# US 2023/0272016 A1 · Peptides for immunotherapy > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2023/0272016 A1 - Document ID: US20230272016A1 - Status: Published application - Kind: A1 - Application number: 18/009,045 - Filed: 2021-06-04 - Published: 2023-08-31 - Earliest claimed: 2020-06-08 - Assignees: Second Genome, Inc. - Applicants: Second Genome, Inc. - Inventors: Bum-Yeol Hwang; Michi Izumi Willcoxon; Helena Kiefel; Toshihiko Takeuchi; Dhwani Haria; Michelle Lin; Roberta L. Hannibal; Joanna Catherine Ceolane Dreux; Jayamary Divya Ravichandar - Web page: https://patentgrep.com/patent/US20230272016A1 ## CPC - C07K 14/195: from bacteria - A61K 39/395: Antibodies (agglutinins A61K38/36 {; as drug carriers A61K47/50}); Immunoglobulins; Immune serum, e.g. antilymphocytic serum - A61P 35/00: Antineoplastic agents - A61P 35/04: specific for metastasis - C07K 16/2818: {against CD28 or CD152} - G01N 33/56911: {Bacteria} - G01N 33/5758: {involving compounds serving as markers for tumours, cancers or neoplasias, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides or metabolites} - C12N 2510/02: Cells for production - G01N 2333/90206: acting on the CH-CH group of donors (1.3) - G01N 2333/988: Lyases (4.), e.g. aldolases, heparinase, enolases, fumarase - G01N 2800/52: Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis - C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00) - A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D) - A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS - G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q) - C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00) ## Abstract The disclosure provides peptides and pharmaceutical compositions thereof. Such peptides can be useful, for example, in treating various human diseases such as immunological diseases. In some embodiments, the peptides are useful as immunotherapeutics for modulating regulatory and effector molecules of the mammalian immune system. ## Claims ### Claim 1 A method for identifying a subject as having a decreased likelihood of positively responding to treatment with an immunomodulator, the method comprising: identifying a subject having a sample that has one or more of: (i) a decreased level of the expression of dgoD, graR, or both relative to the same in a reference sample; (ii) a decreased level of activity of a trans-2-enoyl-CoA reductase, an Acinetobacter tetrose transporter, or both relative to the same in a reference sample; (iii) a decreased flux through the B-ureidopropionase reaction relative to the same in a reference sample; as having a decreased likelihood of having a positive response to treatment with an immunomodulator. ### Claim 2 (depends on 1) The method of claim 1, wherein the method further comprises identifying the subject having a sample that has an increased level of one or more bacterial species selected from the group consisting of: Clostridium clostridioforme, Prevotella sp., Streptococcus parasanguinis, Anaerostipes hadrus, Parasutterella excrementihominis, and Eisenbergiella massiliensis relative to the same in a reference sample. ### Claim 3 (depends on 1) The method of claim 1, wherein the method further comprises identifying the subject having a sample that has a decreased level of one or more bacterial species selected from the group consisting of: Bifidobacterium sp., Collinsella sp., Methanobrevibacter smithii, Oscillibacter sp., Faecalibacterium prausnitzii C, Faecalibacterium prausnitzii I, Intestinimonas timonensis, Faecalibacterium prausnitzii, Bacteroides caccae, Barnesiella intestinihominis, Clostridiaceae bacterium, Clostridium sp., and Bifidobacterium adolescentis relative to the same in a reference sample ### Claim 4 A method for identifying a subject as having an increased likelihood of having a positive response to treatment with an immunomodulator, the method comprising: identifying a subject having a sample that has one or more of: (i) an increased level of the expression of dgoD, graR, or both relative to the same in a reference sample; (ii) an increased level of activity of a trans-2-enoyl-CoA reductase, an Acinetobacter tetrose transporter, or both relative to the same in a reference sample; (iii) an increased flux through the B-ureidopropionase reaction relative to the same in a reference sample; as having an increased likelihood of having a positive response to treatment with an immunomodulator. ### Claim 5 (depends on 4) The method of claim 4, wherein the method further comprises identifying the subject having a sample that has a decreased level of one or more bacterial species selected from the group consisting of: Clostridium clostridioforme, Prevotella sp., Streptococcus parasanguinis, Anaerostipes hadrus, Parasutterella excrementihominis, and Eisenbergiella massiliensis relative to the same in a reference sample. ### Claim 6 (depends on 4) The method of claim 4, wherein the method further comprises identifying the subject having a sample that has an increased level of one or more bacterial species selected from the group consisting of: Bifidobacterium sp., Collinsella sp., Methanobrevibacter smithii, Oscillibacter sp., Faecalibacterium prausnitzii C, Faecalibacterium prausnitzii I, Intestinimonas timonensis, Faecalibacterium prausnitzii, Bacteroides caccae, Barnesiella intestinihominis, Clostridiaceae bacterium, Clostridium sp., and Bifidobacterium adolescentis relative to the same in a reference sample ### Claim 7 (depends on 1, 2, 3, 4, 5, 6) The method of any one of claims 1-6, wherein the immunomodulator is an immune checkpoint inhibitor selected from the group consisting of: ipilimumab, nivolumab, pembrolizumab, atezolizumab, avelumab, durvalumab, cemiplimab, and a combination thereof. ### Claim 8 (depends on 1, 2, 3, 4, 5, 6, 7) The method of any one of claims 1-7, wherein the immunomodulator is a co-stimulatory immune checkpoint agent selected from the group consisting of: IBI101, utomilumab, MEDI1873, and a combination thereof. ### Claim 9 (depends on 1, 2, 3, 4, 5, 6, 7, 8) The method of any one of claims 1-8, wherein the cell therapy is a CAR T cell therapy. ### Claim 10 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9) The method of any one of claims 1-9, wherein the immunomodulator targets one or more of: CTLA-4, PD-1, PD-L1, BTLA, LAG-3, A2AR, TIM-3, B7-H3, VISTA, IDO, OX40, 4-1BB, and GITR. ### Claim 11 A peptide comprising an amino acid sequence having at least 60% sequence identity to SEQ ID NO: 1. ### Claim 12 (depends on 11) The peptide of claim 11, wherein the peptide comprises an amino acid sequence having at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity to SEQ ID NO: 1. ### Claim 13 (depends on 11) The peptide of claim 11, wherein the peptide comprises the amino acid sequence of SEQ ID NO: 1. ### Claim 14 A peptide comprising the amino acid sequence of SEQ ID NO: 1, or a variant thereof comprising one to 15 amino acid substitutions. ### Claim 15 (depends on 11, 12, 13, 14) The peptide of any one of claims 11-14, wherein the methionine at position at 1 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: W, F, V, P, K, R, and S. ### Claim 16 (depends on 11, 12, 13, 14, 15) The peptide of any one of claims 11-15, wherein the leucine at position at 2 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: S, P, G, T, V, A, K, Q, R, W, Y, F, and N. ### Claim 17 (depends on 11, 12, 13, 14, 15, 16) The peptide of any one of claims 11-16, wherein the serine at position at 3 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: Q and R. ### Claim 18 (depends on 11, 12, 13, 14, 15, 16, 17) The peptide of any one of claims 11-17, wherein the threonine at position at 4 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: G, A, and R. ### Claim 19 (depends on 11, 12, 13, 14, 15, 16, 17, 18) The peptide of any one of claims 11-18, wherein the lysine at position at 5 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: A and R. ### Claim 20 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19) The peptide of any one of claims 11-19, wherein the lysine at position at 6 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: R, T, and A. ### Claim 21 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20) The peptide of any one of claims 11-20, wherein the threonine at position at 7 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: G, K, and R. ### Claim 22 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21) The peptide of any one of claims 11-21, wherein the threonine at position at 9 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: W and R. ### Claim 23 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22) The peptide of any one of claims 11-22, wherein the histidine at position at 10 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: K and R. ### Claim 24 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23) The peptide of any one of claims 11-23, wherein the aspartic acid at position at 11 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: F, G, H, I, K, P, R, T, V, W, and Y. ### Claim 25 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24) The peptide of any one of claims 11-24, wherein the histidine at position at 12 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: K and R. ### Claim 26 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25) The peptide of any one of claims 11-25, wherein the tyrosine at position at 13 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: W, N, G, K, R, and W. ### Claim 27 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26) The peptide of any one of claims 11-26, wherein the proline at position at 14 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: G and W. ### Claim 28 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) The peptide of any one of claims 11-27, wherein the serine at position at 15 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: G and R. ### Claim 29 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28) The peptide of any one of claims 11-28, wherein the methionine at position at 18 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: W, H, Y, G, and R. ### Claim 30 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29) The peptide of any one of claims 11-29, wherein the aspartic acid at position at 20 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: P and R. ### Claim 31 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30) The peptide of any one of claims 11-30, wherein the proline at position at 21 of SEQ ID NO:1 is F. ### Claim 32 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31) The peptide of any one of claims 11-31, wherein the glycine at position at 22 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: P, K, and W. ### Claim 33 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32) The peptide of any one of claims 11-32, wherein the aspartic acid at position at 25 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: P and R. ### Claim 34 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33) The peptide of any one of claims 11-33, wherein the arginine at position at 27 of SEQ ID NO:1 is W. ### Claim 35 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34) The peptide of any one of claims 11-34, wherein the alanine at position at 28 of SEQ ID NO:1 is substituted with an amino acid selected from the group consisting of: F, G, V, Y, and W. ### Claim 36 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35) The peptide of any one of claims 11-35, wherein the serine at position at 29 of SEQ ID NO:1 is substituted with R. ### Claim 37 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36) The peptide of any one of claims 11-36, wherein the peptide comprises an amino acid sequence selected from the group consisting of: SEQ ID NOs: 2-35. ### Claim 38 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37) The peptide of any one of claims 11-37, wherein the peptide comprises an amino acid sequence selected from the group consisting of: SEQ ID NOs: 36-93. ### Claim 39 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38) The peptide of any one of claims 11-38, wherein the peptide comprises an amino acid sequence selected from the group consisting of: SEQ ID NOs: 94-114. ### Claim 40 A peptide comprising the amino acid sequence set forth in, X1X2SX4AKX7KX8HDHX12X13X14GRX15RX16PX18WHDWX20X21X22 (SEQ ID NO:115), wherein each of X1-X22 is independently selected from any naturally occurring amino acid. ### Claim 41 (depends on 180) The peptide of claim 180, wherein X1 is an amino acid selected from the group consisting of: M, W, F, V, and P. ### Claim 42 (depends on 40, 41) The peptide of any one of claims 40-41, wherein X2 is an amino acid selected from the group consisting of: L, S, P, G, T, V, and A. ### Claim 43 (depends on 40, 41, 42) The peptide of any one of claims 40-42, wherein X4 is an amino acid selected from the group consisting of: T, G, and A. ### Claim 44 (depends on 40, 41, 42, 43) The peptide of any one of claims 40-43, wherein X7 is an amino acid selected from the group consisting of: G and T. ### Claim 45 (depends on 40, 41, 42, 43, 44) The peptide of any one of claims 40-44, wherein X8 is an amino acid selected from the group consisting of: T and W. ### Claim 46 (depends on 40, 41, 42, 43, 44, 45) The peptide of any one of claims 40-45, wherein X12 is an amino acid selected from the group consisting of: Y, W, and N. ### Claim 47 (depends on 40, 41, 42, 43, 44, 45, 46) The peptide of any one of claims 40-46, wherein X13 is an amino acid selected from the group consisting of: P, G, and W. ### Claim 48 (depends on 40, 41, 42, 43, 44, 45, 46, 47) The peptide of any one of claims 40-47, wherein X14 is an amino acid selected from the group consisting of: S and G. ### Claim 49 (depends on 40, 41, 42, 43, 44, 45, 46, 47, 48) The peptide of any one of claims 40-48, wherein X15 is an amino acid selected from the group consisting of: M, W, H, and Y. ### Claim 50 (depends on 40, 41, 42, 43, 44, 45, 46, 47, 48, 49) The peptide of any one of claims 40-49, wherein X16 is an amino acid selected from the group consisting of: D and P. ### Claim 51 (depends on 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50) The peptide of any one of claims 40-50, wherein X18 is an amino acid selected from the group consisting of: G, P, and K. ### Claim 52 (depends on 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51) The peptide of any one of claims 40-51, wherein X20 is an amino acid selected from the group consisting of: R and W. ### Claim 53 (depends on 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52) The peptide of any one of claims 40-52, wherein X21 is an amino acid selected from the group consisting of: A, F, G, and V. ### Claim 54 (depends on 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53) The peptide of any one of claims 40-53, wherein X22 is an amino acid selected from the group consisting of: R and W. ### Claim 55 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54) The peptide of any one of claims 11-54, wherein the peptide increases activity of a CD2 protein, a BST2 protein, or a TNF protein. ### Claim 56 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54) The peptide of any one of claims 11-54, wherein the peptide binds to a CD2 protein, a BST2 protein, or a TNF protein. ### Claim 57 A peptide comprising an amino acid sequence having at least 60% sequence identity to SEQ ID NO: 117 or SEQ ID NO: 162. ### Claim 58 (depends on 57) The peptide of claim 57, wherein the peptide comprises an amino acid sequence having at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity to SEQ ID NO: 117 or SEQ ID NO: 162. ### Claim 59 (depends on 57) The peptide of claim 57, wherein the peptide comprises the amino acid sequence of SEQ ID NO: 117 or SEQ ID NO: 162. ### Claim 60 (depends on 57, 58, 59) The peptide of any one of claims 57-59, wherein the peptide comprises an amino acid sequence selected from the group consisting of: SEQ ID NOs: 117-160. ### Claim 61 A peptide comprising the amino acid sequence set forth in, X1KX3X4X5SVKX9X10CX12X13CX14X15X16IXBRX20GX22X23X24X25IX27X28X29PX31HKQX35QX37 (SEQ ID NO:161), wherein X1 is optional, each of X2-X25 and X28-X35 is independently a naturally occurring amino acid, X27 is selected from the group consisting of C and CP; and X37 is selected from the group consisting of: G, GN, and DRH. ### Claim 62 (depends on 61) The peptide of claim 61, wherein X1 is the amino acid M. ### Claim 63 (depends on 61, 62) The peptide of any one of claims 61-62, wherein X3 is an amino acid selected from the group consisting of: V, I, and T. ### Claim 64 (depends on 61, 62, 63) The peptide of any one of claims 61-63, wherein X4 is an amino acid selected from the group consisting of: R, K, and Q. ### Claim 65 (depends on 61, 62, 63, 64) The peptide of any one of claims 61-64, wherein X5 is an amino acid selected from the group consisting of: P, S, and A. ### Claim 66 (depends on 61, 62, 63, 64, 65) The peptide of any one of claims 61-65, wherein X9 is an amino acid selected from the group consisting of: P, T, and K. ### Claim 67 (depends on 61, 62, 63, 64, 65, 66) The peptide of any one of claims 61-66, wherein X10 is an amino acid selected from the group consisting of: M and I. ### Claim 68 (depends on 61, 62, 63, 64, 65, 66, 67) The peptide of any one of claims 61-67, wherein X12 is an amino acid selected from the group consisting of: E and D. ### Claim 69 (depends on 61, 62, 63, 64, 65, 66, 67, 68) The peptide of any one of claims 61-68, wherein X13 is an amino acid selected from the group consisting of: K and Y. ### Claim 70 (depends on 61, 62, 63, 64, 65, 66, 67, 68, 69) The peptide of any one of claims 61-69, wherein X15 is an amino acid selected from the group consisting of: K and R. ### Claim 71 (depends on 61, 62, 63, 64, 65, 66, 67, 68, 69, 70) The peptide of any one of claims 61-70, wherein X16 is an amino acid selected from the group consisting of: V and I. ### Claim 72 (depends on 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71) The peptide of any one of claims 61-71, wherein X18 is an amino acid selected from the group consisting of: K and R. ### Claim 73 (depends on 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72) The peptide of any one of claims 61-72, wherein X20 is an amino acid selected from the group consisting of: K, N, and H. ### Claim 74 (depends on 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73) The peptide of any one of claims 61-73, wherein X22 is an amino acid selected from the group consisting of: R, K, H, S, and I. ### Claim 75 (depends on 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74) The peptide of any one of claims 61-74, wherein X23 is an amino acid selected from the group consisting of: V and I. ### Claim 76 (depends on 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75) The peptide of any one of claims 61-75, wherein X24 is an amino acid selected from the group consisting of: M, R, A, and L. ### Claim 77 (depends on 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76) The peptide of any one of claims 61-76, wherein X25 is an amino acid selected from the group consisting of: V and I. ### Claim 78 (depends on 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77) The peptide of any one of claims 61-77, wherein X28 is selected from the group consisting of: E, Q, A, and T. ### Claim 79 (depends on 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78) The peptide of any one of claims 61-78, wherein X29 is an amino acid selected from the group consisting of: N and E. ### Claim 80 (depends on 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79) The peptide of any one of claims 61-79, wherein X31 is an amino acid selected from the group consisting of: K and R. ### Claim 81 (depends on 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80) The peptide of any one of claims 61-80, wherein X35 is an amino acid selected from the group consisting of: K and R. ### Claim 82 (depends on 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81) The peptide of any one of claims 57-81, wherein the peptide modulates activity of a CCR9 protein, a CHRM5 protein, a CXCR3 protein, a CXCR4 protein, a HCRTR2 protein, a MRGPRX2 protein, a SSTR1 protein, or a TSHR(L) protein. ### Claim 83 (depends on 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81) The peptide of any one of claims 57-81, wherein the peptide binds to a CCR9 protein, a CHRM5 protein, a CXCR3 protein, a CXCR4 protein, a HCRTR2 protein, a MRGPRX2 protein, a SSTR1 protein, or a TSHR(L) protein. ### Claim 84 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83) A recombinant host cell comprising an exogenous polynucleotide, the polynucleotide encoding a peptide of any one of claims 11-83. ### Claim 85 (depends on 84) The recombinant host cell of claim 84, wherein the exogenous polynucleotide further encodes a host cell specific signal sequence. ### Claim 86 (depends on 84, 85) The recombinant host cell of claim 84 or claim 85, wherein the exogenous polynucleotide further encodes a heterologous promoter. ### Claim 87 (depends on 86) The recombinant host cell of claim 86, wherein the heterologous promoter is a constitutive promoter. ### Claim 88 (depends on 86) The recombinant host cell of claim 86, wherein the heterologous promoter is an inducible promoter. ### Claim 89 (depends on 84, 85, 86, 87, 88) The recombinant host cell of any one of claims 84-88, wherein the host cell is a prokaryotic cell, a eukaryotic cell, or a fungal cell. ### Claim 90 (depends on 89) The recombinant host cell of claim 89, wherein the host cell is selected from the group consisting of: an Escherichia coli cell, a Lactococcus lactis cell, a Streptomyces coelicolor cell, a Streptomyces lividans cell, a Streptomyces albus cell, a Streptomyces venezuelae cell, or a Bacillus subtilis cell. ### Claim 91 (depends on 89) The recombinant host cell of claim 89, wherein the host cell is a Saccharomyces cerevisiae cell, a Pichia pastoris cell, a Yarrowia lipolytica cell, an Aspergillus niger cell, or a Hansenula polymorpha cell. ### Claim 92 (depends on 89) The recombinant host cell of claim 89, wherein the host cell is a Chinese Hamster Ovary cell. ### Claim 93 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92) A pharmaceutical composition comprising: (a) a peptide of any one of claims 11-83; or a plurality of recombinant host cells of any one of claims 84-92; and (b) a pharmaceutically acceptable carrier. ### Claim 94 (depends on 93) The pharmaceutical composition of claim 93, wherein the pharmaceutical composition further comprises a therapeutically effective amount of a bacterial species selected from the group consisting of: Bifidobacterium sp., Collinsella sp., Methanobrevibacter smithii, Oscillibacter sp., Barnesiella intestinihominis, Faecalibacterium prausnitzii C, Faecalibacterium prausnitzii I, Ruminococcaceae bacterium, Intestinimonas timonensis, Faecalibacterium prausnitzii, Bacteroides caccae, Clostridiaceae bacterium, Clostridium sp., Bifidobacterium adolescentis, and a combination thereof. ### Claim 95 (depends on 93, 94) The pharmaceutical composition of claim 93 or claim 94, wherein the pharmaceutical composition is formulated for oral administration. ### Claim 96 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83) A nucleic acid construct comprising a polynucleotide, wherein the polynucleotide encodes a peptide of any one of claims 11-83. ### Claim 97 (depends on 84, 85, 86, 87, 88, 89, 90, 91, 92) A method of producing a peptide, the method comprising culturing the recombinant host cell of any one of claims 84-92, under conditions sufficient for expression of the encoded peptide. ### Claim 98 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96) A method for treating a disease in a subject in need thereof, the method comprising administering to the subject: (a) a peptide of any one of claims 11-83; (b) a recombinant host of any one of claims 84-92; (c) a pharmaceutical composition of any one of claim 93-95; or (d) a nucleic acid construct of claim 96. ### Claim 99 (depends on 98) The method of claim 98, wherein the peptide modulates the production of at least one cytokine in the subject. ### Claim 100 (depends on 98, 99) The method of claim 98 or claim 99, wherein the cytokine is selected from the group consisting of TNF-α, IL-17, IL-1β, IL-2, IFN-γ, IL-6, IL-12, IL-25, IL-33, IL-8, MCP-1, MIP-3α, CXCL1, IL-23, IL-4, IL-10, IL-13, IFN-α, and TGF-β. ### Claim 101 (depends on 98, 99, 100) The method of any one of claims 98-100, wherein the peptide induces the production of at least one pro-inflammatory cytokine in the subject. ### Claim 102 (depends on 101) The method of claim 101, wherein the at least one pro-inflammatory cytokine is selected from the group consisting of TNF-α, IL-17, IL-1β, IL-2, IFN-γ, IL-6, IL-12, IL-25, IL-33, IL-8, MCP-1, MIP-3α, CXCL1, and IL-23. ### Claim 103 (depends on 98, 99, 100) The method of any one of claims 98-100, wherein the peptide suppresses the production of at least one anti-inflammatory cytokine in the subject. ### Claim 104 (depends on 103) The method of claim 103, wherein the at least one anti-inflammatory cytokine is selected from the group consisting of IL-4, IL-10, IL-13, IFN-α, and TGF-β. ### Claim 105 (depends on 98, 99, 100, 101, 102, 103, 104) The method of any one of claims 98-104, wherein the peptide increases Th1 activation in the subject. ### Claim 106 (depends on 98, 99, 100, 101, 102, 103, 104, 105) The method of any one of claims 98-105, wherein the peptide increases dendritic cell maturation in the subject. ### Claim 107 (depends on 98, 99, 100, 101, 102, 103, 104, 105, 106) The method of any one of claims 98-106, wherein the peptide increases CD70 expression in the subject. ### Claim 108 (depends on 98, 99, 100, 101, 102, 103, 104, 105, 106, 107) The method of any one of claims 98-107, wherein the peptide increases the clonal expansion of Teff in the subject. ### Claim 109 (depends on 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108) The method of any one of claims 98-108, wherein the peptide increases activity of a CD2 protein, a BST2 protein, or a TNF protein. ### Claim 110 (depends on 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108) The method of any one of claims 98-108, wherein the peptide increases activity of a CXCL3 protein. ### Claim 111 (depends on 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108) The method of any one of claims 98-108, wherein the peptide binds to a CD2 protein, a BST2 protein, or a TNF protein. ### Claim 112 (depends on 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108) The method of any one of claims 98-108, wherein the peptide binds to a CXCL3 protein. ### Claim 113 (depends on 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112) The method of any one of claims 98-112, wherein the disease is a neoplasm. ### Claim 114 (depends on 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113) The method of any one of claims 98-113, wherein the disease is cancer. ### Claim 115 (depends on 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114) The method of any one of claims 98-114, wherein the disease is at least one selected from the group consisting of: basal cell carcinoma, biliary tract cancer, bladder cancer, bone cancer, brain and central nervous system cancer, breast cancer, cervical cancer, choriocarcinoma, colon and rectum cancer, connective tissue cancer, cancer of the digestive system, endometrial cancer, esophageal cancer, eye cancer, cancer of the head and neck, gastric cancer, intra-epithelial neoplasm, kidney cancer, larynx cancer, leukemia, liver cancer, small-cell lung cancer, non-small-cell lung cancer, Hodgkin's lymphoma, non-Hodgkins lymphoma, melanoma, myeloma, neuroblastoma, oral cavity cancer, ovarian cancer, pancreatic cancer, prostate cancer, retinoblastoma, rhabdomyosarcoma, rectal cancer, renal cancer, cancer of the respiratory system, sarcoma, skin cancer, stomach cancer, testicular cancer, thyroid cancer, uterine cancer, and cancer of the urinary system. ### Claim 116 (depends on 115) The method of claim 115, further comprising administering a treatment for cancer. ### Claim 117 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91) A method of treating cancer in a subject, the method comprising: (a) identifying a subject having a sample that has one or more of: (i) a decreased level of the expression of dgoD, graR, or both relative to the same in a reference sample; (ii) a decreased level of activity of a trans-2-enoyl-CoA reductase, an Acinetobacter tetrose transporter, or both relative to the same in a reference sample; (iii) a decreased flux through the B-ureidopropionase reaction relative to the same in a reference sample; (iv) an increased level of one or more bacterial species selected from the group consisting of: Clostridium clostridioforme, Prevotella sp., Streptococcus parasanguinis, Anaerostipes hadrus, Parasutterella excrementihominis, and Eisenbergiella massiliensis relative to the same in a reference sample; and (v) a decreased level of one or more bacterial species selected from the group consisting of: Bifidobacterium sp., Collinsella sp., Methanobrevibacter smithii, Oscillibacter sp., Faecalibacterium prausnitzii C, Faecalibacterium prausnitzii I, Intestinimonas timonensis, Faecalibacterium prausnitzii, Bacteroides caccae, Barnesiella intestinihominis, Clostridiaceae bacterium, Clostridium sp., and Bifidobacterium adolescentis relative to the same in a reference sample; and (b) administering a therapy to the identified subject, the therapy comprising a peptide of any one of claims 11-83 or a pharmaceutical composition thereof, or a recombinant host of any one of claims 84-91. ### Claim 118 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91) A method of treating cancer in a subject, the method comprising administering to a subject identified as having one or more of: (i) a decreased level of the expression of dgoD, graR, or both relative to the same in a reference sample; (ii) a decreased level of activity of a trans-2-enoyl-CoA reductase, an Acinetobacter tetrose transporter, or both relative to the same in a reference sample; (iii) a decreased flux through the B-ureidopropionase reaction relative to the same in a reference sample; (iv) an increased level of one or more bacterial species selected from the group consisting of: Clostridium clostridioforme, Prevotella sp., Streptococcus parasanguinis, Anaerostipes hadrus, Parasutterella excrementihominis, and Eisenbergiella massiliensis relative to the same in a reference sample; and (v) a decreased level of one or more bacterial species selected from the group consisting of: Bifidobacterium sp., Collinsella sp., Methanobrevibacter smithii, Oscillibacter sp., Faecalibacterium prausnitzii C, Faecalibacterium prausnitzii I, Intestinimonas timonensis, Faecalibacterium prausnitzii, Bacteroides caccae, Barnesiella intestinihominis, Clostridiaceae bacterium, Clostridium sp., and Bifidobacterium adolescentis relative to the same in a reference sample a therapy comprising a peptide of any one of claims 11-83 or a pharmaceutical composition thereof, or a recombinant host of any one of claims 84-91. ### Claim 119 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91) A method of treating a cancer in a subject that has previously received one or more doses of an immunomodulator, wherein the method comprises administering to a subject identified as having one or more of: (i) a decreased level of the expression of dgoD, graR, or both relative to the same in a reference sample; (ii) a decreased level of activity of a trans-2-enoyl-CoA reductase, an Acinetobacter tetrose transporter, or both relative to the same in a reference sample; (iii) a decreased flux through the B-ureidopropionase reaction relative to the same in a reference sample; (iv) an increased level of one or more bacterial species selected from the group consisting of: Clostridium clostridioforme, Prevotella sp., Streptococcus parasanguinis, Anaerostipes hadrus, Parasutterella excrementihominis, and Eisenbergiella massiliensis relative to the same in a reference sample; and (v) a decreased level of one or more bacterial species selected from the group consisting of: Bifidobacterium sp., Collinsella sp., Methanobrevibacter smithii, Oscillibacter sp., Faecalibacterium prausnitzii C, Faecalibacterium prausnitzii I, Intestinimonas timonensis, Faecalibacterium prausnitzii, Bacteroides caccae, Barnesiella intestinihominis, Clostridiaceae bacterium, Clostridium sp., and Bifidobacterium adolescentis relative to the same in a reference sample a therapy comprising a peptide of any one of claims 11-83 or a pharmaceutical composition thereof, or a recombinant host of any one of claims 84-91. ### Claim 120 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91) A method of treating cancer in a subject, the method comprising: (a) administering to the subject one or more doses of an immunomodulator for a period of time; (b) after (a), determining if a sample obtained from the subject has one or more of: (i) a decreased level of the expression of dgoD, graR, or both relative to the same in a reference sample; (ii) a decreased level of activity of a trans-2-enoyl-CoA reductase, an Acinetobacter tetrose transporter, or both relative to the same in a reference sample; (iii) a decreased flux through the B-ureidopropionase reaction relative to the same in a reference sample; (iv) an increased level of one or more bacterial species selected from the group consisting of: Clostridium clostridioforme, Prevotella sp., Streptococcus parasanguinis, Anaerostipes hadrus, Parasutterella excrementihominis, and Eisenbergiella massiliensis relative to the same in a reference sample; and (v) a decreased level of one or more bacterial species selected from the group consisting of: Bifidobacterium sp., Collinsella sp., Methanobrevibacter smithii, Oscillibacter sp., Faecalibacterium prausnitzii C, Faecalibacterium prausnitzii I, Intestinimonas timonensis, Faecalibacterium prausnitzii, Bacteroides caccae, Barnesiella intestinihominis, Clostridiaceae bacterium, Clostridium sp., and Bifidobacterium adolescentis relative to the same in a reference sample; and (c) administering a therapy to the identified subject, the therapy comprising a peptide of any one of claims 11-83 or a pharmaceutical composition thereof, or a recombinant host of any one of claims 84-91. ### Claim 121 (depends on 12) The method of claim 12, further comprising administering a treatment for cancer. ### Claim 122 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91) A method of treating cancer in a subject, the method comprising: (a) administering to the subject one or more doses of an immunomodulator for a period of time; (b) after (a), identifying a subject having a sample that has one or more of: (i) an increased level of the expression of dgoD, graR, or both relative to the same in a reference sample; (ii) an increased level of activity of a trans-2-enoyl-CoA reductase, an Acinetobacter tetrose transporter, or both relative to the same in a reference sample; (iii) an increased flux through the B-ureidopropionase reaction relative to the same in a reference sample; (iv) a decreased level of one or more bacterial species selected from the group consisting of: Clostridium clostridioforme, Prevotella sp., Streptococcus parasanguinis, Anaerostipes hadrus, Parasutterella excrementihominis, and Eisenbergiella massiliensis relative to the same in a reference sample; and (v) an increased level of one or more bacterial species selected from the group consisting of: Bifidobacterium sp., Collinsella sp., Methanobrevibacter smithii, Oscillibacter sp., Faecalibacterium prausnitzii C, Faecalibacterium prausnitzii I, Intestinimonas timonensis, Faecalibacterium prausnitzii, Bacteroides caccae, Barnesiella intestinihominis, Clostridiaceae bacterium, Clostridium sp., and Bifidobacterium adolescentis relative to the same in a reference sample; and (c) administering a therapy to the identified subject, the therapy comprising a peptide of any one of claims 11-83 or a pharmaceutical composition thereof, or a recombinant host of any one of claims 84-91. ### Claim 123 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91) A method of treating cancer in a subject, the method comprising administering to a subject identified as having one or more of: (i) an increased level of the expression of dgoD, graR, or both relative to the same in a reference sample; (ii) an increased level of activity of a trans-2-enoyl-CoA reductase, an Acinetobacter tetrose transporter, or both relative to the same in a reference sample; (iii) an increased flux through the B-ureidopropionase reaction relative to the same in a reference sample; (iv) a decreased level of one or more bacterial species selected from the group consisting of: Clostridium clostridioforme, Prevotella sp., Streptococcus parasanguinis, Anaerostipes hadrus, Parasutterella excrementihominis, and Eisenbergiella massiliensis relative to the same in a reference sample; and (v) an increased level of one or more bacterial species selected from the group consisting of: Bifidobacterium sp., Collinsella sp., Methanobrevibacter smithii, Oscillibacter sp., Faecalibacterium prausnitzii C, Faecalibacterium prausnitzii I, Intestinimonas timonensis, Faecalibacterium prausnitzii, Bacteroides caccae, Barnesiella intestinihominis, Clostridiaceae bacterium, Clostridium sp., and Bifidobacterium adolescentis relative to the same in a reference sample a therapy comprising a peptide of any one of claims 11-83 or a pharmaceutical composition thereof, or a recombinant host of any one of claims 84-91; wherein the subject has received a therapeutically effective amount of an immunomodulator. ### Claim 124 (depends on 117, 118, 119, 120, 121, 122, 123) The method of any of claims 117-123, the therapy further comprising one or more of: a) a therapeutically effective amount of an immunomodulator; b) an effective amount of one or more bacterial species selected from the group consisting of: Bifidobacterium sp., Collinsella sp., Methanobrevibacter smithii, Oscillibacter sp., Faecalibacterium prausnitzii C, Faecalibacterium prausnitzii I, Ruminococcaceae bacterium, Intestinimonas timonensis, Faecalibacterium prausnitzii, Bacteroides caccae, Barnesiella intestinihominis, Clostridiaceae bacterium, Ruminococcaceae bacterium, Clostridium sp., and Bifidobacterium adolescentis; and c) an additional treatment of cancer excluding an immunomodulator. ### Claim 125 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92) A method of modulating the activity of one or more target proteins in a subject, the method comprising administering to the subject a peptide of any one of claims 11-83; or a plurality of recombinant host cells of any one of claims 84-92; wherein the one or more target protein is selected from the group consisting of a CD2 protein, a BST2 protein, a TNF protein, a CXCL3 protein, a ADRA2A protein, a ADRB2 protein, a CCR6 protein, a CCR9 protein, a CHRM5 protein, a CXCR3 protein, a CXCR4 protein, a EDGE protein, a HCRTR2 protein, a HRH4 protein, a MRGPRX2 protein, a MTNR1A protein, a NPFFR1 protein, a SSTR1 protein, a SSTR3 protein, a TRHR protein, and a TSHR(L) protein. ### Claim 126 (depends on 125) The method of claim 125, wherein the one or more target proteins is selected form the group consisting of a CD2 protein, a BST2 protein, and a TNF protein. ### Claim 127 (depends on 125, 126) The method of any one of claims 125-126, wherein the one or more target proteins is a CXCL3 protein. ### Claim 128 (depends on 125, 126, 127) The method of any one of claims 125-127, wherein the one or more target proteins is selected from the group consisting of a CCR9 protein, a CHRM5 protein, a CXCR3 protein, a CXCR4 protein, a HCRTR2 protein, a MRGPRX2 protein, a SSTR1 protein, and a TSHR(L) protein. ### Claim 129 (depends on 125, 126, 127, 128, 129) The peptide of any one of claims 125-129, wherein the one or more target proteins is selected from the group consisting of a CCR9 protein, a CHRM5 protein, a CXCR3 protein, a CXCR4 protein, a HCRTR2 protein, a MRGPRX2 protein, a SSTR1 protein, or a TSHR(L) protein. ### Claim 130 (depends on 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129) The method of any one of claims 117-129, wherein the method further comprises detecting the level of one or more bacterial species, RNA transcripts, protein activity, or flux though a metabolic pathway in a sample from the subject. ### Claim 131 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91) A method for increasing the response to an immunomodulator in a subject in need thereof comprising administering to the subject a composition comprising a peptide of any one of claims 11-83 or a pharmaceutical composition thereof, or a recombinant host of any one of claims 84-91. ### Claim 132 (depends on 131) The method of claim 131, wherein the subject has cancer. ### Claim 133 (depends on 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91) A method for treating cancer in a subject, the method comprising: (a) detecting a dysbiosis associated with response to therapy with an immunomodulator in a sample from the subject; and (b) administering to the subject a composition comprising a peptide of any one of claims 11-83 or a pharmaceutical composition thereof, or a recombinant host of any one of claims 84-91. ### Claim 134 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 117, 120, 121, 122) The method of any one of claim 1-10, 117, 120-122, or 130-133, wherein the sample is a fecal sample. ### Claim 135 (depends on 134) The method of claim 134, wherein the sample is a tumor biopsy sample. ### Claim 136 (depends on 133, 134, 135) The method of any one of claims 133-135, wherein detecting the dysbiosis associated with response to therapy with an immunomodulator comprises determining bacterial gene expression in the sample from the subject. ### Claim 137 (depends on 133, 134, 135, 136) The method of any one of claims 133-136, wherein detecting the dysbiosis associated with response to therapy with an immunomodulator comprises determining bacterial composition in the sample from the subject. ### Claim 138 (depends on 133, 134, 135, 136, 137) The method of any one of claims 133-137, wherein detecting the dysbiosis associated with response to therapy with an immunomodulator comprises determining bacterial protein activity in the sample from the subject. ### Claim 139 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 119, 120, 121, 122, 124, 130, 131, 132) The method of any one of claim 1-10, 119-122, 124, 130-132, or 136-138, wherein the immunomodulator targets one or more of: CTLA-4, PD-1, PD-L1, BTLA, LAG-3, A2AR, TIM-3, B7-H3, VISTA, IDO, OX40, 4-1BB, and GITR. ### Claim 140 (depends on 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139) The method of any one of claims 98-139, wherein the subject has a solid tumor. ### Claim 141 (depends on 140) The method of claim 140, wherein the subject has a solid tumor selected from the group consisting of: melanoma, lung cancer, kidney cancer, bladder cancer, a head and neck cancer, Merkel cell carcinoma, urothelial cancer, breast cancer, glioblastoma, gastric cancer, a nasopharyngeal neoplasm, colorectal cancer, hepatocellular carcinoma, ovarian cancer, and pancreatic cancer. ### Claim 142 (depends on 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141) The method of any one of claims 98-141, wherein the subject has a hematological malignancy. ### Claim 143 (depends on 142) The method of claim 142, wherein the subject has a hematological malignancy selected from the group consisting of: multiple myeloma, non-Hodgkin lymphoma, Hodgkin lymphoma, diffuse large B-cell lymphoma, and chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL). ### Claim 144 (depends on 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143) The method of any one of claims 98-143, wherein the subject has a cancer selected from one or more of: melanoma, non-small cell lung cancer (NSCLC), small cell lung cancer, squamous cell lung carcinoma, kidney cancer, bladder cancer, a head and neck cancer, Hodgkin lymphoma, Merkel cell carcinoma, urothelial cancer, breast cancer, glioblastoma, gastric adenocarcinoma, transitional cell carcinoma, a biliary tract neoplasm, a nasopharyngeal neoplasm, colorectal cancer, hepatocellular carcinoma, renal cell carcinoma, ovarian cancer, and pancreatic cancer. ### Claim 145 (depends on 115, 116) The method of any of claim 115, 116, or 141-144, wherein the melanoma is unresectable or metastatic melanoma. ### Claim 146 (depends on 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145) The method of any one of claims 133-145, wherein the method comprises administering the composition to the subject once, twice, or three times per day. ### Claim 147 (depends on 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146) The method of any one of claims 133-146, wherein the composition is formulated for oral administration. ### Claim 148 (depends on 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147) The method of any one of claims 133-147, wherein the composition is formulated as a tablet, a capsule, a powder, or a liquid. ### Claim 149 (depends on 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148) The method of any one of claims 133-148, wherein the composition is formulated as a tablet. ### Claim 150 (depends on 149) The method of claim 149, wherein the tablet is coated. ### Claim 151 (depends on 150) The method of claim 150, wherein the coating comprises an enteric coating. ### Claim 152 (depends on 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152) The method of any one of claims 133-152, wherein the composition is formulated for rectal administration. ### Claim 153 (depends on 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152) The method of any one of claims 133-152, wherein the composition is formulated for intravenous administration. ### Claim 154 (depends on 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152) The method of any one of claims 133-152, wherein the composition is formulated for intratumoral administration. ### Claim 155 (depends on 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152) The method of any one of claims 133-152, wherein the method further comprises administering a treatment for cancer, an additional treatment for cancer, and/or other adjunct therapy to the subject. ### Claim 156 (depends on 155) The method of claim 155, wherein the composition comprising the bacterial strain treatment and the treatment for cancer and/or adjunct therapy are administered simultaneously. ### Claim 157 (depends on 156) The method of claim 156, wherein the composition comprising the bacterial strain treatment and the treatment for cancer and/or adjunct therapy are administered sequentially. ### Claim 158 (depends on 156, 157) The method of any one of claims 156-157, wherein the treatment for cancer and/or adjunct therapy comprises a probiotic. ### Claim 159 (depends on 116, 121, 156, 157, 158, 159) The method of any one of claims 116, 121, 156-159, wherein the treatment for cancer and/or adjunct therapy comprises surgery, radiation therapy, or a combination thereof. ### Claim 160 (depends on 116, 121, 149, 155) The method of any one of claims 116, 121, 155-149, wherein the treatment for cancer and/or adjunct therapy comprises a therapeutic agent. ### Claim 161 (depends on 160) The method of claim 160, wherein the therapeutic agent comprises a chemotherapeutic agent, a targeted therapy, an immunotherapy, or a combination thereof. ### Claim 162 (depends on 161) The method of claim 161, wherein the chemotherapeutic agent comprises carboplatin, cisplatin, gemcitabine, methotrexate, paclitaxel, pemetrexed, lomustine, temozolomide, dacarbazine, or a combination thereof. ### Claim 163 (depends on 161, 162) The method of claim 161 or claim 162 wherein the targeted therapy comprises afatinib dimaleate, bevacizumab, cetuximab, crizotinib, erlotinib, gefitinib, sorafenib, sunitinib, pazopanib, everolimus, dabrafenib, aldesleukin, interferon alfa-2b, ipilimumab, peginterferon alfa-2b, trametinib, vemurafenib, or a combination thereof. ### Claim 164 (depends on 161, 162, 163) The method of claim 161-163, wherein the immunotherapy comprises a cell therapy, a therapy with an immunomodulator, or a combination thereof. ### Claim 165 (depends on 164) The method of claim 164, wherein the immunomodulator is an immune checkpoint inhibitor selected from the group consisting of: ipilimumab, nivolumab, pembrolizumab, atezolizumab, avelumab, durvalumab, cemiplimab, and a combination thereof. ### Claim 166 (depends on 165) The method of claim 165, wherein the immunomodulator is a co-stimulatory immune checkpoint agent selected from the group consisting of: IBI101, utomilumab, MEDI1873, and a combination thereof. ### Claim 167 (depends on 164) The method of claim 164, wherein the cell therapy is a CART cell therapy ### Claim 168 (depends on 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167) The method of any one of claims 98-167, wherein the subject is a human.