Microbial consortium and uses thereof

Abstract

To provide a microbial consortium comprising two or more microorganisms, compositions and kits comprising the same, and uses thereof for treating cancer.SOLUTION: A microbial consortium comprising two or more microorganisms is provided, wherein at least one of the two or more microorganisms is present at low abundance in the microbiome of a reference human subject, and at least one other of the two or more microorganisms has at least one of: (i) capability of modulating at least one short chain fatty acid (SCFA); (ii) capability of modulating lactate; and (iii) inclusion of at least one cell envelope component.SELECTED DRAWING: None

Description

Technical Field

[0001] The present invention relates to a consortium of microorganisms and its use, for example, for treating cancer.

Background Art

[0002] References considered relevant as background to the subject matter of the present disclosure are listed below. [1] Lynch, Susan V., and Oluf Pedersen, "The human intestinal microbiome in health and disease.", New England Journal of Medicine, Vol. 375, No. 24 (2016), pp. 2369 - 2379. [2] International Application Publication No. WO2016086208. [3] International Application Publication No. WO2017218680. [4] International Application Publication No. WO2018064165. [5] International Application Publication No. WO2019046646. [6] Takeshi Tanoue et al., "A defined commensal consortium elicits CD8 T cells and anti - cancer immunity", Nature (2019).

[0003] Approval of the above - listed references in this specification should not be construed as an admission that they are in any way relevant to the patentability of the subject matter of the present disclosure.

[0004] Background The human microbiota is a diverse population of over one trillion microorganisms, including bacteria, fungi, archaea, and viruses, that collectively play important roles in various physiological processes within the host that affect human health and disease. For example, the microbiota has been shown to increase energy extraction from food, function as a physical barrier to protect the host from external pathogens, and have the ability to assist in the development of the host immune system [1].

[0005] Compositions of bacterial strains and their use for treating diseases are described [2-6]. SUMMARY OF THE INVENTION MEANS FOR SOLVING THE PROBLEM

[0006] Overview According to some embodiments, the present invention relates to a microbial consortium comprising two or more microorganisms, wherein at least one of the two or more microorganisms is present in low abundance in the microbiota of a reference human subject, and at least one other of the two or more microorganisms has at least one of: (i) the ability to regulate at least one short chain fatty acid (SCFA), (ii) the ability to regulate lactate, and (iii) the ability to contain at least one cell envelope component.

[0007] According to some embodiments, the present invention relates to a pharmaceutical composition comprising a microbial consortium comprising two or more microorganisms, wherein at least one of the two or more microorganisms is present in low abundance in the microbiota of a reference human subject, and at least one other of the two or more microorganisms has at least one of: (i) the ability to regulate at least one SCFA, (ii) the ability to regulate lactate, and (iii) the ability to contain at least one cell envelope component.

[0008] According to some embodiments, the present invention relates to a method of treating, preventing, remitting, alleviating, or delaying the onset or progression of cancer in a human subject in need thereof, the method comprising administering to the subject an effective amount of a microbial consortium comprising two or more isolated or purified microorganisms, wherein at least one of the two or more microorganisms is present in low abundance in the microbiota of a reference human subject, and at least one other of the two or more microorganisms has at least one of: (i) the ability to regulate at least one SCFA, (ii) the ability to regulate lactate, and (iii) the ability to contain at least one cell envelope component.

[0009] According to some aspects, the present invention relates to a method of treating, preventing, remitting, alleviating, or delaying the onset or progression of cancer in a human subject in need thereof, the method comprising administering to the subject an effective amount of a microbial consortium and a therapeutically effective amount of an anti-cancer treatment, the microbial consortium comprising two or more isolated or purified microorganisms, at least one of the two or more microorganisms being present in low abundance in the microbiota of a reference human subject, and at least one other of the two or more microorganisms having at least one of: (i) being able to modulate at least one SCFA, (ii) being able to modulate lactate, and (iii) comprising at least one cell envelope component.

[0010] According to some aspects, the present invention relates to the use of a microbial consortium comprising two or more microorganisms, at least one of the two or more microorganisms being present in low abundance in the microbiota of a reference human subject, and at least one other of the two or more microorganisms having at least one of: (i) being able to modulate at least one SCFA, (ii) being able to modulate lactate, and (iii) comprising at least one cell envelope component, in the preparation of a composition for treating cancer in a subject in need thereof.

[0011] According to some aspects, the present invention relates to a kit comprising a microbial consortium comprising two or more microorganisms, at least one of the two or more microorganisms being present in low abundance in the microbiota of a reference human subject, and at least one other of the two or more microorganisms having at least one of: (i) being able to modulate at least one SCFA, (ii) being able to modulate lactate, and (iii) comprising a composition comprising at least one cell envelope component or the microbial consortium.

[0012] To better understand the subject matter disclosed herein and to illustrate how it can be actually practiced, embodiments are described by way of non-limiting examples only with reference to the accompanying drawings.

Brief Description of the Drawings

[0013]

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Mode for Carrying Out the Invention

[0014] The gut microbiota includes a large number of diverse microorganisms that can affect various physiological processes in the host, including, for example, the development and differentiation, activation or suppression of the host immune system.

[0015] The present disclosure is based on the possible relationship between the immune system and cancer treatment, and aims to use specific microorganisms detected, isolated, or purified from the microbiota, such as the gut microbiota, which contribute to the regulation of the immune system and can thus be used for inhibiting cancer growth and treating cancer.

[0016] For that purpose, the inventors used a series of computational tools utilized for processing high-throughput sequencing data to obtain high-resolution detection and annotation of microbial genes and pathways and microbial taxa. This provided a mechanistic understanding of the relationship between organisms (such as microorganisms) and various human intracellular processes related to cancer and immune function. During the analysis process, several methods such as stringent statistical comparative analysis were applied to enable the identification and selection of specific microorganisms and microbial functions that distinguish cancer patients who were found to respond to immune checkpoint inhibitor therapy from cancer patients who were found to be non-responsive to this therapy.

[0017] The inventors hypothesized that the unique and specific combination of microorganisms identified by the present invention could be used to treat proliferative disorders. Accordingly, the inventors suggested that the computationally identified microorganisms can be administered to a subject, either alone or preferably in a specific combination, to increase the diversity of the microbiota and induce an effective inflammatory immune response to treat cancer. The inventors further suggested that the identified microorganisms can be used for diagnostic and prognostic purposes, for example, to evaluate the responsiveness of a subject to treatment and to determine a treatment protocol.

[0018] Accordingly, the present disclosure provides a microbial consortium. The microbial consortium includes two or more microorganisms that can collectively affect different functional capabilities by regulating a number of processes in both the microorganisms themselves and the host. Such processes can be, for example, the production of short-chain fatty acids (SCFAs), the activation of dendritic cells, and the activation of innate immunity.

[0019] Surprisingly, some of the identified microorganisms were found to be present in low amounts in the human microbiota and were further found to play a major role in immune-mediated processes in the host. As shown in the following examples, these microorganisms are present in low amounts in the human microbiota but, alone and in combination in both in vitro and in vivo experiments, induce a significant inflammatory response.

[0020] Accordingly, the present disclosure provides a microbial consortium comprising two or more microorganisms, wherein at least one of the two or more microorganisms is present in a low abundance in the microbiota of a reference human subject.

[0021] As used herein, a microbial consortium refers to a mixture / cocktail of microorganisms comprising at least one bacterium and / or archaea. When referring to at least one microorganism, it should be understood to refer to one microbial species and / or strain classified into a common scientific classification. The microorganisms that are the subject of the present disclosure are present in the human microbiota and can thus be isolated and / or purified from any microbiota such as the human microbiota by any known method in the art as detailed below or by purification from biological materials (such as fecal materials, such as feces or substances isolated from various segments of the small and large intestines). Thus, the term "microorganism" as used herein, according to some embodiments, refers to at least one of an isolated microorganism, a purified microorganism, or a recombinant microorganism.

[0022] In some embodiments, the microbial consortium comprises isolated microorganisms. In some embodiments, the microbial consortium comprises purified microorganisms. In some embodiments, the microbial consortium comprises recombinant microorganisms. In some embodiments, the microbial consortium comprises isolated microorganisms, purified microorganisms, or any combination thereof. In some embodiments, the microbial consortium comprises isolated microorganisms, purified microorganisms, recombinant microorganisms, or any combination thereof.

[0023] It should be noted that the recombinant microorganisms of the present invention are microorganisms whose genetic structure has been modified by the intentional introduction of new genetic elements. The recombinant microorganisms may maintain the functions (intracellular processes) of the original microorganisms.

[0024] The microorganisms of the present invention can be at least one of living microorganisms, spores of microorganisms, heat-killed non-viable forms, or extracts or components of organisms.

[0025] Although not bound by theory, the inventors have suggested that the selected / identified microorganisms can treat cancer through the regulation of multiple pathways, such as the modification of the host microbiota or the regulation of the production of various biological molecules (e.g., SCFAs).

[0026] The attribution of microorganisms to each of the consortia of the present invention was done by considering the multiple functions and combined functions of each of the microorganisms in order to avoid adverse effects such as damage to the intestinal epithelium. The inventors have suggested that the selected microorganisms can induce an inflammation-inducing effect and inhibit cancer progression, while maintaining the integrity of the intestinal barrier. This can be achieved, for example, by affecting mucin degradation or the regulation of SCFAs in the intestine.

[0027] At least two or more microorganisms within the microbial consortium can have various biological relationships, for example, such that at least one microorganism can benefit from at least one other microorganism. For example, the metabolic products of one microorganism may be used as a substrate by another member of the consortium or additional gut symbionts, thus enhancing the potential for intestinal colonization by the microbial consortium or promoting the desired activity of one or more microorganisms. Thus, the inventors have suggested that combinations of at least two microorganisms in the microbial consortium can achieve an effect that results in immunomodulation through several underlying and overlapping complementary mechanisms. For example, at least one microorganism in the microbial consortium can regulate at least one process, sometimes at least two processes, and further sometimes at least three or at least four processes, as detailed hereinbelow.

[0028] As described herein, at least one microorganism in the microbial consortium is present in low abundance in the microbiota of a reference human subject. Abundance in the context of the present disclosure refers to an expression of the relative amount (content) of a particular microorganism in the microbiota. This amount can be obtained by any method known in the art. For example, various molecular-based methods are available for characterizing and quantifying the gut microbiota, such as conventional clone libraries: direct sequencing using next-generation parallel sequencing technology; denaturing gradient gel electrophoresis and temperature gradient gel electrophoresis; terminal restriction fragment length polymorphism analysis; fluorescence in situ hybridization; and quantitative polymerase chain reaction (PCR). In addition, computational analysis of sequence data containing information about isolated gut microorganisms can be used, for example, by counting the number of reads mapped to a reference genome. Computational tools can be used to determine the relative abundance of each microorganism in the microbiota, defined as the number of reads mapped to the reference genome divided by the total number of microbial reads in a given microbiota sample and normalized by methods known in the art (e.g., genome size).

[0029] As used herein, the term low abundance refers to a microorganism present in a reference microbiota in an amount less than a predetermined standard value(s) or cut-off value(s). The predetermined standard value(s) or cut-off value(s) may be determined as the average value of a large heterogeneous cohort of subjects, or may be determined for a specific population of reference subjects. In some embodiments, the reference human subject is a healthy subject. A healthy subject is a subject who has not been diagnosed with a disease to be treated using the microbial consortium of the present invention. In some other embodiments, the reference human subject is a subject diagnosed with at least one disease, optionally a disease that can be treated using the microbial consortium of the present invention. In some embodiments, the low-abundance microorganism has an average relative abundance of less than 0.5%, sometimes less than 0.4%, sometimes less than 0.3%, sometimes less than 0.2%, and further sometimes less than 0.1%. In some embodiments, the low-abundance microorganism has an average relative abundance of from about 0.00001% to about 0.5%, sometimes from about 0.0001% to about 0.4%, sometimes from about 0.001% to about 0.3%, sometimes from about 0.01% to about 0.2%, sometimes from about 0.01% to about 0.1%, and sometimes from about 0.05% to about 0.1%.

[0030] According to some embodiments, at least one microorganism present in low abundance in a reference human subject has at least one of the following: (i) capable of regulating at least one SCFA, and (ii) containing at least one cell envelope component. The cell envelope components according to the present invention are those recognized by the immune system or epithelial cells of the subject, such as intestinal epithelial cells. According to some other embodiments, at least one microorganism present in low abundance in a reference human subject is capable of regulating lactate.

[0031] Accordingly, in some aspects, the present disclosure provides a microbial consortium comprising two or more microorganisms, wherein at least one of the two or more microorganisms is present in low abundance in the microbiota of a reference human subject and has at least one of (i) the ability to regulate at least one SCFA, (ii) the ability to regulate lactate, and (iii) the ability to contain at least one cell envelope component recognized by the immune system or epithelial cells of the subject, such as intestinal epithelial cells.

[0032] The microbial consortium includes at least one other microorganism. According to some embodiments, the at least one other microorganism has at least one of (i) the ability to regulate at least one SCFA, (ii) the ability to regulate lactate, and (iii) the ability to contain at least one cell envelope component recognized by the immune system or epithelial cells of the subject, such as intestinal epithelial cells.

[0033] Accordingly, in some aspects, the present disclosure provides a microbial consortium comprising two or more microorganisms, wherein at least one of the two or more microorganisms is present in low abundance in the microbiota of a reference human subject, and at least one other of the two or more microorganisms has at least one of (i) the ability to regulate at least one SCFA, (ii) the ability to regulate lactate, and (iii) the ability to contain at least one cell envelope component recognized by the immune system or epithelial cells of the subject, such as intestinal epithelial cells.

[0034] According to some embodiments, the at least one other microorganism that has at least one of (i) the ability to regulate at least one SCFA, (ii) the ability to regulate lactate, and (iii) the ability to contain at least one cell envelope component recognized by the immune system of the subject or epithelial cells, such as intestinal epithelial cells, is at least one microorganism present in low abundance in the microbiota of a reference human subject.

[0035] According to some embodiments, at least one other microorganism having at least one of (i) being able to modulate at least one SCFA, (ii) being able to modulate lactate, and (iii) containing at least one cell envelope component or epithelial cell, such as an intestinal epithelial cell, recognized by the immune system of a subject, is characterized by being present in low abundance in the microbiota of a reference human subject.

[0036] One or more of the microorganisms of the present invention, for example, at least one microorganism present in low abundance in the microbiota of a reference human subject, may be a regulator of a physiological process, i.e., can regulate at least one physiological process in the microorganism and / or the host. As used herein, the term "microorganism capable of modulating" relates to a microorganism that acts directly (e.g., by binding) or indirectly on a biological entity such as a receptor or an enzyme, resulting in the modulation of its activation.

[0037] According to the present invention, modulation, as specified herein, may either activate and increase the activation of a physiological / intracellular process or decrease and inhibit the activation of a physiological / intracellular process, specifically any one of these processes. Thus, the term "modulator" includes inhibitors and activators, and thus the microorganisms of the present invention can be regarded as either inhibitors or activators of a particular process. According to the present invention, an activator is an agent that induces, activates, stimulates, increases, promotes, enhances activation, sensitizes, or upregulates a microorganism that increases / activates a physiological / intracellular process, such as a process or any indirect activator. An inhibitor is an agent that inhibits, partially or completely blocks, reduces, prevents, delays activation, inactivates, desensitizes, or downregulates a microorganism that decreases / reduces a physiological / intracellular process, such as a process or any indirect activator. The term modulation in connection with the present invention may also include, for example, maintaining expression or function. Moreover, for example, the term modulate as used herein may be used to enhance or maintain the secretion of one or more substances as described herein.

[0038] It should be noted that the modulation used in the present invention includes processes (pathways) within the microorganism(s) and / or within the host.

[0039] Processes that are intrinsically regulated in a microorganism, i.e., microorganism-related processes, are all collectively referred to herein as "functional microorganism processes". Functional microorganism processes can occur in at least one specific type (species or microorganism) of microorganism (endogenous process). Such microorganism processes can produce, for example, microorganism products that can be secreted from the microorganism to affect the host. Thus, a microbial consortium can modulate (by activation), for example, a microorganism process that results in the production and subsequent secretion of SCFA or lactate to the host.

[0040] The microorganisms identified by the present inventors have been found to regulate various intracellular processes in the host, which are herein referred to as "functional host processes". These processes can be mediated directly by microbial components (i.e., produced and secreted by the microorganisms) or indirectly via host components. Thus, at least one of two or more microorganisms, for example, at least one microorganism that is present in low abundance in the microbiota of a reference human subject, can regulate intracellular processes (functional host processes) in a host subject. Without being bound by theory, the present inventors have suggested that there is an interaction between a specific process in the microorganism and the intracellular process activated by this specific feature in the host subject. For example, SCFAs such as acetic acid, propionic acid, or butyric acid produced by the microorganism(s) in the microbial components can be secreted from a specific microorganism into the host's intestine and then inhibit the activation of the host's HDAC (histone deacetylase) enzyme or surface components of the immune cells of the host subject. In addition, microbial cell envelope components (such as LPS) can activate the host's TLR (Toll-like receptor). The host component can be, for example, an enzyme. The microbial component can be produced by the microorganism and secreted into the host's intestine.

[0041] As described herein, the regulation of intracellular processes can result in the production of substances. As used herein, production refers to, for example, the production of a substance either directly or indirectly in the microorganism by at least one microorganism (e.g., in the microorganism) or its components (such as an enzyme), or in the host by a host component, and sometimes, when the substance is produced within the microorganism, this can also include the secretion of a specific substance from at least one microorganism into the host's intestine and feces. It should be noted.

[0042] As shown in Examples 1 and 2 below, the identified microorganisms were able to regulate various processes, such as the activation of TLRs, the secretion of various pro-inflammatory cytokines, and the expression of various surface components of immune cells. As also shown in the examples below, surprisingly, microorganisms that are present in low abundance in the microbiota of reference human subjects exhibited profound and substantial regulation (activation, secretion, expression) of various processes in both macrophages and peripheral blood mononuclear cells (PBMCs). Thus, the inventors have suggested that computationally identified and selected low-abundance microorganisms have the ability to induce specific and profound immune responses despite their “natural” low abundance.

[0043] As described herein, a microbial consortium can regulate various processes, including functional microbial processes and / or functional host processes, which are collectively referred to herein as intracellular processes. Intracellular processes relate to (include) the regulation of at least one of the following: (i) Toll-like receptors (TLRs), (ii) surface components of immune cells, (iii) nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), (iv) dendritic cells, (v) pro-inflammatory cytokines, and (vi) intestinal barrier integrity.

[0044] In some embodiments, a microbial consortium can regulate at least one of the following: (i) TLRs, (ii) surface components of immune cells, (iii) NF-κB, (iv) dendritic cells, (v) pro-inflammatory cytokines, and (vi) intestinal barrier integrity.

[0045] In some embodiments, a microbial consortium can regulate at least one of the following: (i) activation of TLRs, (ii) activation of surface components of immune cells, (iii) activation of NF-κB, (iv) activation of dendritic cells, (v) secretion of pro-inflammatory cytokines, and (vi) maintenance or enhancement of intestinal barrier integrity.

[0046] In some embodiments, the microbial consortium can regulate at least one of the following: (i) activation of TLR, (ii) activation of surface components of immune cells, and (iii) maintenance of pro-inflammatory cytokines.

[0047] According to some embodiments, at least one species of microorganism that is present in low abundance in a reference human subject can regulate at least one of (i) TLR, (ii) surface components of immune cells, (iii) NF-κB, (iv) dendritic cells, (v) pro-inflammatory cytokines, and (vi) intestinal barrier integrity.

[0048] According to some embodiments, at least one of two or more species of microorganisms, for example, at least one of two or more species of microorganisms that are present in low abundance in the microbiota of a reference human subject, can regulate at least one of (i) TLR, (ii) surface components of immune cells, and (iii) pro-inflammatory cytokines.

[0049] In some embodiments, the microbial consortium has at least one of the following: (i) can regulate (activate) at least one SCFA, (ii) contains at least one cell envelope component recognized by the immune system of the subject or epithelial cells such as intestinal epithelial cells, (iii) can regulate (activate) at least one TLR, (iv) can regulate (activate) surface components of immune cells, (v) can regulate (activate) NF-κB, (vi) can regulate (activate) dendritic cells, (vii) can secrete pro-inflammatory cytokines, and (viii) can maintain or enhance intestinal barrier integrity.

[0050] In some embodiments, the microbial consortium has at least one of: (i) can regulate at least one SCFA; (ii) includes at least one cell envelope component that can be recognized by the immune system of the subject or epithelial cells such as intestinal epithelial cells; (iii) can regulate at least one TLR; (iv) can regulate surface components of immune cells; and (v) can regulate pro-inflammatory cytokines.

[0051] In some embodiments, at least one of two or more microorganisms, for example, at least one of two or more microorganisms that are present in low abundance in the microbiota of a reference human subject, has at least one of: (i) can regulate at least one SCFA; (ii) includes at least one cell envelope component that can be recognized by the immune system of the subject or epithelial cells such as intestinal epithelial cells; (iii) can regulate at least one TLR; (iv) can regulate surface components of immune cells; and (v) can regulate pro-inflammatory cytokines.

[0052] As described herein, the microbial consortium includes at least one microorganism, for example, at least one of two or more microorganisms that are present in low abundance in the microbiota of a reference human subject, which can regulate / activate at least one SCFA.

[0053] SCFAs produced by the gut microbiota serve as an energy source for the host intestinal epithelium and regulate intestinal motility, inflammation, immune function, glucose homeostasis, and energy harvesting.

[0054] In some embodiments, the SCFA includes at least one of acetic acid, propionic acid, butyric acid, valeric acid, isovaleric acid, formic acid, isobutyric acid, and any combination thereof.

[0055] In some other embodiments, the SCFA includes at least one of acetic acid, propionic acid, butyric acid, and any combination thereof.

[0056] In some embodiments, the microbial consortium comprises at least one microorganism, such as at least one microorganism that is present in low abundance in the microbiota of a reference human subject, which can secrete at least one of acetic acid, propionic acid, butyric acid, valeric acid, isovaleric acid, formic acid, isobutyric acid, lactate, and any combination thereof.

[0057] In some other embodiments, the microbial consortium comprises at least one microorganism, such as at least one microorganism that is present in low abundance in the microbiota of a reference human subject, which can secrete at least one of acetic acid, propionic acid, butyric acid, lactate, and any combination thereof.

[0058] In some embodiments, the microbial consortium comprises at least one microorganism, such as at least one microorganism that is present in low abundance in the microbiota of a reference human subject, which comprises at least one cell envelope component.

[0059] The term cell envelope component refers to a structural / chemical entity that is present on or embedded in the membrane or cell wall or outer membrane of a microorganism. The cell envelope component has the ability to be recognized by the subject (host) immune system according to some embodiments, and has the ability to activate the host immune system or be recognized by the epithelial cells of the subject, such as intestinal epithelial cells, according to some other embodiments.

[0060] Cell envelope components are sometimes shared by microorganisms that are recognized by host immune cell receptors called pattern recognition receptors (PRRs) and are sometimes referred to in the art as pathogen-associated molecular patterns (PAMPs), which are molecules exclusive to microorganisms.

[0061] In some embodiments, the cell envelope component is or comprises at least one of lipoproteins, lipoglycans, peptidoglycans, lipopolysaccharides, polysaccharides, flagellin, proteins, peptides, and sugar residues.

[0062] In some other embodiments, the cell envelope component is or comprises peptidoglycan. In some other embodiments, the peptidoglycan is pseudopeptidoglycan. Pseudopeptidoglycan (also known as pseudomurein) is a major cell wall component of some archaea. In some embodiments, the pseudopeptidoglycan is N-acetylglucosamine, N-acetyltalosaminuronic acid, or any combination thereof.

[0063] In some other embodiments, the cell envelope component is or comprises a polysaccharide. In some embodiments, the polysaccharide is an O antigen or a glucan. The O antigen (also known as the O-specific polysaccharide or O-side chain) is a major component of the surface lipopolysaccharide (LPS) of Gram-negative bacteria and has a highly variable structure. A glucan is a polysaccharide derived from D-glucose linked by glycosidic bonds. Glucans include α-glucans and β-glucans, and the numbers clarify the type of O-glycosidic bond.

[0064] In some other embodiments, the cell envelope component is a biopolymer containing galactose and arabinose residues. In some other embodiments, the biopolymer is arabinogalactan.

[0065] In some other embodiments, the cell envelope component is a lipid residue or comprises a lipid residue. In some embodiments, the lipid residue is or comprises an archaeal lipid or lipid A. Archaeal lipids are characterized by comprising ether-linked lipids based on a 2,3-dialkyl-sn-glycerol backbone. Non-limiting examples of archaeal lipids include archaeol and caldarchaeol.

[0066] In some other embodiments, the cell envelope component is or comprises at least one of a lipoprotein, a lipoglycan, and a lipopolysaccharide. In some other embodiments, the cell envelope component is a lipopolysaccharide comprising lipid A.

[0067] In some other embodiments, the cell envelope component is or comprises at least one of pseudopeptidoglycan, archaeal lipid, O antigen, lipid A, arabinogalactan, and β-glucan.

[0068] The presence of the cell envelope components detailed herein can be determined by any method known in the art, for example, by using computational tools to identify genes encoding the synthesis of specific cell envelope components detailed herein. Moreover, such cell envelope components can be determined by any known method in the art.

[0069] In some embodiments, the microbial consortium can activate at least one TLR.

[0070] The TLR family plays a fundamental role in pathogen recognition and activation of innate immunity. TLRs are highly conserved from Drosophila to humans and share structural and functional similarities. They recognize pathogen-associated molecular patterns (PAMPs) expressed on infectious agents and mediate the production of cytokines necessary for the development of effective immunity. Various TLRs exhibit different expression patterns.

[0071] In some embodiments, the TLR is selected from the group consisting of TLR1, TLR2, TLR3, TLR4, TLR5, TRL6, TLR7, TLR8, TLR9, and any combination thereof.

[0072] In some embodiments, the microbial consortium includes at least one microorganism, such as at least one microorganism that is present in low abundance in the microbiota of a reference human subject, and can modulate at least one of TLR1, TLR2, TLR3, TLR4, TLR5, TRL6, TLR7, TLR8, TLR9, and any combination thereof.

[0073] In some other embodiments, the microbial consortium includes at least one microorganism, such as at least one microorganism that is present in low abundance in the microbiota of a reference human subject, and can modulate at least one of TLR2, TLR4, TLR5, TRL6, and any combination thereof.

[0074] In some further embodiments, the microbial consortium includes at least one microorganism, such as at least one microorganism that is present in low abundance in the microbiota of a reference human subject, and can modulate at least one of TLR2, TLR4, and any combination thereof.

[0075] In some embodiments, the microbial consortium can activate at least one immune cell, such as a T cell, a B cell, a natural killer (NK) cell, an antigen-presenting cell (APC), such as a macrophage or a dendritic cell, or a surface component of an immune cell.

[0076] In some embodiments, the surface component of the immune cell includes at least one cluster of differentiation (CD).

[0077] The term "cluster of differentiation antigens" (also known as a class of determinants for naming or classification) is a nomenclature protocol used for the identification and investigation of cell surface molecules that provide targets for the immunophenotyping of cells. CD molecules often act as important receptors or ligands for cells. In some embodiments, at least one cluster of differentiation antigens is at least one of CD4, CD8, CD40, CD68, CD80, CD86, CD197, CD45, CD11b, CD103, and any combination thereof.

[0078] In some embodiments, the microbial consortium includes at least one microorganism, for example, at least one microorganism that is present in low abundance in the microbiota of a reference human subject, and can regulate the expression of at least one of CD4, CD8, CD40, CD68, CD80, CD86, CD197, CD45, CD11b, CD103, and any combination thereof.

[0079] In some other embodiments, the microbial consortium includes at least one microorganism, for example, at least one microorganism that is present in low abundance in the microbiota of a reference human subject, and can regulate the expression of at least one of CD8 and CD68 and any combination thereof.

[0080] In some embodiments, the microbial consortium can activate NF-κB. NF-κB is a protein complex that controls DNA transcription, cytokine production, and cell survival and plays an important role in regulating the immune response to infection.

[0081] In some embodiments, the microbial consortium can activate dendritic cells. Dendritic cells (DCs) are antigen-presenting cells of the immune system, and their main function is to process antigenic materials and present them to T cells of the immune system on the cell surface. Activated DCs migrate to lymph nodes and interact with T cells and B cells to initiate and form an adaptive immune response.

[0082] In some embodiments, the microbial consortium can activate the inflammasome. The inflammasome is a multi-protein oligomer that is involved in the activation of the inflammatory response and promotes the maturation and secretion of pro-inflammatory cytokines such as interleukin 1β (IL-1β) and interleukin 18 (IL-18).

[0083] In some embodiments, the microbial consortium can regulate pro-inflammatory cytokines.

[0084] Pro-inflammatory cytokines (also called inflammatory cytokines) are a type of signaling molecule (cytokine) secreted from immune cells such as helper T cells (Th) and macrophages, as well as certain other cell types that promote inflammation.

[0085] Non-limiting examples of pro-inflammatory cytokines include interleukin-1 (IL-1), IL-12, IL-18, tumor necrosis factor α (TNF-α), interferon γ (IFNγ), and granulocyte macrophage colony-stimulating factor (GM-CSF).

[0086] In some embodiments, the pro-inflammatory cytokine comprises at least one of interleukin-1 (IL-1), IL-2, IL-1β, IL-6, IL-12, IL-18, IL-22, IL-23 tumor necrosis factor α (TNF-α), interferon γ (IFNγ), and granulocyte macrophage colony-stimulating factor (GM-CSF).

[0087] In some embodiments, the pro-inflammatory cytokine comprises at least one of IL-1β, IL-6, IL-12, TNF-α, IFNγ, and any combination thereof.

[0088] In some embodiments, the microbial consortium comprises at least one microbe, e.g., at least one microbe that is present in low abundance in the microbiota of a reference human subject, and can regulate the secretion of at least one of IL-1, IL-1β, IL-6, IL-12, IL-18, TNF-α, IFNγ, GM-CSF, and any combination thereof.

[0089] In some other embodiments, the microbial consortium comprises at least one microbe, e.g., at least one microbe that is present in low abundance in the microbiota of a reference human subject, and can regulate the secretion of at least one of IL-1β, IL-6, IL-12, TNF-α, and any combination thereof.

[0090] In some embodiments, the microbial consortium can activate the secretion of tumor necrosis factor α (TNFα). TNFα is a cell signaling protein (cytokine) involved in systemic inflammation and is one of the cytokines that make up the acute phase response. The main role of TNF is in the regulation of immune cells.

[0091] In some embodiments, the microbial consortium can activate the secretion of interferon γ (IFNγ). IFNγ is a dimeric soluble cytokine important for innate and adaptive immunity against viruses, some bacteria, and protozoan infections. It is an important activator of macrophages and an inducer of major histocompatibility complex (MHC) class II molecule expression.

[0092] In some embodiments, the microbial consortium can activate mucin degradation. Activation of mucin degradation in the context of the present disclosure refers to functioning to degrade host mucin. Host mucin mainly consists of core 1-4 mucin-type O-glycans containing α and β-linked N-acetyl-galactosamine, galactose, and N-acetyl-glucosamine. These core structures are further elongated and are frequently modified by fucose and sialic acid sugar residues via α1,2 / 3 / 4 and α2,3 / 6 linkages, respectively.

[0093] As described herein, it has been shown in examples that microorganisms present in low abundance can regulate various processes.

[0094] In some embodiments, at least one microorganism present in low abundance in a reference human subject can regulate at least one of acetic acid, propionic acid, and butyric acid.

[0095] In some other embodiments, at least one microorganism present in low abundance in a reference human subject comprises at least one of pseudopeptidoglycan, archaeal lipids, O antigen, lipid A, arabinogalactan, and β-glucan.

[0096] In some further embodiments, at least one microorganism present in low abundance in a reference human subject is capable of at least one of (i) regulating at least one of acetic acid, propionic acid, and butyric acid, and (ii) comprising at least one of pseudopeptidoglycan, archaeal lipids, O antigen, lipid A, arabinogalactan, and β-glucan.

[0097] In some other embodiments, at least one microorganism present in low abundance in a reference human subject can regulate at least one of TLR2, TLR4, TLR5, TLR6, TLR7, and TLR8.

[0098] In some further embodiments, at least one microorganism present in low abundance in the reference human subject can be at least one of (i) modulating at least one of acetic acid, propionic acid, butyric acid, TLR2, TLR4, TLR5, TLR6, TLR7, and TLR8, and (ii) including at least one of pseudopeptidoglycan, archaeal lipids, O antigen, lipid A, arabinogalactan, and β-glucan.

[0099] In some other embodiments, at least one microorganism present in low abundance in the reference human subject can modulate at least one of TLR2 and TLR4.

[0100] In some embodiments, at least one microorganism present in low abundance in the reference human subject can modulate at least one of CD8 and CD68.

[0101] In some other embodiments, at least one microorganism present in low abundance in the reference human subject can modulate at least one of TLR2, TLR4, CD8, and CD68.

[0102] In some embodiments, at least one microorganism present in low abundance in the reference human subject can modulate dendritic cells.

[0103] In some embodiments, at least one microorganism present in low abundance in the reference human subject can modulate at least one of IL-1β, IL-6, IL-12, TNF-α, and IFNγ. In some embodiments, at least one microorganism present in low abundance in the reference human subject can modulate at least one of IL-1β, IL-6, IL-12, and TNF-α.

[0104] According to some further embodiments, at least one microorganism present in low abundance in a reference human subject can regulate at least one of TLR2, TLR4, TLR5, TLR6, TLR7, TLR8, secrete IL-1β, secrete IL-6, secrete IL-12, secrete TNF-α, secrete IFNγ, express CD8, and express CD68.

[0105] According to some further embodiments, at least one microorganism present in low abundance in a reference human subject can regulate at least one of TLR2, TLR4, secrete IL-1β, secrete IL-6, secrete IL-12, secrete TNF-α, secrete IFNγ, express CD8, or express CD68.

[0106] In some embodiments, at least one microorganism present in low abundance in a reference human subject can be at least one of (i) regulating at least one of acetic acid, propionic acid, butyric acid, TLR2, TLR4, TLR5, TLR6, TLR7, TLR8, CD8, CD68, IL-1β, IL-6, IL-12, TNF-α, and IFNγ, and (ii) containing at least one of pseudopeptidoglycan, archaeal lipid, O antigen, lipid A, arabinogalactan, and β-glucan.

[0107] In some embodiments, at least one microorganism present in low abundance in a reference human subject can be at least one of (i) regulating at least one of TLR2, TLR4, CD8, CD68, IL-1β, IL-6, IL-12, and TNF-α, and (ii) containing at least one of pseudopeptidoglycan, archaeal lipid, O antigen, lipid A, arabinogalactan, and β-glucan.

[0108] As detailed above, activation of the immune response is achieved by the identified indigenous microorganisms.

[0109] In some embodiments, the microbial consortium comprises at least one microorganism derived from the genus Methanosphaera, the genus Oenococcus, the genus Cetobacterium, the genus Corynebacterium, and the genus Clostridium.

[0110] In some embodiments, the microbial consortium comprises at least one, at least two, or at least three microorganisms derived from the genus Oenococcus, the genus Cetobacterium, the genus Corynebacterium, and the genus Clostridium.

[0111] In some embodiments, at least one microorganism in low abundance is at least one of the genus Methanosphaera, the genus Oenococcus, the genus Cetobacterium, the genus Corynebacterium, and the genus Clostridium.

[0112] In some embodiments, at least one microorganism in low abundance is at least one of the genus Oenococcus, the genus Cetobacterium, the genus Corynebacterium, and the genus Clostridium.

[0113] In some embodiments, the microbial consortium comprises at least one microorganism derived from the genus Methanosphaera. The genus Methanosphaera can be indicated by Taxonomy ID (or taxid): 2316. Methanosphaera is a genus of microorganisms (archaea) in the family Methanobacteriaceae.

[0114] In some embodiments, the microbial consortium comprises at least one microorganism derived from the genus Oenococcus. The genus Oenococcus can be indicated by Taxonomy ID: 46254. Oenococcus is a genus of Gram-positive bacteria of the family Leuconostocaceae. Non-limiting examples of the genus Oenococcus include Oenococcus oeni and Oenococcus kitaharae.

[0115] In some embodiments, the microbial consortium comprises at least one microorganism derived from the genus Cetobacterium. The genus Cetobacterium can be indicated by Taxonomy ID: 180162. Cetobacterium is a genus of Gram-negative bacteria of the family Fusobacteriaceae.

[0116] In some embodiments, the microbial consortium comprises at least one microbial species (type) derived from the genus Corynebacterium. The genus Corynebacterium can be indicated by Taxonomy ID: 1716. Corynebacterium is a genus of bacteria that are Gram-positive, aerobic, and bacilli.

[0117] In some embodiments, the microbial consortium comprises at least one microorganism derived from the genus Clostridium. The genus Clostridium can be indicated by Taxonomy ID: 1485. Clostridium is a genus of Gram-positive bacteria.

[0118] In some embodiments, the microbial consortium comprises at least one microorganism derived from the species Methanosphaera stadtmanae, the species Oenococcus oeni, the species Clostridium cellulovorans, the species Cetobacterium somerae, the species Corynebacterium glyciniphilum, and the species Clostridium tyrobutyricum.

[0119] In some embodiments, the microbial consortium comprises at least one, at least two, or at least three microorganisms derived from the species Oenococcus oeni, the species Clostridium cellulovorans, the species Cetobacterium somerae, the species Corynebacterium glyciniphilum, and the species Clostridium tyrobutyricum.

[0120] In some embodiments, the at least one microorganism present in low abundance is at least one microorganism derived from the species Methanosphaera stadtmanae, the species Oenococcus oeni, the species Clostridium cellulovorans, the species Cetobacterium somerae, the species Corynebacterium glyciniphilum, and the species Clostridium tyrobutyricum.

[0121] In some embodiments, the at least one microorganism present in low abundance is at least one microorganism from the species Oenococcus oeni, Clostridium cellulovorans, Cetobacterium somerae, Corynebacterium glyciniphilum, and Clostridium tyrobutyricum.

[0122] In some embodiments, the at least one microorganism present in low abundance is at least one microorganism from the species Oenococcus oeni, Cetobacterium somerae, Corynebacterium glyciniphilum, and Clostridium tyrobutyricum.

[0123] In some embodiments, the at least one microorganism present in low abundance is at least one microorganism from the species Clostridium cellulovorans, Cetobacterium somerae, and Clostridium tyrobutyricum.

[0124] In some embodiments, the at least one microorganism present in low abundance is at least one microorganism from the species Clostridium cellulovorans and Cetobacterium somerae.

[0125] In some embodiments, the microbial consortium comprises at least one microorganism derived from the species Methanosphaera stadtmanae. The species Methanosphaera stadtmanae may be indicated by Taxonomy ID: 2317.

[0126] In some embodiments, the microbial consortium comprises at least one microorganism derived from the species Oenococcus oeni. The species Oenococcus oeni may be indicated by Taxonomy ID: 1247.

[0127] In some embodiments, the microbial consortium comprises at least one microorganism derived from the species Cetobacterium somerae. The species Cetobacterium somerae may be indicated by Taxonomy ID: 188913.

[0128] In some embodiments, the microbial consortium comprises at least one microorganism derived from the species Corynebacterium glyciniphilum. The species Corynebacterium glyciniphilum may be indicated by Taxonomy ID: 1404244.

[0129] In some embodiments, the microbial consortium comprises at least one microorganism derived from the species Clostridium tyrobutyricum. The species Clostridium tyrobutyricum may be indicated by Taxonomy ID: 1519.

[0130] In some embodiments, the microbial consortium comprises at least one microorganism derived from the species Clostridium cellulovorans. The species Clostridium cellulovorans may be indicated by Taxonomy ID: 1493.

[0131] In the context of the present disclosure, the identification of microorganisms from a biological sample of a human subject can be performed using any conventional method in the field of microbiology. For example, but not limited to, the identification of bacteria from a biological sample of a human subject can be performed using 16S rRNA (ribosomal RNA) sequencing. The identification of an isolated microorganism can be performed by conducting a similarity analysis between the 16S rRNA gene of the isolated microorganism and the 16S rRNA gene sequences of different microorganisms available in a database. This analysis can be carried out to investigate the similarity between a given sequence and all of the sequences available in the database and obtain the sequence that best matches by calculating a score for the similarity being considered. The identity analysis can be performed using any suitable program, for example, the Basic Local Alignment Search Tool (BLAST (registered trademark)) using a publicly available database such as the National Center for Biotechnology Information (NCBI).

[0132] In some embodiments, at least one of the two or more microorganisms comprises a 16S rRNA sequence having at least 85% to 99%, sometimes 90% to 99%, sometimes 95% to 99%, sometimes 96% to 99%, sometimes 97% to 99%, sometimes 98% to 99% identity with at least one nucleic acid sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, and SEQ ID NO: 6.

[0133] In some embodiments, at least one of the two or more microorganisms comprises at least one nucleic acid sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, and SEQ ID NO: 6, and a 16S rRNA sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5% identity. Note that each of the identity percentages constitutes a separate embodiment of the present invention.

[0134] The threshold sequence identity may be 85%, sometimes 86%, sometimes 87%, sometimes 88%, sometimes 89%, sometimes 90%, sometimes 91%, sometimes 92%, sometimes 93%, sometimes 94%, sometimes 95%, sometimes 96%, sometimes 97%, sometimes 98%, sometimes 99%, sometimes 99.5%, and each of the identity percentages shown herein constitutes a separate embodiment of the present invention.

[0135] As used herein, the term identity (identity %) refers to two or more nucleic acid sequences that are identical. In the context of the present disclosure, sequence identity encompasses transcriptional changes from DNA to RNA; for example, T and U are considered identical. Identity can exist over regions of the sequence that are considered by those skilled in the art to be variable regions of 16S rRNA. In some embodiments, identity exists over the length of the 16S rRNA or a portion of the variable region.

[0136] The percent identity between two or more nucleic acid sequences is determined for the two or more sequences when compared and aligned for maximum correspondence. In the context of the present disclosure, the sequences (nucleic acids) described herein having percent identity are considered to have the same function / activity as the original sequence for which the identity is calculated.

[0137] In some embodiments, the microbial consortium comprises at least Oenococcus oeni PSU-1. Oenococcus oeni PSU-1 may be indicated by Taxonomy ID: 203123. The 16S rRNA sequence of Oenococcus oeni PSU-1 is provided by SEQ ID NO: 1.

[0138] In some embodiments, the microbial consortium comprises at least Clostridium tyrobutyricum KCTC 5387. Clostridium tyrobutyricum KCTC 5387 may be indicated by Taxonomy ID: 1121342. The 16S rRNA sequence of Clostridium tyrobutyricum KCTC 5387 is provided by GenBank accession number NR_044718.2 (SEQ ID NO: 2).

[0139] In some embodiments, the microbial consortium comprises at least Cetobacterium somerae ATCC BAA-474. Cetobacterium somerae ATCC BAA-474 may be indicated by Taxonomy ID: 1319815. The 16S rRNA sequence of Cetobacterium somerae ATCC BAA-474 is provided by GenBank accession number AJ438155.2 (SEQ ID NO: 3).

[0140] In some embodiments, the microbial consortium comprises at least Corynebacterium glyciniphilum AJ 3170. Corynebacterium glyciniphilum AJ 3170 can be indicated by Taxonomy ID: 1404245. The 16S rRNA sequence of Corynebacterium glyciniphilum AJ 3170 is provided by GenBank accession number NR_121782.1 (SEQ ID NO: 4).

[0141] In some embodiments, the microbial consortium comprises at least Clostridium cellulovorans 743B. Clostridium cellulovorans 743B can be indicated by Taxonomy ID: 573061. The 16S rRNA sequence of Clostridium cellulovorans 743B is provided by GenBank accession number NR_119029.1 (SEQ ID NO: 5).

[0142] In some embodiments, the microbial consortium comprises at least Methanosphaera stadtmanae DSM3091. Methanosphaera stadtmanae DSM3091 can be indicated by Taxonomy ID: 339860. The 16S rRNA sequence of Methanosphaera stadtmanae DSM3091 is provided by GenBank accession number NR_028236.1 (SEQ ID NO: 6).

[0143] In some embodiments, the microbial consortium comprises two microorganisms, as shown above. In some embodiments, the microbial consortium comprises a combination of two, three, four, five, or more microorganisms, as shown above.

[0144] In some embodiments, at least one of the two or more microorganisms within the microbial consortium, for example, a microorganism with a low abundance in the reference microbial community, comprises at least one 16S rRNA sequence of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, and SEQ ID NO: 6.

[0145] In some other embodiments, two or more microorganisms in the microbial consortium, for example, a microorganism with a low abundance in the reference microbial community, comprise at least two 16S rRNA sequences of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, and SEQ ID NO: 6.

[0146] In some embodiments, the microbial consortium comprises at least one, at least two, at least three, at least four, and sometimes five microorganisms with low abundance having a 16S rRNA sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, and SEQ ID NO: 5.

[0147] In some embodiments, the microbial consortium comprises at least one, in some embodiments at least two, in some embodiments at least three, in some embodiments at least four microorganisms having the 16S rRNA sequences represented by SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, and SEQ ID NO: 5.

[0148] In some embodiments, the microbial consortium comprises one, in some embodiments two, in some embodiments three, in some embodiments four, in some embodiments five microorganisms having the 16S rRNA sequences represented by SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, and SEQ ID NO: 5.

[0149] In some embodiments, the microbial consortium comprises at least one, at least two, or more microorganisms selected from Methanosphaera stadtmanae DSM3091, Oenococcus oeni PSU-1, Clostridium tyrobutyricum KCTC 5387, Cetobacterium somerae ATCC BAA-474, Corynebacterium glyciniphilum AJ 3170, and Clostridium cellulovorans 743B.

[0150] In some embodiments, the microbial consortium comprises two or more microorganisms selected from Methanosphaera stadtmanae DSM3091, Oenococcus oeni PSU-1, Clostridium tyrobutyricum KCTC 5387, and Cetobacterium somerae ATCC BAA-474.

[0151] In some embodiments, the microbial consortium comprises 1, 2, 3, 4, or 5 microorganisms selected from Oenococcus oeni PSU-1, Clostridium tyrobutyricum KCTC 5387, Cetobacterium somerae ATCC BAA-474, Corynebacterium glyciniphilum AJ 3170, and Clostridium cellulovorans 743B.

[0152] In some embodiments, the microbial consortium comprises 1, 2, 3, or 4 microorganisms selected from Oenococcus oeni PSU-1, Clostridium tyrobutyricum KCTC 5387, Cetobacterium somerae ATCC BAA-474, and Corynebacterium glyciniphilum AJ 3170.

[0153] In some embodiments, the microbial consortium comprises 1, 2, or 3 microorganisms selected from Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, and Clostridium cellulovorans 743B.

[0154] In some embodiments, the microbial consortium comprises 1 or 2 microorganisms selected from Cetobacterium somerae ATCC BAA-474 and Clostridium tyrobutyricum KCTC 5387.

[0155] In some embodiments, the microbial consortium may also include at least one high-abundance microorganism from the human reference microbiota.

[0156] In some embodiments, the high-abundance microorganism may be the same microorganism as the microorganism that secretes at least one of (i) being able to produce at least one SCFA, (ii) being able to regulate lactate, and (iii) containing at least one cell envelope component.

[0157] In some embodiments, the high-abundance microorganism can be a microorganism different from a microorganism that (i) can produce at least one SCFA, (ii) can regulate lactate, and (iii) secretes at least one of the components including at least one cell envelope component.

[0158] In some embodiments, the high-abundance microorganism can be a microorganism different from a microorganism that regulates (produces and / or secretes) short-chain fatty acids (SCFAs).

[0159] In some embodiments, the high-abundance microorganism can be a microorganism different from a microorganism that regulates (produces and / or secretes) lactate.

[0160] In some embodiments, the high-abundance microorganism can be a microorganism different from a microorganism that contains at least one cell envelope component.

[0161] Thus, according to some embodiments, the microbial consortium includes two or more microorganisms, at least one of the two or more microorganisms is present in low abundance in the microbiota of the reference human subject, at least one of the other two or more microorganisms is present in high abundance in the microbiota of the reference human subject, and has at least one of (i) being able to produce at least one SCFA, (ii) being able to regulate lactate, and (iii) containing at least one cell envelope component.

[0162] In some other embodiments, the microbial consortium includes three or more microorganisms, at least one of the three or more microorganisms is present in low abundance in the microbiota of the reference human subject, at least one of the other three or more microorganisms secretes at least one having at least one of (i) being able to produce at least one SCFA, (ii) being able to regulate lactate, and (iii) containing at least one cell envelope component or different bacteria, and at least one of the three or more microorganisms is present in high abundance in the microbiota of the reference human subject.

[0163] As used herein, the term "high abundance" refers to a microorganism present in a microbial community of interest in an amount that exceeds a predetermined standard value(s) or cut-off value(s). The predetermined standard value(s) or cut-off value(s) may be determined as the average value of a large heterogeneous cohort of subjects, or may be determined for a particular population of interest. In some embodiments, the reference human subject is a healthy subject. A healthy subject is a subject not diagnosed with a disease to be treated using the microbial consortium of the present invention. In some other embodiments, the reference human subject is a subject diagnosed with at least one disease, optionally a disease treatable using the microbial consortium of the present invention. In some embodiments, the high-abundance microorganism has an average relative abundance of greater than 0.5%, sometimes greater than 0.6%, sometimes greater than 0.7%, sometimes greater than 0.8%, further sometimes greater than 0.9%, further sometimes greater than 1.5%, and further sometimes greater than 2%. In some embodiments, the high-abundance microorganism has an average relative abundance of from about 0.5% to about 5%, sometimes from about 0.6% to about 5%, sometimes from about 0.7% to about 5%, sometimes from about 1% to about 5%, sometimes from about 1.5% to about 5%, and sometimes from about 2% to about 5%.

[0164] In some embodiments, the high-abundance microorganism possesses cell envelope components recognized by the immune system of the subject. In some embodiments, the high-abundance microorganism possesses cell envelope components that activate the immune system of the subject as described herein.

[0165] In some embodiments, the high-abundance microorganism comprises at least one microorganism from the genus Bacteroides, Ruminococcus, Lactobacillus, Veillonella, Bifidobacterium, Alistipes, and Akkermansia.

[0166] In some embodiments, the high-abundance microorganisms include at least one microorganism from the genus Bacteroides, the genus Lactobacillus, or the genus Veillonella.

[0167] In some embodiments, the high-abundance microorganisms include at least one microorganism from the genus Bacteroides. The genus Bacteroides can be indicated by Taxonomy ID:816. Bacteroides is a genus of Gram-negative obligate anaerobic bacteria.

[0168] In some embodiments, the high-abundance microorganisms include at least one microorganism from the genus Ruminococcus. The genus Ruminococcus can be indicated by Taxonomy ID:1263. Ruminococcus is a genus of bacteria in the class Clostridia, which are anaerobic Gram-positive microorganisms.

[0169] In some embodiments, the high-abundance microorganisms include at least one microbial species or strain derived from the genus Lactobacillus. The genus Lactobacillus can be indicated by Taxonomy ID:1578. Lactobacillus is a genus of Gram-positive bacteria, facultative anaerobic bacteria or microaerophilic bacteria, bacilli, non-spore-forming bacteria that are a major part of the lactic acid bacteria group (i.e., they convert sugars into lactic acid).

[0170] In some embodiments, the high-abundance microorganisms include at least one microbial species or strain derived from the genus Veillonella. The genus Veillonella can be indicated by Taxonomy ID:29465. Veillonella is a genus of anaerobic cocci of Gram-negative bacteria known for its lactate fermentation ability.

[0171] In some embodiments, the high-abundance microorganisms include at least one microbial species or strain derived from the genus Bifidobacterium. The genus Bifidobacterium can be indicated by Taxonomy ID: 1678. Bifidobacterium is a genus of Gram-positive, non-motile, and in some cases branched anaerobic bacteria.

[0172] In some embodiments, the high-abundance microorganisms include at least one microbial species or strain derived from the genus Alistipes. The genus Alistipes can be indicated by Taxonomy ID: 239759. Alistipes is a genus of the Bacteroidetes phylum.

[0173] In some embodiments, the high-abundance microorganisms include at least one microbial species or strain derived from the genus Akkermansia. The genus Akkermansia can be indicated by Taxonomy ID: 239934. Akkermansia is a genus of the Verrucomicrobia phylum.

[0174] In some embodiments, the microbial consortium includes at least one microorganism from the species Bacteroides caccae, Ruminococcus albus, Lactobacillus casei, Veillonella parvula, Alistipes putredinis, Bifidobacterium breve, and Akkermansia muciniphila.

[0175] In some embodiments, the microbial consortium comprises at least one microorganism, at least two microorganisms, or at least three microorganisms derived from the species Bacteroides caccae, Lactobacillus casei, or Veillonella parvula.

[0176] In some embodiments, the microbial consortium comprises at least one microorganism or at least two microorganisms derived from the species Bacteroides caccae or Veillonella parvula.

[0177] In some embodiments, the microbial consortium comprises at least one microorganism derived from the species Ruminococcus albus. The species Ruminococcus albus can be indicated by Taxonomy ID: 1264.

[0178] In some embodiments, the microbial consortium comprises at least one microorganism derived from the species Lactobacillus casei. The species Lactobacillus casei can be indicated by Taxonomy ID: 1582.

[0179] In some embodiments, the microbial consortium comprises at least one microorganism derived from the species Veillonella parvula. The species Veillonella parvula can be indicated by Taxonomy ID: 29466.

[0180] In some embodiments, the microbial consortium comprises at least one microorganism derived from the species Alistipes putredinis. The species Alistipes putredinis can be indicated by Taxonomy ID: 28117.

[0181] In some embodiments, the microbial consortium comprises at least one microorganism derived from the species Bifidobacterium breve. The species Bifidobacterium breve can be indicated by Taxonomy ID: 1685.

[0182] In some embodiments, the microbial consortium comprises at least one microorganism derived from the species Akkermansia muciniphila. The species Akkermansia muciniphila can be indicated by Taxonomy ID: 239935.

[0183] In some embodiments, the microbial consortium comprises at least one microorganism derived from the species Bacteroides caccae. The species Bacteroides caccae can be indicated by Taxonomy ID: 47678.

[0184] In some embodiments, at least one of the two or more microorganisms comprises at least one nucleic acid represented by SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, and SEQ ID NO: 14, sometimes at least one nucleic acid represented by SEQ ID NO: 7, SEQ ID NO: 8, and SEQ ID NO: 9, and has an identity of 85% - 99%, sometimes 90% - 99%, sometimes 95% - 99%, sometimes 96% - 99%, sometimes 97% - 99%, sometimes 98% - 99% with a 16S rRNA sequence.

[0185] In some embodiments, at least one of the two or more microorganisms comprises at least one nucleic acid represented by SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, and SEQ ID NO: 14, sometimes at least one nucleic acid represented by SEQ ID NO: 7, SEQ ID NO: 8, and SEQ ID NO: 9, and comprises a 16S rRNA sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% identity. Note that each of the identity percentages constitutes a separate embodiment of the present invention.

[0186] As described herein, the threshold sequence identity may be 85%, sometimes 86%, sometimes 87%, sometimes 88%, sometimes 89%, sometimes 90%, sometimes 91%, sometimes 92%, sometimes 93%, sometimes 94%, sometimes 95%, sometimes 96%, sometimes 97%, sometimes 98%, sometimes 99%, and each of the identity percentages shown herein constitutes a separate embodiment of the present invention.

[0187] In some embodiments, the high-abundance microorganisms comprise at least one of Bacteroides caccae CL03T12C61, Ruminococcus albus 7, Lactobacillus casei ATCC27139, Veillonella parvula ATCC 17745, Bifidobacterium breve ATCC 15700, Alistipes putredinis DSM 17216, Akkermenia muciniphila ATCC BAA-835, and Akkermansia muciniphila YL44.

[0188] In some embodiments, the high-abundance microorganisms include at least one, at least two of Bacteroides caccae CL03T12C61, Lactobacillus casei ATCC27139, or Veillonella parvula ATCC17745.

[0189] In some embodiments, the high-abundance microorganisms include one, two, or three of Bacteroides caccae CL03T12C61, Lactobacillus casei ATCC27139, or Veillonella parvula ATCC17745.

[0190] In some embodiments, the high-abundance microorganisms include one, two, or three of Bacteroides caccae CL03T12C61 or Veillonella parvula ATCC17745.

[0191] In some embodiments, the high-abundance microorganisms include one, two, or three of Lactobacillus casei ATCC27139 or Veillonella parvula ATCC17745.

[0192] In some embodiments, the high-abundance microorganisms include one, two, or three of Lactobacillus casei ATCC27139 or Bacteroides caccae CL03T12C61.

[0193] In some embodiments, the high-abundance microorganisms include Veillonella parvula ATCC 17745. Veillonella parvula ATCC 17745 can be represented by Taxonomy ID: 686660. The 16S rRNA sequence of Veillonella parvula ATCC 17745 is provided by Gene Bank accession number AY995769.1 (SEQ ID NO: 7).

[0194] In some embodiments, the high-abundance microorganisms include Bacteroides caccae CL03T12C61. Bacteroides caccae CL03T12C61 can be indicated by Taxonomy ID: 997873. The 16S rRNA sequence of Bacteroides caccae CL03T12C61 is provided by SEQ ID NO: 8.

[0195] In some embodiments, the high-abundance microorganisms include Lactobacillus casei ATCC27139. The 16S rRNA sequence of Lactobacillus casei ATCC27139 is provided by Gene Bank accession number AB531131.1 (SEQ ID NO: 9).

[0196] In some embodiments, the high-abundance microorganisms include Ruminococcus albus 7. Ruminococcus albus 7 can be indicated by Taxonomy ID: 697329. The 16S rRNA sequence of Ruminococcus albus 7 is provided by Gene Bank accession number NR_025929.1 (SEQ ID NO: 10).

[0197] In some embodiments, the high-abundance microorganism includes Bifidobacterium breve ATCC 15700. Bifidobacterium breve ATCC 15700 can be indicated by Taxonomy ID: 518634. The 16S rRNA sequence of Veillonella parvula ATCC 17745 is provided by Gene Bank accession number NR_040783.1 (SEQ ID NO: 11).

[0198] In some embodiments, the high-abundance microorganism includes Alistipes putredinis DSM 17216. Alistipes putredinis DSM 17216 can be indicated by Taxonomy ID: 445970. The 16S rRNA sequence of Alistipes putredinis DSM 17216 is provided by Gene Bank accession number NR_025909.1 (SEQ ID NO: 12).

[0199] In some embodiments, the high-abundance microorganism includes Akkermansia muciniphila ATCC BAA-835. Akkermansia muciniphila ATCC BAA-835 can be indicated by Taxonomy ID: 349741. The 16S rRNA sequence of Akkermansia muciniphila ATCC BAA-835 is provided by Gene Bank accession number NR_042817.1 (SEQ ID NO: 13).

[0200] In some embodiments, the high-abundance microorganism includes Akkermansia muciniphila YL44. The 16S rRNA sequence of Akkermansia muciniphila YL44 is provided by SEQ ID NO: 14.

[0201] In another aspect of the invention that can be implemented as a particular embodiment of the microbial consortium of the invention, a microbial consortium is provided that includes two or more purified or isolated microorganisms, wherein at least one of the two or more microorganisms is (i) capable of regulating at least one of acetic acid, propionic acid, butyric acid, TLR2, TLR4, TLR5, TLR6, TLR7, TLR8, CD8, CD68, IL-1β, IL-6, IL-12, and TNF-α and IFNγ, and (ii) contains at least one of pseudopeptidoglycan, archaeal lipid, O antigen, lipid A, arabinogalactan, and β-glucan, and is present in low abundance in a reference human subject, and at least one different microorganism of the two or more microorganisms possesses a cell envelope component recognized by the immune system of the subject. The at least one different microorganism can be a microorganism present in low abundance in the reference human subject or a microorganism present in high abundance in the reference human subject.

[0202] In another aspect of the invention that can be practiced as a particular embodiment of the microbial consortium of the invention, a microbial consortium is provided that comprises two or more purified or isolated microorganisms, wherein at least one of the two or more microorganisms is present in low abundance in a reference human subject and is capable of at least one of (i) modulating at least one of TLR2, TLR4, TLR5, TLR6, TLR7, TLR8, CD8, CD68, IL-1β, IL-6, IL-12, TNF-α, and IFNγ, and (ii) comprising at least one of pseudopeptidoglycan, archaeal lipid, O antigen, lipid A, arabinogalactan, and β-glucan, and at least one of the two or more microorganisms is a different microorganism that comprises at least one of pseudopeptidoglycan, archaeal lipid, O antigen, lipid A, arabinogalactan, and β-glucan. The at least one different microorganism can be a microorganism that is present in low abundance in the reference human subject or a microorganism that is present in high abundance in the reference human subject.

[0203] In another aspect of the invention that can be practiced as a particular embodiment of the microbial consortium of the invention, a microbial consortium is provided that comprises two or more purified or isolated microorganisms, wherein at least one species of microorganism that is present in low abundance in a reference human subject is capable of at least one of (i) modulating at least one of TLR2, TLR4, CD8, CD68, IL-1β, IL-6, IL-12, TNF-α, and IFNγ, and (ii) comprising at least one of pseudopeptidoglycan, archaeal lipid, O antigen, lipid A, arabinogalactan, and β-glucan, and at least one of the different microorganisms bears a cell envelope component that is recognized by the immune system of the subject. The at least one different microorganism can be a microorganism that is present in low abundance in the reference human subject or a microorganism that is present in high abundance in the reference human subject.

[0204] In another aspect of the invention that can be practiced as a particular embodiment of the microbial consortium of the invention, there is provided a microbial consortium comprising two or more purified or isolated microorganisms, wherein at least one of the microorganisms is present in a low abundance in a reference human subject and is capable of (i) modulating at least one of TLR2, TLR4, CD8, CD68, IL-1β, IL-6, IL-12, TNF-α, and IFNγ, and (ii) containing at least one of pseudopeptidoglycan, archaeal lipid, O antigen, lipid A, arabinogalactan, and β-glucan, and at least one different microorganism contains at least one of pseudopeptidoglycan, archaeal lipid, O antigen, lipid A, arabinogalactan, and β-glucan. The at least one different microorganism can be a microorganism present in a low abundance in the reference human subject or a microorganism present in a high abundance in the reference human subject.

[0205] In another aspect of the invention that can be practiced as a particular embodiment of the microbial consortium of the invention, there is provided a microbial consortium comprising two or more purified or isolated microorganisms that are present in a low abundance in a reference human subject and are capable of modulating at least one of TLR2, TLR4, CD8, CD68, IL-1β, IL-6, IL-12, TNF-α, and IFNγ.

[0206] In another aspect of the invention that can be practiced as a particular embodiment of the microbial consortium of the invention, there is provided a microbial consortium comprising two or more purified or isolated microorganisms that are present in a low abundance in a reference human subject and are capable of modulating at least one of TLR2, TLR4, CD8, CD68, IL-1β, IL-6, IL-12, and TNF-α.

[0207] In another aspect of the invention that can be implemented as a specific embodiment of the microbial consortium of the invention, a microbial consortium comprising two or more purified or isolated microorganisms is provided, wherein at least one of the two or more microorganisms has at least one 16S rDNA sequence represented by SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, and SEQ ID NO: 5, and has a 16S rDNA sequence that is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5% identical, and at least one different microorganism of the two or more microorganisms comprises at least one of pseudopeptidoglycan, archaeal lipid, O antigen, lipid A, arabinogalactan, and β-glucan. The at least one different microorganism can be a microorganism that is present in low abundance in a reference human subject or a microorganism that is present in high abundance in a reference human subject.

[0208] In another aspect of the invention that can be implemented as a specific embodiment of the microbial consortium of the invention, a microbial consortium comprising two or more purified or isolated microorganisms is provided, wherein at least one of the two or more microorganisms is present in low abundance in a reference human subject and can regulate at least one of TLR2, TLR4, TLR5, TLR6, TLR7, TLR8, CD8, CD68, IL-1β, IL-6, IL-12, TNF-α, and IFNγ, and at least one different microorganism of the two or more microorganisms having a 16S rDNA sequence has at least one 16S rDNA sequence represented by SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8 and is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5% identical. The at least one different microorganism can be a microorganism that is present in low abundance in a reference human subject or a microorganism that is present in high abundance in a reference human subject.

[0209] In another aspect of the invention that can be implemented as a specific embodiment of the microbial consortium of the present invention, a microbial consortium is provided that includes two or more purified or isolated microorganisms, and at least one of the two or more microorganisms is present in low abundance in a reference human subject that can regulate at least one of TLR2, TLR4, CD8, CD68, IL-1β, IL-6, IL-12, and TNF-α. At least one different microorganism of the two or more microorganisms having a 16S rDNA sequence is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5% identical to at least one 16S rDNA sequence represented by SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8.

[0210] In another aspect of the invention that can be implemented as a specific embodiment of the microbial consortium of the present invention, a microbial consortium is provided that includes two or more purified or isolated microorganisms having a 16S rDNA sequence that is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5% identical to at least one, at least two, at least three, at least four 16S rDNA sequences listed in Table 1.

[0211] In another aspect of the invention that can be implemented as a specific embodiment of the microbial consortium of the present invention, a microbial consortium is provided that includes two or more purified or isolated microorganisms having a 16S rDNA sequence that is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5% identical to at least one, at least two, at least three, at least four 16S rDNA sequences represented by SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8.

[0212] In another aspect of the invention that can be implemented as a specific embodiment of the microbial consortium of the invention, 1, 2, 3, 4, 5, 6, 7, 8 16S rDNA sequences represented by SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8, and at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5% identical 16S rDNA sequences, a microbial consortium comprising two or more purified or isolated microorganisms is provided.

[0213] In some embodiments, the microbial consortium comprises two or more microorganisms selected from Methanosphaera stadtmanae DSM3091, Oenococcus oeni PSU-1, Clostridium tyrobutyricum KCTC 5387, Cetobacterium somerae ATCC BAA-474, Corynebacterium glyciniphilum AJ 3170, Bacteroides caccae CL03T12C61, Ruminococcus albus 7, Lactobacillus casei ATCC27139, Veillonella parvula ATCC 17745, and Clostridium cellulovorans 743B.

[0214] In some embodiments, the microbial consortium comprises three, sometimes four, sometimes five, sometimes six, sometimes seven, sometimes eight, sometimes nine, sometimes ten, or more microorganisms selected from Methanosphaera stadtmanae DSM3091, Oenococcus oeni PSU-1, Clostridium tyrobutyricum KCTC 5387, Cetobacterium somerae ATCC BAA-474, Corynebacterium glyciniphilum AJ 3170, Bacteroides caccae CL03T12C61, Ruminococcus albus 7, Lactobacillus casei ATCC27139, Veillonella parvula ATCC 17745, Clostridium cellulovorans 743B, Bifidobacterium breve ATCC15700, Alistipes putredini DSM 17216, Akkermansia muciniphila ATCC BAA-835, and Akkermansia muciniphila YL44.

[0215] In some embodiments, the microbial consortium comprises at least two isolated or purified microorganisms belonging to a genus, spices, or strain identified by an NCBI Taxonomy ID selected from the group consisting of NCBI Taxonomy ID: 2316, 46254, 180162, 1716, 1485, 2317, 1247, 188913, 1404244, 1519, 1493, 203123, 1121342, 1319815, 1404245, 573061, 339860, 816, 1263, 1578, 29465, 1678, 239759, 239934, 1264, 1582, 29466, 28117, 1685, 239935, 47678, 686660, 997873, 697329, 518634, 445970, 349741.

[0216] In some embodiments, the microbial consortium comprises two or more microorganisms selected from Oenococcus oeni PSU-1, Methanosphaera stadtmanae DSM3091, Clostridium tyrobutyricum KCTC 5387, Cetobacterium somerae ATCC BAA-474, and Corynebacterium glyciniphilum AJ 3170.

[0217] In some embodiments, the microbial consortium comprises two or more microorganisms selected from Oenococcus oeni PSU-1, Methanosphaera stadtmanae DSM3091, Clostridium tyrobutyricum KCTC 5387, and Cetobacterium somerae ATCC BAA-474.

[0218] In some embodiments, the microbial consortium consists of Oenococcus oeni PSU-1, Methanosphaera stadtmanae DSM3091, Clostridium tyrobutyricum KCTC 5387, and Cetobacterium somerae ATCC BAA-474.

[0219] In some embodiments, the microbial consortium comprises two or more microorganisms selected from Oenococcus oeni PSU-1, Methanosphaera stadtmanae DSM3091, Ruminococcus albus 7, Bacteroides caccae CL03T12C61, and Clostridium tyrobutyricum KCTC 5387.

[0220] In some embodiments, the microbial consortium comprises two or more microorganisms selected from Oenococcus oeni PSU-1, Methanosphaera stadtmanae DSM3091, Ruminococcus albus 7, and Bacteroides caccae CL03T12C61.

[0221] In some embodiments, the microbial consortium consists of Oenococcus oeni PSU-1, Methanosphaera stadtmanae DSM3091, Ruminococcus albus 7, and Bacteroides caccae CL03T12C61.

[0222] In some embodiments, the microbial consortium comprises two or more microorganisms selected from Methanosphaera stadtmanae DSM3091, Lactobacillus casei ATCC27139, Veillonella parvula ATCC 17745, and Ruminococcus albus 7.

[0223] In some embodiments, the microbial consortium consists of Methanosphaera stadtmanae DSM3091, Lactobacillus casei ATCC27139, Veillonella parvula ATCC 17745, and Ruminococcus albus 7.

[0224] In some embodiments, the microbial consortium comprises at least one, at least two, at least three, and sometimes all of Corynebacterium glyciniphilum AJ 3170, Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, and Oenococcus oeni PSU-1.

[0225] In some embodiments, the microbial consortium comprises Corynebacterium glyciniphilum AJ 3170, Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, and Oenococcus oeni PSU-1. This microbial consortium containing the four listed bacterial strains is referred to herein as consortium 1 ("Cons.1").

[0226] In some embodiments, the microbial consortium comprises at least one, at least two, at least three, and sometimes at least all of Bacteroides caccae CL03T12C61, Clostridium cellulovorans 743B, Lactobacillus casei ATCC27139, and Veillonella parvula ATCC17745.

[0227] In some embodiments, the microbial consortium comprises Bacteroides caccae CL03T12C61, Clostridium cellulovorans 743B, Lactobacillus casei ATCC27139, and Veillonella parvula ATCC17745. This microbial consortium containing the four listed bacterial strains is referred to herein as consortium 2 ("Cons.2").

[0228] In some embodiments, the microbial consortium comprises at least one, at least two, at least three, at least four, at least five, at least six, at least seven, and sometimes at least all of Corynebacterium glyciniphilum AJ 3170, Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, Oenococcus oeni PSU-1, Bacteroides caccae CL03T12C61, Clostridium cellulovorans 743B, Lactobacillus casei ATCC27139, and Veillonella parvula ATCC 17745.

[0229] In some embodiments, the microbial consortium comprises Corynebacterium glyciniphilum AJ 3170, Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, Oenococcus oeni PSU-1, Bacteroides caccae CL03T12C61, Clostridium cellulovorans 743B, Lactobacillus casei ATCC27139, and Veillonella parvula ATCC 17745. This microbial consortium that includes the eight enumerated bacterial strains is referred to herein as consortium 3 ("Cons. 3"). Consortium 3 includes the microbial strains of both consortium 1 and consortium 2.

[0230] In some embodiments, the microbial consortium comprises at least one, at least two, at least three, or at least all of Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, Clostridium cellulovorans 743B, and Veillonella parvula ATCC 17745.

[0231] In some embodiments, the microbial consortium comprises Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, Clostridium cellulovorans 743B, and Veillonella parvula ATCC 17745. This microbial consortium comprising the four listed bacterial strains is referred to herein as consortium 4 (“Cons. 4”).

[0232] In some embodiments, the microbial consortium comprises at least one, at least two, at least three, or at least all of Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, Bacteroides caccae CL03T12C61, and Veillonella parvula ATCC 17745.

[0233] In some embodiments, the microbial consortium includes Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, Bacteroides caccae CL03T12C61, and Veillonella parvula ATCC 17745. This microbial consortium containing the four listed bacterial strains is referred to herein as consortium 5 ("Cons.5").

[0234] In another aspect of the invention that can be implemented as a specific embodiment of the microbial consortium of the invention, a microbial consortium selected from consortium 1, consortium 2, consortium 3, consortium 4, and consortium 5 is provided.

[0235] In another aspect of the invention that can be implemented as a specific embodiment of the microbial consortium of the invention, a microbial consortium selected from consortium 1, consortium 2, and consortium 3 is provided.

[0236] In another aspect of the invention that can be implemented as a specific embodiment of the microbial consortium of the invention, a microbial consortium that is at least one of consortium 1, consortium 2, consortium 3, consortium 4, and consortium 5 is provided.

[0237] In some embodiments, the microbial consortium includes the same or equivalent amounts of microorganisms that form the consortium. In some further embodiments, the microbial consortium includes different amounts of microorganisms that form the consortium. In some embodiments, the total number (number / amount / cfu of cells) of each microorganism that forms the microbial consortium is about 1×10 ,

[0234] , , ,

[0237] , ,

[0235] , , , ,

[0236] , 5 , , 10 , 3 , 12 ~ about 1×10 12 、1×10 5 ~ about 1×10 10 、1×108 ~ about 5×10 10 、2×10 8 ~ about 4×10 10 、3×10 8 ~ about 3×10 10 、5×10 8 ~ about 1×10 10 is.

[0238] In some embodiments, the total number of microorganisms (number / amount / cfu of cells) that form the microbial consortium is about 1×10 3 ~ about 1×10 12 、1×10 5 ~ about 1×10 10 、1×10 8 ~ about 5×10 10 、2×10 8 ~ about 4×10 10 、3×10 8 ~ about 3×10 10 、5×10 8 ~ about 1×10 10 is.

[0239] As detailed above, two or more microorganisms can be identified in the microbial flora of the reference subject or isolated from the microbial flora of the reference subject, for example, by collecting a biological sample. The biological sample may be any sample capable of isolating a population of microorganisms, such as feces. In yet another embodiment, the sample may be a biopsy of a human organ or tissue, specifically an intestinal biopsy.

[0240] The microbial consortium can be formulated in various forms depending on storage, administration, etc. Non-limiting forms include solid, dry forms such as lyophilized powder, gel form, suspension, cell lysate, or extract. In some embodiments, the microbial consortium can be suspended in a liquid medium (such as PBS or saline) and used in a suspended form.

[0241] The microbial consortium of the present invention can be used for the preparation of pharmaceutical formulations / compositions / suspensions for therapeutic use or in the manufacture of formulations / compositions / suspensions. Accordingly, the formulations / compositions / suspensions of the present invention may contain at least one additional component detailed herein, apart from a therapeutically effective amount of the microbial consortium of the present invention.

[0242] In a further aspect, the present invention relates to a composition (suspension or formulation) comprising the microbial consortium of the present invention. As described herein, the microbial consortium and / or the suspension / composition containing the microbial consortium may form a kit of the present invention. Generally, the compositions and / or suspensions and / or kits described herein, including the microbial consortium and the microbial consortium itself, form part of the present invention. It should be noted that the forms described herein for the microbial consortium itself apply to the compositions and / or suspensions and / or kits containing the microbial consortium.

[0243] In some further embodiments, the composition of the present invention may optionally further comprise at least one of pharmaceutically acceptable carrier(s), excipient(s), additive(s), diluent(s), and adjuvant(s). As used herein, "pharmaceutically acceptable carrier" includes any solvent, dispersion medium, coating, and the like.

[0244] An aqueous suspension may further contain substances that increase the viscosity of the suspension, such as, for example, sodium carboxymethylcellulose, sorbitol, and / or dextran. The suspension may also contain a stabilizer.

[0245] It should be understood that, in addition to the components specifically mentioned above, the formulation may also contain other agents conventional in the art, taking into account the type of formulation in question.

[0246] The microbial consortium of the present invention and / or any suspension / composition comprising the microbial consortium of the present invention can be administered and dosed by the method of the present invention described below in accordance with medical procedures known in the art. For example, the suspensions / compositions used in the methods and kits of the present invention described herein below can be adapted for administration by various interferon administration modes. These include, but are not limited to, injection (e.g., use of subcutaneous, intramuscular, intravenous or intradermal injection), intranasal administration, and oral administration.

[0247] In some embodiments, the microbial consortium of the present invention and / or any suspension / composition comprising the microbial consortium of the present invention can be formulated for oral administration.

[0248] In some embodiments, the microbial consortium of the present invention and / or any suspension / composition comprising the microbial consortium of the present invention can be formulated for delivery to the intestine. In some embodiments, the microbial consortium of the present invention and / or any suspension / composition comprising the microbial consortium of the present invention can be formulated in a food or beverage.

[0249] In some embodiments, the microbial consortium of the present invention and / or any suspension / composition comprising the microbial consortium of the present invention can be formulated to be contained in a carrier.

[0250] In some embodiments, the microbial consortium of the present invention and / or any suspension / composition comprising the microbial consortium of the present invention is enterically coated.

[0251] As described herein, the microbial consortium, the composition comprising the microbial consortium of the present invention, and the kit of the present invention can be useful for various purposes, such as the treatment of a subject in need of treatment by the microbial consortium of the present invention. Specifically, by affecting the immune system of the host subject, for example, the treatment of a proliferative disorder can be achieved.

[0252] As described herein, the microbial consortia, compositions, and kits of the present invention can be administered to a human subject for the treatment of proliferative disorders such as cancer. As shown in the following examples, the microbial consortia of the present invention were able to inhibit tumor growth.

[0253] Accordingly, the present invention further provides a microbial consortium according to the present invention comprising two or more purified or isolated microorganisms of the present invention, and the compositions and kits of the present invention comprising the compositions or kits of the present invention for use in a method of treating a subject suffering from a proliferative disorder.

[0254] In some other embodiments, the microbial consortium is for use in the treatment of a subject diagnosed with a disease treatable by the microbial consortia detailed herein, such as a proliferative disorder.

[0255] A proliferative disorder is a disorder that exhibits cell division and growth that is not part of normal cell turnover, metabolism, growth, or proliferation of an entire organism. Undesirable cell proliferation is seen in tumors and other pathological proliferations of cells, does not perform normal functions, and most continue indefinitely at a growth rate that exceeds the growth rate of normal tissue cells in the absence of external intervention. The pathological conditions that occur due to undesirable cell proliferation are referred to herein as "hyperproliferative diseases" or "hyperproliferative disorders".

[0256] Non-limiting examples of proliferative disorders include cancer, atherosclerosis, rheumatoid arthritis, psoriasis, idiopathic pulmonary fibrosis, scleroderma, and cirrhosis.

[0257] In some embodiments, the microbial consortia of the present invention comprise two or more purified or isolated microorganisms, and the compositions and kits of the present invention comprising the microbial consortia of the present invention are for use in the treatment of cancer.

[0258] As used herein to describe the present invention, "cancer," "tumor," and "malignant tumor" are all related equivalently to hyperplasia of tissues or organs.

[0259] The microbial consortium composition of the present invention or a kit containing the same can be used in the method of the present invention for the treatment of either non-solid tumors or solid tumors.

[0260] Non-limiting examples of cancers include blastoma, carcinoma, lymphoma, leukemia, sarcoma, mesothelioma, glioma, embryonal carcinoma, choriocarcinoma, skin cancer (such as basal-cell skin cancer (BCC), squamous-cell skin cancer (SCC), melanoma, etc.), glioblastoma, lymphoid tumor, squamous cell carcinoma (e.g., squamous epithelial cell carcinoma), lung cancer including small cell lung cancer, non-small cell lung cancer, lung adenocarcinoma and lung squamous cell carcinoma, peritoneal cancer, hepatocellular carcinoma, gastric or stomach cancer including gastrointestinal cancer, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatocellular carcinoma, breast cancer, colon cancer, rectal cancer, colorectal cancer, endometrial cancer or uterine cancer, salivary gland cancer, kidney cancer or renal cancer, prostate cancer, vulvar cancer, thyroid cancer, liver cancer, anal cancer, penile cancer, and head and neck cancer.

[0261] In some embodiments, the cancer is a solid cancer type or a blood cancer type.

[0262] In some embodiments, the cancer is a solid cancer. As used herein, the term solid cancer refers to a solid tumor, which is an abnormal mass of tissue that is usually not cystic or liquid-containing and is malignant. Examples of solid tumors are sarcoma, carcinoma, and lymphoma.

[0263] In some embodiments, the cancer is a blood cancer (also called hematologic cancer). Blood cancers typically begin in blood-forming tissues such as the bone marrow or cells of the immune system. Examples of blood cancers are leukemia, lymphoma, and multiple myeloma.

[0264] In some embodiments, the cancer is at least one of breast cancer, lung cancer, ovarian cancer, prostate cancer, liver cancer, pancreatic cancer, bladder cancer, prostate cancer, cervical cancer, brain cancer, colon cancer, gastrointestinal cancer, skin cancer such as melanoma, lung cancer, kidney cancer, bladder cancer, head and neck cancer, and lymphoma.

[0265] In some embodiments, the cancer is skin cancer. In some embodiments, the cancer is melanoma.

[0266] In some embodiments, the cancer is at least one of breast cancer, lung cancer, pancreatic cancer, bladder cancer, melanoma, kidney cancer, prostate cancer, head and neck cancer, and lymphoma.

[0267] In some embodiments, the cancer is selected from breast cancer, lung cancer, melanoma, and kidney cancer.

[0268] In some embodiments, the cancer is selected from breast cancer and melanoma.

[0269] In some embodiments, the cancer is breast cancer.

[0270] In some embodiments, the cancer is lung cancer. In some embodiments, the cancer is non-small cell lung cancer (NSCLC).

[0271] In some embodiments, the cancer is kidney cancer. In some embodiments, the cancer is renal cell carcinoma (RCC).

[0272] In some embodiments, the cancer is bladder cancer.

[0273] In some embodiments, the cancer is prostate cancer.

[0274] In some embodiments, the cancer is pancreatic cancer.

[0275] In some embodiments, the cancer is a head and neck cancer.

[0276] In some embodiments, the cancer is a lymphoma.

[0277] In some embodiments, the microbial consortium of the present invention comprising two or more purified or isolated microorganisms is administered in combination with an additional therapy.

[0278] As shown in the following examples (e.g., Example 2), the microbial consortium of the present invention was superior to anti-PD-1 inhibitor alone in terms of the ability to inhibit tumor growth and the ability to regulate the activity, expression, and secretion of inflammatory cytokines and differentiation molecules. Specifically, treatment with the microbial consortium of the present invention induced an increase in the secretion of plasma cytokines, INFγ, IL6, and IL12, and an increase in the expression of CD8 and CD68, compared to treatment with anti-PD-1 alone.

[0279] In other words, the microbial consortium of the present invention can be used alone or as an adjuvant therapy, particularly for treating cancer.

[0280] In some embodiments, the microbial consortium can be administered simultaneously with or sequentially to the anti-cancer treatment.

[0281] In some other embodiments, the microbial consortium can be administered simultaneously with the anti-cancer treatment.

[0282] Both the microbial consortium and the anti-cancer treatment can be administered by any administration method and route that are generally known and / or used in the art, and these can be the same or different for the two.

[0283] Non-limiting examples of anti-cancer agents and / or anti-cancer treatments include chemotherapy, radiation therapy, surgery, receptor kinase inhibitors (such as tyrosine), immune checkpoint inhibitors or any other targeted cancer therapy, immunotherapeutic agents, hormonal agents, biological agents, cytokine agents, differentiation factors, anti-angiogenic factors, CAR T cell therapy or any other cell-based therapy, or immunomodulatory therapy.

[0284] In some embodiments, the anti-cancer treatment is an anti-cancer agent.

[0285] In some embodiments, the anti-cancer treatment includes receptor kinase inhibitors (such as tyrosine), immune checkpoint inhibitors or any other targeted cancer therapy, immunotherapeutic agents, hormonal agents, biological agents, cytokine agents, differentiation factors, anti-angiogenic factors, CAR T cell therapy or any other cell-based therapy, or immune stimulatory therapy.

[0286] In some embodiments, the anti-cancer treatment is an immune checkpoint inhibitor.

[0287] Immune checkpoint inhibitors typically block specific proteins made by some types of immune system cells, such as T cells, and some cancer cells. Examples of checkpoint proteins found on T cells or cancer cells include, for example, PD-1 / PD-L1 and CTLA-4 / B7-1 / B7-2. Checkpoint inhibitors can be, for example, immunotherapeutic agents such as monoclonal antibodies.

[0288] In some embodiments, the anti-cancer treatment is a checkpoint inhibitor selected from anti-PD-1 inhibitors, anti-CTLA-4 inhibitors, anti-PD-L1 inhibitors, or combinations thereof. The inhibitor can be a small molecule, antibody, aptamer, oligomer, polymer.

[0289] In some embodiments, the checkpoint inhibitor is selected from anti-PD-1 antibodies, anti-CTLA-4 antibodies, anti-PD-L1 antibodies, or combinations thereof.

[0290] In some embodiments, the checkpoint inhibitor is at least one of ipilimumab, nivolumab, pembrolizumab, atezolizumab, avelumab, durvalumab, and cemiplimab, or any combination thereof.

[0291] In some embodiments, the checkpoint inhibitor is an anti-PD-1 inhibitor.

[0292] In some embodiments, the checkpoint inhibitor is pembrolizumab.

[0293] As shown in the following examples, the microbial consortium of the present invention reduces the tumor growth rate. Therefore, it was suggested that the microbial consortium of the present invention can be used for inhibiting cancer growth and thus for cancer treatment.

[0294] Therefore, in yet another aspect, the present invention provides a method for treating a disorder in a subject in need thereof. In some embodiments, the method of treating, preventing, remitting, alleviating, or delaying the onset of a proliferative disorder in a subject in need thereof comprises administering to such a subject a therapeutically effective amount of the microbial consortium of the present invention or any composition or kit comprising the same.

[0295] According to the method of the present invention, administration of an effective amount of the microbial consortium of the present invention remits one or more signs or symptoms of a proliferative disorder such as cancer. In other words, the method of the present invention is for treating a disorder and may be treatable with the microbial consortium of the present invention.

[0296] In another aspect, the present invention provides a method for treating, preventing, alleviating, reducing, or delaying the onset of a proliferative disorder such as cancer in a human subject in need thereof, the method comprising administering to the subject an effective amount of a microbial consortium comprising two or more isolated or purified microorganisms, wherein at least one of the two or more microorganisms is present in low abundance in the microbiota of a reference human subject. According to some embodiments, the microbial consortium comprises at least one of the other at least one of the two or more microorganisms having at least one of: (i) the ability to modulate at least one SCFA, (ii) the ability to modulate lactate, and (iii) at least one cell envelope component recognized by the immune system or epithelial cells, such as intestinal epithelial cells, of the human subject.

[0297] In yet another aspect, the present invention provides a method for treating, preventing, alleviating, reducing, or delaying the onset of a proliferative disorder such as cancer in a human subject in need thereof, the method comprising administering to the subject an effective amount of a microbial consortium comprising two or more isolated or purified microorganisms, wherein at least one of the two or more microorganisms is present in low abundance in the microbiota of a reference human subject and has at least one of: (i) the ability to modulate at least one SCFA, (ii) the ability to modulate lactate, and (iii) at least one cell envelope component recognized by the immune system or epithelial cells, such as intestinal epithelial cells, of the human subject.

[0298] In some embodiments, the method of the present invention comprises administering a therapeutically effective amount of a microbial consortium comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, and SEQ ID NO: 5 and having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, at least 99.5% identity to a 16S rRNA sequence.

[0299] In some embodiments, the method of the present invention comprises administering a therapeutically effective amount of a microbial consortium comprising 1, 2, 3, 4, or 5 microorganisms selected from Oenococcus oeni PSU-1, Clostridium tyrobutyricum KCTC 5387, Cetobacterium somerae ATCC BAA-474, Corynebacterium glyciniphilum AJ 3170, and Clostridium cellulovorans 743B.

[0300] In some embodiments, the method of the present invention comprises administering a therapeutically effective amount of a microbial consortium comprising at least 1, at least 2, or at least 3 microorganisms derived from the species Bacteroides caccae, the species Lactobacillus casei, or the species Veillonella parvula.

[0301] In some embodiments, the method of the present invention comprises administering a therapeutically effective amount of a microbial consortium comprising at least one microorganism having a 16S rRNA sequence having 85% to 99%, sometimes 90% to 99%, sometimes 95% to 99%, sometimes 96% to 99%, sometimes 97% to 99%, sometimes 98% to 99% identity with a nucleic acid sequence selected from the group consisting of SEQ ID NO: 7, SEQ ID NO: 8, and SEQ ID NO: 9.

[0302] In some embodiments, the method of the present invention comprises administering a therapeutically effective amount of a microbial consortium comprising at least one or at least two of Bacteroides caccae CL03T12C61, Lactobacillus casei ATCC27139, or Veillonella parvula ATCC17745.

[0303]

[0303] In some embodiments, the method of the present invention comprises administering to a subject a therapeutically effective amount of a microbial consortium comprising two or more purified or isolated microorganisms having 1, 2, 3, 4, 5, 6, 7, or 8 16S rDNA sequences listed in Table 1 and 16S rDNA sequences that are at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical.

[0304]

[0303] In some embodiments, the method of the present invention comprises administering to a subject a therapeutically effective amount of a microbial consortium comprising two or more purified or isolated microorganisms having 1, 2, 3, 4, 5, 6, 7, or 8 16S rDNA sequences shown in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8 and 16S rDNA sequences that are at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical.

[0305]

[0303] In some embodiments, the method of the present invention comprises administering to a subject a therapeutically effective amount of a microbial consortium that is at least one of Consortium 1, Consortium 2, Consortium 3, Consortium 4, and Consortium 5.

[0306]

[0303] In another aspect of the present invention that can be implemented as a specific embodiment of the method of the present invention, there is provided a method for treating, preventing, remitting, alleviating, or delaying the onset of a proliferative disorder, such as cancer, in a human subject in need thereof, comprising administering to the microbial consortium of the present invention, which is a therapeutically effective amount, a therapeutically effective amount of an anti-cancer treatment.

[0307]

[0303] In some embodiments, the method comprises administering to the subject the microbial consortium of the present invention, which is a therapeutically effective amount, and an anti-cancer treatment, which is a therapeutically effective amount, simultaneously or sequentially.

[0308] According to some embodiments, the method comprises administering to a subject, simultaneously, a microbial consortium of the invention in a therapeutically effective amount and an anti-cancer treatment in a therapeutically effective amount.

[0309] In some embodiments of the method of the invention for treating, preventing, remitting, alleviating, or delaying the onset of cancer, it comprises administering to a subject in need thereof a microbial consortium of the invention in a therapeutically effective amount and an anti-cancer treatment in a therapeutically effective amount, and the method comprises administering a therapeutically effective amount of the microbial consortium with a therapeutically effective amount of a checkpoint inhibitor, as detailed herein.

[0310] In some embodiments, the cancer is at least one of breast cancer, lung cancer, ovarian cancer, prostate cancer, liver cancer, pancreatic cancer, bladder cancer, prostate cancer, cervical cancer, skin cancer (such as melanoma), brain cancer, colon cancer, gastrointestinal cancer, melanoma, lung cancer, kidney cancer, bladder cancer, head and neck cancer, and lymphoma.

[0311] In some embodiments, the cancer is at least one of breast cancer, lung cancer, pancreatic cancer, bladder cancer, melanoma, kidney cancer, prostate cancer, head and neck cancer, and lymphoma.

[0312] In some embodiments, the cancer is selected from breast cancer, lung cancer, melanoma, and kidney cancer.

[0313] In some embodiments, the cancer is selected from breast cancer and melanoma.

[0314] In some embodiments, the cancer is skin cancer. In some embodiments, the cancer is melanoma.

[0315] In some embodiments, the cancer is breast cancer.

[0316] In some embodiments, the cancer is lung cancer. In some embodiments, the cancer is non-small cell lung cancer (NSCLC).

[0317] In some embodiments, the cancer is kidney cancer. In some embodiments, the cancer is renal cell carcinoma (RCC).

[0318] In some embodiments, the cancer is bladder cancer.

[0319] In some embodiments, the cancer is prostate cancer.

[0320] In some embodiments, the cancer is pancreatic cancer.

[0321] In some embodiments, the cancer is head and neck cancer.

[0322] In some embodiments, the cancer is lymphoma.

[0323] Microbial consortia are known in the art and can be administered to a human subject by any method described herein. According to some embodiments, the methods of the invention include administration of a microbial consortium or a composition comprising a microbial consortium by oral administration. According to some embodiments, the methods of the invention include administration of a microbial consortium or a composition comprising a microbial consortium formulated for delivery to the intestine. A microbial consortium or a composition comprising a microbial consortium can be formulated, for example, into capsules, tablets, foods, or beverages.

[0324] In some embodiments, the method of the invention may comprise administering the microbial consortium of the invention, a composition or kit comprising the microbial consortium of the invention, and optionally additional therapy, as a single one-time dose, or as a single daily dose or multiple daily doses or multiple daily doses, preferably administered every 1 to 7 days. Such applications may be performed once or several times during the patient's lifetime, once, twice, three times, four times, five times, or six times a day, or once a day, once every two days, once every three days, once every four days, once every five days, once every six days, once a week, every two weeks, every three weeks, every four weeks, or even more than one month, which is particularly contemplated.

[0325] The invention further provides the use of the microbial consortium of the invention in the preparation of a composition for treating a proliferative disorder in a subject in need of treatment. Accordingly, the use of a microbial consortium comprising two or more microorganisms is provided, wherein at least one of the two or more microorganisms is present in low abundance in the microbiota of a reference human subject, and at least one of the other two or more microorganisms has at least one of the following in the preparation of a composition for treating a proliferative disorder in a subject in need of treatment: (i) can regulate at least one short-chain fatty acid (SCFA), (ii) can regulate lactate, and (iii) contains at least one cell envelope component.

[0326] The invention further provides the use of the microbial consortium of the invention in the preparation of a composition for treating a proliferative disorder in a subject in need of treatment. Accordingly, the use of a microbial consortium comprising two or more microorganisms is provided, wherein at least one of the two or more microorganisms is present in low abundance in the microbiota of a reference human subject, and in the preparation of a composition for treating a proliferative disorder in a subject in need of treatment, has at least one of the following: (i) can regulate at least one SCFA, (ii) can regulate lactate, and (iii) contains at least one cell envelope component.

[0327] In another aspect, the present invention provides a kit comprising the microbial consortium of the present invention in the preparation of a composition for treating a proliferative disorder in a subject in need thereof. Accordingly, there is provided the use of a microbial consortium comprising two or more microorganisms, wherein at least one of the two or more microorganisms is present in low abundance in the microbiota of a reference human subject, and at least one other of the two or more microorganisms has at least one of: (i) the ability to modulate at least one short-chain fatty acid (SCFA), (ii) the ability to modulate lactate, and (iii) comprises at least one cell envelope component.

[0328] In another aspect, the present invention provides a kit comprising the microbial consortium of the present invention in the preparation of a composition for treating a proliferative disorder in a subject in need thereof. Accordingly, there is provided the use of a microbial consortium comprising two or more microorganisms, wherein at least one of the two or more microorganisms is present in low abundance in the microbiota of a reference human subject, and has at least one of: (i) the ability to modulate at least one SCFA, (ii) the ability to modulate lactate, and (iii) comprises at least one cell envelope component.

[0329] In some embodiments, the kit described herein may comprise the composition / suspension described as a pre-prepared dosage form ready for administration, or may comprise the microbial consortium or a composition comprising the microbial consortium described as a solid pharmaceutical composition (e.g., in lyophilized form) that can be reconstituted with a solvent to provide a liquid dosage form. The kit of the present invention may optionally further comprise instructions for using the kit in the treatment of a proliferative disorder.

[0330] The treatment method provided herein comprises administering a therapeutically effective amount of the microbial consortium of the present invention. The term "effective amount" as used herein is determined by considerations as known to those of ordinary skill in the art.

[0331] The present invention provides a method for treating or preventing a proliferative disorder. The term "treating or preventing" refers to the complete range of therapeutically positive effects of administration to a subject, including inhibition, reduction, alleviation, and relief of proliferative disorder symptoms or undesirable side effects of such proliferative disorder-related disorders.

[0332] As used herein, terms such as "disease," "disorder," and "condition" are used interchangeably since they relate to the health of a subject and have the meaning ascribed to each and all of such terms.

[0333] The present invention relates to a method for treating a subject or patient in need of treatment. "Patient" or "subject in need" means any organism that can be affected by the above-described condition and for which the treatment methods described herein are desired. In particular, in the case of a human subject, it should be further noted that administration of the composition of the present invention to a patient includes both self-administration and administration to the patient by another person.

[0334] The present invention provides a method for treating a proliferative disorder and further relates to disorders associated or related to cancer. The terms "associated" and "related," which are used interchangeably, when referring to pathology herein, mean disorders, diseases, conditions, or any medical condition that share a causal relationship, coexist at a frequency higher than by chance, or at least one disease, disorder, condition, or medical condition is at least one of the locations where it causes a second disease, disorder, condition, or medical condition.

[0335] According to some embodiments shown herein to "increase" or "enhance" activity by modulation in relation to the microbiota consortium of the present invention, such increase or enhancement means, for example, in the absence of treatment, without stimulants as an example (without microorganisms shown as -LPS herein), or without additional anti-cancer agents as an example without anti-PD1, or in the absence of the microbiota consortium of the present invention of the present invention, an increase or elevation in activity of about 5% to 100%, specifically 10% to 100% compared to a suitable control.

[0336] As used herein, the term "about" refers to a value that can deviate from the recited value by up to 1%, more specifically 5%, more specifically 10%, more specifically 15%, and in some cases up to 20%, higher or lower, and this deviation range includes integer values and, where applicable, non-integer values as well to form a continuous range. When used herein, the term "about" refers to ±10%. [Table 1]

[0337] Non-limiting examples: Example 1: In vitro test Example 1A: Toll-like receptor (TLR) activation The purpose of this test was to evaluate TLR activation after incubation with various bacterial strains using InvivoGen's HEK-Blue™ TLR cells (derived from HEK293 cells) and the secreted alkaline phosphatase (SEAP) reporter system.

[0338] Materials and methods HEK-Blue™ TLR2 and HEK-Blue™ TLR4 cells were incubated at 37°C, 5% CO2 for 20 hours with various bacterial strains at increasing concentrations (bacteria:cell ratio 1:2.78, 1:8.33, 1:5). TLR activation was measured as SEAP secretion and quantified at OD630nm using a colorimetric reader. As follows, TLR2 and TLR4 ligands activate NF-κB and AP-1, which induce the production of SEAP. The HEK-Blue™ detection cell culture medium enables the detection of SEAP as a readout of TLR activation.

[0339] Results As can be seen from FIGS. 1A-1E and FIGS. 2A-2C, all of the tested bacterial strains at all of the tested ratios activated TLR4 and TLR2. Specifically, a large increase relative to LPS (the positive control) was observed for TLR4 activation by Cetobacterium somerae ATCC BAA-474 (FIG. 1C) and TLR2 activation by Oenococcus oeni PSU-1 and Corynebacterium glyciniphilum AJ 3170 (FIGS. 2B and 2C). These results suggested that the tested bacterial strains, specifically those present in low abundance, were recognized by specific TLRs and then activated the immune cell response.

[0340] Example 1B: Cytokine Secretion in Macrophage Cell Lines The purpose of this test was to evaluate the effectiveness of various bacterial strains and combinations of bacterial strains in stimulating cytokine secretion from RAW mouse macrophage cell lines compared to lipopolysaccharide (LPS) stimulation.

[0341] Materials and Methods RAW cells were incubated with various bacterial strains (10 8 CFU / mL) at 37° C. and 5% CO2 for 16 hours. The medium (supernatant) was collected and analyzed for cytokine secretion using the R&D DouSet ELISA Development System according to the manufacturer's protocol. Each bacterium was tested in triplicate.

[0342] Results The effects of individual bacterial strains on cytokine secretion showed that all of the tested microorganisms were able to induce cytokine secretion from macrophages compared to the mock (-LPS) (Figures 3A - 3C). Figures 3A and 3B show that Cetobacterium somerae ATCC BAA - 474 induced the greatest secretion of TNFα and IL6, and Figure 3C shows that Veillonella parvula ATCC 17745, followed by Cetobacterium somerae ATCC BAA - 474, induced the greatest secretion of IL1b.

[0343] All of the tested bacterial strains have the ability to induce pro - inflammatory cytokines (TNFα, IL - 6, IL - 1β) at levels higher than LPS stimulation in the macrophage cell line.

[0344] These data collectively suggest an important role of the identified bacterial strains, particularly the low - abundance strains, in inducing cytokine secretion from macrophages.

[0345] Also, various combinations of two bacterial strains were found to induce cytokine secretion, suggesting that combinations of two bacterial strains can increase the signal of the pro - inflammatory response (data not shown).

[0346] The effects of various combinations of bacteria on cytokine secretion were further tested. Figures 4A - 4C show the effects of combinations of bacteria in inducing cytokine secretion. Specifically, the following five combinations (consortia) were tested.

[0347] Consortium 1 ("Cons.1") induces Corynebacterium glyciniphilum AJ 3170, Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, and Oenococcus oeni PSU-1.

[0348] Consortium 2 ("Cons.2") includes Bacteroides caccae CL03T12C61, Clostridium cellulovorans 743B, Lactobacillus casei ATCC27139, and Veillonella parvula ATCC17745.

[0349] Consortium 3 ("Cons.3") includes Corynebacterium glyciniphilum AJ 3170, Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, Oenococcus oeni PSU-1, Bacteroides caccae CL03T12C61, Clostridium cellulovorans 743B, Lactobacillus casei ATCC27139, and Veillonella parvula ATCC 17745.

[0350] Consortium 4 ("Cons.4") includes Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, Clostridium cellulovorans 743B, and Veillonella parvula ATCC 17745.

[0351] Consortium 5 ("Cons.5") includes Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, Bacteroides caccae CL03T12C61, and Veillonella parvula ATCC 17745.

[0352] The results in FIGS. 4A-4C show that all of the tested bacterial consortia induced cytokine secretion, suggesting that the identified combinations of bacterial strains are effective in regulating the pro-inflammatory response. This may suggest an additive effect of the bacterial strains in each consortium.

[0353] Example 1C: Cytokine Secretion from Human Peripheral Blood Mononuclear Cells (PBMCs) The purpose of this test was to evaluate the effectiveness of various bacterial strains and combinations of bacterial strains in stimulating cytokine secretion from PBMCs compared to lipopolysaccharide (LPS) stimulation.

[0354] Materials and Methods Human venous blood (10 - 15 mL) was collected into heparinized vials and thoroughly mixed by gently inverting the tubes several times. The blood was diluted two-fold with PBS. Histopaque was added to a 50 mL centrifuge tube at half the final blood:PBS volume. The blood was gently layered on top of the Histopaque using a 1 mL automatic pipette. Layer formation was done very slowly so that the blood and Histopaque remained as two distinct layers. The tube was centrifuged at 400 × g for 30 minutes at +20 °C in a swing out bucket without any delay. The whitish buffy coat (PBMC) formed at the interface between the Histopaque and the medium was aspirated without any delay. The cells were washed twice with 10 mL of PBS (centrifuged at 800 × g for 10 minutes at +20 °C).

[0355] PBMCs were incubated for 48 hours with each bacterial strain at a final concentration of 10^8 CFU / ml, or vehicle (10% PBS), or positive control (10 ng / mL LPS). Following the incubation period, the supernatants were collected and analyzed for cytokine secretion using the R&D DouSet ELISA development system according to the manufacturer's protocol. Each bacterium was tested in triplicate.

[0356] Results Figures 5A - 5B are bar graphs showing the effectiveness of bacterial strains in stimulating cytokine secretion from PBMC, IL6 (Figure 5A), TNFα (Figure 5B). As can be seen from the figure, most of the bacterial strains containing low abundance bacterial strains stimulated secretion from the cells at increased levels compared to LPS secretion.

[0357] In summary, the in vitro results demonstrate the ability of bacterial strains and combinations of two or more bacterial strains to increase the signal of the inflammatory response from both macrophages and PBMCs.

[0358] Interestingly, the low-abundance bacterial strains were able to activate the pro-inflammatory response better or to a greater extent compared to the high-abundance bacterial strains. These bacterial strains are present in the microbiota in low abundance, suggesting that they have the potential to activate the inflammatory response in the host.

[0359] This type of inflammatory response has been suggested to suppress and limit tumor growth.

[0360] Example 2: In vivo test of mice with breast cancer tumors The purpose of this study was to determine the efficacy of a bacterial consortium treatment in combination with anti-PD-1 therapy (anti-mouse PD-1 (CD279), an equivalent of pembrolizumab for use in mice) against the development of E0771-derived breast cancer tumors in C57BL / 6 female mice.

[0361] Materials and methods On "Day 1" of the study, 50 μL of 1.5×10 5 individual E0771 cells in PBS:Matrigel (1:1) were injected into the right flank of the mice. Tumor volume was measured twice a week from Day 5 until the end of the study. In addition, on Day 1, the mice were started on an antibiotic cocktail (ampicillin (1 g / L), neomycin (1 g / L), metronidazole (1 g / L), and vancomycin (0.5 g / L)) in the drinking water. The antibiotics were administered until Day 13. On Day 14 of the study, the water and water bottles were changed to antibiotic-free water.

[0362] On the 15th day of the experiment, mice were assigned to five groups of 10 or 15 animals. The average tumor volume was similar. The first oral treatment was administered 24 hours after the discontinuation of antibiotics. The bacterial consortium was administered by oral gavage, and anti-PD1 was administered intraperitoneally. Thus, on the "15th" day of the experiment, mice were administered one of these treatments: (1) anti-PD1, (2) Cons.1 + anti-PD1, (3) Cons.2 + anti-PD1, or (4) Cons.3 + anti-PD1, (5) PBS = control group, administered by oral gavage in the same volume as that used to administer the bacterial consortium. During the experiment, mice were further administered oral gavage of bacteria seven times (2 times of gavage / week) and anti-PD1 or anti-PD1 alone.

[0363] The combinations of microorganisms used in this study were as follows:

[0364] Consortium 1 ("Cons.1") was induced by Corynebacterium glyciniphilum AJ 3170, Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, and Oenococcus oeni PSU-1.

[0365] Consortium 2 ("Cons.2") included Bacteroides caccae CL03T12C61, Clostridium cellulovorans 743B, Lactobacillus casei ATCC27139, and Veillonella parvula ATCC17745.

[0366] Consortium 3 ("Cons.3") includes Corynebacterium glyciniphilum AJ 3170, Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, Oenococcus oeni PSU-1, Bacteroides caccae CL03T12C61, Clostridium cellulovorans 743B, Lactobacillus casei ATCC27139, and Veillonella parvula ATCC 17745.

[0367] Starting from the appearance of the tumor (approximately 4 days after cell inoculation), the tumors were measured for length (L) and width (W) twice a week using digital calipers. Tumor volume (mm 3 ) was calculated according to the formula (L × W 2 × 0.5).

[0368] The Th1 cytokine panel was evaluated in plasma samples (IFNγ, IL-6, and IL-12) collected at the end point of each animal.

[0369] At the end of the study, the tumors were excised, placed in formalin, and further processed for histopathological evaluation. Paraffin-embedded 4-μm sections of the tumors were stained with H&E and examined for inflammatory parameters and lymphocyte infiltration graded by an acceptable grading system. In addition, immunohistochemistry (IHC) analysis was performed to detect the expression of CD8 and CD68 using specific antibodies.

[0370] The following parameters were evaluated:

[0371] The inflammatory infiltrates inside or around the nodules were evaluated, characterized in terms of their intensity, and the inflammation was scored from 0 to 3 (0 = slight or absent; 1 = inflammatory cells are clearly present but significantly fewer than other cells; 2 = inflammatory cells approximately equal to melanocytes; 3 = mainly inflammatory cells).

[0372] The lymphocyte infiltration within the tumor was graded on a scale of 0 to 3 (0 = no lymphocytes in the tumor; 1 = less than 5 lymphocytes / high power field (HPF); 2 = more than 5 and less than 20 lymphocytes / HPF; 3 = more than 20 lymphocytes / HPF).

[0373] IHC (immunohistochemistry) scoring grades (CD8, CD68) were performed on a scale of 0 to 4. 0 = no cells were detected 1 = very few cells were detected (1 - 5 cells / 10x magnification) 2 = few cells were detected (6 - 15 cells / 10x magnification) 3 = a moderate number of cells were detected (16 - 50 cells / 10x magnification) 4 = many cells were detected (more than 50 cells / 10x magnification)

[0374] Results Figure 6A shows the reduction in tumor volume for all combinations of three bacterial strains administered with anti - PD1 compared to untreated mice.

[0375] The results shown in Figure 6A also indicated that all combinations of the three bacterial strains administered with anti - PD1 were more effective in reducing tumor volume compared to anti - PD1 alone. As can be seen from the figure, the effects of consortium 1 with anti - PD1 and consortium 2 with anti - PD1 were observed at later time points. This can be attributed to, for example, the period required for colony formation of the combination of bacterial strains and activation of the host immune system by the combination of bacterial strains.

[0376] The results in Figure 6A also show that the effect on tumor volume of Consortium 3, which contains 8 bacterial strains with anti-PD1, was more significant and observed at an earlier time point compared to Consortium 1 with anti-PD1 and Consortium 2 with anti-PD1.

[0377] Collectively, these results suggest that the combination of bacterial strains induces an additive pro-inflammatory response that subsequently suppresses tumor growth.

[0378] These results are further supported in Figure 6B, and thus the time to reach the test endpoint (a tumor volume of 1000 mm 2 ) was longer in the mammary tumors of mice treated with some combinations of anti-PD-1 bacterial strains compared to treatment with anti-PD1 alone.

[0379] Furthermore, analysis of various cytokines in the plasma of mice showed that the combination of anti-PD-1 and bacterial strains induced an increase in the secretion of plasma cytokines, INFγ (Figure 6C), IL6 (Figure 6D), and IL12 (Figure 6E), compared to mice treated with anti-PD-1 alone.

[0380] The histological evaluation of tumors was correlated with the increased pro-inflammatory response induced by the combination of bacterial strains and anti-PD-1. Specifically, the expression of CD8 and CD68 was increased in the tumors of mice treated with the combination of bacterial strains and anti-PD-1 compared to mice treated with anti-PD-1 alone. This response pattern was also evident in the inflammation score.

[0381] Example 3: In vivo test of mice with breast cancer tumors The purpose of this study was to determine the efficacy of bacterial consortium treatment in combination with anti-PD-1 treatment against the development of E0771-derived breast cancer tumors in C57BL / 6 female mice.

[0382] Materials and methods On the "first day" of the test, 50 μL of 1.5×10 in PBS:Matrigel (1:1) was injected into the right flank of the mice.5 Inject individual E0771 cells. Measure tumor volume twice a week starting on day 5 until the end of the test. Additionally, on day 1, the mice are started on an antibiotic cocktail (ampicillin (1 g / L), neomycin (1 g / L), metronidazole (1 g / L), and vancomycin (0.5 g / L)) in the drinking water. Administer the antibiotics until day 13. On day 14 of the test, replace the water and water bottles with water without antibiotics.

[0383] On day 15 of the test, assign the mice into groups of 10 or 15. The average tumor volume is similar. The first oral treatment is administered 24 hours after the discontinuation of the antibiotics. Administer the bacterial consortium by oral gavage and anti-PD1 by intraperitoneal injection. Thus, on day "15" of the test, the mice are administered one of these treatments: (1) anti-PD1, (2) Cons.4 + anti-PD1, (3) Cons.5 + anti-PD1, or (4) PBS = administration by oral gavage with a similar volume is used to administer the bacterial consortium as a control group. During the test, the mice are administered the bacterial oral gavage (gavage twice a week) and anti-PD1 or anti-PD1 only seven more times.

[0384] Consortium 4 ("Cons.4") includes Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, Clostridium cellulovorans 743B, and Veillonella parvula ATCC 17745.

[0385] Consortium 5 ("Cons.5") includes Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, Bacteroides caccae CL03T12C61, and Veillonella parvula ATCC 17745.

[0386] Starting from the appearance of the tumor (approximately 4 days after cell inoculation), the tumor is measured for length (L) and width (W) twice a week using digital calipers thereafter. Tumor volume (mm 3 ) is calculated according to the formula (L × W 2 × 0.5).

[0387] The Th1 cytokine panel is evaluated with plasma samples (IFNγ, IL-6, and IL-12) collected on the end day of each animal.

[0388] At the end of the study, the tumors are excised, placed in formalin, and further processed for histopathological evaluation. 4-μm paraffin-embedded sections of the tumors are stained with H&E and examined for inflammatory parameters and lymphocyte infiltration graded by an acceptable grading system. In addition, immunohistochemistry (IHC) analysis is performed to detect the expression of CD8 and CD68 using specific antibodies.

[0389] The following parameters are evaluated:

[0390] The inflammatory infiltrates inside or around the nodules are evaluated, characterized in terms of their intensity, and the inflammation is scored from 0 to 3 (0 = slight or absent; 1 = inflammatory cells are clearly present but significantly fewer than other cells; 2 = inflammatory cells approximately equal to melanocytes; 3 = mainly inflammatory cells).

[0391] Grade the lymphocyte infiltration in the tumor on a scale of 0 - 3 (0 = no lymphocytes in the tumor; 1 = less than 5 lymphocytes / high power field (HPF); 2 = more than 5 and less than 20 lymphocytes / HPF; 3 = more than 20 lymphocytes / HPF).

[0392] Perform IHC (immunohistochemistry) scoring grade (CD8, CD68) on a scale of 0 - 4. 0 = No cells are detected 1 = A very small number of cells are detected (1 - 5 cells / 10x magnification) 2 = A small number of cells are detected (6 - 15 cells / 10x magnification) 3 = A moderate number of cells are detected (16 - 50 cells / 10x magnification) 4 = A large number of cells are detected (more than 50 cells / 10x magnification)

[0393] Example 4: In vivo test of mice with melanoma The purpose of this test is to determine the efficacy of bacterial consortium treatment combined with anti - PD - 1 treatment against the development of melanoma tumors in C57BL / 6 mice.

[0394] Materials and methods On the "first day" of the test, inject 1.5×10 5 cells of BRAF KO into the right flank of the mouse in 50 μL of PBS:Matrigel (1:1). Measure the tumor volume twice a week from the fifth day until the end of the test. In addition, on the first day, the mice start to be administered an antibiotic cocktail (ampicillin (1 g / L), neomycin (1 g / L), metronidazole (1 g / L), and vancomycin (0.5 g / L)) in the drinking water. Administer the antibiotics until the 13th day. On the 14th day of the test, replace the water and water bottles with water without antibiotics.

[0395] On day 15 of the trial, mice are assigned to groups of 10 or 15. The average tumor volume is the same. The first oral treatment is administered 24 hours after the discontinuation of antibiotics. The bacterial consortium is administered by oral gavage, and anti-PD1 is administered intraperitoneally. Thus, on day "15" of the trial, mice are administered one of these treatments: (1) anti-PD1, (2) Cons.1 + anti-PD1, (3) Cons.2 + anti-PD1, or (4) Cons.3 + anti-PD1, (5) Cons.4 + anti-PD1, (6) Cons.5 + anti-PD1, (7) PBS = control group, administered by oral gavage in the same volume used to administer the bacterial consortium. During the trial, mice are further administered the bacterial oral gavage seven times (2 times gavage / week) and anti-PD1 or anti-PD1 only.

[0396] The combinations of microorganisms used in this trial are as follows:

[0397] Consortium 1 ("Cons.1") induces Corynebacterium glyciniphilum AJ 3170, Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, and Oenococcus oeni PSU-1.

[0398] Consortium 2 ("Cons.2") includes Bacteroides caccae CL03T12C61, Clostridium cellulovorans 743B, Lactobacillus casei ATCC27139, and Veillonella parvula ATCC17745.

[0399] Consortium 3 ("Cons.3") includes Corynebacterium glyciniphilum AJ 3170, Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, Oenococcus oeni PSU-1, Bacteroides caccae CL03T12C61, Clostridium cellulovorans 743B, Lactobacillus casei ATCC27139, and Veillonella parvula ATCC 17745.

[0400] Consortium 4 ("Cons.4") includes Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, Clostridium cellulovorans 743B, and Veillonella parvula ATCC 17745.

[0401] Consortium 5 ("Cons.5") includes Cetobacterium somerae ATCC BAA-474, Clostridium tyrobutyricum KCTC 5387, Bacteroides caccae CL03T12C61, and Veillonella parvula ATCC 17745.

[0402] Starting from the appearance of the tumor (approximately 4 days after cell inoculation), the tumor is measured for length (L) and width (W) twice a week using digital calipers thereafter. Tumor volume (mm 3 3 2 ) is calculated according to the formula (L × W

[0403] × 0.5).

[0404] At the end of the experiment for each animal, the Th1 cytokine panel (IFNγ, IL-6, and IL-12) is evaluated in plasma samples collected.

[0405] At the end of the study, the tumors are excised, placed in formalin, and further processed for histopathological evaluation. Paraffin-embedded 4-μm sections of the tumors are stained with H&E and examined for inflammatory parameters and lymphocyte infiltration graded according to an acceptable grading system. In addition, immunohistochemistry (IHC) analysis is performed to detect the expression of CD8 and CD68 using specific antibodies.

[0405] The following parameters are evaluated:

[0406] The inflammatory infiltrates inside or around the nodules are evaluated, characterized in terms of their intensity, and scored for inflammation from 0 to 3 (0 = slight or absent; 1 = inflammatory cells are clearly present but significantly fewer than other cells; 2 = inflammatory cells approximately equal to melanocytes; 3 = mainly inflammatory cells).

[0407] Lymphocyte infiltration within the tumor is graded on a scale of 0 to 3 (0 = no lymphocytes in the tumor; 1 = less than 5 lymphocytes / high power field (HPF); 2 = more than 5 and less than 20 lymphocytes / HPF; 3 = more than 20 lymphocytes / HPF).

[0408] IHC (immunohistochemistry) scoring grade) CD8, CD68) is performed on a scale of 0 to 4. 0 = cells are not detected 1 = very few cells are detected (1 - 5 cells / 10× magnification) 2 = a few cells are detected (6 - 15 cells / 10× magnification) 3 = A moderate number of cells are detected (16 - 50 cells / magnification 10x) 4 = Many cells are detected (more than 50 cells / magnification 10x)

Sequence Listing Free - Text

[0409] Sequence Listing 2, 6, 12 <223>n is a, c, g, or t.

Claims

**Claim 1** A microbial consortium comprising two or more types of microorganisms, wherein at least one of the two or more types of microorganisms is present in a low abundance in the microbiota of a reference human subject, and at least one other of the two or more types of microorganisms has at least one of the following: (i) can regulate at least one short-chain fatty acid (SCFA), (ii) can regulate lactate, and (iii) contains at least one cell envelope component. **Claim 2** The microbial consortium according to claim 1, wherein the at least one type of microorganism present in a low abundance in a reference human subject has at least one of the following: (i) can regulate at least one SCFA, and (ii) contains at least one cell envelope component. **Claim 3** The microbial consortium according to claim 2, wherein the at least one type of microorganism present in a low abundance in a reference human subject can regulate lactate. **Claim 4** The microbial consortium according to any one of claims 1 to 3, comprising at least one isolated microorganism, purified microorganism, or a combination thereof. **Claim 5** The microbial consortium according to any one of claims 1 to 4, wherein at least one of the two or more types of microorganisms can regulate at least one of the following: (i) Toll-like receptor (TLR), (ii) surface components of immune cells, (iii) nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), (iv) dendritic cells, (v) pro-inflammatory cytokines, and (vi) intestinal barrier integrity. **Claim 6** The microbial consortium according to any one of claims 1 to 5, wherein the at least one type of microorganism present in a low abundance in a reference human subject can regulate at least one of the following: (i) TLR, (ii) surface components of immune cells, and (iii) pro-inflammatory cytokines. **Claim 7** The at least one microorganism that is present in low abundance in the human subject has at least one of the following properties: (i) it can regulate at least one SCFA, (ii) it contains at least one cell envelope component, (iii) it can regulate at least one TLR, (iv) it can regulate surface components of immune cells, (v) it can regulate NF-κB, (vi) it can regulate dendritic cells, (vii) it can regulate pro-inflammatory cytokines, and (viii) it can regulate intestinal barrier integrity. The microbial consortium according to any one of claims 1 to 6.

8. The microbial consortium according to any one of claims 1 to 7, wherein the SCFA comprises at least one of acetic acid, propionic acid, butyric acid, and any combination thereof.

9. The microbial consortium according to any one of claims 1 to 8, wherein the pro-inflammatory cytokine comprises at least one of interleukin-1 (IL-1), IL-1β, IL2, IL-6, IL8, IL-12, IL17, IL-18, IL22, IL23, tumor necrosis factor α (TNF-α), interferon γ (IFNγ), and granulocyte-macrophage colony-stimulating factor (GM-CSF).

10. The microbial consortium according to any one of claims 1 to 9, wherein the cell envelope component is recognized by the immune system of the subject.

11. The microbial consortium according to any one of claims 1 to 10, wherein the cell envelope component is selected from the group consisting of pseudopeptidoglycan, archaeal lipids, O antigen, lipid A, arabinogalactan, and β-glucan.

12. The microbial consortium according to any one of claims 7 to 11, wherein the surface component of the immune cell comprises at least one of the cluster of differentiation (CD).

13. The at least one microorganism that is present in low abundance in a reference human subject is capable of regulating at least one of acetic acid, propionic acid, and butyric acid, and comprises at least one of pseudopeptidoglycan, archaeal lipid, O antigen, lipid A, arabinogalactan, and β-glucan, the microbial consortium according to any one of claims 1 to 12.

14. The at least one microorganism that is present in low abundance in a reference human subject is capable of regulating at least one of TLR2, TLR4, CD4, CD8, IL-1β, IL-6, IL-12, and TNF-α, the microbial consortium according to any one of claims 1 to 13.

15. The at least one microorganism that is present in low abundance in a reference human subject is capable of regulating dendritic cells, the microbial consortium according to any one of claims 1 to 14.

16. Among the two or more microorganisms that are present in low abundance in a reference human subject, one of the microorganisms is capable of regulating at least one of TLR2, TLR4, CD8, CD68, IL-1β, IL-6, IL-12, and TNF-α, and at least one different microorganism among the two or more microorganisms comprises at least one of pseudopeptidoglycan, archaeal lipid, O antigen, lipid A, arabinogalactan, and β-glucan, the microbial consortium according to any one of claims 1 to 15.

17. The at least one microorganism that is in low abundance belongs to at least one of the species Oenococcus oeni, Cetobacterium somerae, Clostridium cellulovorans, Corynebacterium glyciphilum, and Clostridium tyrobutyricum, the microbial consortium according to any one of claims 1 to 16.

18. The at least one microorganism present in low abundance has a 16S rDNA sequence that is at least 95%, at least 96%, at least 97%, at least 98%, at least 99% identical to at least one 16S rDNA sequence represented by SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, and SEQ ID NO:

5. The microbial consortium according to any one of claims 1 to 17, characterized in that it has a 16S rDNA sequence.

19. Among the two or more microorganisms present in low abundance in the reference human subject, one of the microorganisms has a 16S rDNA sequence that is at least 95%, at least 96%, at least 97%, at least 98%, at least 99% identical to at least one 16S rDNA sequence represented by SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, and SEQ ID NO:

5. At least one different microorganism among the two or more microorganisms contains at least one of pseudopeptidoglycan, archaeal lipid, O antigen, lipid A, arabinogalactan, and β-glucan. The microbial consortium according to any one of claims 1 to 18, characterized in that it has a 16S rDNA sequence.

20. The at least one microorganism present in low abundance is at least one of Oenococcus oeni PSU-1, Clostridium tyrobutyricum KCTC 5387, Cetobacterium somerae ATCC BAA-474, Corynebacterium glyciphilum AJ 3170, and Clostridium cellulovorans 743B. The microbial consortium according to any one of claims 1 to 19, characterized in that it is at least one of them.

21. The two or more microorganisms include microorganisms present in high abundance from the microbiota of a human subject. The microorganisms present in high abundance can be the same microorganism having at least one of (i) being capable of producing at least one SCFA, (ii) being able to regulate lactate, and (iii) containing at least one cell envelope component or different bacteria. The microbial consortium according to any one of claims 1 to 20, characterized in that it is the same microorganism having at least one of them.

22. The microbial consortium according to claim 21, wherein the microorganism with a high abundance has a cell envelope component recognized by the immune system of a subject.

23. The microbial consortium according to claim 21 or 22, wherein the microorganism with a high abundance belongs to at least one of the species Bacteroides caccae, Lactobacillus casei, or Veillonella parvula.

24. The microbial consortium according to any one of claims 21 to 23, wherein the microorganism with a high abundance has a 16S rDNA sequence that is at least 95%, at least 96%, at least 97%, at least 98%, at least 99% identical to at least one 16S rDNA sequence represented by SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO:

8.

25. The microbial consortium according to any one of claims 21 to 24, wherein the microorganism with a high abundance contains at least one of Bacteroides caccae CL03T12C61, Lactobacillus casei ATCC27139, or Veillonella parvula ATCC17745.

26. The microbial consortium according to any one of claims 1 to 25, wherein the two or more microorganisms are selected from Oenococcus oeni PSU-1, Clostridium tyrobutyricum KCTC 5387, Cetobacterium somerae ATCC BAA-474, Corynebacterium glyciphilum AJ 3170, Bacteroides caccae CL03T12C61, Lactobacillus casei ATCC27139, Veillonella parvula ATCC 17745, and Clostridium cellulovorans 743B.

27. The microbial consortium according to any one of claims 1 to 26, wherein at least one of the two or more microorganisms present in low abundance in a reference human subject is capable of regulating at least one of TLR2, TLR4, CD8, CD68, IL-1β, IL-6, IL-12, and TNF-α, and at least one different microorganism of the two or more microorganisms has a 16S rDNA sequence that is at least 95%, at least 96%, at least 97%, at least 98%, at least 99% identical to at least one of the 16S rDNA sequences represented by SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO:

8.

28. The microbial consortium according to any one of claims 1 to 26, wherein at least one of the two or more microorganisms present in low abundance in a reference human subject has a 16S rDNA sequence that is at least 95%, at least 96%, at least 97%, at least 98%, at least 99% identical to at least one of the 16S rDNA sequences represented by SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, and SEQ ID NO: 5, and at least one different microorganism of the two or more microorganisms contains at least one of pseudopeptidoglycan, archaeal lipid, O antigen, lipid A, arabinogalactan, and β-glucan.

29. The microbial consortium according to any one of claims 1 to 28, wherein the reference human subject is a healthy subject.

30. The microbial consortium according to any one of claims 1 to 28, wherein the reference human subject is a subject diagnosed with a disease.

31. The microbial consortium according to any one of claims 1 to 30, for use in the treatment of cancer in a human subject.

32. The microbial consortium according to claim 31, wherein the cancer is selected from breast cancer, lung cancer, pancreatic cancer, bladder cancer, malignant melanoma, kidney cancer, head and neck cancer, and lymphoma.

33. The microbial consortium according to any one of claims 1 to 32, for use in the treatment of a subject diagnosed with a disease treatable by the consortium.

34. The microbial consortium according to any one of claims 1 to 33, administered in combination with an anti-cancer treatment.

35. The microbial consortium according to claim 34, wherein the anti-cancer treatment is a checkpoint inhibitor selected from an anti-PD-1 antibody, an anti-CTLA-4 antibody, an anti-PD-L1 antibody, or a combination thereof.

36. The microbial consortium according to claim 35, wherein the checkpoint inhibitor is an anti-PD-1 inhibitor.

37. A pharmaceutical composition comprising a microbial consortium comprising two or more microorganisms, wherein at least one of the two or more microorganisms is present in low abundance in the microbiota of a reference human subject, and at least one other of the two or more microorganisms has at least one of (i) the ability to regulate at least one short-chain fatty acid (SCFA), (ii) the ability to regulate lactate, and (iii) the ability to contain at least one cell envelope component.

38. The pharmaceutical composition according to claim 37, wherein the microbial consortium is the one according to any one of claims 2 to 30.

39. The pharmaceutical composition according to any one of claims 37 or 38, for use in the treatment of cancer.

40. The pharmaceutical composition according to any one of claims 37 to 39, administered in combination with an anti-cancer treatment.

41. The pharmaceutical composition according to claim 40, wherein the anti-cancer treatment is a checkpoint inhibitor selected from an anti-PD-1 antibody, an anti-CTLA-4 antibody, an anti-PD-L1 antibody, or a combination thereof.

42. The pharmaceutical composition according to claim 41, wherein the checkpoint inhibitor is an anti-PD-1 inhibitor.

43. A method of treating, preventing, remitting, alleviating, or delaying the onset of cancer in a human subject in need thereof, the method comprising administering to the subject an effective amount of a microbial consortium comprising two or more isolated or purified microorganisms, wherein at least one of the two or more microorganisms is present in low abundance in the microbiota of a reference human subject, and wherein at least one other of the two or more microorganisms has at least one of (i) the ability to modulate at least one short-chain fatty acid (SCFA), (ii) the ability to modulate lactate, and (iii) at least one cell envelope component recognized by an epithelial cell such as the immune system or intestinal epithelial cells of the human subject, any composition thereof, or a kit comprising the same.

44. The method according to claim 43, wherein the microbial consortium is as defined in any one of claims 2 to 30.

45. The method according to claim 43 or 44, comprising administering to the subject a checkpoint inhibitor in a therapeutically effective amount.

46. The method according to claim 45, wherein the checkpoint inhibitor is selected from an anti-PD-1 antibody, an anti-CTLA-4 antibody, an anti-PD-L1 antibody, or a combination thereof.

47. The method according to any one of claims 43 to 46, wherein the cancer is selected from breast cancer, lung cancer, pancreatic cancer, bladder cancer, melanoma, kidney cancer, head and neck cancer, and lymphoma.

48. Use of a microbial consortium comprising two or more microorganisms in the preparation of a composition for treating cancer in a subject in need thereof, wherein at least one of the two or more microorganisms is present in low abundance in the microbiota of a reference human subject, and at least one other of the two or more microorganisms has at least one of (i) the ability to modulate at least one short-chain fatty acid (SCFA), (ii) the ability to modulate lactate, and (iii) comprising at least one cell envelope component.

49. The use according to claim 48, wherein the microbial consortium is as described in any one of claims 2 to 30.

50. A kit comprising a microbial consortium comprising two or more microorganisms, wherein at least one of the two or more microorganisms is present in a low abundance in the microbiota of a reference human subject, and at least one other of the two or more microorganisms has at least one of: (i) being able to regulate at least one short-chain fatty acid (SCFA), (ii) being able to regulate lactate, and (iii) comprising at least one cell envelope component or a composition comprising the microbial consortium.

51. The kit according to claim 50, wherein the microbial consortium is the one according to any one of claims 2 to 30.

52. The kit according to any one of claims 50 or 51, comprising instructions for use in the treatment of cancer.

53. The kit according to any one of claims 50 to 52, comprising a checkpoint inhibitor.

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