Bacteria Engineered to Treat Diseases that Benefit from Reduced Gut Inflammation and/or Tighten Gut Mucosal Barrier

1 - 31 . (canceled)

32 . A genetically engineered bacterium comprising:

a) at least one non-native copy of a first gene that encodes a transcription factor protein that is regulated by a reactive nitrogen species (RNS), wherein the first gene is operatively linked to a promoter; and

b) at least one of:

i. a second gene encoding a non-native, anti-inflammation molecule;

ii. a second gene encoding a non-native gut barrier function enhancer molecule;

iii. a gene cassette encoding a biosynthetic pathway, wherein a final product of the biosynthetic pathway is an anti-inflammation molecule;

iv. a gene cassette encoding a biosynthetic pathway, wherein a final product of the biosynthetic pathway is a gut barrier function enhancer molecule, wherein

the second gene or gene cassette in b) is expressed under the control of a tunable regulatory region heterologous to the gene or gene cassette, wherein induction of the tunable regulatory region is directly or indirectly controlled by the transcription factor.

33 . The bacterium of claim 32 , wherein at least one of the one or more non-native copies of the gene that encodes the transcription factor is located on a plasmid in the bacterium.

34 . The bacterium of claim 32 , wherein at least one of the one or more non-native copies of the gene that encodes the transcription factor is located on a chromosome in the bacterium.

35 . The bacterium of claim 32 , wherein the promoter that controls expression of at least one of the one or more non-native copies of the gene that encodes the transcription factor is an inducible promoter.

36 . The bacterium of claim 32 , wherein the gene encoding the anti-inflammation molecule, the gut barrier enhancer molecule, or the gene cassette encoding the biosynthetic pathway is located on a plasmid in the bacterium.

37 . The bacterium of claim 32 , wherein the gene encoding the anti-inflammation molecule, the gut barrier enhancer molecule, or the gene cassette encoding the biosynthetic pathway is located on a chromosome in the bacterium.

38 . The bacterium of claim 32 , wherein the gene that encodes the transcription factor protein is nitric oxide sensing repressor NsrR.

39 . The bacterium of claim 32 , wherein the tunable regulatory region that controls expression of the anti-inflammation molecule, the gut barrier enhancer molecule, or the biosynthetic pathway is selected from a native or a modified functional form of a regulatory region from any one of nitric oxide reductase (norB), aniA, nsrR, hmpA, ytfE, ygbA, hcp, hcr, nrfA, and alternative oxidase (aox).

40 . The bacterium of claim 32 , wherein the molecule of b) is selected from propionate, butyrate, acetate, interleukin 10 (IL-10), interleukin 27 (IL-27), transforming growth factor β2 (TGF-ß2), transforming growth factor β1 (TGF-ß1), glucagon-like peptide (GLP-2), N-acylphosphatidylethanolamines (NAPEs), elafin, trefoil factor, and single-chain variable fragment (scFv), antisense RNA, short interfering RNA (siRNA), or short hairpin RNA (shRNA) directed against a pro-inflammatory molecule.

41 . The bacterium of claim 32 , wherein the bacterium is a non-pathogenic bacterium.

42 . The bacterium of claim 41 , wherein the bacterium is selected from the group consisting of Bacteroides, Bifidobacterium, Clostridium, Escherichia, Lactobacillus , and Lactococcus.

43 . The bacterium of claim 42 , wherein the bacterium is Escherichia coli strain Nissle.

44 . The bacterium of claim 32 , wherein the bacterium is an auxotroph in diaminopimelic acid or an enzyme in the thymine biosynthetic pathway.

45 . A pharmaceutically acceptable composition comprising the bacterium of claim 32 ; and a pharmaceutically acceptable carrier.

46 . The composition of claim 45 formulated for oral or rectal administration.

47 . A method of treating or preventing an autoimmune disorder, comprising the step of administering to a patient in need thereof, the composition of claim 45 .

48 . A method of treating a disease or condition associated with gut inflammation and/or compromised gut barrier function, comprising the step of administering to a patient in need thereof, the composition of claim 45 .

49 . The method of claim 47 , wherein the autoimmune disorder is selected from the group consisting of acute disseminated encephalomyelitis (ADEM), acute necrotizing hemorrhagic leukoencephalitis, Addison's disease, agammaglobulinemia, alopecia areata, amyloidosis, ankylosing spondylitis, anti-GBM/anti-TBM nephritis, antiphospholipid syndrome (APS), autoimmune angioedema, autoimmune aplastic anemia, autoimmune dysautonomia, autoimmune hemolytic anemia, autoimmune hepatitis, autoimmune hyperlipidemia, autoimmune immunodeficiency, autoimmune inner ear disease (AIED), autoimmune myocarditis, autoimmune oophoritis, autoimmune pancreatitis, autoimmune retinopathy, autoimmune thrombocytopenic purpura (ATP), autoimmune thyroid disease, autoimmune urticarial, Axonal & neuronal neuropathies, Balo disease, Behcet's disease, Bullous pemphigoid, Cardiomyopathy, Castleman disease, Celiac disease, Chagas disease, Chronic inflammatory demyelinating polyneuropathy (CIDP), Chronic recurrent multifocal ostomyelitis (CRMO), Churg-Strauss syndrome, Cicatricial pemphigoid/benign mucosal pemphigoid, Crohn's disease, Cogan syndrome, Cold agglutinin disease, Congenital heart block, Coxsackie myocarditis, CREST disease, Essential mixed cryoglobulinemia, Demyelinating neuropathies, Dermatitis herpetiformis, Dermatomyositis, Devic's disease (neuromyelitis optica), Discoid lupus, Dressler's syndrome, Endometriosis, Eosinophilic esophagitis, Eosinophilic fasciitis, Erythema nodosum, Experimental allergic encephalomyelitis, Evans syndrome, Fibrosing alveolitis, Giant cell arteritis (temporal arteritis), Giant cell myocarditis, Glomerulonephritis, Goodpasture's syndrome, Granulomatosis with Polyangiitis (GPA), Graves' disease, Guillain-Barre syndrome, Hashimoto's encephalitis, Hashimoto's thyroiditis, Hemolytic anemia, Henoch-Schonlein purpura, Herpes gestationis, Hypogammaglobulinemia, Idiopathic thrombocytopenic purpura (ITP), IgA nephropathy, IgG4-related sclerosing disease, Immunoregulatory lipoproteins, Inclusion body myositis, Interstitial cystitis, Juvenile arthritis, Juvenile idiopathic arthritis, Juvenile myositis, Kawasaki syndrome, Lambert-Eaton syndrome, Leukocytoclastic vasculitis, Lichen planus, Lichen sclerosus, Ligneous conjunctivitis, Linear IgA disease (LAD), Lupus (Systemic Lupus Erythematosus), chronic Lyme disease, Meniere's disease, Microscopic polyangiitis, Mixed connective tissue disease (MCTD), Mooren's ulcer, Mucha-Habermann disease, Multiple sclerosis, Myasthenia gravis, Myositis, Narcolepsy, Neuromyelitis optica (Devic's), Neutropenia, Ocular cicatricial pemphigoid, Optic neuritis, Palindromic rheumatism, PANDAS (Pediatric autoimmune Neuropsychiatric Disorders Associated with Streptococcus ), Paraneoplastic cerebellar degeneration, Paroxysmal nocturnal hemoglobinuria (PNH), Parry Romberg syndrome, Parsonnage-Turner syndrome, Pars planitis (peripheral uveitis), Pemphigus, Peripheral neuropathy, Perivenous encephalomyelitis, Pernicious anemia, POEMS syndrome, Polyarteritis nodosa, Type I, II, & III autoimmune polyglandular syndromes, Polymyalgia rheumatic, Polymyositis, Postmyocardial infarction syndrome, Postpericardiotomy syndrome, Progesterone dermatitis, Primary biliary cirrhosis, Primary sclerosing cholangitis, Psoriasis, Psoriatic arthritis, Idiopathic pulmonary fibrosis, Pyoderma gangrenosum, Pure red cell aplasia, Raynauds phenomenon, reactive arthritis, reflex sympathetic dystrophy, Reiter's syndrome, relapsing polychondritis, restless legs syndrome, retroperitoneal fibrosis, rheumatic fever, rheumatoid arthritis, sarcoidosis, Schmidt syndrome, scleritis, scleroderma, Sjogren's syndrome, sperm & testicular autoimmunity, stiff person syndrome, subacute bacterial endocarditis (SBE), Susac's syndrome, sympathetic ophthalmia, Takayasu's arteritis, temporal arteritis/giant cell arteritis, thrombocytopenic purpura (TTP), Tolosa-Hunt syndrome, transverse myelitis, type 1 diabetes, asthma, ulcerative colitis, undifferentiated connective tissue disease (UCTD), uveitis, vasculitis, vesiculobullous dermatosis, vitiligo, and Wegener's granulomatosis.

50 . The method of claim 49 , wherein the autoimmune disorder is selected from the group consisting of type 1 diabetes, asthma, multiple sclerosis, Crohn's disease, lupus, rheumatoid arthritis, ulcerative colitis, juvenile arthritis, psoriasis, psoriatic arthritis, celiac disease, and ankylosing spondylitis.

51 . The method of claim 48 , wherein the disease or disorder is selected from an inflammatory bowel disease, and a diarrheal disease.