AU2011201420A1 - Beta-1,3(4)-endoglucanohydrolase, beta-1,3(4) glucan, diatomaceous earth, mineral clay and glucomannan to modulate gastrointestinal genes - Google Patents

Abstract

5 Disclosed herein are methods of modulating gastrointestinal gene expression. In one example, the disclosed method includes administering a composition comprising 0 1,3 (4)-endoglucanohydrolase, 3-1,3 (4)glucan, diatomaceous earth, mineral clay, and glucomannan under conditions sufficient to modulate one or more gastrointestinal genes in a human or animal species. The compositions can be fed to any mammalian or avian 10 species including, but not limited to, bovine, equine, ovine, caprine and avian species. When admixed with the feed or food or fed as a supplement, the composition can be used to regulate (e.g., up-regulate or down-regulate) one or more gastrointestinal genes, such as to induce or enhance energy metabolism genes, nutrient transport genes, or a combination thereof. The disclosed methods can also be used to regulate, such as 15 enhance or induce Type I and/or Type II antigen presentation and in turn inducement or enhancement of an immune response. 2619290_1 (GHMatters)

Description

AUSTRALIA Patents Act 1990 COMPLETE SPECIFICATION Standard Patent Applicant(s): OmniGen Research LLC Invention Title: BETA-1, 3(4) -ENDOGLUCANOHYDROLASE, BETA-1, 3(4) GLUCAN, DIATOMACEOUS EARTH, MINERAL CLAY AND GLUCOMANNAN TO MODULATE GASTROINTESTINAL GENES The following statement is a full description of this invention, including the best method for performing it known to us: BETA-1, 3(4)-ENDOGLUCANOHYDROLASE, BETA-1,3(4) GLUCAN, DIATOMACEOUS EARTH, MINERAL CLAY AND GLUCOMANNAN TO MODULATE GASTROINTESTINAL GENES 5 FIELD This disclosure relates to methods and compositions for modulating gastrointestinal gene expression, including genes related to gastrointestinal immune response, nutrient transport and energy metabolism. 10 BACKGROUND The gastrointestinal tract fulfills numerous functions in an intact, healthy organism. Some of the most essential functions provided by the gastrointestinal tract include nutrient digestion and transport, barrier function and the ability to nourish the organism in times of nutrient (energy or protein) deficiency. For the gastrointestinal 15 tract to provide adequately for all of these functions, proper nutrition is fundamental. "Gastrointestional health" is maintained primarily through proper nutrition and hygiene. Recent studies have shown that nutrition has significant potential to improve gastrointestinal health. Thus, a need exists to develop methods to improve gastrointestinal health in efforts to consequently improve gastrointestinal function, 20 quality of life and longevity. It is to be understood that, if any prior art publication is referred to herein, such reference does not constitute an admission that the publication forms a part of the common general knowledge in the art, in Australia or any other country. 25 SUMMARY OF THE DISCLOSURE Disclosed herein are methods of improving gastrointestinal health in mammalian and avian species. The disclosed methods can be used to regulate gastrointestinal gene -2 2619290_ I (GHMatters) expression which can be used to alter gastrointestinal function, including the ability to regulate gastrointestinal transport function, immune function and degradative function. In particular, methods are disclosed for modulating the activity of one or more gastrointestinal genes, such as those provided in FIGS. 1 and/or 2. In some examples, 5 modulating includes up-regulating or down-regulating one or more gastrointestinal genes, including up-regulating one or more genes shown in FIG. 1 or down-regulating one or more genes shown in FIG. 2. In some embodiments, the method includes administering a composition comprising 0-1,3 (4)-endoglucanohydrolase, O-glucan (such as 0- 1,3 (4)glucan), diatomaceous earth, mineral clay, and glucomannan to 10 regulate the one or more gastrointestinal genes in a subject, such as to enhance or induce energy metabolism and/or nutrient transport (such as those provided in Tables 4 and 5). The compositions can be fed to any mammalian or avian species including, but not limited to, bovine, equine, ovine, caprine and avian species. For example, when admixed with the feed or food or fed as a supplement, the composition can be used to 15 regulate (e.g., up regulate or down regulate) one or more gastrointestinal genes. A composition as described can be administered as an additive to feeds or foods or administered directly to the animal or human (e.g., as a supplement). In some embodiments, the disclosed methods are used to improve animal performance (such as increased growth rate and/or increased milk production). In some embodiments, the 20 disclosed methods are used to reduce or inhibit one or more signs or symptoms of a disease, such as an infectious disease (e.g., a bacterial infection). In a first aspect, the present invention provides, a method of modulating expression of one or more gastrointestinal genes in a subject, comprising: administering to the subject a composition comprising 0-glucans, 0-1,3(4)-endoglucanohydrolase, 25 diatomaceous earth, a mineral clay, and glucomannan under conditions sufficient to modulate expression levels of one or more gastrointestinal genes listed in FIGS. 1 and/or 2 as compared to expression levels of the one or more gastrointestinal genes in the absence of the composition, wherein detection of differential expression of one or -3 2619290_1 (GHMatters) more gastrointestinal genes listed in FIGS. 1 and/or 2 indicates modulation of gastrointestinal gene expression. In a second aspect, the present invention provides use of a composition comprising -glucans, 0-1 ,3(4)-endoglucanohydrolase, diatomaceous earth, a mineral 5 clay, and glucomannan for the manufacture of a medicine for the modulation of expression of one or more gastrointestinal genes in a subject comprises administering to the subject a composition comprising -glucans, 0-1,3(4)-endoglucanohydrolase, diatomaceous earth, a mineral clay, and glucomannan under conditions sufficient to modulate expression levels of one or more gastrointestinal genes listed in FIGS. 1 10 and/or 2 as compared to expression levels of the one or more gastrointestinal genes in the absence of the composition, wherein detection of differential expression of one or more gastrointestinal genes listed in FIGS. I and/or 2 indicates modulation of gastrointestinal gene expression. In one example, differential expression of one or more gastrointestinal genes 15 comprises up-regulation of one or more gastrointestinal genes in FIG. 1 and/or down regulation of one or more gastrointestinal genes in FIG. 2. In some examples, the subject is a ruminant animal. In some examples, the mineral clay comprises montmorillonite, bentonite, aluminosilicate, zeolite clays, or a combination thereof. 20 In some embodiments, the method or use includes a composition comprising between about 15% and 40% diatomaceous earth, between about 50% and 80% mineral clay, between about 1.0% and 5.0% 0-glucans, between about 0.05% and 3.0% 0 1,3(4)-endoglucanohydrolase, and between about 1.0% and 8.0% glucomannan. In some embodiments, the method or use includes a composition comprising between 25 about 20% and 30% diatomaceous earth, between about 60% and 75% mineral clay, between about 1.0% and 3.5% 0-glucans, between about 0.1% and 3.0% 0-1,3(4) endoglucanohydrolase, and between about 1.0% and 6.0% glucomannan. In some examples, the method or use further comprises admixing the -4 2619290_1 (GHMatters) composition into foods or animal feedstuffs in a concentration of between about 0.0125% and 5% by weight. In some examples, the method or use further comprises feeding the food and composition combination to one of the group consisting of domestic livestock, ruminant 5 livestock, and avian livestock. In some examples, the method or use further comprises formulating the composition comprising -glucans, 0-1,3(4)-endoglucanohydrolase, diatomaceous earth, a mineral clay, and glucomannan prior to administering the composition. In some examples, the one or more gastrointestinal genes up-regulated comprise 10 one or more genes listed in Tables 4-6. In some examples, the one or more gastrointestinal genes regulated comprise TAP 1, TAP2, HSP70, KIR, MHCI protein, cathepsin B, cathepsin L, cathepsin S, asparaginyl endopeptidase or a combination thereof. In some examples, TAP 1, TAP2 and/or cathepsin L are down-regulated and HSP70, KIR, MHCI protein, cathepsin B, 15 and/or cathepsin S are up-regulated. Disclosed herein are methods of modulating (such as inducing or enhancing) energy metabolism and/or nutrient transport by modulating expression of one or more gastrointestinal genes associated with such processes in a subject, such as by administering to the subject a composition comprising -glucans, 0-1,3(4) 20 endoglucanohydrolase, diatomaceous earth, a mineral clay, and glucomannan under conditions sufficient to modulate expression levels of one or more energy metabolism and/or nutrient transport gastrointestinal genes listed in FIGS. 1 and/or 2 as compared to expression levels of the one or more gastrointestinal genes in the absence of the composition, thereby modulating energy metabolism and/or nutrient transport. In some 25 examples, the one or more gastrointestinal genes up-regulated and associated with nutrient and/or neurotransmitter transport are one or more genes listed in at least Table 4. In some examples, the one or more gastrointestinal genes up-regulated and -5 2619290_I (GHMatters) associated with energy metabolism (such as protein degradation, including one or more genes encoding one or more proteases) are one or more genes listed in at least Table 5. Also disclosed herein is a method of modulating gastrointestinal barrier function by modulating expression of one or more gastrointestinal genes in a subject, such as by 5 administering to the subject a composition comprising -glucans, -1,3(4) endoglucanohydrolase, diatomaceous earth, a mineral clay, and glucomannan under conditions sufficient to modulate expression levels of one or more gastrointestinal genes listed in FIGS. 1 and/or 2 associated with gastrointestinal barrier function as compared to expression levels of the one or more gastrointestinal genes in the absence of the 10 composition, thereby modulating (such as inducing or enhancing gastrointestinal barrier function). Also disclosed herein is a method of enhancing Type I and/or Type II antigen presentation by modulating expression of one or more gastrointestinal genes in a subject, such as by administering to the subject a composition comprising -glucans, 0 15 1,3(4)-endoglucanohydrolase, diatomaceous earth, a mineral clay, and glucomannan under conditions sufficient to modulate expression levels of one or more gastrointestinal genes listed in FIGS. 1 and/or 2 as compared to expression levels of the one or more gastrointestinal genes in the absence of the composition, thereby enhancing Type I and/or Type II antigen presentation. 20 Also provided are methods of inducing an immune response, such as an adaptive immune response, by modulating activity, such as expression, of one or more gastrointestinal genes in a subject. In some examples, methods of increasing barrier function capability of the gastrointestinal tract are provided. In some examples, the one or more gastrointestinal genes up-regulated and associated with immune function are 25 one or more genes listed in Table 6. The foregoing and features of the disclosure will become more apparent from the following detailed description, which proceeds with reference to the accompanying figures. -6 2619290_1 (GHMatters) BRIEF DESCRIPTION OF THE DRAWINGS FIG. 1 is a table listing the gastrointestinal genes which were up-regulated in rat TM jejunum following feeding of OnniGen-AF 5 FIG. 2 is a table listing the gastrointestinal genes which were down-regulated in rat jejunum following feeding of OmniGen-AF M DETAILED DESCRIPTION I. Terms 10 The following explanations of terms and methods are provided to better describe the present disclosure and to guide those of ordinary skill in the art in the practice of the present disclosure. As used herein and in the appended claims, the singular forms "a" or "an" or "the" include plural references unless the context clearly dictates otherwise. For example, reference to "a gastrointestinal gene" includes a plurality of such genes. 15 The term "or" refers to a single element of stated alternative elements or a combination of two or more elements, unless the context clearly indicates otherwise. As used herein, "comprises" means "includes." Thus, "comprising A or B," means "including A, B, or A and B," without excluding additional elements. Unless explained otherwise, all technical and scientific terms used herein have 20 the same meaning as commonly understood to one of ordinary skill in the art to which this disclosure belongs. All publications, patents and patent applications cited herein, whether supra or infra, are hereby incorporated by reference in their entirety. However, publications mentioned herein are cited for the purpose of describing and disclosing the protocols, 25 reagents and vectors which are reported in the publications and which might be used in connection with the invention. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention. -7 2619290_1 (GiMatters) Adjuvant: A vehicle used to enhance antigenicity; such as a suspension of minerals (alum, aluminum hydroxide, aluminum phosphate) on which antigen is adsorbed; or water-in-oil emulsion in which antigen solution is emulsified in oil (MF 59, Freund's incomplete adjuvant), sometimes with the inclusion of killed mycobacteria 5 (Freund's complete adjuvant) to further enhance antigenicity (inhibits degradation of antigen and/or causes influx of macrophages). Adjuvants also include immunostimulatory molecules, such as cytokines, costimulatory molecules, and for example, immunostimulatory DNA or RNA molecules, such as CpG oligonucleotides. Administration: To provide or give a subject a composition that modulates one 10 or more of the gastrointestinal genes (such as those listed in FIGS. 1 and 2) by any effective route. Exemplary routes of administration include, but are not limited to, oral (such as admixed with animal feed), injection (such as subcutaneous, intramuscular, intradermal, intraperitoneal, intravenous, and intratumoral), sublingual, rectal, transdermal, intranasal, vaginal and inhalation routes. 15 Antigen: A compound, composition, or substance that can stimulate the production of antibodies or a B-cell or T-cell response in an animal, including compositions that are injected or absorbed into an animal. Examples include, but are not limited to, peptides, lipids, polysaccharides, and nucleic acids containing antigenic determinants, such as those recognized by an immune cell. In some examples, antigens 20 include peptides derived from a pathogen of interest. Exemplary pathogens include bacteria, fungi, viruses and parasites. An antigen reacts with the products of specific humoral or cellular immunity, including those induced by heterologous immunogens. The term is used interchangeably with the term "immunogen." The term "antigen" includes all related antigenic epitopes. 25 Antigen presentation is a process in the body's immune system by which macrophages, dendritic cells and other cell types capture antigens and then enable their recognition by B-cells and/or T-cells. The basis of adaptive immunity lies in the -8 2619290_1 (GHMatters) capacity of immune cells to distinguish between the body's own cells, and infectious pathogens. Intracellular antigens (Type I antigens) are mainly produced by viruses replicating within a host cell, though antigens here can also derive from cytoplasmic 5 bacteria or the host cell's own proteins. The host cell digests cytoplasmic proteins by a specialized enzyme complex, the proteasome into small peptides. The TAP complex moves the peptide into the endoplasmic reticulum, allowing the antigenic peptide to be coupled to a major histocompatibility complex (MHC) Class I molecule and transported to the cell surface. MHC Class I molecules present antigen to CD8+ cytotoxic T cells. 10 Cytotoxic T cells (also known as TC, killer T cell, or cytotoxic T-lymphocyte (CTL)) are a population of T cells which are specialized for inducing the death of other cells. Recognition of antigenic peptides through Class I by CTLs leads to the killing of the target cell, which is infected by virus, intracytoplasmic bacterium, or are otherwise damaged or dysfunctional. 15 Extracellular antigens (Type II antigens) are usually displayed on MHC Class II molecules, including dendritic cells, activated macrophages, B cells, and several other host cell types in inflammatory conditions. Dendritic cells (DCs) phagocytose exogenous pathogens, such as bacteria, parasites or toxins in the tissues and then migrate, via chemotactic signals, to T cell enriched lymph nodes. During migration, 20 DCs undergo a process of maturation in which they lose phagocytic capacity and develop an increased ability to communicate with B-cells and/or T-cells in the lymph nodes. This maturation process is dependent on signaling from other pathogen associated molecular pattern (PAMP) molecules through pattern recognition receptors, such as the members of the Toll-like receptor family. 25 The DC uses lysosome-associated enzymes to digest pathogen-associated proteins into smaller peptides. In the lymph node, the DC will display these antigenic peptides on its surface by coupling them to MHC Class II molecules. This MHC:antigen complex is then recognized by T cells passing through the lymph node. -9 2619290_1 (GHMatters) Type II antigen presentation plays a role in establishing and maximizing the capabilities of the adaptive immune response. In some embodiments of the disclosed method, administration of a composition comprising 0-1,3 (4)-endoglucanohydrolase, 0-1,3 (4)glucan, diatomaceous earth, 5 mineral clay, and glucomannan induces or enhances Type I or Type II antigen presentation, thereby enhancing an immune response. Antigen peptide transporters 1 and 2 (TAP1 and TAP2): TAPI (also known as ABCB2, PSF1, RING4 or Y3) and TAP2 (also known as ABCB3, PSF2, RING11, Y I) are two proteins which form the Transporter-associated with antigen processing 10 (TAP) transporter. TAP 1 and TAP2 assemble into a heterodimer to form the four domain transporter. TAP is involved in the transport of antigens from the cytoplasm to the endoplasmic reticulum for association with MHC class I molecules. TAP also acts as a molecular scaffold for the final stage of MHC class I folding, namely the binding of peptide. TAPI and TAP2 have been shown to be involved in adaptive immunity. 15 The term TAP 1 includes any TAP 1 gene, cDNA, mRNA, or protein from any organism. The term TAP2 includes any TAP2 gene, cDNA, mRNA, or protein from any organism. In one example, TAP 1 and/or TAP2 expression levels are decreased in the gastrointestinal tract following treatment, such as consumption of an admixture, including 0-1,3 (4)-endoglucanohydrolase, O-glucan (such as 0-1,3 (4)glucan), 20 diatomaceous earth, mineral clay, and glucomannan. Exemplary nucleic acid and protein sequences for TAPI and TAP2 are publicly available (see, for example, GenBank Accession Nos.: NM_000593 and NM_000544). In one example, TAPI includes a full-length wild-type (or native) sequence, as well as TAP1 allelic variants, fragments, homologs or fusion sequences that retain the 25 ability to be regulated by a disclosed composition. In certain examples, TAPI has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to a known TAP I and retains TAPI activity (e.g., the capability to be regulated, such as down-regulated, by 0-1,3 (4)-endoglucanohydrolase, 0-1,3 (4)glucan, - 10 2619290_1 (GHiMatters) diatomaceous earth, mineral clay, and glucomannan and modulate an immune response). In one example, TAP2 includes a full-length wild-type (or native) sequence, as well as TAP2 allelic variants, fragments, homologs or fusion sequences that retain the 5 ability to be regulated by a disclosed composition. In certain examples, TAP2 has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to a known TAP2 and retains TAP2 activity (e.g., the capability to be regulated, such as down-regulated, by 0- 1,3 (4)-endoglucanohydrolase, -glucan (such as 0- 1,3 (4)glucan), diatomaceous earth, mineral clay, and glucomannan and modulate an 10 immune response). Asparaginyl endopeptidase (AEP): A lysosomal cysteine protease that cleaves protein substrates on the C-terminal side of asparagine. AEP plays a role in the endosome/lysosomal degradation system and is implicated in antigen processing. AEP is also known as legumain. This gene encodes a cysteine protease that has a strict 15 specificity for hydrolysis of asparaginyl bonds. This enzyme may be involved in the processing of bacterial peptides and endogenous proteins for MHC class II presentation in the lysosomal/endosomal systems. Enzyme activation is triggered by acidic pH and appears to be autocatalytic. Protein expression occurs after monocytes differentiate into dendritic cells. A fully mature, active enzyme is produced following lipopolysaccharide 20 expression in mature dendritic cells. The term AEP includes any AEP gene, cDNA, mRNA, or protein from any organism. In one example, AEP expression is increased in the gastrointestinal tract following treatment, such as consumption of an admixture, including 0-1,3 (4) endoglucanohydrolase, 0-1,3 (4)glucan, diatomaceous earth, mineral clay, and 25 glucomannan. Exemplary nucleic acid and protein sequences for AEP are publicly available (see, for example, GenBank Accession Nos.: NM_001008530, NM_0 11175, NP_001008530 and NP_035305). - 11 2619290_I (GHMatters) In one example, AEP includes a full-length wild-type (or native) sequence, as well as AEP allelic variants, fragments, homologs or fusion sequences that retain the ability to be modulated by a disclosed composition. In certain examples, AEP has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence 5 identity to a known AEP and retains AEP activity (e.g., the capability to be up-regulated by 0- 1,3 (4)-endoglucanohydrolase, -glucan (such as 0- 1,3 (4)glucan), diatomaceous earth, mineral clay, and glucomannan and modulate an immune response). Bacterial pathogen: A bacteria that causes disease (pathogenic bacteria). Examples of pathogenic bacteria for which infections that can be treated in accordance 10 with the disclosed methods and compositions include without limitation any one or more of (or any combination of) Acinetobacter baumanii, Actinobacillus sp., Actinomycetes, Actinomyces sp. (such as Actinomyces israelii and Actinomyces naeslundii), Aeromonas sp. (such as Aeromonas hydrophila, Aeromonas veronii biovar sobria (Aeromonas sobria), and Aeromonas caviae), Anaplasma phagocytophilum, 15 Alcaligenes xylosoxidans, Acinetobacter baumanii, Actinobacillus actinomycetemcomitans, Bacillus sp. (such as Bacillus anthracis, Bacillus cereus, Bacillus subtilis, Bacillus thuringiensis, and Bacillus stearothermophilus), Bacteroides sp. (such as Bacteroides fragilis), Bartonella sp. (such as Bartonella bacilliformis and Bartonella henselae, Bifidobacterium sp., Bordetella sp. ( such as Bordetella pertussis, 20 Bordetella parapertussis, and Bordetella bronchiseptica), Borrelia sp. (such as Borrelia recurrentis, and Borrelia burgdorferi), Brucella sp. (such as Brucella abortus, Brucella canis, Brucella melintensis and Brucella suis), Burkholderia sp. (such as Burkholderia pseudomallei and Burkholderia cepacia), Campylobacter sp. (such as Campylobacter jejuni, Campylobacter coli, Campylobacter lari and Campylobacter fetus), 25 Capnocytophaga sp., Cardiobacterium hominis, Chlamydia trachomatis, Chlamydophila pneumoniae, Chlamydophila psittaci, Citrobacter sp. Coxiella burneiii, Corynebacterium sp. (such as, Corynebacterium diphtheriae, Corynebacteriumjeikeum and Corynebacterium), Clostridium sp. (such as Clostridium perfringens, Clostridium - 12 2619290_1 (GHMatters) difficile, Clostridium botulinum and Clostridium tetani), Eikenella corrodens, Enterobacter sp. (such as Enterobacter aerogenes, Enterobacter agglomerans, Enterobacter cloacae and Escherichia coli, including opportunistic Escherichia coli, such as enterotoxigenic E. coli, enteroinvasive E. coli, enteropathogenic E. coli, 5 enterohemorrhagic E. coli, enteroaggregative E. coli and uropathogenic E. coli) Enterococcus sp. (such as Enterococcus faecalis and Enterococcusfaecium) Ehrlichia sp. (such as Ehrlichia chafeensia and Ehrlichia canis), Elysipelothrix rhusiopathiae, Eubacterium sp., Francisella tularensis, Fusobacterium nucleatum, Gardnerella vaginalis, Gemella morbillorum, Haemophilus sp. (such as Haemophilus influenzae, 10 Haemophilus ducreyi, Haemophilus aegyptius, Haemophilus parainfluenzae, Haemophilus haemolyticus and Haemophilus parahaemolyticus, Helicobacter sp. (such as Helicobacter pylori, Helicobacter cinaedi and Helicobacterfennelliae), Kingella kingii, Klebsiella sp. ( such as Klebsiella pneumoniae, Klebsiella granulomatis and Klebsiella oxytoca), Lactobacillus sp., Listeria monocytogenes, Leptospira interrogans, 15 Legionella pneumophila, Leptospira interrogans, Peptostreptococcus sp., Moraxella catarrhalis, Morganella sp., Mobiluncus sp., Micrococcus sp., Mycobacterium sp. (such as Mycobacterium leprae, Mycobacterium tuberculosis, Mycobacterium intracelulare, Mycobacterium avium, Mycobacterium bovis, and Mycobacterium marinum), Mycoplasm sp. (such as Mycoplasma pneumoniae, Mycoplasma hominis, 20 and Mycoplasma genitalium), Nocardia sp. (such as Nocardia asteroides, Nocardia cyriacigeorgica and Nocardia brasiliensis), Neisseria sp. (such as Neisseria gonorrhoeae and Neisseria meningitidis), Pasteurella multocida, Plesiomonas shigelloides. Prevotella sp., Porphyromonas sp., Prevotella melaninogenica, Proteus sp. (such as Proteus vulgaris and Proteus mirabilis), Providencia sp. (such as 25 Providencia alcalifaciens, Providencia rettgeri and Providencia stuartii), Pseudomonas aeruginosa, Propionibacterium acnes, Rhodococcus equi, Rickettsia sp. (such as Rickettsia rickettsii, Rickettsia akari and Rickettsia prowazekii, Orientia tsutsugamushi (formerly: Rickettsia tsutsugamushi) and Rickettsia typhi), Rhodococcus sp., Serratia - 13 2619290_1 (GHMatters) marcescens, Stenotrophomonas maltophilia, Salmonella sp. (such as Salmonella enterica, Salmonella typhi, Salmonella paratyphi, Salmonella enteritidis, Salmonella cholerasuis and Salmonella typhimurium), Serratia sp. (such as Serratia marcesans and Serratia liquafaciens), Shigella sp. (such as Shigella dysenteriae, Shigellaflexneri, 5 Shigella boydii and Shigella sonnei), Staphylococcus sp. (such as Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus hemolyticus, Staphylococcus saprophyticus), Streptococcus sp. (such as Streptococcus pneumoniae (for example chloramphenicol-resistant serotype 4 Streptococcus pneumoniae, spectinomycin resistant serotype 6B Streptococcus pneumoniae, streptomycin-resistant serotype 9V 10 Streptococcus pneumoniae, erythromycin-resistant serotype 14 Streptococcus pneumoniae, optochin-resistant serotype 14 Streptococcus pneumoniae, rifampicin resistant serotype 18C Streptococcus pneumoniae, tetracycline-resistant serotype 19F Streptococcus pneumoniae, penicillin-resistant serotype 19F Streptococcus pneumoniae, and trimethoprim-resistant serotype 23F Streptococcus pneumoniae, 15 chloramphenicol-resistant serotype 4 Streptococcus pneumoniae, spectinomycin resistant serotype 6B Streptococcus pneumoniae, streptomycin-resistant serotype 9V Streptococcus pneumoniae, optochin-resistant serotype 14 Streptococcus pneumoniae, rifampicin-resistant serotype 18C Streptococcus pneumoniae, penicillin-resistant serotype 19F Streptococcus pneumoniae, or trimethoprim-resistant serotype 23F 20 Streptococcus pneumoniae), Streptococcus agalactiae, Streptococcus mutans, Streptococcus pyogenes, Group A streptococci, Streptococcus pyogenes, Group B streptococci, Streptococcus agalactiae, Group C streptococci, Streptococcus anginosus, Streptococcus equismilis, Group D streptococci, Streptococcus bovis, Group F streptococci, and Streptococcus anginosus Group G streptococci), Spirillum minus, 25 Streptobacillus moniliformi, Treponema sp. (such as Treponema carateum, Treponema petenue, Treponema pallidum and Treponema endemicum, Tropheryma whippelii, Ureaplasma urealyticum, Veillonella sp., Vibrio sp. (such as Vibrio cholerae, Vibrio parahemolyticus, Vibrio vulnficus, Vibrio parahaemolyticus, Vibrio vulnficus, Vibrio - 14 2619290_1 (GHMatters) alginolyticus, Vibrio mimicus, Vibrio hollisae, Vibriofluvialis, Vibrio metchnikovii, Vibrio damsela and Vibrio furnisii), Yersinia sp. (such asYersinia enterocolitica, Yersinia pestis, and Yersinia pseudotuberculosis) and Xanthomonas maltophilia among others. 5 Biological activity: An expression describing the beneficial or adverse effects of an agent on living matter. When the agent is a complex chemical mixture, this activity is exerted by the substance's active ingredient or pharmacophore, but can be modified by the other constituents. Activity is generally dosage-dependent and it is not uncommon to have effects ranging from beneficial to adverse for one substance when 10 going from low to high doses. In one example, a disclosed composition significantly modulates, such as increase or decreases, the biological activity (such as by altering the expression level) of one or more gastrointestinal genes (such as those listed in FIGS. 1 and 2, respectively) which in turn induces or enhances an immune response. Cathepsin B: An enzymatic protein belonging to the peptidase (or protease) 15 families which is encoded by the CTSB gene. CTSB is a lysosomal cysteine protease composed of a dimer of disulfide-linked heavy and light chains, both produced from a single protein precursor. The term CTSB includes any CTSB gene, cDNA, mRNA, or protein from any organism. In one example, CTSB expression is increased in the gastrointestinal tract 20 following treatment, such as consumption of an admixture, including 0- 1,3 (4) endoglucanohydrolase, 0- 1,3 (4)glucan, diatomaceous earth, mineral clay, and glucomannan. Exemplary nucleic acid and protein sequences for CTSB are publicly available (see, for example, GenBank Accession Nos.: NM_001908, NM_007798, NP_001899 25 and NP 031824). In one example, CTSB includes a full-length wild-type (or native) sequence, as well as CTSB allelic variants, fragments, homologs or fusion sequences that retain the ability to be increased in the gastrointestinal tract following treatment, such as - 15 2619290_1 (GHMatters) consumption of an admixture, including 0-1,3 (4)-endoglucanohydrolase, 0-1,3 (4)glucan, diatomaceous earth, mineral clay, and glucomannan. In certain examples, CTSB has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to a known CTSB and retains CTSB activity (e.g., the capability to be 5 up-regulated by 0-I ,3 (4)-endoglucanohydrolase, 0-glucan (such as 0-1,3 (4)glucan), diatomaceous earth, mineral clay, and glucomannan and modulate an immune response). Cathepsin L: An enzymatic protein (also referred to as cathepsin LI, cathepsin L2 or cathepsin V) belonging to the peptidase (or protease) families which is encoded 10 by the CTSL gene. The term CTSL includes any CTSL gene, cDNA, mRNA, or protein from any organism. In one example, CTSL expression is increased in the gastrointestinal tract following treatment, such as consumption of an admixture, including 0-1,3 (4) endoglucanohydrolase, 0-1,3 (4)glucan, diatomaceous earth, mineral clay, and 15 glucomannan. Exemplary nucleic acid and protein sequences for CTSL are publicly available (see, for example, GenBank Accession Nos.: NM_001912 and NP_001903). In one example, CTSL includes a full-length wild-type (or native) sequence, as well as CTSL allelic variants, fragments, homologs or fusion sequences that retain the 20 ability to be increased in the gastrointestinal tract following treatment, such as consumption of an admixture, including 0- 1,3 (4)-endoglucanohydrolase, 0-1,3 (4)glucan, diatomaceous earth, mineral clay, and glucomannan. In certain examples, CTSL has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to a known CTSL and retains CTSL activity (e.g., the capability to be 25 regulated, such as down-regulated, by 0-1,3 (4)-endoglucanohydrolase, 0-glucan (such as 0-1,3 (4)glucan), diatomaceous earth, mineral clay, and glucomannan and modulate an immune response). - 16 2619290_1 (GHMatters) Cathepsin S (CTSS): A protein which in humans is encoded by the CTSS gene. The protein encoded by this gene, a member of the peptidase C1 family, is a lysosomal cysteine protease that may participate in the degradation of antigenic proteins to peptides for presentation on MHC class II molecules. 5 The term CTSS includes any CTSS gene, cDNA, mRNA, or protein from any organism. In one example, CTSS expression is increased in the gastrointestinal tract following treatment, such as consumption of an admixture, including 0-1,3 (4) endoglucanohydrolase, 0-1,3 (4)glucan, diatomaceous earth, mineral clay, and glucomannan. 10 Exemplary nucleic acid and protein sequences for CTSS are publicly available (see, for example, NM_004079, NM_021281, NP_004070 and NP_067256). In one example, CTSS includes a full-length wild-type (or native) sequence, as well as CTSS allelic variants, fragments, homologs or fusion sequences that retain the ability to be increased in the gastrointestinal tract following treatment, such as 15 consumption of an admixture, including 0-1,3 (4)-endoglucanohydrolase, 0-1,3 (4)glucan, diatomaceous earth, mineral clay, and glucomannan. In certain examples, CTSS has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to a known CTSS and retains CTSS activity (e.g., the capability to be up-regulated by 0-1,3 (4)-endoglucanohydrolase, /-glucan (such as 0-1,3 (4)glucan), 20 diatomaceous earth, mineral clay, and glucomannan and modulate an immune response). Control: A reference standard. A control can be a known value indicative of the level of activity, such as expression of a given molecule, prior to treatment, such as treatment with a disclosed composition comprising /-1,3 (4)-endoglucanohydrolase, / 25 glucan (such as /-1,3 (4)glucan), diatomaceous earth, mineral clay, and glucomannan. A difference between a test sample and a control can be an increase or conversely a decrease. The difference can be a qualitative difference or a quantitative difference, for example a statistically significant difference. In some examples, a - 17 2619290_1 (GHMatters) difference is an increase or decrease, relative to a control, of at least about 5%, such as at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 100%, at least about 150%, at least about 200%, at least about 5 250%, at least about 300%, at least about 350%, at least about 400%, at least about 500%, or greater then 500%. Decrease: To reduce the quality, amount, or strength of something. In one example, administration of a composition comprising 0- 1,3 (4)-endoglucanohydrolase, 1-glucan (such as 0- 1,3 (4)glucan), diatomaceous earth, mineral clay, and glucomannan 10 decreases the biological activity, including decreasing the expression level of one or more gastrointestinal genes in a subject (such as one or more gastrointestinal shown in FIG. 2) as compared to the biological activity prior to the administration of the composition. In a particular example, a decrease results in a decrease in one or more symptoms associated with the presence of a given pathogen, subsequent to the 15 treatment, such as a decrease of at least 10%, at least 20%, at least 50%, or even at least 90%. Such decreases can be measured using the methods disclosed herein as well as those known in the art. Determining expression of a gene product: Detection of a level expression in either a qualitative or quantitative manner. 20 DNA (deoxyribonucleic acid): A long chain polymer which includes the genetic material of most living organisms (some viruses have genes including ribonucleic acid, RNA). The repeating units in DNA polymers are four different nucleotides, each of which includes one of the four bases, adenine, guanine, cytosine and thymine bound to a deoxyribose sugar to which a phosphate group is attached. 25 Triplets of nucleotides, referred to as codons, in DNA molecules code for amino acid in a polypeptide. The term codon is also used for the corresponding (and complementary) sequences of three nucleotides in the mRNA into which the DNA sequence is transcribed. - 18 2619290_I (GHMatters) Differential expression: A difference, such as an increase or decrease, in the conversion of the information encoded in a gene (such as a gastrointestinal gene) into messenger RNA, the conversion of mRNA to a protein, or both. In some examples, the difference is relative to a control or reference value, such as an amount of gene 5 expression that is expected in a subject who has not been given a composition comprising 0-1,3 (4)-endoglucanohydrolase, -glucan (such as 0-1,3 (4)glucan), diatomaceous earth, mineral clay, and glucomannan. Detecting differential expression can include measuring a change in gene expression. Downregulated or inactivation: When used in reference to the expression of a 10 nucleic acid molecule, such as a gene, refers to any process which results in a decrease in production of a gene product. A gene product can be RNA (such as mRNA, rRNA, tRNA, and structural RNA) or protein. Therefore, gene downregulation or deactivation includes processes that decrease transcription of a gene or translation of mRNA. Examples of genes whose expression is downregulated following administration of a 15 composition comprising 0-1,3 (4)-endoglucanohydrolase, 3-glucan (such as -1,3 (4)glucan), diatomaceous earth, mineral clay, and glucomannan can be found in Table 2. Examples of processes that decrease transcription include those that facilitate degradation of a transcription initiation complex, those that decrease transcription 20 initiation rate, those that decrease transcription elongation rate, those that decrease processivity of transcription and those that increase transcriptional repression. Gene downregulation can include reduction of expression above an existing level. Examples of processes that decrease translation include those that decrease translational initiation, those that decrease translational elongation and those that decrease mRNA stability. 25 Gene downregulation includes any detectable decrease in the production of a gene product. In certain examples, production of a gene product decreases by at least 2 fold, for example at least 3-fold or at least 4-fold, as compared to a control (such an amount of gene expression in a sample taken from a subject prior to administration of a - 19 2619290_1 (GHMatters) composition comprising 0-1,3 (4)-endoglucanohydrolase, 0-1,3 (4)glucan, diatomaceous earth, mineral clay, and glucomannan). Enhancing: To increase the quality, amount, or strength of something. In some examples, enhancing can include inducing a certain activity or effect. In one example, a 5 disclosed composition enhances or induces Type I and/or Type II antigen presentation, thereby enhancing or inducing an immune response for example as compared to the response in the absence of the composition. In a particular example, a disclosed composition enhances an immune response by at least 10%, at least 20%, at least 50%, at least 70%, or even at least 90%. Such enhancement can be measured using methods 10 disclosed herein as well as those known to one of ordinary skill in the art. Expression: The process by which the coded information of a gene is converted into an operational, non-operational, or structural part of a cell, such as the synthesis of a protein. Gene expression can be influenced by external signals. For instance, exposure of a cell to a hormone may stimulate expression of a hormone-induced gene. 15 Different types of cells can respond differently to an identical signal. Expression of a gene also can be regulated anywhere in the pathway from DNA to RNA to protein. Regulation can include controls on transcription, translation, RNA transport and processing, degradation of intermediary molecules such as mRNA, or through activation, inactivation, compartmentalization or degradation of specific protein 20 molecules after they are produced. The expression of a nucleic acid molecule can be altered relative to a normal (wild type) nucleic acid molecule. Alterations in gene expression, such as differential expression, include but are not limited to: (1) overexpression; (2) underexpression; or (3) suppression of expression. Alternations in the expression of a nucleic acid molecule 25 can be associated with, and in fact cause, a change in expression of the corresponding protein. Specific examples of gastrointestinal molecules that are up-regulated following administration of a composition comprising 0-1,3 (4)-endoglucanohydrolase, -glucan (such as 0-1,3 (4)glucan), diatomaceous earth, mineral clay, and glucomannan are - 20 2619290_1 (GHMatters) provided FIG. 1. Specific examples of gastrointestinal molecules that are down regulated following administration of a composition comprising 0-1,3 (4) endoglucanohydrolase, O-glucan (such as 0-1,3 (4)glucan), diatomaceous earth, mineral clay, and glucomannan are provided FIG. 2. Protein expression can also be altered in 5 some manner to be different from the expression of the protein in a normal (wild type) situation. This includes but is not necessarily limited to: (1) a mutation in the protein such that one or more of the amino acid residues is different; (2) a short deletion or addition of one or a few (such as no more than 10-20) amino acid residues to the sequence of the protein; (3) a longer deletion or addition of amino acid residues (such as 10 at least 20 residues), such that an entire protein domain or sub-domain is removed or added; (4) expression of an increased amount of the protein compared to a control or standard amount; (5) expression of a decreased amount of the protein compared to a control or standard amount; (6) alteration of the subceellular localization or targeting of the protein; (7) alteration of the temporally regulated expression of the protein (such 15 that the protein is expressed when it normally would not be, or alternatively is not expressed when it normally would be); (8) alteration in stability of a protein through increased longevity in the time that the protein remains localized in a cell; and (9) alteration of the localized (such as organ or tissue specific or subcellular localization) expression of the protein (such that the protein is not expressed where it would normally 20 be expressed or is expressed where it normally would not be expressed), each compared to a control or standard. Controls or standards for comparison to a sample, for the determination of differential expression, include samples believed to be normal (in that they are not altered for the desired characteristic, for example a sample from a subject who has not 25 been administrated a composition comprising 0-1,3 (4)-endoglucanohydrolase, 0-glucan (such as 0-1,3 (4)glucan), diatomaceous earth, mineral clay, and glucomannan) as well as laboratory values, even though possibly arbitrarily set, keeping in mind that such values can vary from laboratory to laboratory. -21 2619290_1 (GHMatters) Laboratory standards and values may be set based on a known or determined population value and can be supplied in the format of a graph or table that permits comparison of measured, experimentally determined values. Gene expression profile (or fingerprint): Differential or altered gene 5 expression can be detected by changes in the detectable amount of gene expression (such as cDNA or mRNA) or by changes in the detectable amount of proteins expressed by those genes. A distinct or identifiable pattern of gene expression, for instance a pattern of high and low expression of a defined set of genes or gene-indicative nucleic acids such as ESTs; in some examples, as few as one or two genes provides a profile, 10 but more genes can be used in a profile, for example at least 3, at least 4, at least 5, at least 6, at least 10, at least 20, at least 25, at least 30, at least 50, at least 80, at least 100, at least 190, at least 200, or more of those listed in any of disclosed Tables. A gene expression profile (also referred to as a fingerprint) can be linked to a tissue or cell type (such as a tissue or cell isolated from the gastrointestinal tract), to a particular stage 15 of normal tissue growth or disease progression, or to any other distinct or identifiable condition that influences gene expression in a predictable way. Gene expression profiles can include relative as well as absolute expression levels of specific genes, and can be viewed in the context of a test sample compared to a baseline or control sample profile (such as a sample from a subject who has not been administered a disclosed 20 composition). In one example, a gene expression profile in a subject is read on an array (such as a nucleic acid or protein array). For example, a gene expression profile is performed using a commercially available array such as a Rat Genome Microarray from AFFYMETRIX* (AFFYMETRIXO, Santa Clara, CA). Gastrointestinal Barrier function: A phrase used to describe the exclusionary 25 properties of the gastric and intestinal mucosa. The gastrointestinal mucosa forms a barrier between the body and a lumenal environment which not only contains nutrients, but is laden with potentially hostile microorganisms and toxins. The challenge is to allow efficient transport of nutrients across the epithelium while rigorously excluding - 22 2619290_I (GHMatters) passage of harmful molecules and organisms into the animal. Meeting these challenges is essential to continued homeostasis. An inadequate immunologic response within the gastrointestinal tract will result in an infection. Conversely, an excessive response to something which is not a pathogen is equally life threatening. Inflammatory bowel 5 disease (IBD) and Crohn's Disease are two examples of pathologies in which the immune system of the gastrointestional tract is over-reacting. The gastrointestinal tract resists infection by pathogens via the combined strategies of both the innate and adaptive immune systems. Innate elements of the gastrointestinal immune system include the physical barrier provided by the functional 10 cell of the mucosal (the enterocyte), secretion of mucus by Goblet cells, the presence of anti-microbial proteins (e.g., defensins) and the presence of antigen presenting cells (APCs; macrophages and dendritic cells) in the villus. Innate detection of pathogen molecules in the gastrointestinal tract is provided by the expression (in enterocytes and underlying tissues) of Toll-like receptors (TLRs; as in other tissues). As a result, 15 penetration of the mucus layer has potential to activate inflammatory processes via the TLRs. This, as in other tissues, would result in infiltration of the affected tissue with white blood cells such as neutrophils that should sequester and arrest the infection. In addition, the innate aspect of the gastrointestinal immune system is supported by APCs. For example, the villus contains dendritic cell populations that extend their 20 dendrites into the lumen of the gastrointestinal tract. In this manner, the higher organism has the ability to monitor the presence and types of microbiota that is present within the gastrointestinal tract. Pathogens and commensals are endocytosed by the dendritic cells after which the dendritic cells migrates to gastrointestinal-associated lymphoid tissues (GALT) and mesentery-associated lymphoid tissues (MALT). Within 25 these lymphoid tissues, antigen fragments are presented, as described above, to naive B and T-lymphocytes. As a result, GALT and MALT tissues are constantly producing plasma cells and cytotoxic T-lymphocytes that home back to the villus. The resident villus plasma cells actively secrete antibodies (primarily in the form of immunoglobulin - 23 2619290_1 (GHMatters) A; IgA) that facilitate recognition and killing of offending pathogen and commensals. Similarly, the presence of cytotoxic T-lymphocytes in the villus provides capability for cell-mediated killing of any invading pathogen via secretion of granzyme isoforms. Heat Shock Protein 70 (HSP70): A member of the heat shock 70 family. 5 HSP70 stabilizes existing proteins against aggregation and mediates the folding of newly translated proteins in the cytosol and in organelles. It is also involved in the ubiquitin-proteasome pathway through interaction with the AU-rich element RNA binding protein 1. The gene is located in the major histocompatibility complex class III region. 10 The term HSP70 includes any HSP70 gene, cDNA, mRNA, or protein from any organism. In one example, HSP70 expression is increased in the gastrointestinal tract following treatment, such as consumption of an admixture, including 0- 1,3 (4) endoglucanohydrolase, 0- 1,3 (4)glucan, diatomaceous earth, mineral clay, and glucomannan. 15 Exemplary nucleic acid and protein sequences for HSP70 are publicly available (see, for example, GenBank Accession Nos.: NM_005345, XM_001002795, NP_005336, and XP_001002795). In one example, HSP70 includes a full-length wild-type (or native) sequence, as well as HSP70 allelic variants, fragments, homologs or fusion sequences that retain the 20 ability to be increased in the gastrointestinal tract following treatment, such as consumption of an admixture, including 0-1,3 (4)-endoglucanohydrolase, 0-glucan (such as 0-1,3 (4)glucan), diatomaceous earth, mineral clay, and glucomannan. In certain examples, HSP70 has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to a known HSP70 and retains HSP70 activity 25 (e.g., the capability to be up-regulated by 0-1,3 (4)-endoglucanohydrolase, O-glucan (such as 0- 1,3 (4)glucan), diatomaceous earth, mineral clay, and glucomannan and modulate an immune response). - 24 2619290_1 (GH Matters) Immune response: A response of a cell of the immune system, such as a B cell, T cell, or monocyte, to a stimulus. In one embodiment, the response is specific for a particular antigen (an "antigen-specific response"). In one embodiment, an immune response is a T cell response, such as a CD4+ response or a CD8+ response. In another 5 embodiment, the response is a B cell response, and results in the production of specific antibodies. Immunogen: An agent (such as an antigen) capable of stimulating a specific immune response against a target, such as a pathogen. Killer cell immunoglobulin-like receptors (KIRs): A family of cell surface 10 proteins found on natural killer (NK) cells. KIRs regulate the killing function of NK cells by interacting with MHC class I molecules, which are expressed on all cell types. This interaction allows them to detect virally infected cells or tumor cells that have a characteristic low level of Class I MHC on their surface. Most KIRs are inhibitory, meaning that their recognition of MHC suppresses the cytotoxic activity of their NK 15 cell. Only a limited number of KIRs have the ability to activate cells. The term KIR includes any KIR gene, cDNA, mRNA, or protein from any organism. In one example, KIR expression is increased in the gastrointestinal tract following treatment, such as consumption of an admixture, including 0-1,3 (4) endoglucanohydrolase, 3-I,3 (4)glucan, diatomaceous earth, mineral clay, and 20 glucomannan. Exemplary nucleic acid and protein sequences for KIRs are publicly available. In one example, KIR includes a full-length wild-type (or native) sequence, as well as KIR allelic variants, fragments, homologs or fusion sequences that retain the ability to be increased in the gastrointestinal tract following treatment, such as consumption of an 25 admixture, including 0-1,3 (4)-endoglucanohydrolase, 0-glucan (such as 0-1,3 (4)glucan), diatomaceous earth, mineral clay, and glucomannan. In certain examples, KIR has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to a known KIR and retains KIR activity (e.g., the capability to be up - 25 2619290_1 (GHMatters) regulated by -1,3 (4)-endoglucanohydrolase, 0-1,3 (4)glucan, diatomaceous earth, mineral clay, and glucomannan and modulate an immune response). Mammal: This term includes both human and non-human mammals. Examples of mammals include, but are not limited to: humans, pigs, cows, goats, cats, 5 dogs, rabbits and mice. Modulate: To alter or induce a change in a cellular function, such as to cause an increase or a decrease in biological activity of a molecule. In a particular activity, an composition including 0-1,3 (4)-endoglucanohydrolase, O-glucan (such as 0-1,3 (4)glucan), diatomaceous earth, mineral clay, and glucomannan modulates the 10 expression level of one or more gastrointestinal genes. In some examples, such modulation in turn modulates immunity, energy metabolism, nutrient and/or neurotransmitter transport or a combination thereof. Nucleic acid: A polymer composed of nucleotide units (ribonucleotides, deoxyribonucleotides, related naturally occurring structural variants, and synthetic non 15 naturally occurring analogs thereof) linked via phosphodiester bonds, related naturally occurring structural variants, and synthetic non-naturally occurring analogs thereof. Thus, the term includes nucleotide polymers in which the nucleotides and the linkages between them include non-naturally occurring synthetic analogs, such as, for example and without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, 20 chiral-methyl phosphonates, 2-0-methyl ribonucleotides, peptide-nucleic acids (PNAs), and the like. Such polynucleotides can be synthesized, for example, using an automated DNA synthesizer. The term "oligonucleotide" typically refers to short polynucleotides, generally no greater than about 50 nucleotides. It will be understood that when a nucleotide sequence is represented by a DNA sequence (i.e., A, T, G, C), this also 25 includes an RNA sequence (i.e., A, U, G, C) in which "U" replaces "T." "Nucleotide" includes, but is not limited to, a monomer that includes a base linked to a sugar, such as a pyrimidine, purine or synthetic analogs thereof, or a base linked to an amino acid, as in a peptide nucleic acid (PNA). A nucleotide is one - 26 2619290_1 (GHMatters) monomer in a polynucleotide. A nucleotide sequence refers to the sequence of bases in a polynucleotide. An HIV envelope polynucleotide is a nucleic acid encoding an HIV envelope polypeptide. Conventional notation is used herein to describe nucleotide sequences: the left 5 hand end of a single-stranded nucleotide sequence is the 5'-end; the left-hand direction of a double-stranded nucleotide sequence is referred to as the 5'-direction. The direction of 5' to 3' addition of nucleotides to nascent RNA transcripts is referred to as the transcription direction. The DNA strand having the same sequence as an mRNA is referred to as the "coding strand;" sequences on the DNA strand having the same 10 sequence as an mRNA transcribed from that DNA and which are located 5' to the 5'-end of the RNA transcript are referred to as "upstream sequences;" sequences on the DNA strand having the same sequence as the RNA and which are 3' to the 3' end of the coding RNA transcript are referred to as "downstream sequences." "Nucleic acid molecules" refers to a deoxyribonucleotide or ribonucleotide 15 polymer including, without limitation, cDNA, mRNA, genomic DNA, and synthetic (such as chemically synthesized) DNA. The nucleic acid molecule can be double stranded or single-stranded. Where single-stranded, the nucleic acid molecule can be the sense strand or the antisense strand. In addition, nucleic acid molecule can be circular or linear. 20 "cDNA" refers to a DNA that is complementary or identical to an mRNA, in either single stranded or double stranded form. "Encoding" refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a 25 defined sequence of nucleotides (for example, rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom. Thus, a gene encodes a protein if transcription and translation of mRNA produced by that gene produces the protein in a cell or other biological system. Both the coding strand, the -27 2619290_1 (GHMatters) nucleotide sequence of which is identical to the mRNA sequence and is usually provided in sequence listings, and non-coding strand, used as the template for transcription, of a gene or cDNA can be referred to as encoding the protein or other product of that gene or cDNA. Unless otherwise specified, a "nucleotide sequence 5 encoding an amino acid sequence" includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence. Nucleotide sequences that encode proteins and RNA may include introns. "Recombinant nucleic acid" refers to a nucleic acid having nucleotide sequences that are not naturally joined together. This includes nucleic acid vectors comprising an 10 amplified or assembled nucleic acid which can be used to transform a suitable host cell. A host cell that comprises the recombinant nucleic acid is referred to as a "recombinant host cell." The gene is then expressed in the recombinant host cell to produce, such as a "recombinant polypeptide." A recombinant nucleic acid may serve a non-coding function (such as a promoter, origin of replication, ribosome-binding site, etc.) as well. 15 A first sequence is an "antisense" with respect to a second sequence if a polynucleotide whose sequence is the first sequence specifically hybridizes with a polynucleotide whose sequence is the second sequence. Terms used to describe sequence relationships between two or more nucleotide sequences or amino acid sequences include "reference sequence," "selected from," 20 "comparison window," "identical," "percentage of sequence identity," "substantially identical," "complementary," and "substantially complementary." For sequence comparison of nucleic acid sequences and amino acids sequences, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences 25 are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters are used. Methods of alignment of sequences for comparison are well known in the art. Optimal alignment of sequences for comparison can be conducted, for example, by the - 28 2619290_1 (GHMatters) local homology algorithm of Smith & Waterman, Adv. Apple. Math. 2:482, 1981, by the homology alignment algorithm of Needleman & Wunsch, J Mol. Biol. 48:443, 1970, by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444, 1988, by computerized implementations of these algorithms (GAP, BESTFIT, 5 FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, WI), or by manual alignment and visual inspection (see for example, Current Protocols in Molecular Biology (Ausubel et al., eds 1995 supplement)). One example of a useful algorithm is PILEUP. PILEUP uses a simplification of 10 the progressive alignment method of Feng & Doolittle, J. Mol. Evol. 35:351-360, 1987. The method used is similar to the method described by Higgins & Sharp, CABIOS 5:151-153, 1989. Using PILEUP, a reference sequence is compared to other test sequences to determine the percent sequence identity relationship using the following parameters: default gap weight (3.00), default gap length weight (0.10), and weighted 15 end gaps. PILEUP can be obtained from the GCG sequence analysis software package, such as version 7.0 (Devereaux et al., Nuc. Acids Res. 12:387-395, 1984. Another example of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and the BLAST 2.0 algorithm, which are described in Altschul et al., J. Mol. Biol. 215:403-410, 1990 and 20 Altschul et al., Nucleic Acids Res. 25:3389-3402, 1977. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information on the worldwide web at ncbi.nlm.nih.gov. The BLASTN program (for nucleotide sequences) uses as defaults a word length (W) of 11, alignments (B) of 50, expectation (E) of 10, M=5, N=-4, and a comparison of both strands. The BLASTP 25 program (for amino acid sequences) uses as defaults a word length (W) of 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915, 1989). - 29 2619290_1 (GHMatters) Another indicia of sequence similarity between two nucleic acids is the ability to hybridize. The more similar are the sequences of the two nucleic acids, the more stringent the conditions at which they will hybridize. The stringency of hybridization conditions are sequence-dependent and are different under different environmental 5 parameters. Thus, hybridization conditions resulting in particular degrees of stringency will vary depending upon the nature of the hybridization method of choice and the composition and length of the hybridizing nucleic acid sequences. Generally, the temperature of hybridization and the ionic strength (especially the Na* and/or Mg++ concentration) of the hybridization buffer will determine the stringency of 10 hybridization, though wash times also influence stringency. Generally, stringent conditions are selected to be about 5oC to 20'C lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Conditions for nucleic acid hybridization and 15 calculation of stringencies can be found, for example, in Sambrook et al., Molecular Cloning: A Laboratoty Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2001; Tijssen, Hybridization With Nucleic Acid Probes, Part I: Theory and Nucleic Acid Preparation, Laboratory Techniques in Biochemistry and Molecular Biology, Elsevier Science Ltd., NY, NY, 1993 and Ausubel et al., Short Protocols in 20 Molecular Biology, 4 th ed., John Wiley & Sons, Inc., 1999. Nutrient digestion and transport: The primary components of foodstuffs include polysaccharides, lipids, proteins, vitamins and minerals. Some of these (polysaccharides, lipids and proteins) need to be hydrolyzed by digestive enzymes/processes into smaller, absorbable components prior to absorption in the small 25 intestine. Other components, such as minerals and vitamins are absorbed largely in the forms in which they enter the gastrointestinal tract. Starches are the most abundant form of polysaccharides in the non-ruminant (monogastric) diet. These include long polymers of glucose molecules linked via alpha 1-4 or alpha 1-6 linkages. Digestion of -30 2619290_1 (GHMatters) starches begins in the mouth via secretion of salivary amylase enzyme and continues in the duodenum. There, pancreatic amylases are secreted and render the polysaccharide completed digested (hydrolyzed) into its constituent monosaccharide components (primary glucose). Other diet polysaccharides are similarly digested to monosaccharide 5 end-products. For example, sucrose, a disaccharide consisting of glucose linked to fructose, is hydrolyzed by intestinal sucrase enzyme into its constituent monosaccharide components. Following this, free monosaccharides are then absorbed across the intestinal mucosal epithelium via sugar-specific transport proteins. These carry sugars into the enterocyte cytosol where they begin to diffuse down a concentration gradient 10 and are ultimately drained from the small intestine via the hepatic portal vein. Proteins include long polymers of amino acids linked together via peptide bonds. These bonds are very similar to those which link sugars in their formation of polysaccharides in that they are formed via condensation reaction. Hydrolysis of these bonds via protein-splitting enzymes (peptidases and proteases), therefore, represents a 15 hydrolytic process. Digestion of proteins begins in the gastric stomach where the low pH provided by gastric acid reduces the H-bonding that causes proteins to fold upon themselves. This causes the protein to unfold after which it is acted upon via a gastric peptidase (pepsin). Pepsin performs limited proteolysis of the protein after which the released peptides enter the small intestine. There, a combination of pancreatic 20 peptidases and proteases and also intestinal exopeptidases digest the protein fragments into small peptides and free amino acids. Amino acids represent the end-point of protein digestion in the gastrointestinal tract and are then absorbed by specific amino acid transporters that are expressed in the enterocyte. Like free sugars, the free amino acids are carried via active transport into the enterocyte after which they diffuse from 25 the basolateral side of the enterocyte via facilitated carriers and eventually reach the portal drainage of the gastrointestinal tract. Free amino acids, like sugars, then are carried to the liver via the portal vein. -31 2619290_1 (GHMatters) Lipids exist in food primarily in the forms of triacylglycerols and mono/di glycerides. Relatively little lipid digestion begins prior to the arrival of lipids into the small intestine. In the small intestine, pancreatic lipases cleave long-chain fatty acids from their glycerol backbone. Free fatty acids then are emulsified with bile acids and 5 form micelles that are then absorbed in the small intestine. Key to this process is the expression of specific fatty acid transport proteins in the enterocyte that facilitate the uptake of fatty acids into the enterocyte. Unlike free amino acids and proteins, fatty acid micelles are transported into the lymphatic drainage of the gastrointestinal tract and make their way into the systemic circulation via the villus lacteal and ultimately are 10 released near the posterior vena cava. Specific transporters for many minerals and vitamins include transport protein family members (e.g., solute carrier families). A characteristic of the gastrointestinal tract is its plasticity. The gastrointestinal tract is capable of rapid hypertrophy and expansion of digestive/absorptive functions 15 during times of nutrient abundance. Conversely, it is also able to rapidly shrink in size (to degrade itself) in times of energy and protein deficiency or during illness. This catabolic response is an important defensive strategy in that it enables an animal to nourish itself (without consuming food) during times of energy/protein inadequacy and during illness (when no food is consumed). 20 The mechanism by which the gastrointestinal tract digests itself during times of nutrient deprivation or during illness is via the expression and activation of proteolytic enzymes and peptidases. The two primary intracellular degradative pathways are the 1) ATP-dependent, ubiquitin (Ub)-dependent proteasomal pathway and the 2) lysosomal pathway. The proteasomal system is ubiquitous and requires the ubiquitination of target 25 proteins prior to degradation. Enhanced ubiquitination thereby increases proteasome dependent digestion of proteins and release of short peptides form the proteasome. These are further digested to free amino acids by cytosolic peptidases. However, the key rate-limiting event in this process is the first step: ubiquitin-tagging of target - 32 2619290 1 (GHMatters) proteins. During fasting and illness, Ub-dependent protein degradation of the gastrointestinal tract is enhanced. Similarly, intracellular proteins are also digested by the more non-specific lysosomal process. This involves endosomal processing of target proteins and subsequent hydrolysis of protein to free amino acids within the lysosome. 5 These free amino acids then diffuse from the gastrointestinal tract and are available to nourish other tissues (e.g., the central nervous system (CNS)). Released amino acids which are "glucogenic" are able to be metabolized directly to glucose which is subsequently used by tissues which have absolute glucose requirements (e.g., CNS and erythrocytes). Similarly, the ketogenic components of the released amino acids can be 10 metabolized into glycolytic and TCA cycle intermediates and metabolized by tissues as an energy (ATP) source. Sample: Biological specimens containing genomic DNA, cDNA, RNA, or protein obtained from the cells of a subject, such as those present in peripheral blood, urine, saliva, semen, tissue biopsy, surgical specimen, fine needle aspriates, and autopsy 15 material. In one example, a sample includes a tissue sample obtained from the gastrointestinal tract of a subject. Subject: Living multicellular vertebrate organisms, a category which includes both human and veterinary subjects which are in need of the desired biological effect, such as inhibition (including prevention) or treatment of an infection. Examples 20 include, but are not limited to: humans, apes, dogs, cats, mice, rats, rabbits, horses, pigs, birds and cows. Toll-like receptors (TLR): A class of proteins that play a role in the innate immune system. They are single membrane-spanning non-catalytic receptors that recognize structurally conserved molecules derived from microbes. Once these 25 microbes have breached physical barriers such as the intestinal tract mucosa, they are recognized by TLRs which activates immune cell responses. "TLR ligand" is a molecule that activates a TLR located on the mucosal surface of the lower gastrointestinal tract, for example a TLR expressed on a dendritic cell. For instance, a - 33 2619290_1 (GHMatters) TLR ligand is a molecule that activates a TLR expressed on a dendritic cell resulting in augmentation of immunity by enhancing the T cell quality (especially avidity). In one particular example, administration of a composition including 0- 1,3 (4) endoglucanohydrolase, O-glucan (such as 0-1,3 (4)glucan), diatomaceous earth, mineral 5 clay, and glucomannan modulates the expression level of one or more gastrointestinal genes which are TLR ligands, such as one or more heat shock proteins, thereby augmenting immunity. Treating a disease: "Treatment" refers to a therapeutic intervention that ameliorates a sign or symptom of a disease or pathological condition, such a sign or 10 symptom of a bacterial or viral infection. Treatment can also induce remission or cure of a condition, such as a bacterial or viral infection. In particular examples, treatment includes preventing a disease or condition, for example by inhibiting the full development of a disease, such as preventing development of an infection (such as a viral or bacterial infection). Prevention of a disease does not require a total absence of 15 an infection. For example, a decrease in the severity or the onset by can be sufficient. Under conditions sufficient for: A phrase that is used to describe any environment that permits the desired activity. In one example, includes administering a disclosed composition including 0-1,3 (4)-endoglucanohydrolase, O-glucan (such as 0 1,3 (4)glucan), diatomaceous earth, mineral clay, and glucomannan to a subject 20 sufficient to allow the desired activity. In some examples, the desired activity is modulating the biological activity (such as the expression) of one or more gastrointestinal genes to thereby invoke or increase an immune response. In a particular example, the desired activity is regulating the biological activity of HSP70, TAP1, TAP2, KIR, asparaginyl endopeptidase, cathepsin B, cathepsin L and cathepsin S or a 25 combination thereof. Upregulated or activation: When used in reference to the expression of a nucleic acid molecule, such as a gene, refers to any process which results in an increase in production of a gene product. A gene product can be RNA (such as mRNA, rRNA, -34 2619290_1 (GHMatters) tRNA, and structural RNA) or protein. Therefore, gene upregulation or activation includes processes that increase transcription of a gene or translation of mRNA. Specific examples of gastrointestinal molecules that are up-regulated following administration of a composition including 0-1,3 (4)-endoglucanohydrolase, 0- 1,3 5 (4)glucan, diatomaceous earth, mineral clay, and glucomannan are provided in FIG. 1. For example, HSP70, KIR, asparaginylendopeptidase and cathepsin B, and/or cathepsin S are up-regulated or increased following administration of a composition including 0 1,3 (4)-endoglucanohydrolase, 0-1,3 (4)glucan, diatomaceous earth, mineral clay, and glucomannan. 10 Examples of processes that increase transcription include those that facilitate formation of a transcription initiation complex, those that increase transcription initiation rate, those that increase transcription elongation rate, those that increase processivity of transcription and those that relieve transcriptional repression (for example by blocking the binding of a transcriptional repressor). Gene upregulation can 15 include inhibition of repression as well as stimulation of expression above an existing level. Examples of processes that increase translation include those that increase translational initiation, those that increase translational elongation and those that increase mRNA stability. Gene upregulation includes any detectable increase in the production of a gene 20 product. In certain examples, production of a gene product increases by at least 2-fold, for example at least 3-fold or at least 4-fold, as compared to a control (such an amount of gene expression prior to administration of a composition including 0-1,3 (4) endoglucanohydrolase, O-glucan (such as 0-1,3 (4)glucan), diatomaceous earth, mineral clay, and glucomannan). In one example, a control is a relative amount of gene 25 expression in a biological sample obtained from a subject that was not provided animal feed including 0-1,3 (4)-endoglucanohydrolase, 0-1,3 (4)glucan, diatomaceous earth, mineral clay, and glucomannan. - 35 2619290_1 (GHMatters) Additional terms commonly used in molecular genetics can be found in Benjamin Lewin, Genes V published by Oxford University Press, 1994 (ISBN 0-19 854287-9); Kendrew et al (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); and Robert A. Meyers (ed.), 5 Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8). I. Methods of Use Disclosed herein are methods of modulating the activity of one or more 10 gastrointestinal genes. In some embodiments, the method includes administering a composition comprising 0-1,3(4)-endoglucanohydrolase, -glucan (such as -1,3(4) glucan), diatomaceous earth, mineral clay, and glucomannan under conditions sufficient to modulate the biological activity of one or more gastrointestinal genes. In some examples, the method includes administering a composition comprising 0-1,3(4) 15 endoglucanohydrolase, -1,3(4) glucan, diatomaceous earth, mineral clay, and glucomannan under conditions sufficient to modulate the expression level of one or more gastrointestinal genes shown in FIGS. I and/or 2, such as to up-regulate the expression level of one or more of the genes shown in FIG. 1 and/or down-regulate one or more of the genes shown in FIG. 2 as compared to expression in the absence of the 20 treatment. In some examples, modulating includes increasing the expression level of one or more gastrointestinal genes shown in FIG. Ior decreasing the expression level of one or more gastrointestinal genes shown in FIG. 2 by at least 10%, at least 20%, at least 50%, at least 70%, or even at least 90%, such between 10% to 200%, 20% to 150%, 30% to about 100%, 40% to 90%, 50% to 70%, including 10%, 15%, 20%, 25%, 25 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 200%, 300%, or 400% as compared to expression levels prior to administration of the composition or to known reference values indicative of the expression of the particular genes in the absence of treatment. In some examples, at least 1, including at least 3, at -36 2619290_1 (GHMatters) least 5, at least 7, at least 10, at least 15, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, such as 1,2,3,4,5,6,7,8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 5 47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 or more gastrointestinal genes in FIGS. 1 and/or 2 are modulated by the method. In some examples, the one or more gastrointestinal genes up-regulated comprise one or more genes listed in Tables 4-6. 10 In some embodiments, the method includes administering a composition comprising -1,3(4)-endoglucanohydrolase, O-glucan (such as 0-1,3(4) glucan), diatomaceous earth, mineral clay, and glucomannan under conditions sufficient to modulate, such as up-regulate the biological activity of gastrointestinal genes which are involved in energy metabolism and nutrient transport. In some examples, the method 15 includes up-regulating one or more gastrointestinal genes provided in Tables 4 and/or 5 relating to energy metabolism, nutrient transport or a combination thereof. In one example, the method includes up-regulating one or more gastrointestinal genes provided in Table 4. In other examples, the method includes up-regulating one or more gastrointestinal genes provided in Table 5. 20 In some embodiments, the disclosed methods of modulating activity of one or more gastrointestinal genes are used to enhance or induce energy metabolism, thereby enhancing or inducing energy metabolism for example, as compared to the response in the absence of the composition. In a particular example, the method comprises administering a disclosed composition under conditions sufficient to enhance energy 25 metabolism by at least 10%, at least 20%, at least 50%, at least 70%, or even at least 90%, such between 10% to 200%, 20% to 150%, 30% to about 100%, 40% to 90%, 50% to 70%, including 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 200%, 300%, 400%. Such - 37 2619290_1 (GHMatters) enhancement can be measured using methods disclosed herein (including detecting expression levels of one or more gastrointestinal genes associated with energy metabolism (such as those provided in Table 5) as well as those known to one of ordinary skill in the art. 5 In some embodiments, the disclosed methods of modulating activity of one or more gastrointestinal genes are used to modulate, such as enhance or induce nutrient transport as compared to the response in the absence of the composition. In a particular example, the method comprises administering a disclosed composition under conditions sufficient to enhance nutrient transport by at least 10%, at least 20%, at least 50%, at 10 least 70%, or even at least 90%, such between 10% to 200%, 20% to 150%, 30% to about 100%, 40% to 90%, 50% to 70%, including 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 200%, 300%, 400%. Such enhancement can be measured using methods disclosed herein (including detecting expression levels of one or more gastrointestinal genes associated 15 with nutrient or neurotransmitter transport (such as one or more genes listed in Table 4) as well as those known to one of ordinary skill in the art. In one example, one or more solute carrier gene family members is up-regulated by the method. For example, one or more genes that encode a solute carrier provided in Table 4 is up-regulated by at least a 2-fold change in expression. In some examples, the one or more genes that encode a 20 solute carrier listed in Table 4 is up-regulated by at l east 10%. In some examples, the method includes administering a composition comprising #-1,3(4)-endoglucanohydrolase, O-glucan (such as 0-1,3(4) glucan), diatomaceous earth, mineral clay, and glucomannan under conditions sufficient to up-regulate the biological activity, such as expression of one or more genes listed in Table 6. In one particular 25 example, the method includes administering a composition comprising 0- 1,3(4) endoglucanohydrolase, -glucan (such as 0-1,3(4) glucan), diatomaceous earth, mineral clay, and glucomannan under conditions sufficient to regulate the biological activity, - 38 2619290_1 (GHMatters) such as expression of HSP70, TAP 1, TAP2, KIR, MHC I protein, asparaginyl endopeptidase, cathepsin B, cathepsin L and cathepsin S or a combination thereof. The provided methods are used to modulate a number of different gastrointestinal functions, including energy metabolism, nutrient and/or 5 neurotransmitter transport, immune function or a combination thereof. In some embodiments, methods for modulating energy metabolism and/or nutrient/neurotransmitter transporters are disclosed. These methods include modulating expression of one or more gastrointestinal genes associated with such processes in a subject, such as by administering to the subject a composition comprising -glucans, 0 10 1,3(4)-endoglucanohydrolase, diatomaceous earth, a mineral clay, and glucomannan under conditions sufficient to modulate expression levels of one or more energy metabolism and/or nutrient transport gastrointestinal genes listed in FIGS. I and/or 2 (including those listed in Tables 4 and/or 5) as compared to expression levels of the one or more gastrointestinal genes in the absence of the composition, thereby modulating 15 energy metabolism and/or nutrient transport. In some examples, the one or more gastrointestinal genes up-regulated and associated with nutrient and/or neurotransmitter transport are one or more genes listed in at least Table 4. In some examples, the one or more gastrointestinal genes up-regulated and associated with energy metabolism (such as protein degradation) are one or more genes listed in at least Table 5. 20 Also disclosed herein is a method of modulating gastrointestinal barrier function by modulating expression of one or more gastrointestinal genes in a subject, such as by administering to the subject a composition comprising 0-glucans, 0-1,3(4) endoglucanohydrolase, diatomaceous earth, a mineral clay, and glucomannan under conditions sufficient to modulate expression levels of one or more gastrointestinal genes 25 listed in FIGS. 1 and/or 2 (such as up-regulating one or more gastrointestinal genes provided in Table 6) associated with gastrointestinal barrier function as compared to expression levels of the one or more gastrointestinal genes in the absence of the - 39 2619290_I (GHMattcrs) composition, thereby modulating (such as inducing or enhancing) gastrointestinal barrier function. The disclosed methods can also be used to regulate, such as enhance or induce Type I and/or Type II antigen presentation and in turn inducement or enhancement of an 5 immune response. The disclosed method can be used to modulate the activity of one or more gastrointestinal genes of any mammalian (including human) or avian species. In a particular embodiment, the compositions are administered to livestock mammals, including both ruminants (e.g., cattle, sheep, goats, cows, deer, bison, buffalo) and non 10 ruminants (e.g., pigs, horses, sows). The provided methods include administrating the composition to modulate one or more gastrointestinal genes (such as those listed in FIGS. 1 and/or 2 and Tables 4-6) by any effective route. Exemplary routes of administration include, but are not limited to, oral (such as admixed with animal feed), injection (such as subcutaneous, 15 intramuscular, intradermal, intraperitoneal, intravenous, and intratumoral), sublingual, rectal, transdermal, intranasal, vaginal and inhalation routes. For example, the compositions can be fed to any mammalian or avian species including, but not limited to, bovine, equine, ovine, caprine and avian species. For example, when admixed with the feed or food or fed as a supplement, the composition can be used to regulate (e.g., 20 up-regulate or down-regulate) one or more gastrointestinal genes. A composition as described can be administered as an additive to feeds or foods or administered directly to the animal or human (e.g., as a supplement). - 40 2619290_1 (GHMatters) In some examples, the method further includes preparing the composition, including preparing the constituents of the composition. The constituents of the composition may be prepared by methods commonly known to those of ordinary skill in the art and obtained from commercial sources. For example, the 0- 1,3 (4) 5 endoglucanohydrolase is produced from submerged fermentation of a commercially available strain of Trichoderma longibrachiatum. Diatomaceous earth is available as a commercially-available acid-washed, product with 95% silica (SiO 2 ) and with its remaining components not assayed but consisting primarily of ash (minerals) as defined by the Association of Analytical 10 Chemists (AOAC, 2002). Diatomaceous earth for use in disclosed methods can be calcined (e.g., at a temperature of at least 900 "C) in some embodiments and can be prepared by methods known in the art. In some examples, 0-1,3 (4)glucan and glucomannan is obtained from commercial preparations of yeast cell wall extract derived from primary inactivated 15 yeast (e.g., Saccharomyces cerevisiae) with the chemical composition shown in Table 1. Table 1 Moisture 2-3% Dry Matter 97-98% Proteins 14-17% Fats 20-22% Phosphorus 1-2% Mannans 22-24% B-1,3 (4)glucan 24-26% Ash 3-5% The yeast cell wall extract can be prepared by a method commonly known to one of ordinary skill in the art. In some examples, the 1-glucans and glucomannan are -41 2619290_1 (GHMatters) derived from boiling and enzyme autolysis of gram positive yeast cell walls from, for example, Saccharomyces cerevisiae. Mineral clays (e.g., aluminosilicates) can be obtained from any of a variety of commercially available clays including, but not limited to, montmorillonite clay, 5 bentonite and zeolite. Some embodiments can comprise hydrated sodium calcium aluminosilicate. In some embodiments, the composition is prepared with various amounts of each constituent relative to one another. In one embodiment, the composition comprises (by weight) between about 0.05% and about 3% 0-1,3(4) 10 endoglucanohydrolase, between about 1% and about 40% diatomaceous earth, between about 0.5% and about 20% 0-1,3 (4)glucan and glucomannan, and between about 40% and about 92% mineral clay. In one embodiment, the composition comprises about 0.1%-3% 3 -1, 3

(

4

)

endoglucanohydrolase, about 5%-40% diatomaceous earth, about 2%-15% yeast cell 15 wall extract, and about 40%-80% mineral clay. In another specific embodiment, the composition comprises about 0.2%-3% 0-1,3(4)-endoglucanohydrolase, about 20% 40% diatomaceous earth, about 4%-10% yeast cell wall extract, and about 50%-70% mineral clay. In some embodiments, the composition includes additional ingredients. For 20 example, the composition includes calcium carbonate, dried kelp, niacin supplement, biotin, d-calcium pantothenate, vitamin B-12 supplement, choline chloride, thiamine mononitrate, pyridoxine hydrochloride, silicon dioxide, riboflavin-5-phosphate, folic acid, soybean oil, or any combination thereof. In some embodiments, the composition can be a dry, free-flowing powder which 25 is suitable for direct inclusion into a feed, food product (e.g., commercially available feeds or food products) or as a supplement to a total mixed ration or diet. In some embodiments, the powder can be mixed with either solid or liquid feed or with water. - 42 2619290_1 (GHMatters) In some embodiments, the composition can be formed into pellets, capsules, and/or tablets. Accordingly, in some methods, the compositions described above are incorporated directly into commercially available feeds or food products. When 5 incorporated directly into feeds, the composition is added to feeds in amounts ranging from about 0.1 kg to about 20 kg per ton of feed. In a particular embodiment, the composition is added to animal feedstuffs or to food in amounts from about 0.5 kg to about 10 kg per ton of feed. In another embodiment, the composition is added to feeds in amounts ranging from about 1 kg to about 5 kg per ton of feed. In one embodiment, 10 the composition is added to feeds in amounts ranging from about 1-2 kg per ton of feed. When expressed as a percentage of dry matter of feed, the composition is added to foodstuffs or feeds in amounts ranging from about 0.0 1% to about 2.5% by weight of feed, preferably from about 0.0125% to about 2% by weight. In one particular embodiment, the composition is added to animal feedstuffs or to food in amounts from 15 about 0.05% to about 1.5% by weight, preferably in amounts of from about 0.0625% to about 1% by weight of feed. In another embodiment, the composition is added in amounts ranging from about 0.1% to about 0.7% by weight, preferably in amounts ranging from about 0.125% to about 0.5% by weight of feed. Alternatively, the compositions described above is fed as a supplement to 20 commercially available feeds or food products in amounts of from about 0.01 gram to about 1 gram per kilogram of live body weight, per day, or preferably from about 0.012 grams/kg to about 0.5 grams/kg of live body weight, per day. For example, in some methods, the composition is fed directly to mammalian or avian species as a supplement in amounts of from about 0.016 grams/kg to about 0.37 grams/kg of live body weight 25 per day. In a particular embodiment, described compositions are provided to a mammalian and avian species in amounts of from about 0.05 grams/kg to about 0.20 grams/kg of body weight per day. One of skill in the art can appreciate that the amount -43 2619290_1 (GHMatters) of the composition fed can vary depending upon the animal species, size of the animal and type of the feedstuff to which the invention is added. As examples, the composition is provided to sheep in the range of from about 2 grams per head per day to about 8 grams per head per day. For bovine animals, the 5 composition is provided in the range of from about 10 grams per head per day to about 60 grams per head per day. One of skill and art can appreciate that the amount of the composition fed can vary depending upon the animal species, size of the animal and type of the feedstuff to which the composition is added. 10 The following example is provided to illustrate certain particular features and/or embodiments. This example should not be construed to limit the disclosure to the particular features or embodiments described. EXAMPLE 15 Compositions comprising 0-1,3(4)-endoglucanohydrolase, 0-1,3(4) glucan, diatomaceous earth, mineral clay, and glucomannan have previously been reported to have a number of properties such as augmenting immune function (see US Patent Application No. 2007/0202092) and inhibiting fungal infections (see US Patent Application No. 2006/0239992). This example describes the ability of a composition 20 comprising 0-1,3(4)-endoglucanohydrolase, 0-1,3(4) glucan, diatomaceous earth, mineral clay, and glucomannan to modulate gastrointestinal gene expression, including genes associated with nutrient and neurotransmitter transporters, protein degradation and immune function. Sixteen male CD rats weighing approximately 200 grams were randomly 25 assigned to two treatments groups: a control group and a test group. The control group was fed ad libitum amounts of powdered rodent diet (Teklad 8604) for a period of 28 days. The test group was fed the same Teklad diet supplemented with 0.5% (w/w) of the composition comprising 0-1,3(4)-endoglucanohydrolase, 0-1,3(4) glucan, - 44 2619290_1 (GHMatters) diatomaceous earth, mineral clay, and glucomannan for the same period of time. Water was available free choice throughout the study. Animals were housed at 20 degrees Celsius and were placed on a 12 hour:12hour light:dark cycle. On Day 28, animals were euthanized by a combination of ketamine and xylazine (for anesthesia) followed 5 by cardiac exsanguination. Intestinal samples were taken from freshly-euthanized animals and immediately frozen on dry ice. RNA was extracted from all tissues using TRIZOL@ and then quantified. Quality of the RNA was assessed using an Agilent Bioanalyzer. RNA from three animals/treatments which was judged to be of adequate "quality" (Abs 260/280 > 1.80) and quantity was then used in a microarray study. RNA 10 from each rat was hybridized to an Affymetrix@ array, each of which contained approximately the entire rat genome (ca. 23,000 genes). Effects of the addition of the composition comprising 0-1,3(4)-endoglucanohydrolase, 0-1,3(4) glucan, diatomaceous earth, mineral clay, and glucomannan to the diet on gastrointestinal gene expression of the 23,000 genes were then assessed. 15 The normalization of probe set intensities was performed using the Robust Multiarray Analysis method (Irizarry et al., Biostatistics 2003, 4(2):249-264). To identify differentially expressed genes, gene expression intensities were compared using a moderated t-test and a Bayes smoothing approach. To correct for the effect of multiple testing, the false discovery rate was estimated from p values derived from the 20 moderated t-test statistics. The analysis was performed using the affylmGUI Graphical User Interface for the Limma microarray package (Wettenhall et al., Bioinformatics 2006, 22(7):897-899), which is available as part of the Bioconductor software package (at world wide web address Bioconductor.org] for the R computing environment. The differential expressed genes were performed functional analysis by DAVID 25 bioinformatics resources (Huang et al., Nature protocol 2009 4 (1):44-56). Of the 23,000 genes printed on the array, 288 genes were significantly up regulated and 385 genes were significantly down-regulated (P<0.05; Table 2 below and FIGS. 1 and 2). After gene functional annotation analysis was completed, of the up - 45 2619290_1 (GHMatters) regulated genes, 204 genes were involved in biological processes, 224 genes belonged to a "molecular function group" and 211 genes belonged to a "cellular component". Of the down-regulated genes, 272 genes were involved in biological processes, 306 genes belonged to a "molecular function group" and 190 genes belonged to a "cellular 5 component". Table 2. Effects of a disclosed composition on expresison and function of several genes. Biological Molecular function Cellular component processes Up-regulated 204 224 211 genes Down-regulated 272 306 190 genes 10 To clarify the pathway for the involvement of differential expressed genes, DAVID bioinformatics resources were used. In total, 13 pathways were identied by the differential expressed genes. Of these pathways, six pathways (complement and coagulation, antigen processing and presentation, autoimmune thyroid disease, allograft 15 rejection, graft versus host disease and viral myocarditis) are related to the immunological reaction, one pathway (starch and sucrose metabolism) was related to energy metabolism and one pathway was related with nutrient transport (endocytosis). These results demonstrate that the modulated gastrointestinal genes are those which are involved in the regulation of immunity (innate and adaptive immunity) and energy 20 metabolism. -46 2619290_1 (GiMatters) Manual analysis of the output revealed that a number of metabolic processes were regulated by the present treatment, including nutrient transport, immune function and protein degradation (Table 3). 5 Table 3. Effects on Expression of Genes involved in Nutrient Transport, Immune function and protein degradation. Physiological Number of up- % of up- Number of % of down process regulated regulated down- regulated (category) genes within genes in regulated genes in this category category genes category Transport 25 9% 12 3% Immunity 16 6% 16 4% Protein 14 5% 12 3% degradation Transport proteins. From this analysis, three times as many transport genes were up 10 regulated (P<0.05) as down-regulated. Up-regulated genes included those involved in the intestinal transport of a broad spectrum of the nutrients that animals require for normal gastrointestinal health; L-amino acids, cationic amino acids, glucose, fructose, fatty acids, carnitine, cholesterol, urea, calcium, cobalt, sodium, phosphorus, potassium, zinc and neurotransmitters. Of interest, 14 genes which are members of the solute 15 carrier gene family were up-regulated. Only 5 members of the solute carrier gene family were down-regulated. A summary of the genes encoding nutrient and neurotransmitter transporters which were up-regulated following the disclosed treatment/feeding is given in Table 4. - 47 2619290 _ (GHMatters) The net result of this regulation would be increased extraction rate and/or efficiency of nutrients from the gastrointestinal tract. In addition, much of gastrointestinal function and communication is coordinated via release of neurotransmitters which act in autocrine, paracrine and endocrine 5 manners. Increased expression of four neutrotransmitter transporters in the gastrointestinal tract is proposed to increase rate and efficacy of neurotransmitter signaling and to thereby improve gastrointestinal health. Table 4. Effects of treatment on expression of nutrient and neurotransmitter transporters 10 in the gastrointestinal tract. Gene name Function Fold P increase value Solute carrier family 43, member L-amino acid transport 1.70 0.002 2 K channel tetramerization domain Potassium transport 2.94 0.019 Solute carrier family 7 Cationic amino acid transport 1.32 0.047 Solute carrier family 2 Facilitated glucose/fructose 1.29 0.039 transport PDZ domain Carnitine and cholesterol 1.27 0.007 transport Solute carrier family 18, member Neurotransmitter transport 1.27 0.026 2 Solute carrier family 39 Zinc transport 1.26 0.045 Solute carrier family 6 Neurotransmitter transport 1.25 0.012 K-voltage gated channel, sub- Potassium transport 1.25 0.028 family Q -48 2619290_1 (GHMatters) Solute carrier family 6 Neurotransmitter transport 1.23 0.031 Solute carrier family 27 Fatty acid transport 1.23 0.012 Cellular retinoic acid binding Intracellular lipid transport 1.23 0.004 protein 2 Sodium leak channel Sodium transport 1.21 0.008 Gastric intrinsic factor Cobalt transport 1.19 0.014 Solute carrier family 25 Phosphorous transport in 1.19 0.048 mitochondria K-intermediate/small conductance Potassium transport 1.18 0.021 Ca-activated channel, sub-family N, member 3 Solute carrier family 12, member Transporter (substrate not 1.18 0.029 6 (Function 2) known) Solute carrier family 22, member Transporter (substrate not 1.17 0.048 25 known) Fatty acid binding protein 7 Fatty acid transport 1.17 0.047 K-intermediate/small conductance Potassium transport 1.17 0.023 Ca-activated channel, sub-family N, Member 2 Solute carrier family 14 Urea transport 1.17 0.038 Solute carrier family 20 Phosphorous transport 1.16 0.042 Clathrin light chain Neurotransmitter release 1.15 0.039 Solute carrier family 25, member Unknown 1.14 0.047 35 Protein degradation (energy metabolism). Adequate gastrointestinal health implies the ability of the tissue to respond to nutritional and disease challenges through the - 49 2619290_1 (GHMatters) mobilization of its protein reserves. Such activity is dependent upon expression of proteolytic systems and their adequate regulation. Three types of protein degradation occur in the gastrointestinal tract: intra-luminal, extracellular and intracellular. The first group is "secreted proteases" (from pancreatic and intestinal tissues) that function in 5 protein digestion. The second group function as secreted proteases (e.g., granzymes) that function within a tissue. The third are intracellular proteolytic systems involved in both the normal turnover of cellular proteins but also in the processing of Type I and II antigens for assembly with MHCI and MHCII on the surfaces of antigen-presenting cells. Surprisingly, feeding of the invention increased expression of all three classes of 10 proteases. A summary of the genes encoding proteases (or proteolytic controlling events) which were up-regulated is given in Table 5. Table 5. Gastrointestinal genes encoding proteolytic enzyme systems that were up regulated by the disclosed treatment/feeding. 15 Gene Function Fold P increase value Ubiquitin D Branding protein. Marks protein for 7.80 0.035 degradation via the proteasome Granzyme F serine proteases that are released by 1.90 0.025 cytoplasmic granules within cytotoxic T cells and natural killer cells Granzyme C serine proteases that are released by 1.52 0.038 cytoplasmic granules within cytotoxic T cells and natural killer cells Chymotrypsin-like Luminal protein digestion 1.31 0.042 elastase family, number 1 - 50 2619290_1 (GiMatters) Preprotrypsinogen Luminal protein digestion 1.30 0.005 IV Cathepsin H Lysosomal protease (intracellular protein 1.26 0.019 degradation) Ubiquitin-specific Intracellular protein degradation 1.26 0.010 peptidase 25 Aspartic Exopeptidase 1.25 0.002 aminopeptidase Cystatin B Intracellular peptidase 1.22 0.031 Cathepsin Q Intracellular lysosomal proteolysis 1.20 0.040 Ubiquitin-specific Proteasomal protein degradation 1.18 0.024 peptidase 20 Endothelial- Intracellular protease 1.16 0.029 converting enzyme The result of the regulation of chymotrypsin and trypsin activities can enhance protein digestion. This suggests that the disclosed treatment may enhance supply of essential amino acids to the host and thereby improve gastrointestinal health and survival 5 capability. Effects of enhanced proteasomal (ubiquitin-dependent) and lysosomal enzyme activities (cathepsin H, cathepsin Q and aspartic aminopeptidase) can include increased Type I and II antigen processing and presentation, respectively. This suggests that the disclosed treatment may enhance the ability of the gastrointestinal tract to mount defenses against both viral (Type I) and bacterial (Type II) pathogens. 10 Immunity and gastrointestinal health. A proper functioning gastrointestinal tract possesses robust immunological capability. In fact, the gastrointestinal tract is regarded as the body's largest immune organ. Many of the genes up- and down-regulated in the gastrointestinal tract by the disclosed treatment/feeding coordinate immune function -51 2619290_1 (GH Matters) (see, for example, Table 6 for specific examples of up-regulated genes), thus suggesting the potential for the disclosed treatment to improve gastrointestinal health through immunoregulation. Because 18 "immune genes" were up-regulated and 16 were down regulated (see FIG. 2), it is likely that there are both immune-stimulatory and 5 immunosuppressive events occurring simultaneously. Table 6. Immune-related genes in the gastrointestinal tract that were up-regulated by the disclosed treatment/feeding. Gene name Function Fold P increase value RT1 Class Ib gene MHC class 1 protein complex (antigen 2.44 0.042 H2-TL-like presentation) RT1 Class lb locus MHC Class 1 protein complex (antigen 3.00 0.018 AW2 presentation) RTI class lb locus MHC 1 antigen presentation 2.39 0.045 AW2 Class 1 CE7 Granzyme F serine proteases that are released by cytoplasmic 1.90 0.025 granules within cytotoxic T cells and natural killer cells Granzyme C serine proteases that are released by cytoplasmic 1.52 0.038 granules within cytotoxic T cells and natural killer cells Histocompatibility 2 MHC Class 1 protein complex 1.46 0.015 T region locus 24 Leukocyte Ig receptor (immunity) 1.37 0.023 immunoglobulin like receptor - 52 2619290_1 (GHMatters) Interleukin-18 Induces cell-mediated immunity 1.37 0.001 Chemokine (C-C Chemokine 1.34 0.016 motif) ligand 20 Arachidonate 5 Arachidonate metabolism/synthesis 1.30 0.029 lipoxygenase activating protein I-kappa B Response to fungus 1.28 0.008 kinase/NF kappa B cascade Keratin 1 Complement activation 1.27 0.012 Chemokine (C-X-C Chemokine 1.26 0.019 motif) ligand 11 Complement Complement cascade 1.20 0.022 component 2 Interleukin 20 Binds IL-20- negative regulator of Type IV 1.17 0.017 receptor hypersensitivity) Complement Complement cascade 1.15 0.028 component 4 binding protein beta Peptidoglycan Pathogen detection. Activated by gram 1.15 0.040 recognition protein positive bacteria. RT1 Class lb, locus Antigen presentation 1.13 0.047 AW2 Of interest, the four genes which were up-regulated the most within this subset of regulated genes were each associated with MHC Class 1 antigen presentation. DAVID pathway analysis indicated that several genes that were regulated were associated with - 53 2619290_1 (GHMatters) both MHC 1 and MHC II antigen-presenting pathways. Up-regulated genes associated with the MHC 1 pathway, in addition to those already presented, included heat shock protein 70 (HSP70; [25% increase in expression, P=0.046], which carries proteasome generated peptides arising from viral antigens to the endoplasmic reticulum for 5 assembly with MHC 1), the MHC 1 antigen presentation protein itself and killer cell lectin-like receptor (19% increase, P<0.0 12). Expression of gastrointestinal genes involved in the presentation of Type II antigens (bacterial) was also enhanced by the present method. These include asparaginyl endopeptidase (AEP) and cathepsins B and S. Each of these are proteolytic 10 enzymes expressed within the lysosome. These lysosomal proteases are involves in the processing of endocytosed pathogen to peptides prior to their assembly with MHCII and presentation on APC surface in association with MHCII. Enhanced processing and presentation of bacterial antigen via this mechanism is proposed to enhance the speed with which the adaptive aspect of the gastrointestinal immune system may develop 15 antibody responses to bacterial pathogens which enter the gastrointestinal tract. Consequences to this regulation can be improved processing and expression of Type I and II antigens on APCs to naive B- and T-lymphocytes in lymphoid tissues and consequent more rapid production of antibodies directed against pathogens from which antigens originated. It is suggested herein that a gastrointestinal tract so-regulated 20 would be better able to repel infections by a broad spectrum of pathogens. Thus, these results support the use of the disclosed method for enhancing the adaptive immune system by enhancing processing and presentation of the bacterial antigens. 25 In view of the many possible embodiments to which the principles of the disclosed invention may be applied, it should be recognized that the illustrated embodiments are only preferred examples of the invention and should not be taken as - 54 2619290_1 (GHMatters) limiting the scope of the invention. Rather, the scope of the invention is defined by the following claims. We therefore claim as our invention all that comes within the scope and spirit of these claims. 5 - 55 2619290_1 (GHMatters)

Claims (14)

1. A method of modulating expression of one or more gastrointestinal genes in a subject, comprising: 5 administering to the subject a composition comprising -glucans, 0-1,3(4) endoglucanohydrolase, diatomaceous earth, a mineral clay, and glucomannan under conditions sufficient to modulate expression levels of one or more gastrointestinal genes listed in FIGS. 1 and/or 2 as compared to expression levels of the one or more gastrointestinal genes in the absence of the composition, wherein detection of 10 differential expression of one or more gastrointestinal genes listed in FIGS. 1 and/or 2 indicates modulation of gastrointestinal gene expression.

2. Use of a composition comprising -glucans, 0-1,3(4) endoglucanohydrolase, diatomaceous earth, a mineral clay, and glucomannan for the manufacture of a medicine for the modulation of expression of one or more 15 gastrointestinal genes in a subject, said use comprising: administering to the subject a composition comprising 0-glucans, 0-1,3(4) endoglucanohydrolase, diatomaceous earth, a mineral clay, and glucomannan under conditions sufficient to modulate expression levels of one or more gastrointestinal genes listed in FIGS. 1 and/or 2 as compared to expression levels of the one or more 20 gastrointestinal genes in the absence of the composition, wherein detection of differential expression of one or more gastrointestinal genes listed in FIGS. 1 and/or 2 indicates modulation of gastrointestinal gene expression.

3. A method according to claim 1 or use according to claim 2, wherein 25 differential expression of one or more gastrointestinal genes comprises up-regulation of one or more gastrointestinal genes in FIG. 1 and/or down-regulation of one or more gastrointestinal genes in FIG. 2. - 56 2619290_I (GHMatters)

4. A method or use according to any one of claims 1-3, wherein the subject is a ruminant animal.

5. A method or use according to any one of claims 1-4, wherein the mineral 5 clay comprises montmorillonite, bentonite, aluminosilicate, zeolite clays, or a combination thereof.

6. A method or use according to any one of claims 1-5, wherein the composition comprises between about 15% and 40% diatomaceous earth, between 10 about 50% and 80% mineral clay, between about 1.0% and 5.0% -glucans, between about 0.05% and 3.0% 0-1,3(4)-endoglucanohydrolase, and between about 1.0% and

8.0% glucomannan. 7. A method or use according to any one of claims 1-5, wherein the 15 composition comprises between about 20% and 30% diatomaceous earth, between about 60% and 75% mineral clay, between about 1.0% and 3.5% 0-glucans, between about 0.1% and 3.0% #-1,3(4)-endoglucanohydrolase, and between about 1.0% and 6.0% glucomannan. 20 8. A method or use according to any one of claims 1-7, further comprising admixing the composition into foods or animal feedstuffs in a concentration of between about 0.0 125% and 5% by weight.

9. A method or use according to claim 8, further comprising feeding the 25 food and composition combination to one of the group consisting of domestic livestock, ruminant livestock, and avian livestock. - 57 2619290_1 (GH Matters)

10. A method or use according to any one of claims 1-9, further comprising formulating the composition comprising #-glucans, 0-1,3(4)-endoglucanohydrolase, diatomaceous earth, a mineral clay, and glucomannan prior to administering the composition. 5

11. A method or use according to any one of claims 1-10, wherein the one or more gastrointestinal genes up-regulated comprise one or more genes listed in FIG. I associated with protein degradation, nutrient and/or neurotransmitter transporters, immune function or a combination thereof. 10

12. A method or use according to any one of claims 1-11, wherein the one or more gastrointestinal genes up-regulated comprise one or more genes listed in Tables 4 6. 15 13. A method or use according to any one of claims 1-11, wherein the one or more gastrointestinal genes modulated comprise TAP 1, TAP2, HSP70, KIR, MHC1 protein, cathepsin B, cathepsin L, cathepsin S, asparaginyl endopeptidase or a combination thereof. 20 14. A method of enhancing Type I and/or Type II antigen presentation by modulating expression of one or more gastrointestinal genes in a subject according to any one of claims 1-13.

15. A method of inducing or enhancing an immune response by modulating 25 expression of one or more gastrointestinal genes in a subject according to any one of claims 1-14. - 58 2619290_I (GHMatters)

16. A method according to claim 15, wherein the immune response is an adaptive immune response.

17. A method of inducing or enhancing energy metabolism and/or nutrient 5 transport by modulating expression of one or more gastrointestinal genes in a subject according to any one of claims 1-13. - 59 2619290_1 (GHMatters)