Synthetic microbiome consortia and use thereof

Abstract

The present invention provides a system for diagnosing, treating, or both, a condition or a disease associated therewith, in a subject in need thereof, the system including a synthetic microbiome including recombinant cells. Further provided are a composition including the system, a kit, a method of using same.

Description

SYNTHETIC MICROBIOME CONSORTIA AND USE THEREOFCROSS REFERENCE TO RELATED APPLICATION

[0001] This Application claims the benefit of priority of U.S. Provisional Patent Application No. 63 / 643,504, entitled “SYNTHETIC MICROBIOME CONSORTIA AND USE THEREOF”, filed 7 May 2024, the contents of which are incorporated herein by reference in their entirety.FIELD OF THE INVENTION

[0002] The present invention, in some embodiments, thereof, is in the field of molecular biology and genetic engineering.BACKGROUND

[0003] Synthetic microbiome design offers promising diagnostic and therapeutic applications for treating various intestinal inflammations, including inflammatory bowel disease (IBD). IBD encompasses chronic conditions like Crohn's disease (CD) and ulcerative colitis (UC), characterized by persistent inflammation in different sections of the intestine; UC affects the colon uniformly, whereas CD targets varied intestinal areas. Common symptoms include pain, fatigue, dysbiosis (disrupted intestinal microbiota), diarrhea, and increased GI tract sensitivity.

[0004] Patients with these conditions often have decreased levels of bacteria that ferment short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate in their intestinal mucosa and stools compared to healthy individuals. SCFAs play vital roles in maintaining intestinal homeostasis and modulating the immune system. Their reduced levels in IBD patients have been documented, and butyrate, in particular, is known for its significant immunomodulatory effects through activation of G-protein coupled receptors (GPRs), influencing various signaling pathways in immune cells.

[0005] Another interesting metabolite to study in the analysis of the stool of patients with chronic inflammations is L-lactate. It is one of the lactate isomers predominantly producedby human cells and has a significant role in the regulation of inflammatory diseases, including IBD, as well as in the regulation of intestinal homeostasis. An increase in the concentration of L-lactate in the intestines and patients' stool indicates the presence of inflammatory processes in them. Studies show that in patients with CD and UC, the concentration of L-lactate in the stool increases.

[0006] There is still a great need for the integration of synthetic biology in developing microbial systems and use of same, such as in diagnosing and / or treating intestinal inflammation.SUMMARY

[0007] According to the first aspect, there is provided a system for diagnosing, treating, or both, a condition or a disease associated therewith, in a subject in need thereof, the system comprising: (a) a first recombinant cell comprising at least one first exogenous DNA molecule comprising at least one first promoter and at least one first nucleic acid sequence encoding a detectable polypeptide, at least one first enzyme synthesizing a cell communication molecule, or both, and being operably linked to the at least one first promoter, and wherein the at least one first promoter is responsive to a biomarker of the condition or disease; and (b) a second recombinant cell comprising at least one second exogenous DNA molecule comprising at least one second promoter and at least one nucleic acid sequence encoding at least one second enzyme synthesizing a therapeutic molecule alleviating the condition or disease and being operably linked to the at least one second promoter, and wherein the at least one second promoter is responsive to the cell communication molecule.

[0008] According to another aspect, there is provided a composition comprising the system of the invention, and an acceptable carrier.

[0009] According to another aspect, there is provided a method for diagnosing, treating, or both, a condition or a disease associated therewith, in a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of the pharmaceutical composition of the invention, thereby diagnosing, treating, or both, the condition or the disease associated therewith, in a subject.

[0010] According to another aspect, there is provided a kit comprising: (a) a first recombinant cell comprising at least one first exogenous DNA molecule comprising at least one first promoter and at least one first nucleic acid sequence encoding a detectable polypeptide, at least one first enzyme synthesizing a cell communication molecule, or both, and being operably linked to the at least one first promoter, and wherein the at least one first promoter is responsive to a biomarker of the condition or disease; and (b) a second recombinant cell comprising at least one second exogenous DNA molecule comprising at least one second promoter and at least one nucleic acid sequence encoding at least one second enzyme synthesizing a therapeutic molecule alleviating the condition or disease and being operably linked to the at least one second promoter, and wherein the at least one second promoter is responsive to the cell communication molecule.[Oi l] In some embodiments, any one of the at least one first promoter and the at least one second promoter is directly or indirectly responsive to the biomarker and the cell communication molecule, respectively.

[0012] In some embodiments, the detectable polypeptide, the at least one first enzyme, or both, is expressed upon activation of the at least one first promoter.

[0013] In some embodiments, the at least one second enzyme is expressed upon activation of the at least one second promoter.

[0014] In some embodiments, any one of the at least one first promoter, the at least one second promoter, and both, comprise a plurality of promoters.

[0015] In some embodiments, any one of the at least one first enzyme, the at least one second enzyme, and both, comprise a plurality of enzymes.

[0016] In some embodiments, the at least one first exogenous DNA molecule comprises at least one second nucleic acid sequence encoding at least one polypeptide capable of transporting the biomarker into the first recombinant cell, binding the biomarker in the first recombinant cell, or both.

[0017] In some embodiments, the biomarker is derived, produced, secreted, or any combination thereof, by the subject.

[0018] In some embodiments, the first recombinant cell, the second recombinant cell, or both, is a prokaryote cell or a eukaryote cell.

[0019] In some embodiments, both the first recombinant cell and the second recombinant cell are recombinant bacterial cells.

[0020] In some embodiments, the at least one first promoter comprises a primary first promoter and a secondary first promoter.

[0021] In some embodiments, the primary first promoter controls or regulates expression / transcription of the at least one second nucleic acid sequence.

[0022] In some embodiments, the at least one second nucleic acid sequence is encoding a first polypeptide being a transporter of the biomarker and a second polypeptide being a repressor of the secondary first promoter.

[0023] In some embodiments, the secondary first promoter controls or regulates expression / transcription of the at least one first nucleic acid sequence.

[0024] In some embodiments, binding of the biomarker to the second polypeptide being a repressor activates the secondary first promoter such that the detectable polypeptide, at least one first enzyme synthesizing a cell communication molecule, or both, are produced by the first recombinant cell.

[0025] In some embodiments, the at least one second nucleic acid sequence is encoding a polypeptide being a transcription factor responsive to the biomarker.

[0026] In some embodiments, binding of the biomarker to the polypeptide being a transcription factor responsive to the biomarker activates the secondary first promoter such that the detectable polypeptide, at least one first enzyme synthesizing a cell communication molecule, or both, are produced by the first recombinant cell.

[0027] In some embodiments, the at least one second promoter comprises a primary second promoter, a secondary second promoter, and a tertiary second promoter.

[0028] In some embodiments, the primary second promoter and the tertiary second promoter control or regulate expression / transcription of the at least one nucleic acid sequenceencoding at least two second enzymes of the plurality of enzymes synthesizing the therapeutic molecule alleviating the condition or disease.

[0029] In some embodiments, the secondary second promoter controls or regulates expression of a nucleic acid sequence encoding a polypeptide being a transcription factor capable of activating the tertiary second promoter.

[0030] In some embodiments, binding of the cell communication molecule to a cytoplasmic receptor in the second recombinant cell activates the tertiary second promoter such that the therapeutic molecule alleviating the condition or disease is synthesized by the second recombinant cell.

[0031] In some embodiments, the biomarker is selected from the group consisting of: heme, L-lactate, hydrogen peroxide, and any combination thereof.

[0032] In some embodiments, the cell communication molecule is a quorum sensing signaling molecule.

[0033] In some embodiments, the quorum sensing signaling molecule is an N-acyl homoserine lactone (AHL).

[0034] In some embodiments, the therapeutic molecule is a short-chain fatty acid (SCFA).

[0035] In some embodiments, the SCFA is butyrate.

[0036] In some embodiments, the condition is inflammation.

[0037] In some embodiments, the disease associated with inflammation is an autoimmune disease.

[0038] In some embodiments, the autoimmune disease is an inflammatory bowel disease (IBD).

[0039] In some embodiments, any one of the at least one first exogenous DNA molecule, the at least one second exogenous DNA molecule, and both, are integrated in a vector or a plasmid.

[0040] In some embodiments, the vector or plasmid being introduced into any one of the first recombinant cell, the second recombinant cell, and both.

[0041] In some embodiments, the composition is a pharmaceutical composition.

[0042] In some embodiments, the pharmaceutical composition is for use in diagnosis, treatment, or both, of a condition or a disease associated therewith, in a subject in need thereof.

[0043] In some embodiments, the pharmaceutical composition is formulated for any one of oral delivery and colonic delivery.

[0044] In some embodiments, the administering is enterally administering.

[0045] In some embodiments, the method further comprises a step comprising determining the abundance of the detectable polypeptide in the subject or sample derived therefrom, wherein an abundance above a predetermined threshold of the detectable polypeptide in the subject or the sample derived therefrom is indicative of the subject being afflicted with the condition or the disease associated therewith.

[0046] In some embodiments, the method further comprises administering to the subject a therapeutically effective amount of an anti-inflammatory drug.

[0047] In some embodiments, the kit further comprises instruction for administering the first recombinant cell and the second recombinant cell to a subject in need thereof.

[0048] In some embodiments, the administering is sequentially administering or simultaneously administering.

[0049] In some embodiments, the kit is for diagnosing, treating, or both, a condition or a disease associated therewith, in a subject in need thereof.

[0050] In some embodiments, the diagnosing is in a sample obtained or derived from the subject.

[0051] In some embodiments, the diagnosing is in vitro or ex vivo.

[0052] Unless otherwise defined, all technical and / or scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the invention, exemplary methods and / or materials are described below. In case of conflict, the patent specification,including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be necessarily limiting.

[0053] Further embodiments and the full scope of applicability of the present invention will become apparent from the detailed description given hereinafter. However, it should be understood that the detailed description and specific examples, while indicating preferred embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.

[0054] In addition to the exemplary aspects and embodiments described above, further aspects and embodiments will become apparent by reference to the figures and by study of the following detailed description.BRIEF DESCRIPTION OF THE FIGURES

[0055] Fig. 1 includes a non-limiting scheme showing a representation of a synthetic engineered microbiome comprising sensory-sender bacteria and responder bacteria for biosynthetic drug production and release in real-time. The communication between sender and responder is carried out by signaling molecules and natural bacterial quorum sensing mechanism.

[0056] Fig. 2 includes non-limiting schemes and a graph showing a heme sensor design based on MG 1655 wild type strain, and fecal sample measurement procedure. The fecal samples were measured in microplate reader, and the results can be seen on the right graph. The inventors used a healthy germ-free (GF) murine fecal sample and at the time 0 manually added heme 2.5 pM - blue positive control curve. The red curve represents the negative control - healthy GF mice w / o heme the design. The green curve is a test curve, wherein the inventors used dextran sodium sulfate (DSS)-induced GF murine model, and collected stool on day 4-6 after DSS-induction.

[0057] Fig. 3 includes a non-limiting scheme and a graph showing L-Lactate sensor in vitro results. This sensor is working in the dynamic range of 5-100 mM which corresponds to the physiological range.

[0058] Fig. 4 includes an enzymatic synthetic pathway and non-limiting schemes showing the engineered design of the probiotic E. coli Nissle 1917 that produce butyrate. The current mutated genotype is NOM006: E. coli Nissle 1917 AfrdA, AldhA, Apta, AadhE, AmgsA::pTetO(LBL)-TetR. On the left is the synthetic pathway with main genes to be inserted. On the right is the bacterial design which harbors production genes, when the strain itself was mutated using CRISPR / Cas9 to knock-out and knock-in certain genes.

[0059] Fig. 5 includes non-limiting schemes and a graph showing an in vivo experimental design and fecal samples measurement protocol on the top left and bottom left, respectively. The inventors used a healthy GF murine model, which was monocolonized with a certain bacterial strain on day 0. On the day 0, by means of gavage, the inventors inoculated mice with different bacterial strains: with butyrate non-producing NOM006 strains for negative and positive controls, NC and PC, respectively, and with butyrate producing NOM006 strain as a test strain. On day 2 the appropriate murine groups were supplied with inducers in drinking water (NC group, test +inducer group) for the circuit activation. Every 2 days the inducers supply was repeated. The fecal samples were collected every 2 days after activation. The bar graph on the right represents the gas chromatography-mass spectrometry (GC-MS) measurements after animal scarification on day 8, on samples of the cecum. Further, butyrate production levels were measured in fecal samples and colon feces (data not shown).

[0060] Fig. 6 includes a non-limiting schemes, micrographs, and graphs. On the top left is a non-limiting in vivo experimental design with the DSS-induced GF murine models. Here mice were monocolonized with a certain strains on day - 1. As a control strain the inventors used E. coli Nissle 1917 WT non-producing strain, and as a test the inventors used an engineered strain NOM006 with butyrate production system. On day 0, the inventors collected the control feces, and induced murine models with DSS for the next 6 days. On day 3 the inventors added inducers to activate the butyrate production bacterial model. On day 21 the mice were sacrificed. During the experiment every 3 days samples for colony formation factor (CFU), calprotectin concentration, and cytokines, were collected. Additionally, every 3 days mice from each group were weighed. On the bottom left, histological analysis from the sacrificed mice on day 9 is presented. It can be seen that intestines of the test group looks less inflamed than the control one. On the right there are the three graphs for the calprotectin concentration, weight, and CFU dynamic changes.DETAILED DESCRIPTIONSystem

[0061] According to a first aspect, there is provided a system for diagnosing, treating, or both, a condition or a disease associated therewith, in a subject in need thereof.

[0062] In some embodiments, the system is an artificial or a synthetic system. In some embodiments, the composition is an artificial or a synthetic microbiome. In some embodiments, a microbiome comprises a heterogenous population of cells comprising at least two distinct sub-populations of cells. In some embodiments, each sub -population of cells of the microbiome disclosed herein comprises at least one exogenous DNA molecule. In some embodiments, each one of the sub-populations of cells comprises a different exogenous DNA molecule. In some embodiments, different exogenous DNA molecules comprises different nucleic acid sequences.

[0063] In some embodiments, the system comprises a first recombinant cell and a second recombinant cell.

[0064] In some embodiments, the first recombinant cell comprises at least one first exogenous DNA molecule. In some embodiments, the second recombinant cell comprises at least one second exogenous DNA molecule.

[0065] In some embodiments, the at least one first exogenous DNA molecule comprises at least one first promoter and at least one first nucleic acid sequence.

[0066] In some embodiments the at least one first nucleic acid sequence encodes a detectable polypeptide, at least one first enzyme, or both.

[0067] In some embodiments, the at least one first enzyme is capable of synthesizing a cell communication molecule.

[0068] In some embodiments, the at least one first nucleic acid sequence is operably linked to the at least one first promoter. In some embodiments, the at least one first promoter is responsive to a biomarker of a condition or disease.

[0069] In some embodiments, the at least one second exogenous DNA molecule comprises least one second promoter and at least one nucleic acid sequence (a third nucleic acid sequence).

[0070] In some embodiments, the at least one nucleic acid encodes at least one second enzyme.

[0071] In some embodiments, the at least one second enzyme synthesizes a therapeutic molecule alleviating a condition or disease.

[0072] In some embodiments, the at least one second nucleic acid sequence is being operably linked to the at least one second promoter. In some embodiments, the at least one second promoter is responsive to a cell communication molecule.

[0073] In some embodiments, the at least one first promoter the at least one second promoter, or both, is directly or indirectly responsive to the biomarker or the cell communication molecule, respectively.

[0074] In some embodiments, directly refers to the biomarker or the cell communication molecule being bound to a transcription factor, repressor, operator, enhancer, or the like, which interacts and / or binds to the at least one first promoter or the at least one second promoter, respectively, upon which transcription activated.

[0075] In some embodiments, indirectly refers to activation of the at least one first promoter or the at least one second promoter in a manner wherein the biomarker or the cell communication molecule either being bound to a transcription factor, repressor, operator, enhancer (or the like) or not, does not interact and / or bind to the at least one first promoter or the at least one second promoter, respectively, so as to activate transcription.

[0076] In some embodiments, the detectable polypeptide, the at least one first enzyme, or both, is expressed upon activation of the at least one first promoter.

[0077] In some embodiments, a detectable polypeptide comprises any polypeptide which can be detected by a skilled artisan. In some embodiments, the detectable polypeptide is a fluorescent, bioluminescent, chemiluminescent, colorimetric, or any equivalent thereof, polypeptide. In some embodiments, the detectable polypeptide is a fluorescent protein.

[0078] In some embodiments, the at least one second enzyme is expressed upon activation of the at least one second promoter.

[0079] In some embodiments, any one of the at least one first promoter, the at least one second promoter, and both, comprise a plurality of promoters. In some embodiments, any one of the at least one first enzyme, the at least one second enzyme, and both, comprise a plurality of enzymes.

[0080] As used herein, the term “plurality” refers to any integer being equal to or greater than 2.

[0081] In some embodiments, the at least one first exogenous DNA molecule comprises at least one second nucleic acid sequence encoding at least one polypeptide capable of transporting the biomarker into the first recombinant cell, binding the biomarker in the first recombinant cell, or both. In some embodiments, binding is in the cytoplasm of the first recombinant cell.

[0082] In some embodiments, the biomarker is derived, produced, secreted, or any combination thereof, by a or the subject.

[0083] In some embodiments, the first recombinant cell, the second recombinant cell, or both, is a prokaryote cell or a eukaryote cell. In some embodiments, a eukaryote cell comprises or is fungus or yeast. In some embodiments, the first recombinant cell and the second recombinant cell are recombinant bacterial cells. In some embodiments, the first recombinant cell, the second recombinant cell, or both, are E. coli cells.

[0084] In some embodiments, the at least one first promoter comprises a primary first promoter and a secondary first promoter.

[0085] In some embodiments, the primary first promoter controls or regulates expression / transcription of the at least one second nucleic acid sequence.

[0086] In some embodiments, the at least one second nucleic acid sequence is encoding a first polypeptide being a transporter of the biomarker. In some embodiments, the at least one second nucleic acid sequence is encoding a second polypeptide being a repressor of the secondary first promoter. In some embodiments, the at least one second nucleic acidsequence is encoding a first polypeptide being a transporter of the biomarker and a second polypeptide being a repressor of the secondary first promoter.

[0087] In some embodiments, the secondary first promoter controls or regulates expression / transcription of the at least one first nucleic acid sequence.

[0088] In some embodiments, binding of the biomarker to the second polypeptide being a repressor activates the secondary first promoter such that the detectable polypeptide, at least one first enzyme synthesizing a cell communication molecule, or both, are produced by the first recombinant cell.

[0089] In some embodiments, the at least one enzyme synthesizing a cell communication molecule belongs to the homoserine lactone(s) biosynthesis pathway. In some embodiments, a homoserine lactone is or comprises N-acyl homoserine lactone(s) (AHL).

[0090] In some embodiments, the at least one second nucleic acid sequence is encoding a polypeptide being a transcription factor responsive to the biomarker.

[0091] In some embodiments, binding of the biomarker to the polypeptide being a transcription factor responsive to the biomarker activates the secondary first promoter such that the detectable polypeptide, at least one first enzyme synthesizing a cell communication molecule, or both, are produced by the first recombinant cell.

[0092] In some embodiments, the at least one second promoter comprises a primary second promoter, a secondary second promoter, and a tertiary second promoter.

[0093] In some embodiments, the primary second promoter and the tertiary second promoter control or regulate expression / transcription of the at least one nucleic acid sequence encoding at least two second enzymes of the plurality of enzymes synthesizing a therapeutic molecule alleviating the condition or disease.

[0094] In some embodiments, the at least two second enzymes of the plurality of enzymes synthesizing a therapeutic molecule alleviating the condition or disease belong to the butyrate biosynthetic pathway. In some embodiments, the at least two enzymes comprise at least 3, at least 4, at least 5, or at least 6 enzymes, or any value and range therebetween. Each possibility represents a separate embodiment of the invention.

[0095] In some embodiments, the at least two enzymes are selected from: acetyl-CoA acetyltransferase, hydroxybutyryl-CoA dehydrogenase, crotonase, butyryl CoA dehydrogenase, phosphotransbututylase, butyrate kinase, or any combination thereof.

[0096] In some embodiments, the secondary second promoter controls or regulates expression / transcription of a nucleic acid sequence encoding a polypeptide being a transcription factor capable of activating the tertiary second promoter.

[0097] In some embodiments, the binding of the cell communication molecule to a cytoplasmic receptor in the second recombinant cell activates the tertiary second promoter such that the therapeutic molecule alleviating the condition or disease is synthesized by the second recombinant cell.

[0098] In some embodiments, the second recombinant cell further comprises a gene or a transcript thereof encoding a cytoplasmic receptor of the cell communication molecule. In some embodiments, the second recombinant cell further comprises a polypeptide being a cytoplasmic receptor of the cell communication molecule.

[0099] In some embodiments, the biomarker comprises any molecule being indicative of oxidative stress. In some embodiments, the biomarker comprises any compound known to be enriched or abundant above a pre-determined threshold in a subject or a cell thereof, in or under oxidative stress. In some embodiments, the biomarker is selected from: heme, L- lactate, hydrogen peroxide, or any combination thereof.

[0100] In some embodiments, the cell communication molecule comprises a quorum sensing signaling molecule. In some embodiments, a quorum sensing signaling molecule comprises any compound known, capable of, or both, to induce quorum sensing.

[0101] As used herein, the term “quorum sensing” refers to a cell’s ability to detect and respond to population density by gene regulation. In some embodiments, quorum sensing is bacterial quorum sensing.

[0102] In some embodiments, a quorum sensing signaling molecule comprises or is N-acyl homoserine lactone(s) (AHL), or a combination thereof.

[0103] In some embodiments, the therapeutic molecule is or comprises a short-chain fatty acid (SCFA). In some embodiments, the SCFA is or comprises butyrate.

[0104] In some embodiments, the condition is inflammation. In some embodiments, the disease associated with inflammation is an autoimmune disease. In some embodiments, the autoimmune disease is an inflammatory bowel disease (IBD).

[0015] In some embodiments, the at least one first exogenous DNA molecule, the at least one second exogenous DNA molecule, or both, are integrated in a vector or a plasmid.

[0016] In some embodiments, the vector or plasmid is introduced into any one of the first cell, the second cell, or both, thereby rendering or resulting in a first recombinant cell and / or a second recombinant cell. In some embodiments, the vector or plasmid is integrated into the genome of the recombinant cell after introduction into the cell. In some the vector or plasmid is not integrated into the genome of the recombinant cell after introduction into the cell.

[0107] In some embodiments, the vector or plasmid in an expression vector.

[0108] In some embodiments, the vector is a viral vector.

[0109] The term "nucleic acid" is well known in the art. A "nucleic acid" as used herein will generally refer to a molecule (i.e., a strand) of DNA, RNA or a derivative or analog thereof, comprising a nucleobase. A nucleobase includes, for example, a naturally occurring purine or pyrimidine base found in DNA (e.g., an adenine "A," a guanine "G," a thymine "T" or a cytosine "C") or RNA (e.g., an A, a G, an uracil "U" or a C).

[0110] The terms “nucleic acid molecule” include but not limited to singlestranded RNA (ssRNA), double-stranded RNA (dsRNA), single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), small RNA such as miRNA, siRNA and other short interfering nucleic acids, snoRNAs, snRNAs, tRNA, piRNA, tnRNA, small rRNA, hnRNA, circulating nucleic acids, fragments of genomic DNA or RNA, degraded nucleic acids, ribozymes, viral RNA or DNA, nucleic acids of infectious origin, amplification products, modified nucleic acids, plasmidical or organellar nucleic acids and artificial nucleic acids such as oligonucleotides.

[0111] The terms "polynucleotide," "polynucleotide sequence," "nucleic acid sequence," and "nucleic acid molecule" are used interchangeably herein. These terms encompass nucleotide sequences and the like. A polynucleotide may be a polymer of RNA or DNA thatis single- or double-stranded, that optionally contains synthetic, non-natural, or altered nucleotide bases.

[0112] As used herein, the terms “peptide”, "polypeptide" and "protein" are used interchangeably to refer to a polymer of amino acid residues. In another embodiment, the terms "peptide", "polypeptide" and "protein" as used herein encompass native peptides, peptidomimetics (typically including non-peptide bonds or other synthetic modifications) and the peptide analogues peptoids and semipeptoids or any combination thereof. In another embodiment, the peptides polypeptides and proteins described have modifications rendering them more stable while in the body or more capable of penetrating into cells. In one embodiment, the terms “peptide”, "polypeptide" and "protein" apply to naturally occurring amino acid polymers. In another embodiment, the terms “peptide”, "polypeptide" and "protein" apply to amino acid polymers in which one or more amino acid residue is an artificial chemical analogue of a corresponding naturally occurring amino acid.

[0113] Expressing a gene within a cell is well known to one skilled in the art. It can be carried out by, among many methods, transfection, viral infection, or direct alteration of the cell’s genome. In some embodiments, the gene is in an expression vector such as plasmid or viral vector. One such example of an expression vector containing pl6-Ink4a is the mammalian expression vector pCMV pl 6 INK4A available from Addgene.

[0114] A vector nucleic acid sequence generally contains at least an origin of replication for propagation in a cell and optionally additional elements, such as a heterologous polynucleotide sequence, expression control element (e.g., a promoter, enhancer), selectable marker (e.g., antibiotic resistance), poly-Adenine sequence.

[0115] The vector may be a DNA plasmid delivered via non-viral methods or via viral methods. The viral vector may be a retroviral vector, a herpesviral vector, an adenoviral vector, an adeno-associated viral vector or a poxviral vector. The promoters may be active in mammalian cells. The promoters may be a viral promoter.

[0116] In some embodiments, the gene is operably linked to a promoter. The term “operably linked” is intended to mean that the nucleotide sequence of interest is linked to the regulatory element or elements in a manner that allows for expression of the nucleotide sequence (e.g.,in an in vitro transcription / translation system or in a host cell when the vector is introduced into the host cell).

[0117] In some embodiments, the vector is introduced into the cell by standard methods including electroporation (e.g., as described in From et al., Proc. Natl. Acad. Sci. USA 82, 5824 (1985)), Heat shock, infection by viral vectors, high velocity ballistic penetration by small particles with the nucleic acid either within the matrix of small beads or particles, or on the surface (Klein et al., Nature 327. 70-73 (1987), and / or the like.

[0118] The term "promoter" as used herein refers to a group of transcriptional control modules that are clustered around the initiation site for an RNA polymerase i.e., RNA polymerase II. Promoters are composed of discrete functional modules, each consisting of approximately 7-20 bp of DNA, and containing one or more recognition sites for transcriptional activator or repressor proteins.

[0119] In some embodiments, nucleic acid sequences are transcribed by RNA polymerase II (RNAP II and Pol II). RNAP II is an enzyme found in eukaryotic cells. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA.

[0120] In some embodiments, mammalian expression vectors include, but are not limited to, pcDNA3, pcDNA3.1 (±), pGL3, pZeoSV2(±), pSecTag2, pDisplay, pEF / myc / cyto, pCMV / myc / cyto, pCR3.1, pSinRep5, DH26S, DHBB, pNMTl, pNMT41, pNMT81, which are available from Invitrogen, pCI which is available from Promega, pMbac, pPbac, pBK- RSV and pBK-CMV which are available from Strategene, pTRES which is available from Clontech, and their derivatives.

[0121] In some embodiments, expression vectors containing regulatory elements from eukaryotic viruses such as retroviruses are used by the present invention. SV40 vectors include pSVT7 and pMT2. In some embodiments, vectors derived from bovine papilloma virus include pBV-lMTHA, and vectors derived from Epstein Bar virus include pHEBO, and p2O5. Other exemplary vectors include pMSG, pAV009 / A+, pMTO10 / A+, pMAMneo- 5, baculovirus pDSVE, and any other vector allowing expression of proteins under the direction of the SV-40 early promoter, SV-40 later promoter, metallothionein promoter, murine mammary tumor virus promoter, Rous sarcoma virus promoter, polyhedrin promoter, or other promoters shown effective for expression in eukaryotic cells.

[0122] In some embodiments, recombinant viral vectors, which offer advantages such as lateral infection and targeting specificity, are used for in vivo expression. In one embodiment, lateral infection is inherent in the life cycle of, for example, retrovirus and is the process by which a single infected cell produces many progeny virions that bud off and infect neighboring cells. In one embodiment, the result is that a large area becomes rapidly infected, most of which was not initially infected by the original viral particles. In one embodiment, viral vectors are produced that are unable to spread laterally. In one embodiment, this characteristic can be useful if the desired purpose is to introduce a specified gene into only a localized number of targeted cells.

[0123] Various methods can be used to introduce the expression vector of the present invention into cells. Such methods are generally described in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Springs Harbor Laboratory, New York (1989, 1992), in Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1989), Chang et al., Somatic Gene Therapy, CRC Press, Ann Arbor, Mich. (1995), Vega et al., Gene Targeting, CRC Press, Ann Arbor Mich. (1995), Vectors: A Survey of Molecular Cloning Vectors and Their Uses, Butterworths, Boston Mass. (1988) and Gilboa et at. [Bio techniques 4 (6): 504-512, 1986] and include, for example, stable or transient transfection, lipofection, electroporation and infection with recombinant viral vectors. In addition, see U.S. Pat. Nos. 5,464,764 and 5,487,992 for positive-negative selection methods.

[0124] In one embodiment, plant expression vectors are used. In one embodiment, the expression of a polypeptide coding sequence is driven by a number of promoters. In some embodiments, viral promoters such as the 35S RNA and 19S RNA promoters of CaMV [Brisson et al., Nature 310:511-514 (1984)], or the coat protein promoter to TMV [Takamatsu et al., EMBO J. 6:307-311 (1987)] are used. In another embodiment, plant promoters are used such as, for example, the small subunit of RUBISCO [Coruzzi et al., EMBO J. 3: 1671-1680 (1984); and Brogli et al., Science 224:838-843 (1984)] or heat shock promoters, e.g., soybean hspl7.5-E or hspl7.3-B [Gurley et al., Mol. Cell. Biol. 6:559-565 (1986)]. In one embodiment, constructs are introduced into plant cells using Ti plasmid, Ri plasmid, plant viral vectors, direct DNA transformation, microinjection, electroporation, and other techniques well known to the skilled artisan. See, for example, Weissbach &Weissbach [Methods for Plant Molecular Biology, Academic Press, NY, Section VIII, pp 421-463 (1988)]. Other expression systems such as insects and mammalian host cell systems, which are well known in the art, can also be used by the present invention.

[0125] In some embodiments, an exogenous DNA molecule as disclosed herein comprises or is a synthetic DNA molecule or a synthetic polynucleotide.

[0126] As used herein, the term "synthetic" refers to something that is artificial or manmade. In some embodiments, a synthetic DNA molecule as disclosed herein, is not present, made, or both, in nature. In some embodiments, synthetic excludes a product of nature, e.g., obtained or produced only by man.

[0127] According to another aspect, there is provided a composition comprising the system of the invention, and an acceptable carrier.

[0128] In some embodiments, the carrier is a biologically acceptable carrier. In some embodiments, the carrier is a pharmaceutically acceptable carrier.

[0129] In some embodiments, the composition is a pharmaceutical composition.

[0130] In some embodiments, the pharmaceutical composition is for use in diagnosis, treatment, or both, of a condition or a disease associated therewith, in a subject in need thereof.

[0131] In some embodiments, the condition is inflammation. In some embodiments, the disease associated with inflammation comprises an autoimmune disease. In some embodiments, the autoimmune disease is IBD.

[0132] In some embodiments, IBD comprises ulcerative colitis, Chron’s disease, or both.

[0133] The term “autoimmune disease" as used herein refers to any disorder resulting from an immune response against the subject's own tissue or tissue components or to antigens that are not intrinsically harmful to the subject.

[0134] The symptoms and degree of severity can vary. Autoimmune diseases include, but are not limited to, autoimmune diseases that are frequently designated as involving single organ or single cell-type autoimmune disorder and autoimmune diseases that are frequently designated as involving systemic autoimmune disorder. Non-limiting examples of singleorgan or single cell-type autoimmune disorders include Hashimoto's thyroiditis, autoimmune hemolytic anemia, autoimmune atrophic gastritis of pernicious anemia, autoimmune encephalomyelitis, autoimmune orchitis, Goodpasture's disease, autoimmune thrombocytopenia, sympathetic ophthalmia, myasthenia gravis (MG), Graves' disease, primary biliary cirrhosis, chronic aggressive hepatitis, and membranous glomerulopathy. Non-limiting examples of autoimmune diseases involving systemic autoimmune disorder include systemic lupus erythematosis (SLE), rheumatoid arthritis (RA), multiple sclerosis (MS), Sjogren's syndrome, Reiter's syndrome, polymyositis-dermatomyositis, systemic sclerosis, polyarteritis nodosa, and bullous pemphigoid. Each possibility represents a separate embodiment of the invention.

[0135] As used herein, the terms “carrier,” “excipient,” or “adjuvant” are interchangeable, and refer to any component of a pharmaceutical composition that is not the active agent. As used herein, the term “pharmaceutically acceptable carrier” refers to non-toxic, inert solid, semi-solid liquid filler, diluent, encapsulating material, formulation auxiliary of any type, or simply a sterile aqueous medium, such as saline. Some examples of the materials that can serve as pharmaceutically acceptable carriers are sugars, such as lactose, glucose and sucrose, starches such as corn starch and potato starch, cellulose and its derivatives such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt, gelatin, talc; excipients such as cocoa butter and suppository waxes; oils such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; glycols, such as propylene glycol, polyols such as glycerin, sorbitol, mannitol and polyethylene glycol; esters such as ethyl oleate and ethyl laurate, agar; buffering agents such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline, Ringer's solution; ethyl alcohol and phosphate buffer solutions, as well as other non-toxic compatible substances used in pharmaceutical formulations. Some non-limiting examples of substances which can serve as a carrier herein include sugar, starch, cellulose and its derivatives, powered tragacanth, malt, gelatin, talc, stearic acid, magnesium stearate, calcium sulfate, vegetable oils, polyols, alginic acid, pyrogen-free water, isotonic saline, phosphate buffer solutions, cocoa butter (suppository base), emulsifier as well as other non- toxic pharmaceutically compatible substances used in other pharmaceutical formulations. Wetting agents and lubricants such as sodium lauryl sulfate, as well as coloring agents,flavoring agents, excipients, stabilizers, antioxidants, and preservatives may also be present. Any non-toxic, inert, and effective carrier may be used to formulate the compositions contemplated herein. Suitable pharmaceutically acceptable carriers, excipients, and diluents in this regard are well known to those of skill in the art, such as those described in The Merck Index, Thirteenth Edition, Budavari et al., Eds., Merck & Co., Inc., Rahway, N.J. (2001); the CTFA (Cosmetic, Toiletry, and Fragrance Association) International Cosmetic Ingredient Dictionary and Handbook, Tenth Edition (2004); and the “Inactive Ingredient Guide,” U.S. Food and Drug Administration (FDA) Center for Drug Evaluation and Research (CDER) Office of Management, the contents of all of which are hereby incorporated by reference in their entirety. Examples of pharmaceutically acceptable excipients, carriers, and diluents useful in the present compositions include distilled water, physiological saline, Ringer's solution, dextrose solution, Hank's solution, and DMSO. These additional inactive components, as well as effective formulations and administration procedures, are well known in the art and are described in standard textbooks, such as Goodman and Gillman’s: The Pharmacological Bases of Therapeutics, 8th Ed., Gilman et al. Eds. Pergamon Press (1990); Remington’s Pharmaceutical Sciences, 18th Ed., Mack Publishing Co., Easton, Pa. (1990); and Remington: The Science and Practice of Pharmacy, 21st Ed., Lippincott Williams & Wilkins, Philadelphia, Pa., (2005), each of which is incorporated by reference herein in its entirety. The presently described composition may also be contained in artificially created structures such as liposomes, ISCOMS, slow- releasing particles, and other vehicles which increase the half-life of the peptides or polypeptides in serum. Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. Liposomes for use with the presently described peptides are formed from standard vesicle - forming lipids which generally include neutral and negatively charged phospholipids and sterol, such as cholesterol. The selection of lipids is generally determined by considerations such as liposome size and stability in the blood. A variety of methods are available for preparing liposomes as reviewed, for example, by Coligan, J. E. et al, Current Protocols in Protein Science, 1999, John Wiley & Sons, Inc., New York, and see also U.S. Pat. Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369.

[0136] The carrier may comprise, in total, from about 0.1% to about 99.99999% by weight of the pharmaceutical compositions presented herein.Methods of use

[0137] According to another aspect, there is provided a method for diagnosing, treating, or both, a condition or a disease associated therewith, in a subject in need thereof.

[0138] In some embodiments, the method comprises administering to the subject a therapeutically effective amount of the pharmaceutical composition of the invention, thereby diagnosing, treating, or both, the condition or the disease associated therewith, in a subject.

[0139] In some embodiments, the pharmaceutical composition is formulated for oral delivery, colonic delivery, or both.

[0140] In some embodiments, administering comprises enterally administering. In some embodiments, enterally administering comprises orally administering, administering to the colon (such as of a subject), or both.

[0141] In some embodiments, the method further comprises a step comprising determining the abundance of a detectable polypeptide in the subject or sample derived therefrom.

[0142] In some embodiments, the determining is ex vivo or in vitro determining.

[0143] In some embodiments, an abundance of the detectable polypeptide being above a predetermined threshold in the subject or a sample derived therefrom is indicative of the subject being afflicted with the condition or the disease associated therewith. In some embodiments, an abundance of the detectable polypeptide being above a predetermined threshold in the subject or a sample derived therefrom is indicative of the subject being suitable for, in need of, or both, treatment for the condition or the disease associated therewith.

[0144] In some embodiments, an abundance of the detectable polypeptide being equal to or below a predetermined threshold in the subject or a sample derived therefrom is indicative of the subject being unafflicted with the condition or the disease associated therewith. In some embodiments, an abundance of the detectable polypeptide being equal to or below a predetermined threshold in the subject or a sample derived therefrom is indicative of the subject being unsuitable for treatment for the condition or the disease associated therewith.

[0145] In some embodiments, the method further comprises administering to the subject a therapeutically effective amount of an anti-inflammatory drug.

[0146] As used herein, the terms “treatment” or “treating” of a disease, disorder, or condition encompasses alleviation of at least one symptom thereof, a reduction in the severity thereof, or inhibition of the progression thereof. Treatment need not mean that the disease, disorder, or condition is totally cured. To be an effective treatment, a useful composition herein needs only to reduce the severity of a disease, disorder, or condition, reduce the severity of symptoms associated therewith, or provide improvement to a patient or subject’s quality of life.

[0017] In some embodiments, treating comprises preventing. In some embodiments, treating comprises preventing and treating.Kit

[0148] According to another aspect, there is provided a kit comprising: (a) a first recombinant cell comprising at least one first exogenous DNA molecule comprising at least one first promoter and at least one first nucleic acid sequence encoding a detectable polypeptide, at least one first enzyme synthesizing a cell communication molecule, or both, and being operably linked to the at least one first promoter, and wherein the at least one first promoter is responsive to a biomarker of the condition or disease; and (b) a second recombinant cell comprising at least one second exogenous DNA molecule comprising at least one second promoter and at least one nucleic acid sequence encoding at least one second enzyme synthesizing a therapeutic molecule alleviating the condition or disease and being operably linked to the at least one second promoter, and wherein the at least one second promoter is responsive to the cell communication molecule.

[0149] In some embodiments, the kit further comprises instruction for administering the first recombinant cell and the recombinant second cell to a subject in need thereof.

[0150] In some embodiments, administering is sequentially administering or simultaneously administering.

[0151] In some embodiments, the kit is for preparing the pharmaceutical composition of the invention. In some embodiments, the pharmaceutical composition is suitable for and / or foruse in diagnosing, treating, or both, a condition or a disease associated therewith, in a subject in need thereof.

[0152] In some embodiments, the kit is for diagnosing, treating, or both, a condition or a disease associated therewith, in a subject in need thereof.

[0153] In some embodiments, the diagnosing is in a sample obtained or derived from the subject. In some embodiments, diagnosing is in vitro or ex vivo.General

[0154] Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.

[0155] As used herein, the term "about" when combined with a value refers to plus and minus 10% of the reference value. For example, a length of about 1,000 nucleobases refers to a length of 1,000 nucleobases ± 100 nucleobases.

[0156] In those instances where a convention analogous to "at least one of A, B, and C, etc." is used, in general such a construction is intended in the sense one having skill in the art would understand the convention (e.g., "a system having at least one of A, B, and C" would include but not be limited to systems that have A alone, B alone, C alone, A and B together, A and C together, B and C together, and / or A, B, and C together, etc.). It will be further understood by those within the art that virtually any disjunctive word and / or phrase presenting two or more alternative terms, whether in the description, claims, or drawings, should be understood to contemplate the possibilities of including one of the terms, either of the terms, or both terms. For example, the phrase "A or B" will be understood to include the possibilities of "A" or "B" or "A and B."

[0157] In the discussion unless otherwise stated, adjectives such as “substantially” and “about” modifying a condition or relationship characteristic of a feature or features of an embodiment of the invention, are understood to mean that the condition or characteristic is defined to within tolerances that are acceptable for operation of the embodiment for an application for which it is intended. Unless otherwise indicated, the word “or” in the specification and claims is considered to be the inclusive “or” rather than the exclusive or, and indicates at least one of, or any combination of items it conjoins.

[0158] It should be understood that the terms “a” and “an” as used above and elsewhere herein refer to “one or more” of the enumerated components. It will be clear to one of ordinary skill in the art that the use of the singular includes the plural unless specifically stated otherwise. Therefore, the terms “a”, “an” and “at least one” are used interchangeably in this application.

[0159] For purposes of better understanding the present teachings and in no way limiting the scope of the teachings, unless otherwise indicated, all numbers expressing quantities, percentages or proportions, and other numerical values used in the specification and claims, are to be understood as being modified in all instances by the term “about.” Accordingly, unless indicated to the contrary, the numerical parameters set forth in the following specification and attached claims are approximations that may vary depending upon the desired properties sought to be obtained. At the very least, each numerical parameter should at least be construed in light of the number of reported significant digits and by applying ordinary rounding techniques.

[0160] In the description and claims of the present application, each of the verbs, “comprise”, “include” and “have” and conjugates thereof, are used to indicate that the object or objects of the verb are not necessarily a complete listing of components, elements or parts of the subject or subjects of the verb.

[0161] Other terms as used herein are meant to be defined by their well-known meanings in the art.

[0162] Unless specifically stated or obvious from context, as used herein, the term "or" is understood to be inclusive.

[0163] Throughout this specification and claims, the word “comprise” or variations such as “comprises” or “comprising,” indicate the inclusion of any recited integer or group of integers but not the exclusion of any other integer or group of integers.

[0164] As used herein, the term “consists essentially of’, or variations such as “consist essentially of’ or “consisting essentially of’ as used throughout the specification and claims, indicate the inclusion of any recited integer or group of integers, and the optional inclusion of any recited integer or group of integers that do not materially change the basic or novel properties of the specified method, structure, or composition.

[0165] As used herein, the terms "comprises", "comprising", "containing", "having" and the like can mean "includes", "including", and the like; "consisting essentially of or "consists essentially" likewise has the meaning ascribed in U.S. patent law and the term is open-ended, allowing for the presence of more than that which is recited so long as basic or novel characteristics of that which is recited is not changed by the presence of more than that which is recited, but excludes prior art embodiments. In one embodiment, the terms "comprises", "comprising", "having" are / is interchangeable with "consisting".

[0166] Additional objects, advantages, and novel features of the present invention will become apparent to one ordinarily skilled in the art upon examination of the following examples, which are not intended to be limiting. Additionally, each of the various embodiments and aspects of the present invention as delineated hereinabove and as claimed in the claims section below finds experimental support in the following examples.EXAMPLES

[0167] Generally, the nomenclature used herein, and the laboratory procedures utilized in the present invention include chemical, molecular, biochemical, computational, statistics and cell biology techniques. Such techniques are thoroughly explained in the literature. See, for example, "Molecular Cloning: A laboratory Manual" Sambrook et al., (1989); "Current Protocols in Molecular Biology" Volumes I-III Ausubel, R. M., ed. (1994); "Cell Biology: A Laboratory Handbook", Volumes I-III Cellis, J. E., ed. (1994); The Organic Chemistry of Biological Pathways by John McMurry and Tadhg Begley (Roberts and Company, 2005); Organic Chemistry of Enzyme-Catalyzed Reactions by Richard Silverman (Academic Press,2002); Organic Chemistry (6thEdition) by Leroy "Skip" G Wade; Organic Chemistry by T. W. Graham Solomons and, Craig Fryhle.

[0168] The inventors are developing a microbiome platform designed for both diagnostics and treatment. This system can be segmented into three primary components. The first is the sensing bacterial strain, which serves as a sender to communicate with other parts of the synthetic microbiome. This strain has the ability to detect biomarkers relevant to the host's disease state within the physiological dynamic range.

[0019] The second component is the responder strain. This strain is capable of recognizing signaling molecules from the sender strain, and in response can controllably activate a drugproducing biosynthetic pathway within itself.

[0170] The third component involves the integration and quorum sensing -based communication between the members of the consortium. This sophisticated interaction ensures coordinated functioning among the different bacterial strains, enhancing the overall efficacy of the diagnostic and therapeutic processes.

[0171] Firstly, the inventors show the sender results. The inventors used previously published designs and checked them on the DSS-induced germ-free (GF) murine models versus non-induced ones (Fig. 2). In Fig. 3, the inventors demonstrate the capabilities of the current L-Lactate sensor. This sensor operates effectively within a realistic concentration range in vitro using the MG1655 strain. In Fig. 4, the inventors present the finalized model for the herein disclosed butyrate production system. The strain, NOM006, was tested both in vitro and in vivo to verify its production capabilities. In Fig. 5 the inventors demonstrate the protocol and results of in vivo GF non-induced murine model experiment, showing significant butyrate production upon supplementation of the inducer. In Fig. 6 the inventors show the same implementation as in Fig. 6 but in a DSS-induced IBD murine model. Notably, clear therapeutic effects, e.g., reduced calprotectin levels, increased body weight (or inhibition of body weight loss), normal intestine histopathology.

[0172] While the present invention has been particularly described, persons skilled in the art will appreciate that many variations and modifications can be made. Therefore, the invention is not to be construed as restricted to the particularly described embodiments, and the scopeand concept of the invention will be more readily understood by reference to the claims, which follow.

Claims

CLAIMSWhat is claimed:

1. A system for diagnosing, treating, or both, a condition or a disease associated therewith, in a subject in need thereof, the system comprising:(a) a first recombinant cell comprising at least one first exogenous DNA molecule comprising at least one first promoter and at least one first nucleic acid sequence encoding a detectable polypeptide, at least one first enzyme synthesizing a cell communication molecule, or both, and being operably linked to said at least one first promoter, and wherein said at least one first promoter is responsive to a biomarker of said condition or disease; and(b) a second recombinant cell comprising at least one second exogenous DNA molecule comprising at least one second promoter and at least one nucleic acid sequence encoding at least one second enzyme synthesizing a therapeutic molecule alleviating said condition or disease and being operably linked to said at least one second promoter, and wherein said at least one second promoter is responsive to said cell communication molecule.

2. The system of claim 1, wherein any one of said at least one first promoter and said at least one second promoter is directly or indirectly responsive to said biomarker and said cell communication molecule, respectively.

3. The system of claim 1 or 2, wherein said detectable polypeptide, said at least one first enzyme, or both, is expressed upon activation of said at least one first promoter.

4. The system of any one of claims 1 to 3, wherein said at least one second enzyme is expressed upon activation of said at least one second promoter.

5. The system of any one of claims 1 to 4, wherein any one of said at least one first promoter, said at least one second promoter, and both, comprise a plurality of promoters.

6. The system of any one of claims 1 to 5, wherein any one of said at least one first enzyme, said at least one second enzyme, and both, comprise a plurality of enzymes.

7. The system of any one of claims 1 to 6, wherein said at least one first exogenous DNA molecule comprises at least one second nucleic acid sequence encoding at least onepolypeptide capable of transporting said biomarker into said first recombinant cell, binding said biomarker in said first recombinant cell, or both.

8. The system of any one of claims 1 to 7, wherein said biomarker is derived, produced, secreted, or any combination thereof, by said subject.

9. The system of any one of claims 1 to 8, wherein said first recombinant cell, said second recombinant cell, or both, is a prokaryote cell or a eukaryote cell.

10. The system of any one of claims 1 to 9, wherein both said first recombinant cell and said second recombinant cell are recombinant bacterial cells.

11. The system of any one of claim 1 to 10, wherein said at least one first promoter comprises a primary first promoter and a secondary first promoter.

12. The system of claim 11, wherein said primary first promoter controls or regulates expression / transcription of said at least one second nucleic acid sequence.

13. The system of claim 12, wherein said at least one second nucleic acid sequence is encoding a first polypeptide being a transporter of said biomarker and a second polypeptide being a repressor of said secondary first promoter.

14. The system of any one of claims 11 to 13, wherein said secondary first promoter controls or regulates expression / transcription of said at least one first nucleic acid sequence.

15. The system of claim 13 or 14, wherein binding of said biomarker to said second polypeptide being a repressor activates said secondary first promoter such that said detectable polypeptide, at least one first enzyme synthesizing a cell communication molecule, or both, are produced by said first recombinant cell.

16. The system of claim 11 or 12, wherein said at least one second nucleic acid sequence is encoding a polypeptide being a transcription factor responsive to said biomarker.

17. The system of claim 16, wherein binding of said biomarker to said polypeptide being a transcription factor responsive to said biomarker activates said secondary first promoter such that said detectable polypeptide, at least one first enzyme synthesizing a cell communication molecule, or both, are produced by said first recombinant cell.

18. The system of any one of claims 1 to 17, wherein said at least one second promoter comprises a primary second promoter, a secondary second promoter, and a tertiary second promoter.

19. The system of claim 18, wherein said primary second promoter and said tertiary second promoter control or regulate expression / transcription of said at least one nucleic acid sequence encoding at least two second enzymes of said plurality of enzymes synthesizing said therapeutic molecule alleviating said condition or disease.

20. The system of claim 18 or 19, wherein said secondary second promoter controls or regulates expression of a nucleic acid sequence encoding a polypeptide being a transcription factor capable of activating said tertiary second promoter.

21. The system of any one of claims 18 to 20, wherein binding of said cell communication molecule to a cytoplasmic receptor in said second recombinant cell activates said tertiary second promoter such that said therapeutic molecule alleviating said condition or disease is synthesized by said second recombinant cell.

22. The system of any one of claims 1 to 21, wherein said biomarker is selected from the group consisting of: heme, L-lactate, hydrogen peroxide, and any combination thereof.

23. The system of any one of claims 1 to 22, wherein said cell communication molecule is a quorum sensing signaling molecule.

24. The system of claim 23, wherein said quorum sensing signaling molecule is an N- acyl homoserine lactone (AHL).

25. The system of any one of claims 1 to 24, wherein said therapeutic molecule is a shortchain fatty acid (SCFA).

26. The system of claim 25, wherein said SCFA is butyrate.

27. The system of any one of claims 1 to 26, wherein said condition is inflammation.

28. The system of claim 27, wherein the disease associated with said inflammation is an autoimmune disease.

29. The system of claim 28, wherein said autoimmune disease is an inflammatory bowel disease (IBD).

30. The system of any one of claims 1 to 29, wherein any one of said at least one first exogenous DNA molecule, said at least one second exogenous DNA molecule, and both, are integrated in a vector or a plasmid.

31. The system of claim 30, wherein said vector or plasmid being introduced into any one of said first recombinant cell, said second recombinant cell, and both.

32. A composition comprising the system of any one of claims 1 to 31, and an acceptable carrier.

33. The composition of claim 32, being a pharmaceutical composition.

34. The pharmaceutical composition of claim 33, for use in diagnosis, treatment, or both, of a condition or a disease associated therewith, in a subject in need thereof.

35. The pharmaceutical composition for use according to claim 34, wherein said condition is inflammation.

36. The pharmaceutical composition for use according to claim 35, wherein the disease associated with said inflammation is an autoimmune disease.

37. The pharmaceutical composition for use according to claim 36, wherein said autoimmune disease is IBD.

38. A method for diagnosing, treating, or both, a condition or a disease associated therewith, in a subject in need thereof, the method comprising administering to said subject a therapeutically effective amount of the pharmaceutical composition of claim 33, thereby diagnosing, treating, or both, the condition or the disease associated therewith, in a subject.

39. The method of claim 38, wherein said pharmaceutical composition is formulated for any one of oral delivery and colonic delivery.

40. The method of claim 38 or 39, wherein said administering is enterally administering.

41. The method of claim 40, wherein said condition is inflammation.

42. The method of claim 41 , wherein the disease associated with said inflammation is an autoimmune disease.

43. The method of claim 42, wherein said autoimmune disease is IBD.

44. The method of any one of claims 38 to 43, further comprising a step comprising determining the abundance of said detectable polypeptide in said subject or sample derived therefrom, wherein an abundance above a predetermined threshold of said detectable polypeptide in said subject or said sample derived therefrom is indicative of said subject being afflicted with said condition or the disease associated therewith.

45. The method of any one of claims 38 to 44, further comprising administering to said subject a therapeutically effective amount of an anti-inflammatory drug.

46. A kit comprising:(a) a first recombinant cell comprising at least one first exogenous DNA molecule comprising at least one first promoter and at least one first nucleic acid sequence encoding a detectable polypeptide, at least one first enzyme synthesizing a cell communication molecule, or both, and being operably linked to said at least one first promoter, and wherein said at least one first promoter is responsive to a biomarker of said condition or disease; and(b) a second recombinant cell comprising at least one second exogenous DNA molecule comprising at least one second promoter and at least one nucleic acid sequence encoding at least one second enzyme synthesizing a therapeutic molecule alleviating said condition or disease and being operably linked to said at least one second promoter, and wherein said at least one second promoter is responsive to said cell communication molecule.

47. The kit of claim 46, further comprising instruction for administering said first recombinant cell and said second recombinant cell to a subject in need thereof.

48. The kit of claim 47, wherein said administering is sequentially administering or simultaneously administering.

49. The kit of any one of claims 46 to 48, for diagnosing, treating, or both, a condition or a disease associated therewith, in a subject in need thereof.

50. The kit of claim 49, wherein said diagnosing is in a sample obtained or derived from said subject.

51. The kit of claim 50, wherein said diagnosing is in vitro or ex vivo.

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