Method and use of microbiome composition

Abstract

Methods and uses of compositions (eg, comprising one or more microbial strains) are disclosed.

Description

[Technical Field]

[0001] Cross-reference of related applications This application claims priority to U.S. Provisional Patent Application No. 63 / 077,544, filed on 11 September 2020, the entirety of which is incorporated herein by reference. [Background technology]

[0002] Generally, the metabolome is understood to be the metabolites present in an organism, cell, or tissue. The levels of one or more metabolites present in an organism, cell, or tissue may be associated with a particular disease, disorder, or condition. [Overview of the project]

[0003] This disclosure provides insight into the possibility of modulating the metabolome of subjects (e.g., mammals (e.g., humans, mice, etc.)) using the compositions described herein. In particular, this disclosure describes techniques that can be used to evaluate the effects of administering compositions (e.g., microbiome compositions) to subjects, and to identify or characterize the effects and / or modulation of metabolites or metabolome levels of subjects upon administration of such compositions. In some embodiments, the metabolites that may be modulated may be associated with certain diseases, disorders, or illnesses. Such techniques may be useful for identifying differences in metabolite levels in specific subjects (e.g., patients) or populations (e.g., before and after administration of the disclosed compositions). Thus, this disclosure also provides techniques that may be useful for evaluating the properties and effects of the disclosed compositions in specific subjects (e.g., patients), and thereby for providing subject-specific information on how the metabolome of individual subjects differentially affects the health status of those subjects. For example, in some embodiments, the techniques provided herein may be useful for identifying diseases, disorders, or illnesses that a subject may be susceptible to based on the metabolome in a subject-specific sample, and for treating and / or preventing such diseases, disorders, or illnesses by administering the disclosed compositions (e.g., to modulate the subject's metabolome). Therefore, the techniques described herein may be useful as diagnostic tools for screening for specific diseases, disorders, or illnesses, and for treating and / or preventing such diseases, disorders, or illnesses.

[0004] In particular, the present disclosure provides a method for measuring the level of one or more metabolites in a sample derived from a subject. In some embodiments, the subject ingests a composition comprising a composition comprising one or more microbial strains. In some embodiments, the subject ingests a composition comprising one or more lipopolysaccharides. In some embodiments, the subject ingests a composition comprising one or more microbial strains and one or more lipopolysaccharides. In some embodiments, the subject ingests a composition comprising one or more microbial strains and one or more lipopolysaccharides.

[0005] In some embodiments, the subjects are mammals. In some embodiments, the subjects are humans. In some embodiments, the subjects have or are at risk of developing a disease, disorder, or illness.

[0006] In some embodiments, one or more microbial strains originate from the mammalian microbiome. In some embodiments, one or more microbial strains originate from the human microbiome. In some embodiments, one or more microbial strains originate from the microbiome of the subject described above.

[0007] In some embodiments, one or more microbial strains are selected from Table 5.

[0008] In some embodiments, one or more microbial strains are Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, Acidaminococcus sp., or a combination thereof. In some embodiments, the composition includes or comprises Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, and Acidaminococcus sp.

[0009] In some embodiments, the composition contains two or more microbial strains. In some embodiments, the composition contains five or more microbial strains. In some embodiments, the composition contains ten or more microbial strains.

[0010] In some embodiments, one or more lipopolysaccharides are derived from Escherichia coli, Salmonella sp., Shigella sp., Pseudomonas sp., Moraxella sp., Helicobacter sp., Stenotrophomonas sp., Bdellovibrio sp., Legionella sp., acetic acid bacteria, cyanobacteria, spirochetes, green sulfur bacteria, green non-sulfur bacteria, or a combination thereof. In some embodiments, one or more lipopolysaccharides are derived from E. coli. In some embodiments, one or more lipopolysaccharides are derived from E. coli 0111.B4.

[0011] In some embodiments, one or more metabolites include one or more metabolites from Table 1, Table 2, Table 3, Table 4, or a combination thereof. In some embodiments, one or more metabolites are selected from Table 1, Table 2, Table 3, Table 4, or a combination thereof. In some embodiments, at least one of the one or more metabolites is associated with a disease, disorder, or illness.

[0012] In some embodiments, the sample is or contains cells or tissues. In some embodiments, the sample is or contains amniotic fluid, aqueous humor, ascites, bile, bone marrow, blood, breast milk, cerebrospinal fluid, earwax, chyle, keems, ejaculate, endolymph, exudate, feces, gastric acid, gastric juice, lymph, mucus, pericardial fluid, perilymph, ascites, pleural fluid, pus, mucosal secretions, saliva, sebum, semen, serum, smegma, sputum, synovial fluid, sweat, tears, urine, vaginal secretions, vitreous fluid, vomit, interstitial fluid, lymph, plasma, mucus, digestive fluid, feces, and / or combinations or components thereof.

[0013] In some embodiments, measuring the level of one or more metabolites in a sample derived from the target includes quantifying the level of one or more metabolites in the sample derived from the target. In some embodiments, the level is the presence or absence of one or more metabolites. In some embodiments, the level is the concentration of one or more metabolites.

[0014] In some embodiments, the method includes administering a composition containing one or more microbial strains to the subject. In some embodiments, the method further includes administering a composition containing one or more lipopolysaccharides to the subject. In some embodiments, the method further includes administering a composition containing one or more microbial strains and one or more lipopolysaccharides to the subject.

[0015] In some embodiments, the method involves administering to the subject a composition containing one or more microbial strains and a composition containing one or more lipopolysaccharides. In some embodiments, the composition containing one or more microbial strains and the composition containing one or more lipopolysaccharides are administered simultaneously. In some embodiments, the composition containing one or more microbial strains and the composition containing one or more lipopolysaccharides are administered sequentially. In some embodiments, the composition containing one or more microbial strains and the composition containing one or more lipopolysaccharides are administered via different administration routes.

[0016] In some embodiments, the method includes comparing the level of one or more metabolites in a sample derived from the subject to a reference value. In some embodiments, the reference value is a control reference value. In some embodiments, the control reference value is a proven value, such as a previously measured value or a value in the literature. In some embodiments, the reference value is the level of one or more metabolites in a control sample derived from the subject, obtained from the subject before the subject ingested one or more microbial strains, one or more lipopolysaccharides, or both.

[0017] In some embodiments, the method includes measuring the percentage difference between the levels of one or more metabolites in the measured sample and a control reference value.

[0018] In some embodiments, the method includes determining whether one or more microbial strains modulate the levels of one or more metabolites in a subject. In some embodiments, if it is determined that the administered one or more microbial strains modulate the levels of one or more metabolites in the subject, the method includes administering at least a subset of one or more microbial strains to the subject. In some embodiments, the one or more metabolites are associated with a disease, disorder, or illness that the subject has or is at risk of developing.

[0019] In some embodiments, the method is a method for regulating one or more metabolites in a subject.

[0020] In some embodiments, the method is a method for characterizing the ability of one or more microbial strains to modulate one or more metabolites in a subject.

[0021] In some embodiments, the method is a method for characterizing the metabolome of a subject.

[0022] In some embodiments, the method is a method for treating or ameliorating a disease, disorder, or illness in a subject, wherein the disease, disorder, or illness is related to one or more metabolites.

[0023] The present disclosure provides, among other things, compositions comprising one or more microbial strains. In some embodiments, the one or more microbial strains are one or more of the microbial strains listed in Table 5. In some embodiments, the one or more microbial strains are two or more of the microbial strains listed in Table 5. In some embodiments, the one or more microbial strains are five or more of the microbial strains listed in Table 5. In some embodiments, the one or more microbial strains are ten or more of the microbial strains listed in Table 5.

[0024] The present disclosure provides a composition comprising Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, Acidaminococcus sp., or a combination thereof. In some embodiments, the composition comprises at least two microbial strains selected from the group consisting of Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, and Acidaminococcus sp. In some embodiments, the composition comprises at least five microbial strains selected from the group consisting of Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, and Acidaminococcus sp. In some embodiments, the composition comprises or consists of Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, and Acidaminococcus sp.

[0025] In some embodiments, the composition is a pharmaceutical composition. In some embodiments, the composition contains a pharmaceutically acceptable carrier.

[0026] In some embodiments, the composition is ingestible Goods That is the case.

[0027] This disclosure specifies that the compositions described herein are intended for use in modulating one or more metabolites in a subject.

[0028] This disclosure specifies that the compositions described herein are intended for use in characterizing the ability of one or more microbial strains to regulate one or more metabolites in a subject.

[0029] This disclosure specifies that the compositions described herein are intended for use in characterizing the metabolome under consideration.

[0030] This disclosure specifies that the compositions described herein are intended for use in treating or improving a disease, disorder, or illness in which one or more metabolites are associated with a subject.

[0031] This disclosure provides the use of the compositions described herein for modulating one or more metabolites in a subject.

[0032] This disclosure provides the use of the compositions described herein for characterizing the ability of one or more microbial strains to regulate one or more metabolites in a target.

[0033] This disclosure provides the use of the compositions described herein for characterizing a target metabolome.

[0034] This disclosure provides the use of the compositions described herein for treating or improving a disease, disorder, or illness in a subject, wherein the disease, disorder, or illness is related to one or more metabolites.

[0035] These and other embodiments included in this disclosure are further described below and in the claims. This disclosure relates, for example, to the following: [1] A method comprising measuring the level of one or more metabolites in a sample derived from a target, The aforementioned subject is, (i) A composition containing one or more microbial strains, (ii) A composition containing one or more lipopolysaccharides, (iii) combinations of those The method described above, which involves ingesting [the substance]. [2] The method according to item 1, wherein the subject is a mammal. [3] The method according to item 1 or 2, wherein the subject is a human. [4] The method according to any one of items 1 to 3, wherein one or more microbial strains are derived from the mammalian microbiome. [5] The method according to any one of items 1 to 4, wherein one or more microbial strains are derived from the human microbiome. [6] The method according to any one of items 1 to 5, wherein one or more microbial strains are derived from the target microbiome. [7] The method according to any one of items 1 to 6, wherein one or more microbial strains are selected from Table 5. [8] The method according to any one of claims 1 to 7, wherein the one or more microbial strains are Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, Acidaminococcus sp., or a combination thereof. [9] The method according to any one of claims 1 to 8, wherein the composition comprises two or more microbial strains.

[10] The method according to any one of claims 1 to 9, wherein the composition comprises five or more microbial strains.

[11] The method according to any one of claims 1 to 10, wherein the composition comprises 10 or more microbial strains.

[12] The method according to any one of claims 1 to 11, wherein the composition comprises Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, and Acidaminococcus sp.

[13] The method according to any one of items 1 to 12, wherein one or more of the aforementioned lipopolysaccharides are derived from E. coli.

[14] The method according to any one of items 1 to 13, wherein the one or more lipopolysaccharides are derived from E. coli 0111.B4.

[15] The method according to any one of items 1 to 14, wherein the one or more metabolites are selected from Table 1, Table 2, Table 3, Table 4, or a combination thereof.

[16] The method according to any one of claims 1 to 15, wherein at least one of the one or more metabolites is associated with a disease, disorder, or illness.

[17] The method according to paragraph 16, wherein the subject is suffering from or at risk of suffering from the disease, disability, or illness.

[18] The method according to any one of items 1 to 17, wherein the sample is cells or tissue, or includes them.

[19] The method according to any one of items 1 to 18, wherein the sample is a body fluid or contains a body fluid.

[20] The method according to any one of claims 1 to 19, wherein the sample is amniotic fluid, aqueous humor, ascites, bile, bone marrow, blood, breast milk, cerebrospinal fluid, earwax, chyle, keems, ejaculate, endolymph, exudate, feces, gastric acid, gastric juice, lymph, mucus, pericardial fluid, perilymph, ascites, pleural fluid, pus, mucosal secretions, saliva, sebum, semen, serum, smegma, sputum, synovial fluid, sweat, tears, urine, vaginal secretions, vitreous fluid, vomit, interstitial fluid, lymph, plasma, mucus, digestive fluid, feces, and / or combinations or components thereof.

[21] The method according to any one of claims 1 to 20, wherein measuring the level of one or more metabolites in a sample derived from the subject is equivalent to quantifying the level of one or more metabolites in the sample derived from the subject.

[22] The method according to any one of claims 1 to 21, further comprising administering the composition containing one or more microbial strains to the subject.

[23] The method according to any one of claims 1 to 22, further comprising comparing the level of one or more metabolites in the sample derived from the subject with a reference value.

[24] The method according to item 23, wherein the aforementioned reference value is a control reference value.

[25] The method according to claim 23, wherein the reference value is the level of one or more metabolites in a control sample derived from the subject, obtained from the subject before the subject ingests one or more microbial strains, one or more lipopolysaccharides, or both.

[26] A method for regulating one or more metabolites in a subject, as described in any one of items 1 to 25.

[27] A method for characterizing the ability of one or more microbial strains to regulate one or more metabolites in a target, as described in any one of items 1 to 25.

[28] A method for characterizing the target metabolome, as described in any one of items 1 to 25.

[29] A method for treating or improving a disease, disorder, or illness in a subject, wherein the disease, disorder, or illness is related to one or more metabolites, according to any one of claims 1 to 25.

[30] A composition containing one or more microbial strains listed in Table 5.

[31] The composition according to item 30, comprising two or more microbial strains listed in Table 5.

[32] The composition according to item 30 or 31, comprising five or more microbial strains listed in Table 5.

[33] A composition according to any one of items 30 to 32, comprising 10 or more microbial strains listed in Table 5.

[34] A composition comprising Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, Acidaminococcus sp., or a combination thereof.

[35] The composition according to claim 34, comprising at least two microbial strains selected from the group consisting of Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, and Acidaminococcus sp.

[36] The composition according to claim 34 or 35, comprising at least five microbial strains selected from the group consisting of Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, and Acidaminococcus sp.

[37] A composition according to any one of claims 34 to 36, comprising Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, and Acidaminococcus sp.

[38] The composition according to any one of claims 30 to 37, wherein the composition is a pharmaceutical composition.

[39] The composition according to any one of claims 30 to 38, wherein the composition is an article that can be ingested.

[40] A composition according to any one of claims 30 to 39, for use in modulating one or more metabolites in a subject.

[41] A composition according to any one of claims 30 to 39, for use in characterizing the ability of one or more microbial strains to regulate one or more metabolites in a target.

[42] A composition according to any one of sections 30 to 39, for use in characterizing the metabolome of interest.

[43] A composition according to any one of sub-sub

[44] Use of any one of the compositions described in subsections 30 to 39 for modulating one or more metabolites in a subject.

[45] Use of any one of the compositions described in subsections 30 to 39 for characterizing the ability of one or more microbial strains to regulate one or more metabolites in a target.

[46] Use of any one of the compositions described in items 30 to 39 for characterizing the target metabolome.

[47] Use of a composition according to any one of paragraphs 30 to 39 for the treatment or improvement of a disease, disorder, or illness in a subject, wherein the disease, disorder, or illness is related to one or more metabolites.

[0036] Definition The scope of the present invention is defined by the claims appended herein and is not limited by any specific embodiment described herein. A person skilled in the art will recognize, upon reviewing this specification, various modifications that may be equivalent to or otherwise within the scope of the described embodiments. In general, terms used herein have their understood meanings in the art unless otherwise explicitly indicated. Explicit definitions of certain terms are provided below, but the meanings of these terms and other terms in specific cases throughout this specification will be clear to a person skilled in the art from the context.

[0037] The use of sequential terms such as “first,” “second,” “third,” etc., that modify elements of a claim in the claims does not in itself imply any priority, superiority, or order or temporal order in which the actions of a method are performed over any element of one claim, but rather is simply used as a label to distinguish one element of a claim having a particular name from another element having the same name (except for the use of sequential terms).

[0038] As used herein, the articles “a” and “an” should be understood to include plural referents unless explicitly indicated to the contrary. Any claim or description containing “or” between one or more members of a group is considered to be applicable if one, more than one, or all of the members of that group are present in, used in, or otherwise associated with a given product or process, unless otherwise indicated or evident from the context. In some embodiments, exactly one member of a group is present in, used in, or otherwise associated with a given product or process. In some embodiments, more than one, or all members of a group are present in, used in, or otherwise associated with a given product or process. Unless otherwise indicated, or unless it is obvious to those skilled in the art that a contradiction or inconsistency would occur, the present invention should be understood to encompass all variations, combinations, and permutations in which one or more limitations, elements, clauses, descriptive terms, etc., from one or more of the enumerated claims are introduced into another claim (or any other claim, where relevant) that depends on the same basic claim. Where elements are presented as a list (e.g., in a Markush group or similar form), each subgroup of the element is also disclosed, and any element(s) may be removed from such subgroup. Generally, where an embodiment or aspect is said to "comprising" a particular element, feature, etc., it should be understood that a particular embodiment or aspect "consist" of such element, feature, etc., or "consist essentially of" them. For the purposes of simplification, these embodiments are not explicitly defined in every example herein. It should also be understood that any embodiment or aspect may be expressly excluded from the claims, regardless of whether such particular exclusions are enumerated in the specification.

[0039] Administration: As used herein, the term “administration” typically refers to the administration of a composition to a subject or system to achieve the delivery of a drug to that subject or system. In some embodiments, the drug is a composition or is contained within a composition. In some embodiments, the drug is produced through the metabolism of the composition or one or more of its components. Those skilled in the art will recognize the various routes that may be used for administration to a subject, e.g., a human, under appropriate circumstances. For example, in some embodiments, administration may be ocular, oral, parenteral, topical, etc. In some specific embodiments, administration may be via the bronchi (e.g., by bronchial infusion), buccal, skin (this may be, or include, one or more of the following: dermis, intradermal, interdermal, transdermal, etc.), enteral, intra-arterial, intradermal, gastric, intramedullary, intramuscular, intranasal, intraperitoneal, intrathecal, intravenous, ventricle, within a specific organ (e.g., within the liver), mucosa, nasal cavity, oral, rectal, subcutaneous, sublingual, topical, trachea (e.g., by intratracheal infusion), vagina, vitreous humor, etc. In many embodiments provided by this disclosure, administration is oral administration. In some embodiments, administration may involve only a single dose. In some embodiments, administration may involve the application of a number of doses. In some embodiments, administration may involve intermittent (e.g., multiple doses spaced apart) dosing and / or cyclical (e.g., individual doses spaced apart) dosing. In some embodiments, administration may involve continuous drug delivery (e.g., perfusion) over a selected period of time. Cell administration may be by any suitable route that results in delivery to a desired site in the subject, in which at least a portion of the delivered cells or cellular components remain viable. The viability period of cells after administration to the subject can range from as short as a few hours (e.g., 24 hours) to several days or even as long as several years (i.e., long-term engraftment). In some embodiments, administration may involve the delivery of a bacterial extract or preparation containing one or more bacterial metabolites and / or by-products, but lacking fully viable bacterial cells.

[0040] Analogue: As used herein, the term “analogue” refers to a substance that shares one or more specific structural features, elements, components, or parts with a reference substance. Typically, an “analogue” exhibits a remarkable structural similarity to the reference substance, for example, by sharing a core or consensus structure, but at the same time differs in a particular individual way. In some embodiments, an analogue is a substance that can be produced from a reference substance, for example, by a chemical manipulation of the reference substance. In some embodiments, an analogue is a substance that can be produced through the implementation of a synthetic process that is substantially similar to (for example, sharing several steps with) the synthetic process that produces the reference substance. In some embodiments, an analogue is produced or can be produced through the implementation of a synthetic process different from the synthetic process used to produce the reference substance.

[0041] Approximately: When applied to one or more values ​​of interest, this includes values ​​similar to the defined baseline. In certain embodiments, the terms "approximately" or "about" refer to a range of values ​​that fall within ±10% (more than or less than) the defined baseline, unless otherwise specified or evident from the context (unless such number exceeds 100% of the possible values).

[0042] Equivalent: As used herein, the term “equivalent” means two or more drugs, entities, states, conditions, subjects, etc., that may not be identical to one another but are similar enough to allow comparison between them, so that a person skilled in the art can reasonably draw conclusions based on observed differences or similarities. In some embodiments, equivalent sets of conditions, situations, individuals, or groups are characterized by several substantially identical features and one or a few variable features. A person skilled in the art will understand, in context, what degree of identity is required for two or more such drugs, entities, states, conditions, etc., to be considered equivalent under any given situation. For example, a person skilled in the art will understand that a set of situations, individuals, or groups are equivalent if they are characterized by a sufficient number and variety of substantially identical features to guarantee a reasonable conclusion that differences in results or observed phenomena under different situations, individuals, or groups, or under different situations, individuals, or groups, are caused by or exhibit variations in the variable features.

[0043] Conservative: As used herein, this refers to cases where a conservative amino acid substitution involves the substitution of one amino acid residue with another amino acid residue having a side-chain R group with similar chemical properties (e.g., charge or hydrophobicity). Generally, conservative amino acid substitutions do not substantially alter the desired functional properties of a protein, such as the ability of a receptor to bind to a ligand. Examples of amino acids with side chains having similar chemical properties include aliphatic side chains such as glycine (Gly, G), alanine (Ala, A), valine (Val, V), leucine (Leu, L), and isoleucine (Ile, I); aliphatic-hydroxyl side chains such as serine (Ser, S) and threonine (Thr, T); amide-containing side chains such as asparagine (Asn, N) and glutamine (Gln, Q); aromatic side chains such as phenylalanine (Phe, F), tyrosine (Tyr, Y), and tryptophan (Trp, W); basic side chains such as lysine (Lys, K), arginine (Arg, R), and histidine (His, H); acidic side chains such as aspartic acid (Asp, D) and glutamic acid (Glu, E); and sulfur-containing side chains such as cysteine ​​(Cys, C) and methionine (Met, M). Conservative amino acid substituents include, for example, valine / leucine / isoleucine (Val / Leu / Ile, V / L / I), phenylalanine / tyrosine (Phe / Tyr, F / Y), lysine / arginine (Lys / Arg, K / R), alanine / valine (Ala / Val, A / V), glutamic acid / aspartic acid (Glu / Asp, E / D), and asparagine / glutamine (Asn / Gln, N / Q). In some embodiments, the conservative amino acid substitution may be the substitution of any native residue in a protein with alanine, for example, as used in alanine scanning mutagenesis. In some embodiments, the conservative substitution is one that has a positive value in the PAM250 log-likelihood matrix disclosed in Gonnet, GH et al., 1992, Science 256:1443-1445 (the entire document is incorporated herein by reference). In some embodiments, the permutation is a moderately conservative permutation, and the permutation has a non-negative value in the PAM250 log-likelihood matrix.

[0044] [Table 1]

[0045] Control: As used herein, "control" refers to the meaning of "control" as understood in the art, which is a standard against which results are compared. Typically, controls are used to enhance the integrity of an experiment by isolating such variable in order to draw conclusions about it. In some embodiments, a control is a reaction or assay performed concurrently with the test reaction or assay to provide a comparator. "Control" also includes "control animals." "Control animals" may have modifications as described herein, modifications different from those described herein, or may not have modifications (i.e., wild-type animals). In one experiment, the "test" (i.e., the variable being tested) is applied. In a second experiment, the "control," i.e., the variable being tested, is not applied. In some embodiments, the control is an existing control (i.e., a previously performed test or assay, or of a known quantity or result). In some embodiments, the control is or includes a printed or otherwise preserved record. A control may be a positive control or a negative control.

[0046] Determine, measure, evaluate, assess, assay, and analyze: Determine, measure, evaluate, assess, assay, and analyze are used interchangeably herein to refer to any form of measurement and include determining whether or not an element is present. These terms include both quantitative and / or qualitative determinations. Assays can be relative or absolute. "Assay in relation to the presence" can mean determining the quantity of something that is present and / or determining whether or not it is present or absent.

[0047] Dosage Form: Those skilled in the art will understand that the term “dosage form” can be used to refer to a physically distinct unit of a drug (e.g., a therapeutic agent) for administration to a subject. Typically, each such unit contains a predetermined amount of the drug. In some embodiments, such amount is a unit dose (or the whole) appropriate for administration according to a drug regimen (i.e., a therapeutic drug regimen) that has been determined to correlate with a desired or beneficial outcome when administered to a relevant population. Those skilled in the art will understand that the total amount of a therapeutic composition or therapeutic agent to be administered to a particular subject may be determined by one or more attending physicians and may involve administration in multiple dosage forms.

[0048] Dosage regimen: Those skilled in the art will understand that the term “dosage regimen” can be used to refer to a set of unit doses (typically more than one) administered individually to a subject, typically at intervals. In some embodiments, a given drug has a recommended dosage regimen, which may consist of one or more doses. In some embodiments, a dosage regimen comprises multiple doses, each of which is timed apart from the others. In some embodiments, individual doses are spaced apart by the same duration, and in some embodiments, a dosage regimen comprises multiple doses, each of which is spaced apart by at least two different durations. In some embodiments, all doses in a dosage regimen are of the same unit dose. In some embodiments, different doses in a dosage regimen are of different amounts. In some embodiments, a dosage regimen comprises a first dose, followed by one or more additional doses, each a second dose different from the first dose. In some embodiments, the drug regimen comprises a first dose, followed by one or more additional doses at a second dose equal to the first dose. In some embodiments, the drug regimen correlates with a desired or beneficial outcome when administered across a relevant population.

[0049] Manipulated: Generally, the term “manipulated” refers to a form of artificial manipulation. For example, a cell or organism is considered “manipulated” if its genetic information is altered (e.g., new genetic material that was not previously present is introduced, for example, by transformation, mating, somatic hybridization, transfection, transduction, or other mechanisms, or if previously present genetic material is altered or removed, for example, by substitution or deletion mutations, or by a mating protocol). By convention and as understood by those skilled in the art, the offspring of a manipulated polynucleotide or cell are typically still referred to as “manipulated,” even if the actual manipulation was performed on the original entity.

[0050] Excipients: When used herein, this refers to inert (e.g., non-therapeutic) agents that may be included in a pharmaceutical composition to provide or assist in providing, for example, a desired consistency or stabilizing effect. In some embodiments, suitable pharmaceutical excipients may include, for example, starch, glucose, lactose, sucrose, gelatin, malt, rice, fine powder, chalk, silica gel, sodium stearate, glyceryl monostearate, talc, sodium chloride, skim milk powder, glycerol, propylene glycol, water, ethanol, and the like.

[0051] Functional: As used herein, a “functional” biomolecule is a biomolecule in a form that exhibits its characteristic properties and / or activity. A biomolecule may have two functions (i.e., difunctional) or many functions (i.e., polyfunctional).

[0052] Gene: As used herein, refers to a DNA sequence in a chromosome that codes for a product (e.g., an RNA product and / or a polypeptide product). In some embodiments, a gene includes a coding sequence (i.e., a sequence that codes for a particular product). In some embodiments, a gene includes a non-coding sequence. In some specific embodiments, a gene may include both coding (e.g., exon) and non-coding (e.g., intron) sequences. In some embodiments, a gene may include one or more regulatory sequences (e.g., promoters, enhancers, etc.) and / or intron sequences that can control or influence one or more modes of gene expression (e.g., cell-type-specific expression, inducible expression, etc.). For clarity, note that as used in this disclosure, the term “gene” generally refers to a portion of a nucleic acid that codes for a polypeptide or a fragment thereof. As will be clear to those skilled in the art from the context, this term may optionally include regulatory sequences. This definition is not intended to exclude the application of the term “gene” to non-protein-coding expression units, but is intended to clarify that as used herein, this term most often refers to polypeptide-coding nucleic acids.

[0053] To improve, increase, enhance, inhibit, or reduce: As used herein, the terms “improve,” “increase,” “enhance,” “inhibit,” “reduce,” or their grammatical equivalents, indicate a value relative to a baseline or other reference measure. In some embodiments, the value is a statistically significant difference from the baseline or other reference measure. In some embodiments, a suitable reference measure may be, or include, a measurement in a particular system (e.g., in a single individual) under otherwise equivalent conditions, except in the presence of a particular drug or treatment (e.g., before and / or after), or in the presence of a suitable equivalent reference drug. In some embodiments, a suitable reference measure may be, or include, a measurement in an equivalent system known or expected to respond in a particular manner in the presence of a relevant drug or treatment. In some embodiments, the suitable reference is a negative reference, and in some embodiments, the suitable reference is a positive reference.

[0054] Isolated: As used herein, isolated means a substance and / or entity that (1) has been separated from at least a portion of the components to which it was originally produced (whether in nature and / or in an experimental environment) and / or (2) has been artificially designed, produced, prepared and / or manufactured. In some embodiments, the isolated substance or entity may be concentrated, and in some embodiments, the isolated substance or entity may be pure. In some embodiments, the isolated substance and / or entity may be separated from about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more than about 99% of the other components to which they were originally produced. In some embodiments, the isolated drug is ultrapure of about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 99%. When used herein, a substance is “pure” if it substantially contains no other components. In some embodiments, as will be understood by those skilled in the art, a substance may still be considered “concentrated,” “isolated,” or even “pure” after being combined with certain other components, such as one or more carriers or excipients (e.g., buffers, solvents, water, etc.). In such embodiments, the isolation or purity percentage of the substance is calculated without including such carriers or excipients. Those skilled in the art are aware of the various techniques for isolating (e.g., concentrating or purifying) a substance or drug (e.g., using one or more of fractional distillation, extraction, precipitation, or other separation methods).

[0055] Level: As used herein, the term “level” refers to a measure of the amount or quantity of a substance (e.g., a metabolite). In some embodiments, the level may simply be the presence or absence of a substance. The level of a substance can be expressed in multiple ways or forms. For example, in some embodiments, the level may be expressed as a percentage (%), a measure of weight (e.g., mg, μg, ng, etc.), a measure of concentration (e.g., mg / mL, μg / mL, ng / mL, etc.), a measure of volume (e.g., mL, μL, nL, etc.), a rate of change, etc.

[0056] Metabolites: As used herein, the term “metabolites” refers to substances (e.g., small molecules, macromolecules, organic compounds, or inorganic compounds) that are produced or used during metabolism. Metabolism is generally understood as the process by which substances (e.g., foods, drugs, chemicals, cells, or tissues) are chemically broken down. In some embodiments, metabolites are end products. In some embodiments, metabolites are intermediates. Exemplary metabolites are shown herein, e.g., in Annex 1-1, and in Figures 1-4 and 7-14. Exemplary metabolic pathways are shown herein, e.g., in Annex 1-2, and in Figures 7-14.

[0057] Pharmaceutical Composition: As used herein, the term “pharmaceutical composition” refers to a composition in which an active agent is formulated together with one or more pharmaceutically acceptable carriers. In some embodiments, the active agent is present in a unit dose appropriate for administration in a therapeutic regimen that exhibits a statistically significant probability of achieving a predetermined therapeutic effect when administered to a relevant population. In some embodiments, the pharmaceutical composition may be specifically formulated for administration in solid or liquid form, including those adapted for: oral administration, e.g., oral tablets (aqueous or non-aqueous solutions or suspensions), tablets, e.g., those intended for buccal, sublingual, and systemic absorption, pills, powders, granules, pastes for application to the tongue, capsules, etc. In some embodiments, the active agent may be or contain cells or cell populations (e.g., cultures of EES microorganisms). In some embodiments, the active agent may be or contain extracts or components of cells or cell populations (e.g., cultures). In some embodiments, the active agent may be or contain isolated, purified, or pure compounds. In some embodiments, the active agent may be synthesized in vitro (e.g., via chemical synthesis and / or enzymatic synthesis). In some embodiments, the active agent may be a natural product (whether isolated from its natural source or synthesized in vitro) or may contain one.

[0058] pharmaceutically acceptable: When used herein, the term “pharmaceutically acceptable,” which may be used, for example, in reference to a carrier, diluent, or excipient used to formulate a pharmaceutical composition such as those disclosed herein, means that such carrier, diluent, or excipient is compatible with the other components of the composition and is not harmful to its recipient.

[0059] pharmaceutically acceptable carrier: As used herein, the term “pharmaceutically acceptable carrier” means a pharmaceutically acceptable material, composition, or vehicle, such as a liquid or solid filler, diluent, excipient, or solvent encapsulant, that is involved in transporting or delivering the compound of interest from one organ or body part to another. Each carrier must be compatible with the other components of the formulation and “acceptable” in the sense that it is not harmful to the subject (e.g., the patient). Some examples of materials that can serve as pharmaceutically acceptable carriers include sugars such as lactose, glucose, and sucrose; starches such as corn starch and potato starch; celluloses and their derivatives such as sodium carboxymethylcellulose, ethylcellulose, and cellulose acetate; tragacanth powder; malt; gelatin; talc; excipients such as cocoa butter and suppository waxes; oils such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil, and soybean oil; glycols such as propylene glycol; polyols such as glycerin, sorbitol, mannitol, and polyethylene glycol; esters such as ethyl oleate and ethyl laurate; agar; buffers such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline; Ringer's solution; ethyl alcohol; pH buffer solutions; polyesters, polycarbonates, and / or polyanhydrides; and other non-toxic, suitable substances used in pharmaceutical formulations.

[0060] Prevention: As used herein, the term “prevention” refers to the delay of the onset of one or more symptoms of a particular disease, disorder, or illness, and / or a reduction in their frequency and / or severity. In some embodiments, prevention is evaluated against a population such that a drug is considered to “prevent” a particular disease, disorder, or illness if a statistically significant reduction in the onset, frequency, and / or intensity of one or more symptoms of the disease, disorder, or illness is observed in a population susceptible to the disease. In some embodiments, prevention may be considered complete, for example, if the onset of the disease, disorder, or illness is delayed for a predetermined period of time.

[0061] Reference: This describes the standard or control against which a comparison is made when used herein. For example, in some embodiments, the drug, animal, individual, population, sample, sequence, or value of interest is compared to a reference or control drug, animal, individual, population, sample, sequence, or value. In some embodiments, the reference or control is tested and / or determined substantially simultaneously with the test or determination of interest. In some embodiments, the reference or control is an existing reference or control, optionally embodied in a tangible medium. Typically, as will be understood by those skilled in the art, the reference or control is determined or characterized under conditions or circumstances equivalent to those being evaluated. Those skilled in the art will understand when there is sufficient similarity to demonstrate reliability and / or justification for comparison with a particular possible reference or control. In some embodiments, the reference is a negative control reference, and in some embodiments, the reference is a positive control reference.

[0062] Risk: As understood from context, “risk” of a disease, disability, and / or illness refers to the likelihood that a particular individual will develop the disease, disability, and / or illness. In some embodiments, risk is expressed as a percentage. In some embodiments, risk is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or up to 100%. In some embodiments, risk is expressed as a relative risk to the risk associated with a reference sample or reference sample group. In some embodiments, the reference sample or reference sample group has a known risk of the disease, disability, illness, and / or event. In some embodiments, the reference sample or reference sample group is derived from individuals equivalent to a particular individual. In some embodiments, the relative risk is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or greater.

[0063] Sample: As used herein, the term “sample” typically refers to an aliquot of material obtained from or derived from the source of interest. In some embodiments, the source of interest is a biological or environmental source. In some embodiments, the source of interest may be, or may include, cells or organisms, such as microorganisms, plants, or animals (e.g., humans). In some embodiments, the source of interest may be, or may include, biological tissue or biological fluids. In some embodiments, biological tissue or bodily fluid may be amniotic fluid, aqueous humor, ascites, bile, bone marrow, blood, breast milk, cerebrospinal fluid, earwax, chyle, ovoid, ejaculate, endolymph, exudate, feces, gastric acid, gastric juice, lymph, mucus, pericardial fluid, perilymph, peritoneal fluid, pleural fluid, pus, mucosal secretions, saliva, sebum, semen, serum, smegma, sputum, synovial fluid, sweat, tears, urine, vaginal secretions, vitreous fluid, vomit, plasma, mucus, digestive fluid, feces, and / or combinations or components thereof, or may include them. In some embodiments, biological fluid may be intracellular fluid, extracellular fluid, intravascular fluid (plasma), interstitial fluid, lymph, and / or cell permeable fluid, or may include them. In some embodiments, biological fluid may be plant exudate, or may include it. In some embodiments, biological tissue or specimens may be obtained, for example, by aspiration, biopsy (e.g., microneedle or tissue biopsy), swab (e.g., oral, nasal, skin, or vaginal swabs), scraping, surgery, washing or lavage (e.g., bronchoalveolar epithelium, tubules, nasal cavity, eye, oral cavity, uterus, vagina, or other washing or lavage). In some embodiments, the biological specimen is or contains cells obtained from an individual. In some embodiments, the specimen is a “primary specimen” obtained directly from the source of interest by any suitable means. In some embodiments, as will be clear from the context, the term “specimen” refers to a preparation obtained by processing a primary specimen (e.g., by removing one or more components of the primary specimen and / or by adding one or more agents to the primary specimen). For example, filtration using a semipermeable membrane.Such “processed sample” may include, for example, nucleic acids or proteins extracted from the sample, or obtained by subjecting the primary sample to one or more techniques such as nucleic acid amplification or reverse transcription, isolation and / or purification of a specific component.

[0064] Low molecular weight: As used herein, the term “low molecular weight” refers to small organic or inorganic molecules having a molecular weight of less than approximately 3,000 daltons. Generally, low molecular weight may have a molecular weight of less than 3,000 daltons (Da). Small molecules may be, for example, at least about 100 Da to about 3,000 Da (e.g., about 100 to about 3,000 Da, about 100 to about 2,500 Da, about 100 to about 2,000 Da, about 100 to about 1,750 Da, about 100 to about 1,500 Da, about 100 to about 1,250 Da, about 100 to about 1,000 Da, about 100 to about 750 Da, about 100 to about 500 Da, about 200 to about 1,500, about 500 to about 1,000, about 300 to about 1,000 Da, or about 100 to about 250 Da).

[0065] Subject: As used herein, the term “subject” refers to the individual to whom the treatment provided is applied. In some embodiments, the subject is an animal. In some embodiments, the subject is a mammal, for example, a mammal that is experiencing or susceptible to one or more diseases, disorders, or illnesses as described herein. In some embodiments, the animal is a vertebrate, for example, a non-human primate (especially a higher primate), a mammal such as a sheep, a dog, a rodent (e.g., a mouse or a rat), a guinea pig, a goat, a pig, a cat, a rabbit, or a cow. In some embodiments, the animal is a non-mammalian such as a chicken, an amphibian, a reptile, or an invertebrate model such as C. elegans. In some embodiments, the subject is a human. In some embodiments, the subject is suffering from or susceptible to one or more diseases, disorders, or illnesses as described herein. In some embodiments, the subject exhibits one or more symptoms of one or more diseases, disorders, or illnesses as described herein. In some embodiments, the subject has been diagnosed with one or more diseases, disorders, or illnesses as described herein. In some embodiments, the subject is currently receiving or has received a specific therapy for diagnosing and / or treating a disease, disorder, or illness. In other embodiments, the subject is an experimental animal or surrogate animal used as a disease model.

[0066] "Substantially," as used herein, refers to a qualitative state that indicates the entire or nearly entire range or degree of the desired characteristic or property. Those skilled in the biological art will understand that it is rare, if any, for biological and chemical phenomena to progress toward completion and / or completeness, or to achieve or avoid absolute results. The term "substantially" is therefore used herein to capture the potential lack of completeness inherent in many biological and chemical phenomena.

[0067] Treatment regimen: When the term “treatment regimen” is used herein, it means a drug regimen whose administration across a relevant population may correlate with a desired or beneficial treatment outcome.

[0068] Therapeutic dose: As used herein, this means the amount that produces the desired effect for which it is administered. In some embodiments, this term refers to an amount sufficient to treat a disease, disorder, and / or disease when administered to a population that is suffering from or susceptible to the disease, disorder, and / or disease, according to a therapeutic drug regimen. In some embodiments, a therapeutic dose is an amount that reduces the incidence and / or severity of one or more symptoms of a disease, disorder, and / or disease, and / or delays their onset. Those skilled in the art will understand that the term “therapeutic dose” does not actually require that successful treatment be achieved in a particular individual. Rather, a therapeutic dose may be an amount that, when administered to patients requiring such treatment, provides a particular desired pharmacological response in a significant number of subjects. In some embodiments, a reference to a therapeutic dose may refer to an amount measured in one or more specific tissues (e.g., tissues affected by the disease, disorder, or disease) or fluids (e.g., blood, saliva, serum, sweat, tears, urine, etc.). Those skilled in the art will understand that in some embodiments, a therapeutically effective amount of a particular drug or therapy may be formulated and / or administered as a single dose. In some embodiments, a therapeutically effective drug may be formulated and / or administered in multiple doses, for example, as part of a drug regimen.

[0069] Treatment: As used herein, the term “treatment” (and also “to treat” or “to treat”) refers to any application of therapy that partially or completely alleviates, improves, reduces, inhibits, delays the onset of, reduces the severity of, and / or reduces the incidence of one or more symptoms, features, and / or causes of a particular disease, disorder, and / or illness. In some embodiments, such treatment may be the treatment of subjects who do not exhibit signs of the relevant disease, disorder, and / or illness, and / or subjects who exhibit only the initial signs of the disease, disorder, and / or illness. Alternatively or in addition, such treatment may be the treatment of subjects who exhibit one or more established signs of the relevant disease, disorder, and / or illness. In some embodiments, treatment may be the treatment of subjects diagnosed with the relevant disease, disorder, and / or illness. In some embodiments, treatment may be the treatment of subjects known to have one or more susceptibility factors that statistically correlate with an increased risk of developing the relevant disease, disorder, and / or illness. [Brief explanation of the drawing]

[0070] [Figure 1] (Table 1) This table shows the percentage change in metabolite levels in female mice treated with the CT10 composition compared to sham treatment, and the corresponding levels of metabolites in each microbial species present in the CT10 composition. Microbial species with the highest metabolite levels are shown in bold and shaded. [Figure 2] (Table 2) This table shows the percentage change in metabolite levels in male mice treated with the CT10 composition compared to sham treatment, and the corresponding levels of metabolites in each microbial species present in the CT10 composition. Microbial species with the highest metabolite levels are shown in bold and shaded. [Figure 3](Table 3) This table shows the percentage change in metabolite levels measured in female mice injected with the LPS composition, compared to treatment with a dummy injection. It also shows the percentage change in metabolite levels measured in female mice treated with the CT10 composition and then injected with the LPS composition, compared to treatment with a dummy injection. [Figure 4] (Table 4) This table shows the percentage change in metabolite levels measured in female mice injected with the LPS composition, compared to treatment with a dummy injection. It also shows the percentage change in metabolite levels measured in male mice treated with the CT10 composition and then injected with the LPS composition, compared to treatment with a dummy injection. [Figure 5] This figure contains data showing the results of PCA. PC1 and PC2 represent the first and second principal components, respectively. The numbers in parentheses are the measured contribution rates. The plot labels are the sample names. "PCA Score" contains the measured contribution rates for each component. "Factor Loadings" contains the factor loadings used for each component. [Figure 6] This figure contains data showing the results of detected hierarchical cluster analysis (HCA). The horizontal and vertical axes represent sample names and peaks, respectively. HCA was performed at the peaks. The distances between peaks are then displayed in a tree diagram. The heatmap includes the normalized HCA detection values. [Figure 7] This figure shows an exemplary pathway map (overview of primary metabolism). The metabolites detected in this study are plotted on the pathway map. The bars / lines represent the relative area of ​​each metabolite in the control (blue) and treatment (red) groups, respectively. ND indicates that the metabolite was not detected. [Figure 8] This figure shows an exemplary pathway map (central carbon metabolism). The metabolites detected in this study are plotted on the pathway map. The bars / lines represent the relative area of ​​each metabolite in the control (blue) and treatment (red) groups, respectively. ND indicates that the metabolite was not detected. [Figure 9]This figure shows an exemplary pathway map (urea cycle-related metabolism). The metabolites detected in this study are plotted on the pathway map. The bars / lines represent the relative area of ​​each metabolite in the control (blue) and treatment (red) groups, respectively. ND indicates that the metabolite was not detected. [Figure 10] This figure shows an exemplary pathway map (lipid and amino acid metabolism). The metabolites detected in this study are plotted on the pathway map. The bars / lines represent the relative area of ​​each metabolite in the control (blue) and treatment (red) groups, respectively. ND indicates that the metabolite was not detected. [Figure 11] This figure shows exemplary pathway maps (branched chains and aromatic amino acids). The metabolites detected in this study are plotted on the pathway map. The bars / lines represent the relative area of ​​each metabolite in the control (blue) and treatment (red) groups, respectively. ND indicates that the metabolite was not detected. [Figure 12] This figure shows an exemplary pathway map (nucleotide metabolism). The metabolites detected in this study are plotted on the pathway map. The bars / lines represent the relative area of ​​each metabolite in the control (blue) and treatment (red) groups, respectively. ND indicates that the metabolite was not detected. [Figure 13] This figure shows an exemplary pathway map (coenzyme metabolism). The metabolites detected in this study are plotted on the pathway map. The bars / lines represent the relative area of ​​each metabolite in the control (blue) and treatment (red) groups, respectively. indicates that the metabolite was not detected. [Figure 14] This figure shows the levels of other metabolites detected in the control and treatment groups. The bars / lines represent the relative area of ​​each metabolite in the control (blue) and treatment (red) groups, respectively. [Modes for carrying out the invention]

[0071] Microbial preparations(s) and / or constituent(s)(s) This disclosure provides systems and methods for evaluating, characterizing, and identifying one or more microbial strains of a microbiome. Such systems and methods may be useful for evaluating, characterizing, and identifying one or more microbial strains that affect the health of humans, livestock, and / or pets by modulating their respective metabolomes. In some embodiments, one or more microbial strains from the microbiomes of snakes, lizards, fish, or birds are evaluated, characterized, and identified. In some embodiments, one or more microbial strains from the microbiomes of mammals are evaluated, characterized, and identified. The mammalian microbiome may be the microbiome of dogs, cats, horses, cattle, sheep, goats, or pigs. In some embodiments, the microbiomes used in the systems or methods described herein may prevent or treat diseases or illnesses.

[0072] Microbiomes can be isolated from any system or tissue of organisms that support microbial growth. For example, a microbiome may be a skin microbiome, oral microbiome, nasal microbiome, gastrointestinal microbiome, brain microbiome, lung microbiome, or urogenital microbiome. A list of exemplary microbial strains found in the gastrointestinal microbiome is included in Table 5 below. Those skilled in the art will understand that microbiome samples can be obtained in various ways known in the art. For example, skin, oral, nasal, lung, or urogenital microbiome samples can be obtained using swabs or tissue scrapings. In some embodiments, gastrointestinal microbiomes can be sampled from feces. Skin microbiomes, oral microbiomes, nasal microbiomes, gastrointestinal microbiomes, brain microbiomes, lung microbiomes, or urogenital microbiome samples can be obtained via biopsy.

[0073] In some embodiments, the microbiome is that of a healthy individual, or an individual who does not have a particular disease or disorder or is not at risk of developing one. In some embodiments, the microbiome is that of an individual who has a particular disease or disorder or is at risk of developing one. In some embodiments, the microbiome is that of an individual who is known to have a particular disease or disorder. In some embodiments, the human microbiome is that of a human who is not at risk of one or more diseases or illnesses.

[0074] In some embodiments, the microbiome is a reference microbiome. The reference microbiome may be from a healthy individual or an individual that does not have a particular disease or disorder, or is not at risk of developing one. In some cases, the reference microbiome may originate from the same individual as the microbiome being evaluated or characterized, but be obtained at a different time. In some cases, the reference microbiome may originate from the same individual as the microbiome being evaluated or characterized, but be obtained from a different system or tissue.

[0075] In some embodiments, individual microbial strains or combinations of microbial strains may be evaluated, characterized, or identified in relative amounts different from those found in a microbiome if such strains (single or multiple species) were present. For example, the effect of regulating the levels of one or more metabolites of a cell or organism in response to a single strain may be evaluated, characterized, or identified using the in vitro methods described herein (e.g., mammalian cells) or in vivo methods using mammals (e.g., mice, humans, etc.), even if such single strain naturally exists in a microbiome together with other microbial strains. As another example, the effect of regulating the levels of one or more metabolites of a cell or organism in response to two microbial strains may be evaluated, characterized, or identified using the methods described herein, even if such two microbial strains naturally exist in a microbiome together with further microbial strains.

[0076] Furthermore, extracts, components, or compounds of microbial strains may be evaluated, characterized, or identified using the methods described herein. In some examples, extracts, components, or compounds of microbial strains determined to affect the levels of one or more metabolites in an organism (e.g., a mammal) may be evaluated, characterized, or identified. Evaluating, characterizing, or identifying extracts, components, or compounds of microbial strains that affect the levels of one or more metabolites in an organism (e.g., a mammal) may provide further information about potential biomarkers, targets, or protective factors in the microbiome.

[0077] Various techniques are known in the art that can be used to prepare extracts of microbial strains and / or isolate or process extracts, components, or compounds from microbial strains (for example, to isolate and / or purify one or more components or compounds therefrom). To name just a few examples, such techniques may include one or more of the following: organic extraction, vacuum concentration, chromatography, etc.

[0078] Assessment of biological impacts This disclosure provides insight that it is possible to identify, characterize, or modulate one or more levels of metabolites (e.g., metabolome) of an organism (e.g., mammal (e.g., human)) by using the compositions described herein (e.g., microbiome compositions) and bringing the composition(s) into contact with an organism (e.g., by feeding or administering the composition to the organism). In some embodiments, the organism may be suffering from or at risk of suffering from a disease, disorder, or illness. To determine whether one or more compositions affect the level of one or more metabolites (e.g., metabolites that may be indicators of a disease, disorder, or illness), the levels of one or more metabolites in a sample brought into contact with one or more compositions may be observed, measured, or evaluated. To determine whether the compositions disclosed herein may affect the metabolome of the organism, various metabolite levels of the organism may be observed, measured, or evaluated. As just a few examples, metabolites whose levels may be observed, measured, or evaluated in order to determine whether the compositions disclosed herein affect living organisms include, for example, the metabolites listed in Appendix 1-1 and in Figures 1-4 and 7-14.

[0079] In some embodiments, the methods described herein utilize a first sample and a second sample. In some embodiments, the first sample is a reference sample. In some embodiments, the reference sample may be a sample obtained from a subject that has come into contact with the composition, e.g., the CT10 composition (e.g., administered or ingested the composition). In some embodiments, the reference sample may be a sample obtained from a subject that has come into contact with the composition, e.g., the CT10 composition (e.g., administered or ingested the composition) at a first time point. In some embodiments, the reference sample may be a sample obtained from a subject before coming into contact with the composition, e.g., the CT10 composition (e.g., administered or ingested the composition). In some embodiments, the reference sample may be a sample obtained from a healthy individual. In some embodiments, the reference sample may be a sample obtained from an individual that has a disease, disability, or illness, or is at risk of having them. In some embodiments, the reference sample is a control sample. In some embodiments, the reference sample is a negative control sample. In some embodiments, the reference sample is a positive control sample. In some embodiments, the reference sample may be a proven baseline value (e.g., a value across the entire control sample). In some embodiments, the reference sample may be derived from a published publication (e.g., a textbook, a magazine, etc.).

[0080] In some embodiments, the second sample may be a test sample. In some embodiments, the test sample may be a sample obtained from a subject that has come into contact with the composition, e.g., the CT10 composition (e.g., administered or ingested the composition). In some cases, the subject (patient or population) may have a disease, disorder, or illness, or be at risk thereof. In some cases, the subject may have one or more diseases, disorders, or unknown risks to illness. In some embodiments, the test may be a sample obtained from a subject that has come into contact with the composition, e.g., the CT10 composition (e.g., administered or ingested the composition) at a second time point.

[0081] In some embodiments, the methods described herein include comparing the level of one or more metabolites (e.g., metabolome) obtained from a test sample with the level of one or more metabolites (e.g., metabolome) obtained from a reference sample. In some embodiments, by comparing the level of one or more metabolites obtained from a test sample with the level of one or more metabolites obtained from a reference sample, the compositions disclosed herein can be evaluated, characterized, or identified as useful for modulating metabolite levels. In some embodiments, by comparing the level of one or more metabolites obtained from a test sample with the level of one or more metabolites obtained from a reference sample, it can be determined that the compositions disclosed herein increase the severity or incidence of a disease, disorder, or disease phenotype. In some embodiments, by comparing the level of one or more metabolites obtained from a test sample with the level of one or more metabolites obtained from a reference sample, it can be determined that the compositions disclosed herein decrease the severity or incidence of a disease, disorder, or disease phenotype. In some embodiments, by comparing the level of one or more metabolites obtained from a test sample with the level of one or more metabolites obtained from a reference sample, it can be determined that the compositions disclosed herein do not affect the severity or incidence of a disease, disorder, or disease phenotype.

[0082] The compositions and methods provided herein may be useful in evaluating, characterizing, or identifying levels of one or more metabolites that affect a disease, disorder, or illness in a mammal. This disclosure also provides the recognition that the compositions and methods provided herein can be used to define and / or characterize metabolome signatures associated with a disease, disorder, or illness. Furthermore, this disclosure also provides the recognition that the compositions and methods provided herein can be used to define and / or characterize metabolome signatures associated with one or more characteristics of a disease, disorder, or illness (e.g., severity, responsiveness to therapy, etc.). For example, if levels of several metabolites are determined to be associated with an increased severity of a disease, disorder, or illness across multiple individuals, the levels of such metabolites, as well as their relative amounts, can be used as signatures to identify individuals at risk of developing a disease, disorder, or illness with increased severity. As another example, if the levels of several metabolites are determined to be associated with an increased severity of a disease, disorder, or illness in a single individual at a specific point in time (e.g., after discontinuation of treatment), then the levels of those metabolites, as well as their relative amounts, can be used as signatures to identify when that individual is at risk of developing an increased severity of the disease, disorder, or illness.

[0083] This disclosure also provides the recognition that individuals can be diagnosed with a disease, disorder, or illness using the compositions and methods provided herein. In fact, individuals can be identified as individuals with early diagnosis and / or at risk using metabolome signatures associated with a disease, disorder, or illness determined through the use of the compositions and methods provided herein.

[0084] This disclosure also provides the recognition that it is possible to monitor the progression of disease, impairment, or illness in an individual using the compositions and methods provided herein. For example, if the relative amount decreases by the level of a metabolite determined to increase the severity of disease, impairment, or illness, it may indicate that the disease, impairment, or illness is being mitigated, for example, by treatment or an immune response.

[0085] This disclosure also provides insight that the compositions and methods provided herein can be used to tailor treatments (e.g., therapeutic agents, nutritional supplements, and / or probiotics) to individual patients. In some embodiments, the compositions and methods provided herein can provide “personalized” therapeutic agents. In some cases, levels of metabolites within an individual can be assessed, characterized, or identified to determine whether the individual has a disease, disorder, or illness. Based on the results, the individual can be treated with one or more compositions to adjust the levels of metabolites (i.e., the individual’s metabolome). In some cases, this would affect the disease, disorder, or illness that the individual has or is at risk of developing. For example, if an individual is determined to have relatively low levels of one or more metabolites that are determined to reduce the severity of a disease, disorder, or illness, then administration of one or more compositions that are determined to reduce the severity of a disease, disorder, or illness to the individual (or their extracts, components, or compounds) may alleviate the severity of the disease or illness in that individual.

[0086] This disclosure provides insight that it is possible to recursively treat, prevent or improve diseases, disorders, or illnesses using the compositions and methods provided herein. In some embodiments, for example, one or more compositions disclosed herein may be administered to a subject (e.g., by feeding, injection, etc.) after measuring the effect of one or more compositions on the levels of a target metabolite. In some embodiments, the compositions may be administered once. In some embodiments, the compositions may be administered multiple times. In some embodiments, the compositions may be administered daily, weekly, bi-weekly, monthly, bi-monthly, etc. In each of these cases, the levels of one or more metabolites may be monitored. In some embodiments, the levels of one or more metabolites (e.g., metabolome) may be monitored before administration of the compositions. In some embodiments, the levels of one or more metabolites (e.g., metabolome) may be monitored after administration of the compositions.

[0087] Pharmaceutical composition Compositions comprising individual microbial strains or combinations of microbial strains are provided herein. In some embodiments, the composition comprises individual microbial strains or combinations of microbial strains, extracts thereof, and / or components thereof, derived from the mammalian microbiome, evaluated, identified, characterized, or assayed using the methods herein. In some embodiments, compositions comprising two or more, three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, or ten or more microbial strains, extracts thereof, and / or components thereof, derived from the mammalian microbiome, evaluated, identified, characterized, or assayed using the methods herein.

[0088] In some embodiments, the compositions provided herein include two or more, three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, or ten or more microbial strains listed in Table 5 below.

[0089] [Table 2-1] Table 2-2 Table 2-3 Table 2-4 Table 2-5 Table 2-6 Table 2-7

[0090] In some embodiments, compositions comprising Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, Acidaminococcus sp., or combinations thereof are provided herein. In some embodiments, the composition comprises at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or all of the following: Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, and Acidaminococcus sp. In some embodiments, for example, the composition may include, but is not limited to, Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, and Acidaminococcus sp., and may also be called by other names, including, but not limited to, CT10 compositions, CT10 cocktails, etc.

[0091] In some embodiments, the individual microbial strains or combinations of microbial strains from the mammalian microbiome are killed (e.g., by heat). Alternatively, in some embodiments, the individual microbial strains or combinations of microbial strains from the mammalian microbiome may include viable or living cells.

[0092] In some embodiments, one or more microbial strains include, for example, individual viable or living microbial strains or combinations of microbial strains derived from the mammalian microbiome.

[0093] In some embodiments, one or more microbial strains include, for example, individual viable or living microbial strains or combinations of microbial strains derived from a mammalian microbiome, as described herein, and are formulated including one or more cell cultures and / or their supernatants or pellets, and / or powders formed therefrom, and / or through the use thereof.

[0094] In some embodiments, compositions for use in accordance with this disclosure are, for example, pharmaceutical compositions for administration to mammals (e.g., humans) (e.g., oral administration). Pharmaceutical compositions typically comprise an active agent (e.g., individual microbial strains or combinations of microbial strains derived from the mammalian microbiome, their extracts, and / or components) and a pharmaceutically acceptable carrier. Certain exemplary pharmaceutically acceptable carriers include, for example, salines, solvents, dispersion media, coatings, antimicrobial and antifungal agents, isotonic agents, and absorption retarders that are compatible with pharmaceutical administration.

[0095] In some embodiments, a pharmaceutical composition for use in accordance with this disclosure may contain and / or be administered in combination with one or more co-active compounds. In certain embodiments, such auxiliary activators include ginger, curcumin, probiotics (e.g., one or more probiotic strains from the following genera: Lactobacillus, Bifidobacterium sp., Saccharomyces, Enterococcus, Streptococcus, Pediococcus, Leuconostoc, Bacillus, and / or Escherichia coli (see Fijan, Int J Environ Res Public Health. 2014 May; 11(5): 4745-4767 (this document is incorporated herein by reference)); prebiotics (indigestible food components that help support the growth of probiotic bacteria, e.g., fructans such as fructooligosaccharides (FOS) and inulin, galactans such as galactooligosaccharides (GOS), indigestible starch, pectin, beta-glucan, and dietary fiber such as xylooligosaccharides (Hutkins et al., Curr Opin This may include Biotechnol. 2016 Feb;37:1-7 (the same document is incorporated herein by reference), and combinations thereof.

[0096] Pharmaceutical compositions are typically formulated to be compatible with their intended route of administration. An example of a route of administration is oral administration. Methods for formulating suitable pharmaceutical compositions are known in the art; see, for example, Remington: The Science and Practice of Pharmacy, 21st ed., 2005, and the series of books, Drugs and the Pharmaceutical Sciences: A Series of Textbooks and Monographs (Dekker, NY). Oral compositions generally contain an inert diluent or an edible carrier. To give just a few examples, in some embodiments, oral formulations may be or may contain syrups, liquids, tablets, lozenges, gummies, capsules, such as gelatin capsules, powders, gels, or films.

[0097] In some embodiments, pharmaceutically compatible binders and / or adjuvant materials may be included as part of the pharmaceutical composition. In some specific embodiments, the pharmaceutical composition may contain, for example, one or more of the following inert components or compounds of similar nature: binders such as microcrystalline cellulose, tragacanth gum, or gelatin; excipients such as starch or lactose; disintegrants such as alginic acid, Primogel, or corn starch; lubricants such as magnesium stearate or Sterotes; flow enhancers such as colloidal silicon dioxide; sweeteners such as sucrose or saccharin; or flavorings such as peppermint, methyl salicylate, or orange flavor. In some embodiments, the composition may be ingested as is, or sprinkled on or mixed into food or liquids (such as water). In some embodiments, compositions that can be administered to mammals as described herein include (e.g., supplemented with) individual microbial strains or combinations of microbial strains derived from the mammalian microbiome, their extracts, and / or their components, and are available for ingestion. Goods It may be (for example, food or beverage) or may include it.

[0098] In some embodiments, the food may be one or more of the following: bars, candies, baked goods, cereals, salty snacks, pasta, chocolate, and other solid foods; liquid or semi-solid foods including yogurt, soups, and stews; and beverages such as smoothies, shakes, juices, and other carbonated or non-carbonated beverages. In some embodiments, the food is prepared by the subject by mixing individual microbial strains or combinations of microbial strains derived from the mammalian microbiome, their extracts, and / or their components.

[0099] The composition may be contained in a kit, container, pack, or dispenser, along with instructions for administration or use as described herein.

[0100] Those skilled in the art, upon reviewing this disclosure, will understand that in some embodiments, a composition as described herein (e.g., a pharmaceutical composition) may be, or include, one or more cells, tissues, or organisms (e.g., plant or microbial cells, tissues, or organisms) that produce (e.g., have produced and / or are producing) the relevant compound.

[0101] Those skilled in the art will understand that in some embodiments, techniques for preparing compositions and / or preparations (and in particular for preparing pharmaceutical compositions) may include one or more steps of evaluating or characterizing the compound, preparation, or composition, for example, as part of quality control. In some embodiments, if the assayed material does not meet the predetermined specifications for the relevant evaluation, it is discarded. In some embodiments, if such assayed material actually meets the predetermined specifications, it continues to be processed as described herein.

[0102] In some embodiments, the pharmaceutical compositions provided herein may promote colonization of individual microbial strains or combinations of microbial strains derived from the mammalian microbiome, in particular, strains(s) identified, characterized, or evaluated as reducing the severity or incidence of mammalian diseases or illnesses in mammals that have or are at risk of having a mammalian disease or illness. In some embodiments, the pharmaceutical compositions provided herein may attenuate colonization of individual microbial strains or combinations of microbial strains derived from the mammalian microbiome, in particular, strains(s) identified, characterized, or evaluated as increasing the severity or incidence of mammalian diseases or illnesses in mammals that have or are at risk of having a mammalian disease or illness. In some embodiments, the pharmaceutical compositions provided herein may promote colonization of individual microbial strains or combinations of microbial strains originating from the mammalian microbiome, particularly those strains identified, characterized, or evaluated as being able to defeat one or more microbial strains that do not affect the severity or incidence of mammalian disease or illness, but increase the severity or incidence of mammalian disease or illness in mammals that are affected or at risk of such disease.

[0103] In some embodiments, each of the one or more microbial strains in the composition is 10 1 ~10 15 Contains colony-forming units (CFUs). In some embodiments, each of one or more microbial strains in the composition is 10 6 ~10 15 Contains CFU. In some embodiments, each of the one or more microbial strains in the composition contains the same number of CFUs. In some embodiments, some of the one or more microbial strains in the composition contain different numbers of CFUs.

[0104] In some embodiments, the composition totals 10 6 ~10 15 Including CFU

[0105] In some embodiments, the pharmaceutical composition is adapted to a specific mammal (e.g., a specific human, e.g., a patient) based on the microbiome of that specific mammal (e.g., a human). In some embodiments, the pharmaceutical composition is specific to the microbiome of an individual mammal (e.g., a human). In some embodiments, the pharmaceutical composition is specific to the microbiome of a population of mammals (e.g., humans). A population of mammals may include, but is not limited to, a family, mammals in the same geographical location (e.g., neighborhood, city, state, or country), mammals with the same disease or illness, mammals of a specific age or age range, or mammals that consume a specific diet (e.g., food, food source, or calorie intake).

[0106] Treatment method This disclosure acknowledges that the compositions described herein may be useful in the treatment of a particular condition. The methods provided by this disclosure include methods for the treatment of a particular disease, disorder, and illness. In some embodiments, the relevant disease, disorder, and illness may be, or include, a neurodegenerative disease, disorder, or illness. In some embodiments, the neurodegenerative disease, disorder, or illness may be Alzheimer's disease. In some embodiments, the relevant disease, disorder, and illness may be, or include, an intraocular neovascular disease, disorder, or illness. In some embodiments, the neurodegenerative disease, disorder, or illness may be diabetic retinopathy, retinopathy of prematurity, age-related macular degeneration, or glaucoma.

[0107] Generally, the therapeutic methods provided by this disclosure involve administering a therapeutically effective amount of a composition described herein, alone or in combination with other compositions and / or treatments, to a subject that requires or has been determined to require such treatment.

[0108] In some embodiments, the therapeutic methods provided herein are prophylactic or preventative and may be administered to a subject, for example, before the onset of significant symptoms and / or before exposure to certain anticipated triggers associated with a neurodegenerative disease, disorder, or illness. In some embodiments, the therapeutic methods provided herein are therapeutic and may be administered to a subject, for example, after the onset of significant symptoms associated with a neurodegenerative disease, disorder, or illness.

[0109] In some embodiments, the therapeutic method provided is administered to a subject, which is a mammal, for example, a mammal experiencing a disease, disorder, or illness as described herein. In some embodiments, the subject is a human subject or a non-human veterinary subject, for example, an ape, cat, dog, monkey, or pig.

[0110] In many embodiments, treatment involves improving at least one symptom of a neurodegenerative disease, disorder, or disease associated with the disorder, disorder, or disease. In some embodiments, the treatment method may be preventative.

[0111] In some embodiments, the method may involve administering a therapeutically effective amount of the composition disclosed herein before, during (e.g., concurrently with), or after the application of a treatment expected to be associated with a neurodegenerative disease, disorder, or illness.

[0112] In some embodiments, subjects receiving treatment as described herein may be receiving and / or have received other treatments (e.g., drug therapy, surgery, etc.) intended to treat one or more symptoms or characteristics of a disease, disorder, or illness (e.g., neurodegenerative disease, disorder, or illness) as described herein, and thereby the composition provided may be administered in combination with such other therapy (i.e., treatment) to treat the relevant disease, disorder, or illness.

[0113] In some embodiments, the compositions described herein may be administered in a form containing one or more pharmaceutically acceptable carriers. Suitable carriers have been previously described and vary depending on the desired form and mode of administration of the composition. For example, pharmaceutically acceptable carriers may include diluents or excipients such as fillers, binders, wetting agents, disintegrants, surfactants, flow enhancers, and lubricants. Typically, the carrier may be solid (including powder), liquid, or any combination thereof. Each carrier is preferably "acceptable" in the sense that it is compatible with the other components in the composition and is not harmful to the subject. The carrier may be bioacceptable and inert (for example, it may allow the composition to maintain the viability of the biomaterial until it is delivered to the appropriate site).

[0114] Tablets, pills, capsules, lozenges, etc., may contain any of the following ingredients or compounds of similar properties: binders such as microcrystalline cellulose, tragacanth gum, or gelatin; excipients such as starch or lactose; disintegrants such as alginic acid, Primogel, or corn starch; lubricants such as magnesium stearate or Sterotet; flow promoters such as colloidal silicon dioxide; sweeteners such as sucrose or saccharin; or flavoring agents such as peppermint, methyl salicylate, orange flavor, or other suitable flavors. These are merely examples and not intended to be limiting.

[0115] Oral compositions may include inert diluents or food carriers. For therapeutic oral administration, the active compound may be incorporated with excipients and used in the form of tablets, lozenges, medicinal drops, troches, or capsules, such as gelatin capsules. Oral compositions may also be prepared by combining the compositions of this disclosure with food products. In some embodiments, microorganisms may be formulated in food products. Some non-limiting examples of food products used with the methods and compositions described herein include popsicles, cheese, cream, chocolate, milk, meat, beverages, pickles, kefir, miso, sauerkraut, and the like. In other embodiments, the food product may be juice, soft drink, tea beverage, drink preparation, jelly drink, and functional beverage; alcoholic beverages such as beer; carbohydrate-containing foods such as rice processed foods, noodles, bread, and pasta; processed fish products such as fish, ham, sausage, and processed seafood products; retort pouch products such as curry, food with thick sauce, and Chinese soup; soup; dairy products such as milk, milk beverages, ice cream, and yogurt; fermented products such as miso, fermented beverages, and pickles; soy products; various confectionery products such as biscuits, cookies, candy, chewing gum, and gummies; cold desserts such as jelly, custard pudding, and frozen desserts; instant foods such as instant soup and instant miso soup; and equivalents thereof. Preferably, the food preparation does not require cooking after mixing with the microbial strain(s) to avoid killing any microorganisms. In one embodiment, the food product used for administration is chilled, for example, ice-cold flavored water. In certain embodiments, the foodstuffs are not potentially allergenic foodstuffs (e.g., not soy, wheat, peanuts, tree nuts, dairy products, eggs, shellfish, or fish). Pharmaceutically compatible binders and / or adjuvant materials may be included as part of the composition.

[0116] In some such embodiments, the compositions described herein are administered to a subject according to a dosage regimen that achieves a population of the subject's microbiome with administered cells. In some embodiments, the composition is administered to the subject in a single dose. In some embodiments, the composition is administered to the subject in multiple doses. In some embodiments, the dosage of the composition is administered to the subject twice daily, daily, weekly, or monthly.

[0117] In some embodiments, each of one or more microbial strains in a dose comprises 10 1 ~10 15 colony forming units (CFU). In some embodiments, each of one or more microbial strains in a dose comprises 10 6 ~10 15 CFU. In some embodiments, each of one or more microbial strains in a dose comprises the same number of CFU. In some embodiments, some of one or more microbial strains in a dose comprise different numbers of CFU.

[0118] In some embodiments, one dose of one or more microbial strains comprises a total of 10 6 ~10 15 CFU. In some embodiments, one dose of one or more microbial strains comprises a total of 10 7 ~10 15 CFU. In some embodiments, one dose of one or more microbial strains comprises 50 to 200 billion CFU. In some embodiments, one dose of one or more microbial strains comprises 50 to 50 billion CFU. In some embodiments, one dose of one or more microbial strains comprises 50 to 20 billion CFU. In some embodiments, one dose of one or more microbial strains comprises 500 to 1000 billion CFU. In some embodiments, one dose of one or more microbial strains comprises 1000 to 2000 billion CFU.

Example

[0119] The following examples are provided to illustrate to those skilled in the art how to make and use the methods and compositions described herein and are not intended to limit the scope of the present disclosure.

[0120] Example 1: Metabolome profile of mouse plasma Objective of the study: Analysis of ionic metabolites in mouse plasma using capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS).

[0121] Summary: Metabolome analysis was performed on 10 mouse plasma samples using CE-TOFMS in two modes: cationic and anionic. 196 metabolites were detected (119 in cationic mode and 77 in anionic mode).

[0122] Materials and methods: Materials: Mice were treated with either a control or a therapeutic agent (CT10 composition), and changes in metabolite levels in blood / plasma samples from these mice were then analyzed. 30–50 microliters of phosphate-buffered saline (PBS) were used as a control (depending on the animal's body weight). For CT10, 10 6 Each individual bacterial strain of the CFU was mixed in PBS and administered to mice once daily via oral gastric tube feeding. The total bacterial concentration was 10 7 The sample was CFU. Metabolome analysis was performed on the above sample. The above sample is shown in Table 6 below.

[0123] [Table 3]

[0124] Sample preparation: Each 50 μL sample was mixed with 200 μL of methanol containing an internal standard (20 μM). Then, 150 μL of Milli-Q water was added and thoroughly mixed. This solution (300 μL) was filtered through a 5 kDa cutoff filter (ULTRAFREE-MC-PLHCC, Human Metabolome Technologies, Yamagata, Japan) to remove polymers. The filtrate was concentrated by centrifugation and resuspended in 50 μL of ultrapure water immediately before measurement.

[0125] Measurement: The compounds were measured by metabolomics based on cation and anion mode CE-TOFMS under the following conditions. To improve the analytical quality of the CE-MS analysis, the samples were diluted during measurement as shown in Table 6. Cationic metabolites (cationic metabolites) Device Agilent CE-TOFMS system (Agilent Technologies Inc.), equipment number 3 Capillary: Fused silica capillary, inner diameter 50 μm x 80 cm Analysis conditions Analytical buffer solution: Cation buffer solution (p / n: H3301-1001) Washing buffer solution: Cationic buffer solution (p / n: H3301-1001) Sample injection: Pressurized injection 50 mbar, 10 seconds CE voltage: positive, 30kV MS ionization: ESI positive MS capillary voltage: 4,000V MS scanning range: m / z 50~1,000 Sheath fluid: HMT sheath fluid (p / n: H3301-1020) Anionic metabolites (anionic mode) Device Agilent CE-TOFMS system (Agilent Technologies Inc.) Equipment number 2 Capillary: Fused silica capillary, inner diameter 50 μm x 80 cm Analysis conditions Analytical buffer solution: Anion buffer solution (p / n: I3302-1023) Washing buffer: Anion buffer solution (p / n: I3302-1023) Sample injection: Pressurized injection 50 mbar, 22 seconds CE voltage: positive, 30kV MS ionization: ESI negative MS capillary voltage: 3,500V MS scanning range: m / z 50~1,000 Sheath fluid: HMT sheath fluid (p / n: H3301-1020)

[0126] Data processing and analysis: Data Processing: Peaks detected in CE-TOFMS analysis were extracted using automated integration software (MasterHands ver.2.17.1.11, developed by Keio University) to obtain peak information including m / z, migration time (MT), and peak area. The peak area was then converted to relative peak area using the following formula. The peak detection limit was determined based on the signal-to-noise ratio (S / N) = 3.

[0127]

number

[0128] Peak Annotation: Next, based on m / z and MT, estimated metabolites were assigned from the HMT standard library and known / unknown peak libraries. The tolerance was ±0.5 min for MT and ±10 ppm for m / z (mass error was calculated using the following formula). If several peaks were assigned to the same candidate, a sub-number was assigned to that candidate.

number

[0129] Quantitative estimation of target metabolites: Absolute quantification of target metabolites was performed. All metabolite concentrations were calculated by normalizing the peak area of ​​each metabolite relative to the area of ​​an internal standard and using a calibration curve obtained by single-point (100 μM or 50 μM) calibration.

[0130] Statistical Analysis (PCA, HCA): Hierarchical cluster analysis (HCA) and principal component analysis (PCA) were performed using statistical analysis software (developed by HMT). The analysis results are shown in detail in the attached Excel file.

[0131] Plotting on Pathway Map: Using VANTED (Visualization and Analysis of Networks containing Experimental Data) 4 software, the peak profiles containing estimated metabolites were plotted on a metabolic pathway map. Some abbreviations for metabolites used in the above pathway map differ from those in the HMT standard library (Appendix 1). The above pathway map was created based on metabolic pathways known to exist in human cells.

[0132] result: Estimated metabolites: 196 peaks (119 in cation mode and 77 in anion mode) were detected by CE-TOFMS measurement and annotated (Table 7).

[0133] Comparative analysis between test groups: The results for the 196 detected peaks are summarized in Table 7.

[0134] Quantitative estimation of target metabolites: Of the target metabolites, 64 types (40 in cationic mode and 24 in anionic mode) were detected and quantified (Table 8).

[0135] Statistical analysis (PCA, HCA): The results of PCA are shown in Figure 5. The results of HCA are displayed using a heatmap (Figure 6).

[0136] Plotting onto pathway maps: Graphs of the obtained metabolome data were created and overlaid on the following metabolic pathway maps, namely, an overview of primary metabolism, central carbon metabolism, urea cycle, lipid metabolism, amino acid metabolism, nucleotide metabolism, and coenzyme metabolism (Figures 7-14).

[0137] These results indicate that the microbiome compositions disclosed herein may modulate the metabolome of mammals (e.g., mice) and may have therapeutic aspects.

[0138] Example 2: Characterization of microbial strains affecting the levels or metabolome of one or more metabolites. Example 2.1: Metabolome analysis of mice treated with one or more compositions Male and female mice were administered either (i) Group I: CT10 composition, (ii) Group II: E. coli Ol11: lipopolysaccharide (LPS) derived from B4, (iii) Group III: placebo as a negative control, or (iv) Group IV: LPS composition followed by CT10 composition. Each group contained 5 mice. For Groups I and IV, 10 of the CT10 composition was administered. 6 Each individual bacterial strain of the CFU was mixed in PBS and administered to mice once daily via oral gastric tube feeding. Therefore, the total bacterial concentration was 10 7 The results were CFU. Groups II and IV received 1 microgram / mL of LPS in PBS via intraperitoneal injection. Group III received 30 mL of PBS as a placebo solution, also administered via intraperitoneal injection. 24 hours after injection, the mice were sacrificed and plasma samples were collected.

[0139] Metabolic analysis was performed on mouse plasma samples using CE-TOFMS (Agilent Technologies Inc.) in two modes for cationic and anionic metabolites. Compared to the levels of each metabolite in the control / placebo group, levels of 104 metabolites increased in female mice treated with the CT10 composition, while levels of 88 metabolites increased in male mice (see Figures 1 and 2, Tables 1 and 2). Of these metabolites, 19 increased regardless of sex.

[0140] Metabolome analyses were also performed on each of the 10 microbial species derived from the CT10 cocktail. Specifically, metabolome analyses were performed on both cells and the corresponding spent culture media for each microbial species. This data was used to map the potential origins of each metabolite that increased in mouse plasma (see Figures 1 and 2, Tables 1 and 2). Of the 104 metabolites that increased in the plasma of female mice treated with the CT10 composition compared to other bacterial species in the CT10 composition, 93 were detected at high levels in at least one bacterium. Furthermore, 11 metabolites were not detected in any microorganism (see Table 1). It can be hypothesized that these metabolites were likely produced in vivo in response to treatment with the CT10 composition. Similarly, of the 88 metabolites that increased in the plasma of male mice treated with the CT10 composition compared to other bacterial species in the CT10 composition, 74 were detected at high levels in at least one bacterium. In both male and female animals treated with the CT10 composition, 75 metabolites were detected at high levels.

[0141] Furthermore, metabolome analysis was performed on plasma samples from male and female mice administered either a placebo or an LPS composition. In response to LPS treatment, levels of 37 metabolites increased in females and 97 metabolites increased in males (see Figures 3 and 4, Tables 3 and 4). Of these metabolites, 17 increased in response to LPS injection, regardless of sex. In female mice, of the 37 metabolites whose levels increased in response to LPS injection, levels of 34 metabolites decreased in group IV, which was administered the LPS composition and the CT10 composition (Table 3). In male mice, of the 97 metabolites whose levels increased in response to LPS injection, levels of 89 metabolites decreased in group IV, which was administered the LPS composition and the CT10 composition (Table 4).

[0142] These results indicate that microbiome compositions and / or LPS compositions modulate the metabolome of both male and female mammals (e.g., mice), albeit in different forms.

[0143] Other Embodiments Those skilled in the art will understand that various modifications, alterations, and improvements to the present disclosure will be readily conceivable. Such modifications, alterations, and improvements are intended to be part of the present disclosure and to be within the spirit and scope of the invention. Accordingly, the above description and drawings are merely examples, and any invention described herein is further detailed by the appended claims.

[0144] Those skilled in the art will understand the typical standard deviation or error resulting from values ​​obtained in assays or other processes as described herein. Publications, websites, and other reference materials referenced herein to explain the background of the invention and to provide additional details relating to its implementation are incorporated herein by reference in their entirety. Embodiments of the present invention are described in conjunction with modes for carrying out the invention; however, the above description is intended to be illustrative and not to limit the scope of the invention, and it should be understood that the scope of the invention is defined by the appended claims. Other embodiments, advantages, and modifications are within the scope of the appended claims.

[0145] [Table 4-1] [Table 4-2] [Table 4-3]

[0146] [Table 5-1] Table 5-2

[0147] Table 6-1 Table 6-2

[0148] Table 7-1 Table 7-2

[0149] Table 8

[0150] Table 9-1 Table 9-2 Table 9-3

[0151] Table 10-1 Table 10-2

[0152] Table 11-1

Table 11-2

[0153]

Table 12-1

Table 12-2

Table 12-3

[0154]

Table 13

[0155]

Table 14

[0156]

Table 15

[0157]

Table 16

[0161]

Table 19

Table 20

Table 21

Table 22

[0162]

Table 23

Table 24

Claims

1. An edible article comprising Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, and Acidaminococcus sp., wherein the edible article is a food or beverage suitable for human consumption.

2. An ingestible article according to claim 1, for use in regulating one or more metabolites in a subject.

3. An ingestible article according to claim 1 or 2 for use in characterizing the ability of Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp., Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp., Veillonella sp., Bifidobacterium sp., Bacillus subtilis, and Acidaminococcus sp. to regulate one or more metabolites in a subject.

4. An ingestible article according to claim 1 or 2 for use in characterizing the metabolome of a target.

5. An ingestible article according to any one of claims 1 to 4, further comprising one or more lipopolysaccharides, wherein the one or more lipopolysaccharides are derived from E. coli.

6. The ingestible article according to claim 5, wherein one or more lipopolysaccharides are derived from E. coli 0111. B4.

7. Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp. , Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp. , Veillonella sp. , Bifidobacterium sp. , Bacillus subtilis and Acidaminococcus sp. each of 10 ６ ~10 １５ An ingestible article according to any one of claims 1 to 6, comprising colony-forming units (CFUs).

8. Gluconacetobacter hansenii, Terrisporobacter glycolicus, Coprococcus sp. , Lactobacillus plantarum, Clostridium butyricum, Paenibacillus sp. , Veillonella sp. , Bifidobacterium sp. , Bacillus subtilis and Acidaminococcus sp. each of 10 １ ~10 １５ An ingestible article according to any one of claims 1 to 6, comprising CFU.

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