WHAT IS CLAIMED IS: 1. A genetically engineered bacterium, wherein the genetically engineered bacterium comprises an exogenous nucleic acid encoding an enzyme that produces a diffusible signal factor (DSF) by introducing a cis-2 double bond to a fatty acid. 2. The genetically engineered bacterium of claim 1, wherein the enzyme is selected from the group consisting of an enzyme encoded by the AAO28287 (rpfF) locus of Xylella fastidiosa, and an enzyme encoded by the CAR54439 locus from Burkholderia cenocepacia, an enzyme encoded by the TWR33075 locus of Cronobacter turicensis, an enzyme encoded by the WP_129362672 locus of Enterobacter cloacae, an enzyme encoded by the NP_249436 locus of Pseudomonas aeruginosa, an enzyme encoded by the WP_005416390 locus of Stenotrophomonas maltophilia, an enzyme encoded by the AAM41146 locus of Xanthomonas campestris pathovar campestris, an enzyme encoded by the WP_054444565 locus of Achromobacter xylosoxidans, an enzyme encoded by the WP_085344885 locus of Cronobacter sakazakii, an enzyme encoded by the WP_124890011 locus of Pantoea agglomerans, an enzyme encoded by the WP_148874552 locus of Serratia marcescens, and an enzyme encoded by the AKF40192 locus of Yersinia enterocolitica. 3. The genetically engineered bacterium of claim 1, wherein the enzyme is an enzyme encoded by the AAO28287 (rpfF) locus of Xylella fastidiosa. 4. The genetically engineered bacterium of claim 1, wherein the exogenous nucleic acid comprises a sequence that is at least 80% identical to a sequence selected from the group consisting of SEQ ID NOs: 2, 3, 4, 5, 6, 8, 9, 11, 12, 14, 15, and 17. 5. The genetically engineered bacterium of claim 1, wherein the exogenous nucleic acid encodes an amino acid sequence that is at least 80% identical to a sequence selected from the group consisting of SEQ ID NOs: 1, 7, 10, 13, 16, and 18-24. 6. The genetically engineered bacterium of any one of claims 1-5, wherein the genetically engineered bacterium is a probiotic bacterium. 7. The genetically engineered bacterium of claim 6, wherein the probiotic bacterium is selected from the group consisting of genera Escherichia, Propionibacterium, Lactobacillus, Bifidobacterium and Streptococcus. 8. The genetically engineered bacterium of claim 7, wherein the probiotic bacterium is selected from the group consisting of Escherichia coli strain Nissle 1917, Escherichia coli strain MG1655, Lactobacillus acidophilus, Lactobacillus brevis, Lactobacillus bulgaricus, Lactobacillus casei, Lactobacillus helveticus, Lactobacillus plantarum, Lactobacillus reuteri, Lactobacillus rhamnosus, Bifidobacterium bifidum, Bifidobacterium infantis, Bifidobacterium lactis, Bifidobacterium longum, Streptococcus thermophilus; and Propionibacterium freudenreichii. 9. The genetically engineered bacterium of any one of claims 1-5, wherein the genetically engineered bacterium is from the genus Salmonella. 10. The genetically engineered bacterium of claim 2 or claim 5, wherein the nucleic acid encoding the selected enzyme is codon-optimized for expression in the genetically engineered bacterium. 11. The genetically engineered bacterium of claim 1, wherein the enzyme is expressed in the bacteria. 12. The genetically engineered bacterium of any one of claims 1-11, wherein the exogenous nucleic acid comprises a promoter selected from an endogenous promoter, a constitutive promoter and an inducible promoter. 13. The genetically engineered bacterium of any one of claims 1-12, wherein the exogenous nucleic acid is stably integrated in the bacterial genome. 14. The genetically engineered bacterium of claim 13, wherein a single copy of the exogenous nucleic acid is integrated in the bacterial genome. 15. A composition, comprising the genetically engineered bacterium according to any one of claims 1-14, and a pharmaceutically or veterinarily acceptable carrier. 16. The composition of claim 15, wherein the composition is an animal feed composition. 17. A method for treating or preventing a Salmonella infection comprising administering to a subject in need of treatment a genetically engineered bacterium, wherein the genetically engineered bacterium comprises an exogenous nucleic acid encoding an enzyme that produces a diffusible signal factor (DSF) by introducing a cis-2 double bond to a fatty acid. 18. The method of claim 17, wherein the enzyme is selected from an enzyme encoded by the AAO28287 (rpfF) locus of Xylella fastidiosa, and an enzyme encoded by the CAR54439 locus from Burkholderia cenocepacia, an enzyme encoded by the TWR33075 locus of Cronobacter turicensis, an enzyme encoded by the WP_129362672 locus of Enterobacter cloacae, an enzyme encoded by the NP_249436 locus of Pseudomonas aeruginosa, an enzyme encoded by the WP_005416390 loc-us of Stenotrophomonas maltophilia, an enzyme encoded by the AAM41146 locus of Xanthomonas campestris pathovar campestris, an enzyme encoded by the WP_054444565 locus of Achromobacter xylosoxidans, an enzyme encoded by the WP_085344885 locus of Cronobacter sakazakii, an enzyme encoded by the WP_124890011 locus of Pantoea agglomerans, an enzyme encoded by the WP_148874552 locus of Serratia marcescens, and an enzyme encoded by the AKF40192 locus of Yersinia enterocolitica. 19. The method of claim 17, wherein the enzyme is an enzyme encoded by the AAO28287 (rpfF) locus of Xylella fastidiosa. 20. The method of claim 17, wherein the exogenous nucleic acid comprises a sequence that is at least 80% identical to a sequence selected from the group consisting of SEQ ID NOs: 2, 3, 4, 5, 6, 8, 9, 11, 12, 14, 15, and 17. 21. The method of claim 17, wherein the exogenous nucleic acid encodes an amino acid sequence that is at least 80% identical to a sequence selected from the group consisting of SEQ ID NOs: 1, 7, 10, 13, 16, and 18-24. 22. The method of claim 17, wherein the genetically engineered bacterium is probiotic bacteria. 23. The method of claim 22, wherein the probiotic bacterium is selected from the group consisting of genera Escherichia, Propionibacterium, Lactobacillus, Bifidobacterium and Streptococcus. 24. The method of claim 22, the probiotic bacterium is selected from the group consisting of Escherichia coli strain Nissle 1917, Escherichia coli strain MG1655, Lactobacillus acidophilus, Lactobacillus brevis, Lactobacillus bulgaricus, Lactobacillus casei, Lactobacillus helveticus, Lactobacillus plantarum, Lactobacillus reuteri, Lactobacillus rhamnosus, Bifidobacterium bifidum, Bifidobacterium infantis, Bifidobacterium lactis, Bifidobacterium longum, Streptococcus thermophilus; and Propionibacterium freudenreichii. 25. The method of claim 17, wherein the genetically engineered bacterium is from the genus Salmonella. 26. The method of claim 18 or claim 20, wherein the nucleic acid encoding the selected enzyme is codon-optimized for expression in the genetically engineered bacterium. 27. The method of any one of claims 17-21, wherein the enzyme is expressed in the bacterium. 28. The method of any one of claims 17-27, wherein the exogenous nucleic acid comprises a promoter selected from an endogenous promoter, a constitutive promoter and an inducible promoter. 29. The method of any one of claims 17-28, wherein the exogenous nucleic acid is stably integrated in the bacterial genome. 30. The method of claim 29, wherein a single copy of the exogenous nucleic acid is integrated in the bacterial genome. 31. The method of any one of claims 17-30, wherein the genetically engineered bacterium or a spore of the genetically engineered bacterium is within a capsule when administered. 32. The method of any one of claims 17-31, wherein the subject is a human. 33. The method of any one of claims 17-31, wherein the subject is a non-human animal. 34. The method of claim 33, wherein the non-human animal is a domesticated animal. 35. A vector comprising a nucleic acid encoding an enzyme selected from the group consisting of an enzyme encoded by the AAO28287 (rpfF) locus of Xylella fastidiosa, and an enzyme encoded by the CAR54439 locus from Burkholderia cenocepacia, an enzyme encoded by the TWR33075 locus of Cronobacter turicensis, an enzyme encoded by the WP_129362672 locus of Enterobacter cloacae, an enzyme encoded by the NP_249436 locus of Pseudomonas aeruginosa, an enzyme encoded by the WP_005416390 locus of Stenotrophomonas maltophilia, an enzyme encoded by the AAM41146 locus of Xanthomonas campestris pathovar campestris, an enzyme encoded by the WP_054444565 locus of Achromobacter xylosoxidans, an enzyme encoded by the WP_085344885 locus of Cronobacter sakazakii, an enzyme encoded by the WP_124890011 locus of Pantoea agglomerans, an enzyme encoded by the WP_148874552 locus of Serratia marcescens, and an enzyme encoded by the AKF40192 locus of Yersinia enterocolitica. 36. The vector of claim 35, wherein the enzyme is an enzyme encoded by the AAO28287 (rpfF) locus of Xylella fastidiosa. 37. The vector of claim 35, wherein the nucleic acid encoding the selected enzyme is codon-optimized for expression in a bacterium. 38. The vector of claim 35, wherein the nucleic acid comprises a sequence that is at least 80% identical to a sequence selected from the group consisting of SEQ ID NOs: 2, 3, 4, 5, 6, 8, 9, 11, 12, 14, 15, and 17. 39. The vector of claim 35, wherein the nucleic acid encodes an amino acid sequence that is at least 80% identical to a sequence selected from the group consisting of SEQ ID NOs: 1, 7, 10, 13, 16, and 18-24. 40. The vector of claim 35, further comprising a promoter selected from a native promoter, a heterologous promoter, a constitutive promoter or an inducible promoter. 41. A method of producing a diffusible signal factor (DSF), comprising culturing the genetically engineered bacterium of any one of claims 1-14 under conditions that allow the genetically engineered bacterium to express the enzyme that produces a DSF, thereby producing the DSF. 42. The method of claim 41, further comprising purifying the produced DSF from the cell culture. |
[0079] In some embodiment, the enzyme comprises an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 20. [0080] In some embodiment, the enzyme comprises an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 21. [0081] In some embodiment, the enzyme comprises an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 22. [0082] In some embodiment, the enzyme comprises an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 23. [0083] In some embodiment, the enzyme comprises an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 24. Genetically Engineered Bacterium [0084] In one aspect, disclosed herein is a genetically engineered bacterium that comprises an exogenous nucleic acid encoding an enzyme that produces a diffusible signal factor (DSF), as described herein. As used herein, the term "genetically engineered" or "genetically modified" used in connection with a microorganism means that the microorganism comprises a genome that has been modified (relative to the original or natural-occurring genome of the microorganism), or comprises an exogenous introduced nucleic acid. [0085] The recombinant bacteria disclosed herein, · prevents Salmonella infection by disrupting an essential virulence function, rather than by killing or inhibiting the growth of the organism. · is effective at very low concentrations (less than 1 mM in vitro). · targets specifically Salmonella; unlikely to have deleterious effects on resident intestinal bacteria. · produces compounds that eliminate the requirement for costly and time-consuming chemical synthesis. · can be employed as a probiotic organism, administered to humans or non-human animals (e.g., sheep, turkeys, goats, dogs, cats, cattle, swine, chicken, ducks and other commercially-important domesticated animals) to prevent Salmonella carriage and disease. [0086] In some embodiments, the exogenous nucleic acid comprises a gene that is codon- optimized for expression in a host genetically engineered bacterium (such as E. coli and Salmonella). In some embodiments, the exogenous nucleic acid is expressed in a bacterium, to produce DSFs. As used herein, the term "codon-optimized" refers to nucleic acid molecules that are modified based on the codon usage of the host species (e.g., a specific E. coli, Salmonella or probiotic bacterium species used), but without altering the polypeptide sequence encoded by the nucleic acid. [0087] In some embodiments, the exogenous nucleic acid comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 2, 3, 4, 5, 6, 8, 9, 11, 12, 14, 15, and 17. [0088] In some embodiments, the exogenous nucleic acid comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 2. [0089] In some embodiments, the exogenous nucleic acid comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 3. [0090] In some embodiments, the exogenous nucleic acid comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 4. [0091] In some embodiments, the exogenous nucleic acid comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 5. [0092] In some embodiments the exogenous nucleic acid comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 6. [0093] In some embodiments, the exogenous nucleic acid comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 8. [0094] In some embodiments, the vector comprises a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 9. [0095] In some embodiments, the exogenous nucleic acid comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 11. [0096] In some embodiments, the exogenous nucleic acid comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 12. [0097] In some embodiments, the exogenous nucleic acid comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 14. [0098] In some embodiments, the exogenous nucleic acid comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 15. [0099] In some embodiments, the exogenous nucleic acid comprises a sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 17. [0100] In some embodiments, the exogenous nucleic acid encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 1, 7, 10, 13, 16, and 18- 24. [0101] In some embodiment, the exogenous nucleic acid encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 1. [0102] In some embodiment, the exogenous nucleic acid encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 7. [0103] In some embodiment, the exogenous nucleic acid encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 10. [0104] In some embodiment, the exogenous nucleic acid encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 13. [0105] In some embodiment, the exogenous nucleic acid encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 16. [0106] In some embodiment, the exogenous nucleic acid encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 18. [0107] In some embodiment, the exogenous nucleic acid encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 19. [0108] In some embodiment, the exogenous nucleic acid encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 20. [0109] In some embodiment, the exogenous nucleic acid encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 21. [0110] In some embodiment, the exogenous nucleic acid encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 22. [0111] In some embodiment, the exogenous nucleic acid encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 23. [0112] In some embodiment, the exogenous nucleic acid encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 24. [0113] In some embodiments, the exogenous nucleic acid further comprises a promoter. In some embodiments, the promoter is a native promoter. In some embodiments, the promoter is a heterologous promoter (i.e., the promoter is of a different origin as compared to the nucleic acid). In a specific embodiment, the native promoter is the promoter of the rpfF gene from Xylella fastidiosa. In some embodiments, the promoter is a constitutive promoter. In some embodiments, the promoter is an inducible promoter. In some embodiments the inducible promoter is selected from a tacI, a tacII and an araBAD promoter. tacI and tacII promoters are inducible with the chemical O-Nitrophenyl-β-D- galactopyranoside (ONPG). araBAD promoter is inducible with the sugar arabinose. In some embodiments, the inducible promoter is a lac operon, which can be induced by Isopropyl β-D-1-thiogalactopyranoside (IPTG). [0114] In some embodiments, the exogenous nucleic acid is provided in a plasmid for introduction into a recipient bacteria strain. In some embodiments, the plasmid is pUC57. In some embodiments, plasmid vectors other than pUC57 are used to control production of cis-2 fatty acids. rpfF or homologs can be expressed from plasmids of differing copy number or stability to optimize production. [0115] In some embodiments, the exogenous nucleic acid is integrated into the genome of a bacterium. Conventional methods of gene integration can be used to integrate these genes in single copy into the chromosome of the bacteria. Genomic integration is more advantageous than plasmid-based expression, as integrated constructs are stable and do not require antibiotic selection to be maintained. In a specific embodiment, the exogenous nucleic acid is integrated into the genome of Salmonella, thus creating strains of Salmonella deficient in virulence. In some embodiments, the exogenous nucleic is cloned into Pantoea agglomerans to produce several DSFs. [0116] In some embodiments, the bacterium is a probiotic bacterium. In some embodiments, the probiotic bacterium is selected from genera Escherichia, Propionibacterium, Lactobacillus, Bifidobacterium and Streptococcus. In some embodiments, the probiotic bacterium is selected from Escherichia coli strain Nissle 1917, Escherichia coli strain MG1655, Lactobacillus acidophilus, Lactobacillus brevis, Lactobacillus bulgaricus, Lactobacillus casei, Lactobacillus helveticus, Lactobacillus plantarum, Lactobacillus reuteri, Lactobacillus rhamnosus, Bifidobacterium bifidum, Bifidobacterium infantis, Bifidobacterium lactis, Bifidobacterium longum, Streptococcus thermophilus; and Propionibacterium freudenreichii. In a specific embodiment, the bacterium is E. coli. In a specific embodiment, the bacterium is a species of genera Salmonella or Pantoea. Composition [0117] Another aspect of this disclosure is directed to a composition, comprising a genetically engineered bacterium described herein. In some embodiments, the composition further comprises a pharmaceutically or veterinarily acceptable carrier. [0118] For the purposes of this disclosure, "a pharmaceutically acceptable carrier" means any of the standard pharmaceutical carriers. [0119] "Veterinarily acceptable carrier," as used herein, refers to a carrier medium that does not interfere with the effectiveness of the biological activity of the active ingredient, and is not toxic to the veterinary subject to whom it is administered. [0120] Examples of suitable carriers are well known in the art and may include, but are not limited to, any of the standard pharmaceutical carriers such as a phosphate buffered saline solution and various wetting agents. Other carriers may include additives used in tablets, granules and capsules, and the like. Typically such carriers contain excipients such as starch, milk, sugar, certain types of clay, gelatin, stearic acid or salts thereof, magnesium or calcium stearate, talc, vegetable fats or oils, gum, glycols or other known excipients. Such carriers may also include flavor and color additives or other ingredients. Compositions comprising such carriers are formulated by well-known conventional methods. [0121] Some examples of pharmaceutically acceptable liquid carriers include alcohols (e.g., ethanol), glycols (e.g., propylene glycol and polyethylene glycols), polyols (e.g., glycerol), oils (e.g., mineral oil or a plant oil), paraffins, and aprotic polar solvents acceptable for introduction into a mammal (e.g., dimethyl sulfoxide or N-methyl-2- pyrrolidone) any of which may or may not include an aqueous component (e.g., at least, above, up to, or less than 10, 20, 30, 40, or 50 vol% water). Some examples of pharmaceutically acceptable gels include long-chain polyalkylene glycols and copolymers thereof (e.g., poloxamers), cellulosic and alkyl cellulosic substances (as described in, for example, U.S. Patent 6,432,415), and carbomers. The pharmaceutically acceptable wax may be or contain, for example, carnauba wax, white wax, bees wax, glycerol monostearate, glycerol oleate, and/or paraffins, such as described in, for example, PCT International Publication WO2009/117130. [0122] In specific embodiments, a pharmaceutically/veterinarily acceptable carrier is a dietary supplement or food. Examples of food that can be used to deliver a composition comprising recombinant bacterial spores include, but are not limited to, baby formula, yogurt, milk cheese, kefir, sauerkraut, and chocolate. [0123] In a specific embodiment, the composition is an animal feed composition. In a specific embodiment, the composition is a food product for humans (e.g., yogurt, kefir or other probiotic-containing food product) or a nutritional supplement. [0124] Another aspect of this disclosure is directed to preventatives for infection and carriage by non-typhoidal serovars of Salmonella. Compounds can be consumed by humans or be fed to livestock and poultry to prevent the colonization of the intestine by Salmonella. Recombinant bacteria such as E. coli producing cis-2 unsaturated fatty acids (DSFs) can be directly administered to animals or humans to prevent Salmonella infection. Methods for Treating or Preventing Salmonella Infections [0125] Another aspect of this disclosure is directed to a method for treating or preventing a Salmonella infection (e.g., a Salmonella enterica infection) comprising administering to a subject in need of treatment or prevention an effective amount of a genetically engineered bacterium, wherein the genetically engineered bacterium comprises an exogenous nucleic acid encoding an enzyme that produces a DSF. [0126] As used herein, the term "effective amount" means the total amount of each active component of a pharmaceutical composition or method that is sufficient to show a meaningful patient benefit, i.e., treatment, healing, prevention of the relevant medical condition, amelioration of the symptoms, or an increase in rate of treatment, healing, prevention or amelioration of such conditions, or inhibition of the progression of the condition. [0127] In the method, genetically engineered bacterium, typically in the form of a pharmaceutical composition, as described herein, is enterally administered to the subject. In some embodiments, the subject has already contracted Salmonella when the subject is administered the genetically engineered bacterium, in which case the method of treating functions to inhibit or prevent Salmonella invasion of the intestinal epithelium in the subject, thereby inhibiting or preventing infection of the subject by Salmonella. In other embodiments, the subject has not contracted Salmonella when the subject is administered the genetically engineered bacterium, in which case the method of treating functions as a preventative measure to inhibit or prevent Salmonella invasion in the subject, thereby preventing or inhibiting Salmonella infection, should the subject contract Salmonella. [0128] In some embodiments, the genetically engineered bacterium is administered as a composition in a pharmaceutically or veterinarily-acceptable carrier, as described herein. [0129] In some embodiments, an effective amount of a genetically engineered bacterium is 1 x 101 , 1 x 102 , 1 x 103, 1 x 104 , 1 x 105, 1 x 106, 1 x 107, 1 x 108, 1 x 109 or more said genetically engineered bacterium or its spores. [0130] In some embodiments, the subject is a mammal. In some embodiments, the subject is a human. In some embodiments, the subject is a non-human animal. In some embodiments, the non-human animal is a domesticated animal. In some embodiments, the domesticated animal is selected from a horse, a camel, a dog, a cat, a pig, a cow, a goat and a sheep. Expression Vector [0131] Another aspect of this disclosure is directed to a vector comprising a nucleic acid encoding an enzyme that capable of producing a DSF. [0132] In some embodiments the vector comprises a nucleic acid that encodes an enzyme that is selected from the group consisting of an enzyme encoded by the AAO28287 (rpfF) locus of Xylella fastidiosa, and an enzyme encoded by the CAR54439 locus from Burkholderia cenocepacia, an enzyme encoded by the TWR33075 locus of Cronobacter turicensis, an enzyme encoded by the WP_129362672 locus of Enterobacter cloacae, an enzyme encoded by the NP_249436 locus of Pseudomonas aeruginosa, an enzyme encoded by the WP_005416390 locus of Stenotrophomonas maltophilia, an enzyme encoded by the AAM41146 locus of Xanthomonas campestris pathovar campestris, an enzyme encoded by the WP_054444565 locus of Achromobacter xylosoxidans, an enzyme encoded by the WP_085344885 locus of Cronobacter sakazakii, an enzyme encoded by the WP_124890011 locus of Pantoea agglomerans, an enzyme encoded by the WP_148874552 locus of Serratia marcescens, and an enzyme encoded by the AKF40192 locus of Yersinia enterocolitica. [0133] In some embodiment, the vector comprises a nucleic acid that encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to a sequence selected from SEQ ID NOs: 1, 7, 10, 13, 16. [0134] In some embodiment, the vector comprises a nucleic acid that encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 1. [0135] In some embodiment, the vector comprises a nucleic acid that encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 7. [0136] In some embodiment, the vector comprises a nucleic acid that encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 10. [0137] In some embodiment, the vector comprises a nucleic acid that encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 13. [0138] In some embodiment, the vector comprises a nucleic acid that encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 16. [0139] In some embodiment, the vector comprises a nucleic acid that encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 18. [0140] In some embodiment, the vector comprises a nucleic acid that encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 19. [0141] In some embodiment, the vector comprises a nucleic acid that encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 20. [0142] In some embodiment, the vector comprises a nucleic acid that encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 21. [0143] In some embodiment, the vector comprises a nucleic acid that encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 22. [0144] In some embodiment, the vector comprises a nucleic acid that encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 23. [0145] In some embodiment, the vector comprises a nucleic acid that encodes an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 24. [0146] In some embodiments, the vector comprises a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to a sequence selected from the group consisting of SEQ ID NOs: 2, 3, 4, 5, 6, 8, 9, 11, 12, 14, 15, and 17. [0147] In some embodiments, the vector comprises a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 2. [0148] In some embodiments, the vector comprises a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 3. [0149] In some embodiments, the vector comprises a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 4. [0150] In some embodiments, the vector comprises a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 5. [0151] In some embodiments, the vector comprises a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 6. [0152] In some embodiments, the vector comprises a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 8. [0153] In some embodiments, the vector comprises a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 9. [0154] In some embodiments, the vector comprises a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 11. [0155] In some embodiments, the vector comprises a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 12. [0156] In some embodiments, the vector comprises a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 14. [0157] In some embodiments, the vector comprises a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 15. [0158] In some embodiments, the vector comprises a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more identical to SEQ ID NO: 17. [0159] In some embodiments, the vector comprises a nucleic acid sequence that is codon optimized based on the codon usage of a host species (e.g., a specific E. coli, Salmonella or probiotic bacterium species), but without altering the polypeptide sequence encoded by the nucleic acid sequence. Methods of Producing DSFs [0160] Another aspect of this disclosure is directed to a method of producing a diffusible signal factor (DSF), comprising culturing a genetically engineered bacterium described herein (which comprises an exogenous nucleic acid encoding an enzyme that produces a DSF) under conditions that allow the genetically engineered bacterium to express the enzyme that produces a DSF, thereby producing the DSF. In some embodiment, the method further comprises purifying the produced DSF from the cell culture. [0161] In some embodiments, DSFs are produced in a probiotic bacterial strain. In some embodiments, the probiotic strain is selected from genera Escherichia, Propionibacterium, Lactobacillus, Bifidobacterium and Streptococcus. In some embodiments, the probiotic strain is selected from Escherichia coli strain Nissle 1917, Escherichia coli strain MG1655, Lactobacillus acidophilus, Lactobacillus brevis, Lactobacillus bulgaricus, Lactobacillus casei, Lactobacillus helveticus, Lactobacillus plantarum, Lactobacillus reuteri, Lactobacillus rhamnosus, Bifidobacterium bifidum, Bifidobacterium infantis, Bifidobacterium lactis, Bifidobacterium longum, Streptococcus thermophilus; and Propionibacterium freudenreichii. In a specific embodiment, the probiotic strain is a strain of E. coli. In a specific embodiment, rpfF or its homologs are expressed in E. coli strains known to colonize the intestine of animals, including the recognized probiotic stain Nissle 1917. [0162] In some embodiments, DSFs are produced from a species of Samonella or Pantoea. EXAMPLES Example 1: Materials and Methods rpfF Constructs and Recombinant strains [0163] The rpfF gene of Xylella fastidiosa and the BCAM0581 gene of Burkholderia cenocepacia were modified to optimize expression in E. coli by altering their codons to those most frequently used in E. coli. Each was fused to a modified tac promoter lacking the lac operator region and with a consensus ribosome-binding site to create a constitutive promoter. Constructs were generated and cloned onto the EcoRV restriction enzyme site of plasmid pUC57 by a commercial source. The plasmid constructs were introduced by transformation into the K12 strain of E. coli MG1655, and into Salmonella serovar Typhimurium strain ATCC 14028s. These recombinant strains were grown in co-culture with a strain derived from Salmonella serovar Typhimurium strain ATCC 14028s that harbors a plasmid carrying a fusion of the invasion gene hilA to the luxCDABE reporter. The ability of recombinant strains to repress hilA expression in the co-cultured strain was assessed by reduction in light production from the luxCDABE genes. The specific compound produced was determined by gas chromatography. Sequences [0164] SEQ ID NO: 1: Xylella fastidiosa Temecula1 rpfF amino acid sequence. SEQ ID NO: 2: Xylella fastidiosa Temecula1 rpfF gene nucleotide sequence. SEQ ID NO: 3: Codon-optimized nucleotide sequence of rpfF from Xylella fastidiosa. Position 1-68: constitutive promoter based upon the tac promoter. Position 69-941: rpfF open reading frame (ORF). Position 942-947: BglII cloning site SEQ ID NO: 4: Codon-optimized nucleotide sequence (version 2) of rpfF from Xylella fastidiosa. Position 1-82: tacI promoter. Position 83-955: ORF. Position 956-961: BglII cloning site. SEQ ID NO: 5: Codon-optimized nucleotide sequence (version 3) of rpfF of Xylella fastidiosa. SEQ ID NO: 6: rpfF homolog gene nucleotide sequence in Cronobacter turicensis strain MOD1_Md1sN. SEQ ID NO: 7: Cronobacter turicensis rpfF homolog amino acid sequence. SEQ ID NO: 8: rpfF homolog gene nucleotide sequence in Xanthomonas campestris pv. campestris. SEQ ID NO: 9: Codon-optimized nucleotide sequence of rpfF homolog of Xanthomonas campestris pv. campestris. SEQ ID NO: 10: Xanthomonas campestris pv. campestris rpfF homolog amino acid sequence. SEQ ID NO: 11: rpfF homolog gene nucleotide sequence in Stenotrophomonas maltophilia K279a. SEQ ID NO: 12: Codon-optimized nucleotide sequence of rpfF homolog of Stenotrophomonas maltophilia K279a. SEQ ID NO: 13: Stenotrophomonas maltophilia rpfF ho log amino acid sequence. SEQ ID NO: 14: rpfF homolog gene nucleotide sequence in Pseudomonas aeruginosa. SEQ ID NO: 15: Codon-optimized nucleotide sequence of rpfF hom og in Pseudomonas aeruginosa. SEQ ID NO: 16: Pseudomonas aeruginosa rpfF homolog amino acid sequence. SEQ ID NO: 17: rpfF homolog gene nucleotide sequence in Enterobacter cloacae subsp. cloacae (ATCC 13047). SEQ ID NO: 18: Burkholderia cenocepacia rpfF homolog amino acid sequence. SEQ ID NO: 19: Yersinia enterocolitica rpfF homolog amino acid sequence. SEQ ID NO: 20: Serratia marcescens rpfF homolog amino acid sequence. SEQ ID NO: 21: Pantoea agglomerans rpfF homolog amino acid sequence. SEQ ID NO: 22: Cronobacter sakazakii rpfF homolog amino acid sequence. SEQ ID NO: 23: Achromobacter xylosoxidans rpfF homolog amino acid sequence. SEQ ID NO: 24: Enterobacter cloacae subsp. cloacae rpfF homolog amino acid sequence. Cloning and expression of cis-2 fatty acid production genes [0165] Genes termed BCAM0581 in Burkholderia cenocepacia and rpfF in Xylella fastidiosa encode homologous enoyl-CoA hydratase proteins that introduce a cis-2 double bond into long-chain fatty acids, producing a diffusible signal factor. In Burkholderia cenocepacia the primary product is cis-2-dodecenoic acid, while in Xylella fastidiosa they are 2-cis-hexadecenoic and 2-cis-tetradecenoic acids. The inventors codon-optimized these two genes for expression in E. coli and expressed each under the control of a constitutive promoter as constructs cloned into the EcoRV site of the pUC57 plasmid. The inventors then used gas chromatography (GC) to assess the presence of 2-cis- hexadecenoic acid in culture supernatants by comparing it to a commercially obtained preparation of this chemical (FIG.7). The expression of rpfF produced a peak of the appropriate retention time to be 2-cis-hexadecenoic acid. This peak was absent in the control sample (E. coli with the pUC57 plasmid). It was also absent in the strain expressing BCAM0581. [0166] To assess the functional significance of recombinant enoyl-CoA hydratase expression, a Salmonella Typhimurium strain carrying a hilA-lux reporter fusion was co- cultured with E. coli expressing BCAM0581 or rpfF (FIG.5). HilA is a central regulator of invasion and is required for virulence. E. coli expressing rpfF (purple triangles) repressed hilA expression to a level similar to that using 2.5 mM 2-cis-hexadecenoic acid in the culture medium (black circles). 2-cis-dodecenoic acid (brown squares) reduced expression to a lesser degree, but BCAM0581 (yellow diamonds), predicted to produce 2- cis-dodecenoic acid, did not repress. [0167] A single gene, rpfF of Xylella fastidiosa, is sufficient to produce a DSF of the 2-cis fatty-acid class in Enterobacteriaceae. Codon-optimizied rpfF expression by either E. coli or Salmonella produces a diffusible signal that can be sensed by neighboring bacteria. Expression of rpfF by E. coli or Salmonella reduces Salmonella invasion gene expression. In some embodiments, the rpfF gene (or a homolog thereof, e.g., a gene listed in Table 1) is integrated into the genome of probiotic bacterial strains to assess the effects on Salmonella invasion. Electro mobility shift assays (EMSAs) [0168] Electrophoretic mobility shift assays (EMSAs). EMSAs were performed as previously described (Y. A. Golubeva et al., MBio, 7(1), 2016). Briefly, 10 nM of hilA promoter DNA was mixed with 150 μM HilD, HilC or RtsA in a binding buffer containing 20 mM KCl, 1% glycerol, 1mM DTT, 0.04 mM EDTA, 0.05% Tergitol™ NP-40 and 20 mM HEPES, pH 7.3. cis-2-hexadecenoic acid was tested at concentrations of 1 to 200 μM. Binding was performed at room temperature for 20 minutes. Samples were separated on 6% Novex® TBE DNA retardation gels, and DNA was stained using SYBR® green (Invitrogen). Example 2: 2-cis-hexadecenoic acid reduces the percentage of Salmonella expressing an invasion gene in the gut. [0169] The ability of orally administered 2-cis-hexadecenoic acid to inhibit Salmonella invasion-gene expression in the complex chemical environment of the gut was determined. Only a portion of bacteria activate invasion genes in the gut. To improve the sensitivity of the assay, the inventors used a strain carrying a hilD UTR A25 to a G single base mutation, resulting in increased invasion-gene expression due to altered mRNA stability. This strain additionally carried a constitutively expressed ΔphoN::BFP construct for Salmonella identification, and a sicA-GFP reporter fusion to monitor SPI1 expression. The administration of 2-cis-hexadecenoic acid to mice at 1.5 mM in drinking water significantly reduced the percentage of bacteria expressing an invasion gene in the caecum by 2-fold. The proportion of a ΔhilD null mutant expressing the invasion gene was 5-fold lower than the untreated A25G strain, indicating the importance of HilD for invasion activation in the gut. As fatty acids are rapidly absorbed in the upper gastrointestinal tract, it is presumed that low amounts of 2-cis-hexadecenoic acid were available in the caecum. Compared to the in vitro potency of 2-cis-hexadecenoic acid, an estimated concentration of between 2.5 µM and 10 µM would repress invasion to the percentage observed in the caecum. These results demonstrate that the DSF 2-cis-hexadecenoic acid can signal to inhibit invasion gene expression in the gut (FIG.8). Example 3: 2-cis-unsaturated fatty acids destabilize HilD. [0170] The effects of DSFs on HilD protein stability were assessed. See FIG.9. A strain carrying hilD under a tetracycline-controlled promoter and a C-terminal 3XFLAG tag was used to measure the stability of HilD. The half-life of HilD from bacteria grown in the absence of DSFs was 112 minutes, but addition of 2-cis-hexadecenoic acid to the culture drastically reduced that half-life, to 1 minute. cis-2-eicosenoic acid reduced HilD half-life by a lesser extent, to 18 minutes, and oleic acid did so to 92 minutes. These data indicate that DSFs destabilize HilD. Lon protease is known to be responsible for HilD degradation, but genetic approaches indicated that lon was not required for the repressive effects of the 2-cis-hexadecenoic acid. The inventors therefore tested the role of Lon by assessing HilD protein half-life in a lon mutant. In the absence of lon, HilD protein accumulated, and the DSF had no effect on its stability. However, the DSF continued to repress hilA expression even in the absence of lon. It is therefore likely that DSFs inactivate HilD with consequent degradation by Lon, but that Lon plays no direct role in the repression of invasion genes by DSFs. Example 4: cis-2-unsaturated fatty acids inhibit HilD, HilC and RtsA from binding their target DNA. [0171] The results presented in FIG.10 indicate that cis-2-unsaturated fatty acids repressed HilD through an inactivation mechanism followed by protein degradation. It is hypothesized that these compounds directly interact with HilD, thus impairing its function. HilD binds to the hilA promoter (I. N. Olekhnovich et al., J. Bacteriol., 184(15), 4148- 4160, 2002). The present research examined the effects of cis-2-unsaturated compounds on the binding of purified HilD to the hilA promoter using electrophoretic mobility shift assays (EMSA). In the absence of DSF, the expected binding of HilD to the hilA promoter was demonstrated by the retarded migration of this DNA fragment through the polyacrylamide gel (FIG.7). Addition of 20 μM 2-cis-hexadecenoic acid, however, prevented the binding of HilD to the hilA promoter, whereas concentrations of 1, 2, 5, and 10 μM partially inhibited binding. HilC and RtsA also bind to the hilA promoter and induce expression of hilA. Addition of 100 μM 2-cis-hexadecenoic acid preventing binding of each of these two proteins to the hilA promoter, while concentrations of 10, 25, 50 and 75 μM partially inhibited binding. Therefore, the cis-2-unsaturated fatty acids directly inhibit the ability of HilD, HilC and RtsA to interact with their DNA target. Example 5: Specific amino acid residues of HilD are essential for repression by 2-cis- unsaturated DSFs. [0172] The inventors used in silico methods to visualize the interaction of 2-cis- hexadecenoic acid with HilD. In the absence of an established structure of HilD, the X- ray crystal of its structural and functional homolog, ToxT of Vibrio cholerae, was used to create a virtual HilD replica by homology modeling. Virtual docking of 2-cis- hexadecenoic acid onto this HilD model found two amino acid residues (K293 and K294) whose side-chains were predicted to be in close proximity to the ligand. To test these predictions, each was replaced with an alanine, expressing the mutant constructs on a low copy-number plasmid. To isolate the effects of the hilD mutations from other invasion activators, these constructs were introduced into a Salmonella strain with null mutations in chromosomal hilC, rtsA, and hilD, thus eliminating all components of the invasion feed- forward regulatory loop. Using sipB::lacZY, a representative HilD-regulated gene, as a reporter, invasion-gene expression in cultures grown with 20 µM 2-cis-hexadecenoic acid was examined. The hilD mutants retained their full capacity to induce sipB in the absence of 2-cis-hexadecenoic acid, complementing the chromosomal hilD null mutant, and demonstrating that the point mutations did not reduce transcriptional activation by HilD. HilD mutants K293A and K294A were resistant to the repressive effects of 2-cis- hexadecenoic acid. No significant repression of sipB was observed in these mutants, compared to almost 11-fold reduction in the strain with a wild type HilD. The effect of disrupting residues K293 and K294 on invasion gene expression was specific only to LCFAs with a cis-2 unsaturation. The LCFA 2-cis-dodecenoic acid (c2-DDA), which reduced sipB expression by 4.1-fold in the wild type HilD strain, produced no significant reduction in the K293A and K294A mutants. Conversely, 2-trans-hexadecenoic acid (t2- HDA), which differs from 2-cis-hexadecenoic acid only in the spatial orientation of unsaturation at the second carbon, repressed sipB expression in mutant K293A (4.7-fold) and mutant K294A (4.5-fold) as well as wild type HilD (5.2-fold). These results thus identify the amino acids of HilD important for invasion gene repression by the 2-cis class of fatty acids. Example 6: Recombinant expression of rpfF by E. coli reduces Salmonella invasion gene expression in co-culture. [0173] Variants of rpfF found in several bacterial species encode homologous proteins with enoyl-CoA dehydratase and thioesterase activities that introduce a cis-2 double bond into long-chain fatty acids, generating diffusible signal factors. The inventors codon- optimized five of these genes for expression in E. coli K-12 (from the genera Pseudomonas, Xanthomonas, Stenotrophomonas, Cronobacter and Xylella) and expressed each under the control of a constitutive promoter as constructs cloned into the pUC57 plasmid. To assess the functional significance of recombinant RpfF production, a S. Typhimurium strain carrying a hilA-luxCDABE reporter fusion was co-cultured with E. coli expressing each construct (FIG.13). As a stringent test of function, the Salmonella outnumbered the recombinant E. coli by 10 to 1. The RpfF homologs repressed the hilA reporter expression to varying degrees, with those from Cronobacter and Xylella being the most potent. The observed repression was equivalent to addition of high concentrations of 2-cis-hexadecenoic acid (1-2 µM) directly to growth media. These findings (shown in FIG.13) thus demonstrate that the expression of a single gene, rpfF, in E. coli is necessary and sufficient to produce adequate 2-cis-hexadecenoic acid that can be secreted to inhibit the expression of invasion genes among neighboring Salmonella present in excess.