

X - 12212 0.5426 9.74E-08 3607 229.1 indolepropionate 0.5355 1.54E-07 1925 202.1

X - 15636 0.5102 7.14E-07 3814 243.1

X - 15728 0.4442 2.31E-05 3972 231.1

X - 11541 0.4292 4.62E-05 4984 399

X - 16015 0.4259 5.37E-05 3788 268.1 campesterol 0.4223 6.30E-05 2353 343.4

X - 12236 0.4159 8.35E-05 1321 245.1

1-linoleoylglycerophosphoethanolamine 0.3896 0.0002 5725 476.3

2-oleoylglycerophosphoethanolamine 0.3987 0.0002 5848 478.3 catechol sulfate 0.3949 0.0002 1928 188.9

4-acetylphenol sulfate 0.385 0.0003 2399 215 ornithine 0.3772 0.0004 1763.8 141.9

7-ketodeoxycholate 0.3774 0.0004 4840 405.4

10-heptadecenoate (17:ln7) 0.3752 0.0004 5558 267.3 pentadecanoate (15:0) 0.3728 0.0005 1853.5 299.2 carnosine 0.3625 0.0007 813 225.2

3-(4-hydroxyphenyl)propionate 0.3591 0.0008 1727.9 179.1 benzoate 0.3525 0.001 1291.5 179

3-dehydrocarnitine 0.3491 0.0011 1020 160.2

12-dehydrocholate 0.3411 0.0015 4866 405.4

X - 17612 0.3402 0.0015 4298.5 567.4

3 -(3 -hydroxyphenyl)propionate 0.3278 0.0023 2000 165.1 cis-vaccenate (18:ln7) 0.3262 0.0025 1987 339.3

X - 18570 0.3258 0.0025 3243.1 207

X - 17314 0.3244 0.0026 2595 266.2

X - 11843 0.3248 0.0026 2710 230.1 hydroquinone sulfate -0.3247 0.0026 1383 189

X - 15461 0.3135 0.0037 2125 160.1

2-arachidonoylglycerophosphoethanolamine 0.312 0.0039 5674 500.3

X - 11852 0.3043 0.0049 3324 233.1 chenodeoxycholate 0.3025 0.0052 5250 391.4 myristoleate (14:ln5) 0.301 0.0054 5338 225.3 3 -dehydrocholate 0.2938 0.0067 5050 405.4 cholate 0.2933 0.0068 5148 407.4

X - 11909 0.2925 0.0069 5272 297.3

X - 12668 0.2912 0.0072 2318 246.1 myristate (14:0) 0.291 0.0073 5439 227.3 deoxycholate 0.2882 0.0079 5268 391.4 oleate (18:ln9) 0.2867 0.0082 1984.4 339.2

15-methylpalmitate (isobar with 2-methylpalmitate) 0.283 0.0091 5698 269.4 phenylalanyltryptophan 0.2818 0.0094 3349 352.2

N-acetyltyrosine -0.2813 0.0095 1677 222.2

Table 11. Compound levels present in diets A and B. Values represent scaled imputed values fdata are scaled such that the median value measured across all samples was set to 1.0 and missing values (if any) were imputed with the observed minimum for that particular compound).

ID A B indoleacrylate 0.06 0.06 equol sulfate 0.08 0.08

X - 12212 0.21 0.21 indolepropionate 0.07 0.07 .

X - 15636 0.2 0.2

X - 15728 0.32 0.32

X - 11541 0.36 0.36

X - 16015 0.02 0.02 campesterol 1.56 0.72

X - 12236 0.1 0.1

1-linoleoylglycerophosphoethanolamine 0.48 2.77

2-oleoylglycerophosphoethanolamine 0.43 6.03 catechol sulfate 0.02 0.02

4-acetylphenol sulfate 0.4 0.56 ornithine 4.31 15.34

7-ketodeoxycholate 2.65 0.38

10-heptadecenoate (17:ln7) 0.09 0.33 pentadecanoate (15:0) 0.34 0.7 carnosine 0.38 1.28

3 -(4-hydroxyphenyl)propionate 14.94 0.38 benzoate 0.03 0.03

3-dehydrocarnitine 0.54 0.34

12-dehydrocholate 0.22 0.17

X - 17612 0.21 0.3

3-(3-hydroxyphenyl)propionate 0.1 0.1 cis-vaccenate (18:ln7) 0.32 0.73

X - 18570 0.08 0.08

X - 17314 0.42 0.13

X - 11843 0.19 0.19 hydroquinone sulfate 0.03 0.03

X - 15461 0.97 0.35

2-arachidonoylglycerophosphoethanolamine 0.33 10.33

X - 11852 0.1 0.1 chenodeoxycholate 7.78 0.79 myristoleate (14: ln5) 0.12 0.41

3-dehydrocholate 0.8 0.39 cholate 25.83 0.83

X - 11909 0.16 0.2

X - 12668 0.13 0.13 myristate (14:0) 0.15 0.4 deoxycholate 0.19 0.19 oleate (18: ln9) 0.34 1

15-methylpalmitate (isobar with 2-methylpalmitate) 0.37 0.19 phenylalanyltryptophan 0.29 0.29

N-acetyltyrosine 0.82 0.32

Table 12. Bifidobacterium in response to diet A and Diet B.

Table 13. Compounds validated by dietary change. ID Retention Mass

Index

campesterol 2529 186.1

7-ketodeoxycholate 3625 321.2

3 -(4-hydroxyphenyl)propionate 3607 229.1

3-dehydrocarnitine 1925 202.1

12-dehydrocholate 3814 243.1

X - 17314 3972 231.1

X - 15461 4984 399 chenodeoxycholate 3788 268.1

3-dehydrocholate 2353 343.4 cholate 1321 245.1

15-methylpalmitate (isobar with 2-methylpalmitate) 5725 476.3

[0075] It should be understood that various changes and modifications to the presently preferred embodiments described herein will be apparent to those skilled in the art. Such changes and modifications can be made without departing from the spirit and scope of the present subject matter and without diminishing its intended advantages. It is therefore intended that such changes and modifications be covered by the appended claims.