Combined mechanical, chemical and biologic preparations of mucosal surfaces to enhance a microbial or microbiome engraftment

Abstract

In alternative embodiments, provided are products of manufacture and methods for treating, ameliorating and preventing diseases and conditions related to infected or dysfunctional mucosal surfaces, including mucosal surfaces in the gastrointestinal (GI) tract, respiratory tract, and other mucosal surfaces, for example, mucosal surfaces in the stomach, nasal sinuses, nasopharyngeal area, lungs, bladder or the vagina. Provided are methods and products of manufacture for preparing the GI tract for a microbiota engraftment, then infusing a colonic microbiota engraftment, for example, a fecal microbiota transplant (FMT). In alternative embodiments, provided are methods and products of manufacture for mechanical disruption of a biofilm followed by the chemical and / or biologic dissolution of a mucus layer or a biofilm, and subsequent implantation of FMT material into or onto a mucosal surface such as a GI tract. In alternative embodiments, provided are delivery devices which permit the FMT material to reach the various mucosal surfaces, for example, mucosal surfaces in the GI tract. In alternative embodiments, provided are methods and products of manufacture for replacing an individual's microbiome, where the individual's microbiome may be infected, including replacing the individual's microbiome in colonic, intestinal, gastric, respiratory or vaginal spaces or environments, with that of a healthy or not infected microbiome, where the healthy or not infected microbiome can be donor-derived or cultured. Provided herein are methods for the treatment, amelioration and / or prevention of numerous conditions characterized by an in situ microbiome super-infection, including microbiome super-infections, for example, conditions characterized as gastrointestinal (GI) disease.

Description

COMBINED MECHANICAL, CHEMICAL AND BIOLOGIC PREPARATIONS OF MUCOSAL SURFACES TO ENHANCE A MICROBIAL OR MICROBIOME ENGRAFTMENTTechnical Field

[0001] This application claims the benefit of priority to United States Provisional Application No (USSN) 63 / 551,747, filed on 9 February 2024 and United States Provisional Application No (USSN) 63 / 640,199, filed on 29 April 2024, the entire disclosures of which are incorporated herein by cross-reference.

[0002] This invention generally relates to mucosal surfaces in the body; and in particular, provided are products of manufacture and methods for treating, ameliorating and preventing diseases and conditions related to infected or dysfunctional mucosal surfaces, including mucosal surfaces in the gastrointestinal (GI) tract, respiratory tract, and other mucosal surfaces, for example, mucosal surfaces in the stomach, nasal sinuses, nasopharyngeal area, lungs, bladder or the vagina. Provided are methods and products of manufacture for preparing the GI tract for a microbiota engraftment, then infusing a colonic microbiota engraftment, for example, a fecal microbiota transplant (FMT). In alternative embodiments, provided are methods and products of manufacture for mechanical disruption of a biofilm followed by the chemical and / or biologic dissolution of a mucus layer or a biofilm, and subsequent implantation of FMT material into or onto a mucosal surface such as a GI tract. In alternative embodiments, provided are delivery devices which permit the FMT material to reach the various mucosal surfaces, for example, mucosal surfaces in the GI tract. In alternative embodiments, provided are methods and products of manufacture for replacing an individual’s microbiome, where the individual’s microbiome may be infected, including replacing the individual’s microbiome in colonic, intestinal, gastric, respiratory or vaginal spaces or environments, with that of a healthy or not infected microbiome, where the healthy or not infected microbiome can be donor-derived or cultured. Provided herein are methods for the treatment, amelioration and / or prevention of numerous conditions characterized by an in situ microbiome super- infection, including microbiome super- infections, for example, conditions characterized as gastrointestinal (GI) disease.Background

[0003] Currently numerous conditions for example colitis, Crohn’s disease, irritable bowel syndrome of its various forms, constipation, autism, gastro-intestinal (GI) infection, collagenous colitis, Multiple Sclerosis (MS), Parkinson’s disease (PD) and other Gl-related conditions have been found to be difficult to cure with administration of a fecal microbiota transplant (FMT). Researchers have attempted various methods of achieving implantation, even using multiple infusions and antibiotic pre-treatment and the use of so called super donors, with short term success that is not lasting and not a cure; for example, for constipation, a patient cure rate after several months of FMT can be achieved in no more than 20 to 30% of patients treated. This poor success rate is similar to current FMT treatments for irritable bowel syndrome (IBS), chronic abdominal pain of unknown origin, autism, colitis, and Crohn’s disease.

[0004] Fecal Microbiota Transplantation (FMT) has a long history of use, initially going back to China in the 4th century where the healthy flora was introduced through the mouth as a liquid “soup”. Current methodologies for delivering a microbiota population, for example, an FMT, into a bowel or GI tract has progressed and several methods can be used. For example, these include use of trans-gastroscopic, trans-colonoscopic, trans- enteroscopic, naso-jejunal tube infusions or even use a per-endoscopic gastrostomy (PEG) opening which would accommodate the tube that would go down distally to the jejunum or ileum. For example, equipment or devices for delivery of high flow liquids to the colon has been described by for example US Patent nos. 10,244,980; 10,314,536; 10,881,277; 11,185,625; 11,484,632, and U.S. patent application publication no. US 20210076906 Al.Summary of Invention

[0005] In alternative embodiments, provided are methods for microbiome transplantation and engraftment in a mucosal environment in an individual in need thereof, the method comprising: removing of some (substantially all) or all microbiome from a mucosal environment in the individual in need thereof,wherein optionally the microbiome in the mucosal environment is an infected, diseased or dysfunctional microbiome, or a microbiome causing, aggravating or perpetuating a disease or condition, and optionally the mucosal environment is a gastrointestinal (GI) tract, respiratory tract, stomach, nasal sinus, nasopharyngeal, lung, bladder or vaginal mucosal environment, wherein if the mucosal environment is the colon, removing of some (substantially all) or all colonic fecal material from the colon of the individual in need thereof by washing out colonic fecal material from the colon, wherein the washing out of some (substantially all) or all microbiome comprises administering a formulation comprising a biofilm dissolving or disrupting agent to the mucosal environment in the individual in need thereof, and administering a normal or non-diseased microbiome population, or a fecal microbiota transplantation (FMT) material, to the washed mucosal environment in the individual in need thereof, wherein optionally the normal or non-diseased microbiome population, or a fecal microbiota transplantation (FMT) material, is administered or formulated as a liquid, a solution, a freeze-dried or lyophilized formulation, wherein the removing of some (substantially all) or all microbiome from a mucosal environment in the individual in need thereof comprising administration of a formulation comprising:(a) bromelain and acetylcysteine, or(b) bromelain and acetylcysteine, and any one or several of: a solution of soap in water, N-acetylcysteine, dispersin, ribonucleic-acid-III inhibiting peptide (RIP), Salvadora persica extracts, competence- stimulating peptide (CSP) patulin (PAT), penicillic acid (PA) / EDTA, cathelicidin-derived peptides, small lytic peptide PTP-7, nitric oxide, cys-2-decenoic acid, sodium nitroprusside, s-nitroso- 1-glutathione(GSNfaO), s-nitroso -N-acetylpenicillamine (SNAP), chlorhexidine, povidone-iodine (PI), a nanoemulsion, a lytic bacteriophage, a lactoferrin, a xylitol hydrogel, a synthetic iron chelator, a cranberry component, a curcumin, acetyl- 11-keto-boswellic acid (AKBA), a barley coffee (BC) component, silver nanoparticles, a probiotic (for example, a Bacillus), sinefungin, N-acetyl-cysteine, S-adenosylmethionine, S-adenosyl- homocysteine, a Delisea furanone, a N-sulfonyl homoserine lactone, iron salts, ionic silver salts, arsenicals, selenium, titanium dioxide, gallium nitrate, ethanol, hydrogen peroxide, hydrochloric acid, formaldehyde, luminal formalin in low concentrations, ozonated water, super-oxidized aqueous solution, nitrofurantoin, hexamine hippurate, potassium hydroxide, mercuric chloride, iodine or iodopovidone (for example, povidone- iodine (PVP-I) and / or polyhexamethylene biguanide (PHMB)), disodium EDTA, ozone insufflation, and a combination of selenium and gentamicin; or is selected from the group consisting of azithromycin, clarithromycin, gentamicin, vancomycin, rifaximin, rifabutin, rifampicin, streptomycin, erythromycin, roxithromycin, DEA-CP, bismuth thiols, bismuth subcitrate; bismuth subsalicylate; a bismuth ethanondiothol, a bismuth dimercaprol, a bismuth dimercapropranol, an antibiotic (for example, a secnidazole, nitazoxanide, furazolidone, a nitroimidazole (for example, metronidazole, tinidazole, nimorazole, dimetridazole, pretomanid, ornidazole, megazol, and / or azanidazole), paromomycin, iodoquinol, doxycycline, norfloxacin, ciprofloxacin, levofloxacin, a P-lactam antibiotic such as penicillin (or penicillin G or penicillin V) and / or neomycin), a vitamin (for example, vitamin C), a nanoparticle (for example, a silver nanoparticle), a micropore particle or any combination thereof.

[0006] In one embodiment, provided are methods of microbiome transplantation and engraftment in a mucosal environment in an individual in need thereof, the method comprising: removing of some (substantially all) or all microbiome from a mucosal environment in the individual in need thereof, wherein optionally the microbiome in the mucosal environment is an infected, diseased or dysfunctional microbiome, or a microbiome causing, aggravating or perpetuating a disease or condition,and optionally the mucosal environment is a gastrointestinal (GI) tract, respiratory tract, stomach, nasal sinus, nasopharyngeal, lung, bladder or vaginal mucosal environment, wherein if the mucosal environment is the colon, removing of some (substantially all) or all colonic fecal material from the colon of the individual in need thereof by washing out colonic fecal material from the colon, and administering a normal or non-diseased microbiome population, or a fecal microbiota transplantation (FMT) material, to the washed mucosal environment in the individual in need thereof, wherein optionally the normal or non-diseased microbiome population, or a fecal microbiota transplantation (FMT) material, is administered or formulated as a liquid, a solution, a freeze-dried or lyophilized formulation, wherein the removing of some (substantially all) or all microbiome from a mucosal environment in the individual in need thereof comprises administration of a formulation comprising a biofilm dissolving or disrupting agent selected from:(a) bromelain and acetylcysteine, or(b) bromelain and acetylcysteine, and any one or several of: a solution of soap in water, N-acetylcysteine, dispersin, ribonucleic-acid-III inhibiting peptide (RIP), Salvadora persica extracts, competence-stimulating peptide (CSP) patulin (PAT), penicillic acid (PA) / EDTA, cathelicidin-derived peptides, small lytic peptide PTP-7, nitric oxide, cys-2-decenoic acid, sodium nitroprusside, s-nitroso- 1-glutathione (GSNfaO), s-nitroso -N- acetylpenicillamine (SNAP), chlorhexidine, povidone-iodine (PI), a nanoemulsion, a lytic bacteriophage, a lactoferrin, a xylitol hydrogel, a synthetic iron chelator, a cranberry component, a curcumin, acetyl- 11-keto-boswellic acid (AKBA), a barley coffee (BC) component, silver nanoparticles, a probiotic (optionally the probiotic comprises a Bacillus), sinefungin, N-acetyl-cysteine, S-adenosylmethionine, S-adenosyl- homocysteine, a Delisea furanone, a N-sulfonyl homoserine lactone, iron salts, ionic silver salts, arsenicals, selenium, titanium dioxide, gallium nitrate, ethanol, hydrogenperoxide, hydrochloric acid, formaldehyde, luminal formalin in low concentrations, ozonated water, super-oxidized aqueous solution, nitrofurantoin, hexamine hippurate, potassium hydroxide, mercuric chloride, an iodine- or iodopovidone-comprising formulation (optionally the iodine- or iodopovidone-comprising formulation comprises povidone-iodine (PVP-I) and / or polyhexamethylene biguanide (PHMB)), disodium EDTA, ozone insufflation, and a combination of selenium and gentamicin; or is selected from the group consisting of azithromycin, clarithromycin, gentamicin, vancomycin, rifaximin, rifabutin, rifampicin, streptomycin, erythromycin, roxithromycin, DEA-CP, bismuth thiols, bismuth subcitrate; bismuth subsalicylate; a bismuth ethanondiothol, a bismuth dimercaprol, a bismuth dimercapropranol, an antibiotic (and optionally the antibiotic comprises a secnidazole, nitazoxanide, furazolidone, a nitroimidazole (for example, metronidazole, tinidazole, nimorazole, dimetridazole, pretomanid, omidazole, megazol, and / or azanidazole), paromomycin, iodoquinol, doxycycline, norfloxacin, ciprofloxacin, levofloxacin, a P-lactam antibiotic such as penicillin (or penicillin G or penicillin V) and / or neomycin), a vitamin (and optionally the vitamin comprises vitamin C), a nanoparticle (and optionally the nanoparticle comprises a silver nanoparticle), a micropore particle or any combination thereof.

[0007] In alternative embodiments, provided are methods of microbiome transplantation and engraftment in a mucosal environment in an individual in need thereof, the method comprising: removing of some (substantially all) or all microbiome from a mucosal environment in the individual in need thereof, wherein optionally the microbiome in the mucosal environment is an infected, diseased or dysfunctional microbiome, or a microbiome causing, aggravating or perpetuating a disease or condition, and optionally the mucosal environment is a gastrointestinal (GI) tract, respiratory tract, stomach, nasal sinus, nasopharyngeal, lung, bladder or vaginal mucosal environment,wherein if the mucosal environment is the colon, removing of some (substantially all) or all colonic fecal material from the colon of the individual in need thereof by washing out colonic fecal material from the colon, and administering a normal or non-diseased microbiome population, or a fecal microbiota transplantation (FMT) material, to the washed mucosal environment in the individual in need thereof, wherein optionally the normal or non-diseased microbiome population, or a fecal microbiota transplantation (FMT) material, is administered or formulated as a liquid, a solution, a freeze-dried or lyophilized formulation, wherein the removing of some (substantially all) or all microbiome from a mucosal environment in the individual in need thereof comprises administration of a formulation comprising a biofilm dissolving or disrupting agent selected from:(a) bromelain and acetylcysteine.

[0008] In alternative embodiments, said removing of some, substantially all or all infected or diseased or dysfunctional microbiome, or colonic fecal material, and / or said administering a normal or non-diseased microbiome, or a fecal microbiota transplantation (FMT), is carried out using a device as described in U.S. Patent Application Publication serial no. US / 2018 / 0235448 Al; U.S. Patent Application Publication serial no.US / 2018 / 0344907 Al; U.S. Patent no. 10,022,488; U.S. Patent no. 10,080,487; U.S. Patent no. 10,179,202; U.S. Patent no. 10,265,461; U.S. Patent no. 10,322,226; and / or U.S. Patent no. 9,949,618.

[0009] In alternative embodiments, said removing of some, substantially all or all infected or diseased or dysfunctional microbiome, or colonic fecal material, and / or said administering a normal or non-diseased microbiome, or a fecal microbiota transplantation (FMT), is carried out using a colonoscope, optionally, an OLYMPUS EVIS EXERA III GIF-HQ190 VIDEO GASTROSCOPE™ (KenMed Surgical) or equivalents; or an ELUXEO 700 SERIES® colonoscope (Fuji) or equivalents; or a SLIM DEC DUODENOSCOPE™ (Pentax Medical) or equivalents.

[0010] In alternative embodiments, said removing of some, substantially all or all infected or diseased or dysfunctional microbiome, or colonic fecal material, and / or said administering a normal or non-diseased microbiome, or a fecal microbiota transplantation (FMT), is carried out using an AQUANET™ or equivalent thereof, or a MOTUS PURE- VU EVS SYSTEM™ or equivalent thereof.

[0011] In alternative embodiments, the normal or non-diseased microbiome, or fecal microbiota transplantation (FMT) material, liquid, formulation or solution, is administered to the individual in need thereof immediately after the removing of some, substantially all or all of the infected or diseased or dysfunctional microbiome, or colonic fecal material.

[0012] In alternative embodiments, the fecal microbiota transplantation (FMT) material, liquid, formulation or solution, or a normal or non-diseased microbiome, is administered to the individual in need thereof less than 1 hour after the removing of some, substantially all or all of the infected or diseased or dysfunctional microbiome, or colonic fecal material.

[0013] In alternative embodiments, the fecal microbiota transplantation (FMT) material, liquid, formulation or solution, or a normal or non-diseased microbiome, is administered to the individual in need thereof less than 15 minutes after the removing of some, substantially all or all of the infected or diseased or dysfunctional microbiome, or colonic fecal material.

[0014] In alternative embodiments, provided are methods for treating, ameliorating, or preventing a gastrointestinal (GI) disease initiated by or exacerbated by a pathological colonic microbiome in an individual in need thereof, the method comprising carrying out the method as provided herein. In alternative embodiments, the gastrointestinal (GI) disease initiated by or exacerbated by a pathological colonic microbiome is constipation or ulcerative colitis. In alternative embodiments, the gastrointestinal (GI) disease initiated by or exacerbated by a pathological colonic microbiome is irritable bowel syndrome.

[0015] In alternative embodiments, provided are methods for treating, ameliorating, or preventing: colitis (such as a microscopic colitis or allergic colitis, or pouchitis), Crohn’sdisease, irritable bowel syndrome, constipation, autism (optionally, autism spectrum disorder), also a GI infection, collagenous colitis, Multiple Sclerosis (MS), Parkinson’s disease (PD), any Gl-related condition, the method comprising carrying out the method as provided herein.

[0016] In alternative embodiments, provided are methods for treating, ameliorating, lessening the severity of or decreasing the symptoms of, or preventing: a diarrhea (for example, an antibiotic-associated diarrhea), Alzheimer’s disease (AD); Alopecia, Anorexia nervosa; Celiac disease; Chronic intestinal pseudo-obstruction (CIPO); Cytomegalovirus (CMV) infection; Chronic obstructive pulmonary disease (COPD); a viral infection (for example, a norovirus, Epstein-Barr virus (EBV) or influenza infection, or COVID- 19 infection, Coronavirus disease 2019 or long COVID); a fungal infection; a bacterial infection (for example, Helicobacter pylori infection or sepsis or a multi-drug resistant infection); lung abscess, pyogenic liver abscess, Diversion colitis; Drug-induced hypersensitivity syndrome (DIHS); D-lactic acidosis; Essential tremor; Hepatic encephalopathy; Immune dysregulation polyendocrinopathy enteropathy X-linked syndrome (IPEX syndrome); Immune thrombocytopenia; Multiple organ dysfunction syndrome (MODS); Multiple sclerosis (MS); Nonalcoholic fatty liver disease; Primary sclerosing cholangitis; Severe alcoholichepatitis; Systemic sclerosis; Primary Sclerosing Cholangitis (PSC); radiation enteritis, hypertension, graft versus host disease, Crohn’s disease (CD), intraperitoneal infection, urinary tract infection, cirrhosis, Non-alcoholic fatty liver disease (NAFLD), Subarachnoid Hemorrhage (SAH), chronic fatigue syndrome, depression, anxiety, epilepsy, bipolar disorder, alcoholism (or alcohol use disorder), Tourette syndrome, atopic dermatitis, a cancer (for example, melanoma, adenocarcinoma, a gastric, intestinal or colon cancer, such as a gastro-esophageal cancer), gut fermentation syndrome, food intolerance, small intestine bacterial overgrowth, nonerosive reflux disease, colitis (optionally collagenous colitis or early onset colitis), metabolic syndrome, diabetes, gout, obesity, and / or trimethylaminuria (TMAU), Good’s syndrome, a chemotherapy induced diarrhea such as a TKI-induced diarrhea, dry eye, alopecia, kidney disease (such as chronic kidney disease), arthropathy, psoriasis, irritable bowel syndrome, constipation, and / or any disease or condition as set forth in FIG. 2 the method comprising carrying out a method as provided herein.

[0017] In alternative embodiments, provided are pharmaceutical compositions or formulations comprising:(a) bromelain and acetylcysteine, or(b) bromelain and acetylcysteine, and any one or several of: a solution of soap in water, N-acetylcysteine, dispersin, ribonucleic-acid-III inhibiting peptide (RIP), Salvadora persica extracts, competence- stimulating peptide (CSP) patulin (PAT), penicillic acid (PA) / EDTA, cathelicidin-derived peptides, small lytic peptide PTP-7, nitric oxide, cys-2-decenoic acid, sodium nitroprusside, s-nitroso- 1-glutathione (GSNfaO), s-nitroso-N-acetylpenicillamine (SNAP), chlorhexidine, povidone-iodine (PI), a nanoemulsion, a lytic bacteriophage, a lactoferrin, a xylitol hydrogel, a synthetic iron chelator, a cranberry component, a curcumin, acetyl- 11-keto-boswellic acid (AKBA), a barley coffee (BC) component, silver nanoparticles, a probiotic (for example, a Bacillus), sinefungin, N-acetyl-cysteine, S-adenosylmethionine, S-adenosyl- homocysteine, a Delisea furanone, a N-sulfonyl homoserine lactone, iron salts, ionic silver salts, arsenicals, selenium, titanium dioxide, gallium nitrate, ethanol, hydrogen peroxide, hydrochloric acid, formaldehyde, luminal formalin in low concentrations, ozonated water, super-oxidized aqueous solution, nitrofurantoin, hexamine hippurate, potassium hydroxide, mercuric chloride, iodine or iodopovidone (for example, povidone- iodine (PVP-I) and / or polyhexamethylene biguanide (PHMB)), disodium EDTA, ozone insufflation, and a combination of selenium and gentamicin; or is selected from the group consisting of azithromycin, clarithromycin, gentamicin, vancomycin, rifaximin, rifabutin, rifampicin, streptomycin, erythromycin, roxithromycin, DEA-CP, bismuth thiols, bismuth subcitrate; bismuth subsalicylate; a bismuth ethanondiothol, a bismuth dimercaprol, a bismuth dimercapropranol, an antibiotic (for example, a secnidazole, nitazoxanide, furazolidone, a nitroimidazole (for example, metronidazole, tinidazole, nimorazole, dimetridazole, pretomanid, ornidazole, megazol, and / or azanidazole), paromomycin, iodoquinol, doxycycline, norfloxacin, ciprofloxacin, levofloxacin, a P-lactam antibiotic such as penicillin (or penicillin G or penicillin V) and / or neomycin), a vitamin (for example, vitamin C), a nanoparticle (for example, a silver nanoparticle), a micropore particle or any combination thereof.

[0018] In alternative embodiments the pharmaceutical compositions or formulations are formulated into a capsule or a tablet, a solid, a liquid (optionally saline), a powder or an aerosol.

[0019] In alternative embodiments, provided are uses of a pharmaceutical composition or formulation as provided herein for treating, ameliorating, lessening the severity of or decreasing the symptoms of, or preventing a disease or condition as provided herein.

[0020] In alternative embodiments, provided are pharmaceutical compositions or formulations for use in treating, ameliorating, lessening the severity of or decreasing the symptoms of, or preventing a disease or condition as provided herein, wherein the pharmaceutical compositions or formulations comprise a pharmaceutical compositions or formulations as set forth herein.

[0021] In alternative embodiments, provided are trans-colonoscopic devices comprising a lumen having an aspiration port lumen of between about 2 mm and 20 mm, or having an aspiration port lumen between about 3 and 10 mm, or having an aspiration port lumen of about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 4, 15, 16, 17, 18, 19 or 20 or more mm in diameter, wherein the device further comprises or is combined with multiple (or a plurality of) waterjets or channels circumferentially positioned or situated around the tip / edge of the device. In alternative embodiments the trans-colonoscopic devices as provided herein further comprise multiple (or a plurality of) waterjets or channels circumferentially positioned or situated within between about 0.5 and 20 cm of the tip or end of the tip / end / or edge of the instrument or device, or between about 1 mm and 15 cm of the tip or end of the tip / end / or edge of the instrument or device, or between about 10 mm and 10 cm of the tip or end of the tip / end / or edge of the instrument or device, optionally also being positioned at the tip of the device / instrument.

[0022] In alternative embodiments, provided are trans-colonoscopic devices comprising a removable (or replaceable) external layer or sleeve comprising multiple or a plurality of fluid streaming channels; this external layer or sleeve is removable (replaceable) to accommodate for the degeneration or dissolving of plastic tubing by some biofilm dissolving agents.

[0023] The details of one or more exemplary embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.

[0024] All publications, patents, patent applications cited herein are hereby expressly incorporated by reference in their entireties for all purposes.Brief Description of Drawings

[0025] The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

[0026] Figure 1 describes the mechanism of mucolytic action with bromelain and acetylcysteine.

[0027] Figure 2 depicts conditions, diseases or infections caused by or aggravated by an infected or dysfunctional mucosal biofilm.

[0028] Figure 3 depicts a device having a large aspiration port lumen.

[0029] The drawings set forth herein are illustrative of exemplary embodiments provided herein and are not meant to limit the scope of the invention as encompassed by the claims.

[0030] Figures are described in detail herein.

[0031] Like reference symbols in the various drawings indicate like elements.Detailed Description

[0032] In alternative embodiments, provided are products of manufacture and methods for treating, ameliorating and preventing diseases and conditions related to infected or dysfunctional mucosal surfaces, including mucosal surfaces in the gastrointestinal (GI)tract, respiratory tract, and other mucosal surfaces, for example, mucosal surfaces in the stomach, nasal sinuses or the vagina. Provided are methods and products of manufacture for preparing the GI tract for a microbiota engraftment, then infusing a colonic microbiota engraftment, for example, a fecal microbiota transplant (FMT). In alternative embodiments, provided are methods and products of manufacture for the chemical and / or biologic dissolution of a mucus layer or biofilm and / or mechanical disruption of the biofilm, and subsequent implantation of FMT material onto or into a mucosal surface such as a GI tract.

[0033] In alternative embodiments, products of manufacture and methods as provided herein address the problems and failures of researchers and clinicians in attempting various methods of achieving FMT implantation, where even using multiple infusions and antibiotic pre-treatment and the use of so called super donors have failed. In alternative embodiments, products of manufacture and methods as provided herein focus on mucosal biofilm and its substantial removal. Inventor has trialed multiple infusions and surprisingly found that substantially dissolving of the mucous layer or biofilm of a GI tract, for example, in a colon, can markedly prolong the success of an FMT implantation.Triple component therapy

[0034] In alternative embodiments, products of manufacture and methods as provided herein comprise use of serial, almost simultaneous, or simultaneous use of several components. In alternative embodiments, provided herein is a triple component therapy comprising: use of equipment or devices for delivery of high flow liquids to a mucosal surface in vivo / in situ, for example, for delivery in the colon; formulations for the chemical / biologic dissolution of a mucus layer or a biofilm in an individual in need thereof; and, microbiome replacement therapy or in vivo administration (or patient delivery) of FMT material.Devices used to practice exemplary methods

[0035] In alternative embodiments, devices or products of manufacture used to practice exemplary methods as provided herein can include methods and / or equipment or devices for delivery of high flow liquids to a mucosal surface in vivo / in situ, for example, fordelivery in the colon, as described by for example US Patent nos. 10,244,980;10,314,536; 10,881,277; 11,185,625; 11,484,632, 11,766,464; and, U.S. patent application publication no. US 20210076906 Al.

[0036] In alternative embodiments, devices or products of manufacture used to practice exemplary methods, for example, to deliver a chemical / biologic dissolution formulation and / or a microbiome transplant (such as an FMT), can include or comprise a component of any colonoscope, for example, an OLYMPUS EVIS EXERA III GIF-HQ190 VIDEO GASTROSCOPE™ (KenMed Surgical) or equivalents; or an ELUXEO 700 SERIES® colonoscope (Fuji Holdings) or equivalents; or a SLIM DEC DUODENOSCOPE™ (Pentax Medical) or equivalents; or ENDOCHOICE FUSE™ colonoscopy devices (Boston Scientific), or equivalents.

[0037] In alternative embodiments, devices or products of manufacture used to practice exemplary methods, for example, to deliver a chemical / biologic dissolution formulation and / or a microbiome transplant (such as an FMT), can include or comprise a component of a PURE-VU EVS SYSTEM™ (Motus GI Holdings, Inc.), any standard colonic washout device, for example, by cleansing devices (BCDs) by for example AQUANET™, various oro- and naso-jejunal tubes, and / or gastrostomy-to-jejunum tubes.

[0038] All these devices make up one of the three components of an exemplary combination therapy package as provided herein, which can achieve effective treatments and in some cases cures in over 80 conditions known to be mediated or exacerbated by an infected microbiome.

[0039] For example, in alternative embodiments, in chronic vaginal infections a simplified ‘enema-like’ tube with or without balloon / s may be used to deliver the other two components for cure. In alternative embodiments, for a nasopharyngeal area, nasal or nasopharyngeal catheters or sprays can be used as the device component for the exemplary triple therapy to approach cure. In alternative embodiments, for chronic lung infections intubation, bronchoscopic delivery, nebulizer masks, or puffers can deliver the other components. In alternative embodiments, for treating chronic bladder infections, balloon-carrying urinary catheters are used as a delivery device.

[0040] In alternative embodiments, one or several devices singly or in combination are used to deliver a liquid to a biofilm-comprising mucosa, for example, to a bowel or a nasopharyngeal area, the lungs, vagina or bladder, and these devices are used as delivery vehicles for the dissolving agents which clear the biofilm.

[0041] For example, the device described by MOTUS GI HOLDINGS INC™ medical technology company can be used for cleansing of the bowel stool, and in alternative embodiments as provided herein is repurposed to remove more than just the gut stool or microbiome but also to remove the closely adherent biofilm; MOTUS GI HOLDINGS INC™ did not develop the device to remove biofilm, and it is FDA approved to remove luminal stool.

[0042] In alternative embodiments, one or several devices used to practice methods as provided herein comprise use of a waterjet and / or aspiration or multiple jets with large volume of infusion and large volume aspiration; for example, a device such as a PURE- VU EVS SYSTEM™ device; which is designed for reducing colonoscopy failures due to leftover stool; and in alternative embodiments as provided herein, this device is repurposed and used to remove biofilm, including very thin pm sized biofilm.

[0043] In alternative embodiments, the washing out phase uses a nasojejunal tube, or the patient can wear a vibrating jacket to agitate the intraluminal contents, thus accelerating biofilm dissolution.

[0044] In alternative embodiments, one or several devices used to practice methods as provided herein, for example to administer biofilm dissolving or disruption agents, comprise use of a nasojejunal tube, a per-endoscopic gastrostomy (PEG) tube, or for delivery to the rectum upwards (as high as the terminal ileum) using a MOTUS PURE- VU EVS SYSTEM™ or equivalent thereof.

[0045] As an alternative design which improves on the MOTUS PURE-VU EVS SYSTEM™ or equivalent thereof devices or instruments, or any of the devices or instruments described above, or similar or equivalent devices or instruments, provided herein is a novel endoscopic instrument or device which avoids having (or does not need to have to work effectively) an attached “add-on” tube or external sleeve for fluidinfusion / aspiration as it uses a very large or wide lumen for an aspiration port (as illustrated in FIG. 3) (for example, having an aspiration port lumen of between about 2 mm and 20 mm, or having an aspiration port lumen between about 3 and 10 mm, or having an aspiration port lumen of about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 4, 15, 16, 17, 18, 19 or 20 or more mm in diameter) trans-colonoscopic device combined with multiple (or a plurality of) water jets or channels circumferentially positioned or situated around, at and / or near the tip / end / or edge of the instrument or device (for example, the multiple (or a plurality of) waterjets or channels are circumferentially positioned situated within between about 0.5 and 20 cm of the tip or end of the tip / end / or edge of the instrument or device, or between about 1 mm and 15 cm of the tip or end of the tip / end / or edge of the instrument or device, or between about 10 mm and 10 cm of the tip or end of the tip / end / or edge of the instrument or device, optionally also being positioned at the tip of the device / instrument). These novel improvements to endoscopes as provided herein can be built to include the design of any currently produced endoscope or colonoscope, and also comprising a circle of jets. These novel improvements to endoscopes as provided herein can be applied to any available devices or instruments known in the art, and / or as described herein, including for example, devices from PENTAX™, OLYMPUS™, FUJI™, WOLF™, STORZ™, STRYKER™, HO YA™, or other brands of endoscopic devices.

[0046] In alternative embodiments, the devices or instruments are wider to accommodate a large aspiration lumen. Through the length of the novel instrument there will be a large diameter aspirating channel or channels equivalent or larger than that on the current MOTUS PURE-VU EVS SYSTEM™ system. This way, no specific external sleeve or over-tube would be required because it causes its use to be complicated, convoluted, tangled, with numerous tubes attached in almost a disorganised manner. This tends to make the procedure luminal examination more difficult.

[0047] In alternative embodiments, these improvements are done in gastroscopes, endoscopic retrograde cholangiopancreatography (ERCP) instruments, colonoscopes and / or pediatric colonoscopes, and the like; and in alternative embodiments the equipment may require specialized pumps attached so that large volumes of fluid can be injected into the bowel and large volumes aspirated.

[0048] In alternative embodiments, the devices or instruments as provided herein comprise a removable (or replaceable) external layer or sleeve comprising multiple or a plurality of fluid streaming channels; this external layer or sleeve is removable (replaceable) to accommodate for the degeneration or dissolving of plastic tubing by some biofilm dissolving agents.

[0049] In alternative embodiments, novel devices or instruments as provided herein are used for biofilm removal, and these instruments and devices are capable of delivering large volumes of biofilm-dissolving and mucolytic agents. In alternative embodiments, the large volume of biofilm-dissolving and mucolytic agents delivered can be any known in the art, for example, biofilm-dissolving and mucolytic agents as described herein, for example, including large volume of soap and water, bromelain and acetylcysteine (or BROM AC™), iodine or an iodine formulation, a recombinant human deoxyribonuclease I (rhDNase) or domase alfa (or PULMOZYME™), N-acetylcysteine (NAC), glutathione, or any known biofilm dissolving chemical such as classic and peptide mucolytics including carbocysteine (or carbocisteine) ((R)-2-Amino-3- (carboxymethylsulfanyl)propanoic acid), erdosteine, fudosteine (or S-(3-Hydroxypropyl)- L-cysteine, or CLEANAL™), thymosin beta 4 (or timbetasin), and F-actin.

[0050] The biofilm and / or mucolytics can also be delivered through a naso-jejunal tube in combination of using a colonoscope from below the nasojejunal tube from above to cover the distal small bowel by removing the biofilm there, or naso-jejunal tube alone.

[0051] In alternative embodiments, one or several devices used to practice methods as provided herein, for example to administer biofilm dissolving or disruption agents, comprise use of an enteroscope, although it will take a long time to have to be passed and will be uncomfortable or require prolonged sedation.

[0052] In alternative embodiments, an AQUANET™ pre-wash can be used prior to the MOTUS PURE-VU EVS SYSTEM™ or equivalent thereof. In alternative embodiments, soap and water and bromelain and acetylcysteine (for example, BROMAC™) to dissolve the hard forms of mucus distally.

[0053] In alternative embodiments, prior to administration of biofilm dissolving or disruption agents, the methods comprise administration of one to four weeks or more of vancomycin plus rifaximin to kill some of the bacteria inside the biofilm.Biofilm dissolving agents

[0054] In alternative embodiments, a second component of a triple component therapy (comprising: a delivery device, for example, a coloscope as provided herein; biofilm dissolver(s); and, fecal matter transplantation (FMT)) as provided herein is the chemical and / or biologic dissolution of a mucus layer or biofilm, including biofilms that have about a 5 to 400 pm thick layer comprising bacterial cells surrounded by extracellular polymers including polysaccharides, proteins and extracellular DNA (also called eDNA). The biofilm protects the bacteria which can better survive in the hostile environment, and the biofilm is notoriously difficult to dissolve completely and even when dissolved any remaining bacteria in concert with the surface epithelial cells can regenerate a biofilm in between about 20 to 60 minutes. Because a single dissolving agent may be inadequate to achieve dissolution, methods and formulations as provided herein comprise a combination of chemical agents for substantial biofilm removal, and can also comprise use of local agitation of the mucosal layer. Because a single dissolving agent may be inadequate to achieve dissolution, methods and formulations as provided herein comprise a combination of chemical agents for substantial biofilm removal, and can also comprise use of local agitation of the mucosal layer, for example, using a vibrating belt (for example, using VIBROBELT™) or a similar device to agitate intraluminal fluid.

[0055] In alternative embodiments, methods as provided herein use biofilm disrupting and / or dissolution formulation or agents, which can be used singly or combined, and biofilm disrupting and / or dissolution formulation or agents as provided herein comprise use of saline, the combination of bromelain and acetylcysteine (which can be BROM AC™), soap and water, ethanol, acetic acid and iodine and / or any combination thereof.

[0056] In alternative embodiments, the term "bromelain" refers to either of two protease enzymes extracted from the plants of the family Bromeliaceae, or extracted from pineapple, or Ananas comosus, or it may refer to a combination of those enzymes alongwith other compounds produced in an extract. In alternative embodiments, bromelain extract is a mixture of protein-digesting (proteolytic) enzymes and several other substances in smaller quantities; and, the proteolytic enzymes are sulfhydryl proteases; a free sulfhydryl group of a cysteine amino acid side chain is required for function. In alternative embodiments the two main enzymes in bromelain are: stem bromelain, or EC 3.4.22.32; and, fruit bromelain (or BROMELASE™), or EC 3.4.22.33, which catalyses the hydrolysis of proteins with broad specificity for peptide bonds, for example, Bz-Phe- Val-Arg-NHMec is a synthetic substrate of fruit bromelain.

[0057] In alternative embodiments, the combination of bromelain and acetylcysteine (for example, BROMAC™) is particularly important in removing the mucus layer. While the invention is not limited by any particular mechanism of action, FIG. 1 describes the mechanism of mucolytic action with bromelain and acetylcysteine (for example, BROMAC™). Mucin polymers (as in biofilms) comprise a peptide backbone held together by glycosidic linkages, with glycoprotein tails which interact through disulphide bonds. Bromelain acts on the glycoside linkages within the peptide chain, whilst acetylcysteine cleaves the disulphide bridges between oligosaccharide side chains. The combined effect of bromelain and acetylcysteine is to synergistically interact to provide a greater mucolytic effect. Bromelain has also been theorised to promote the growth of good bacteria as well as suppressing the growth and toxic secretions of bad bacteria. In some embodiments, Bromelain may aid in the implantation of the donor microbiome while suppressing the hosts pre FMT microbiome.

[0058] In alternative embodiments, formulations as provided herein, or formulations or combinations of biofilm dissolving or disrupting agents as used in methods and products of manufacture as provided herein, comprise one or any combination of: bromelain, a combination of bromelain and acetylcysteine, a solution of soap in water, N- acetylcysteine, dispersin, ribonucleic-acid-III inhibiting peptide (RIP), Salvadora persica extracts, competence- stimulating peptide (CSP) patulin (PAT), penicillic acid (PA) / EDTA, cathelicidin-derived peptides, small lytic peptide PTP-7, nitric oxide, cys-2- decenoic acid, sodium nitroprusside, s-nitroso- 1-glutathione (GSNfaO), s-nitroso -N- acetylpenicillamine (SNAP), chlorhexidine, povidone-iodine (PI), a nanoemulsion, a lytic bacteriophage, a lactoferrin, a xylitol hydrogel, a synthetic iron chelator, a cranberry component, a curcumin, acetyl- 11-keto-boswellic acid (AKBA), a barley coffee (BC)component, silver nanoparticles, a probiotic (for example, a Bacillus), sinefungin, N- acetyl-cysteine, S-adenosylmethionine, S-adenosyl-homocysteine, a Delisea furanone, a N-sulfonyl homoserine lactone, iron salts, ionic silver salts, arsenicals, selenium, titanium dioxide, gallium nitrate, ethanol, hydrogen peroxide, hydrochloric acid, formaldehyde, luminal formalin in low concentrations, ozonated water, super-oxidized aqueous solution, nitrofurantoin, hexamine hippurate, potassium hydroxide, mercuric chloride, iodine or iodopovidone (for example, povidone-iodine (PVP-I) and / or polyhexamethylene biguanide (PHMB)), disodium EDTA, ozone insufflation, and a combination of selenium and gentamicin; or is selected from the group consisting of azithromycin, clarithromycin, gentamicin, vancomycin, rifaximin, rifabutin, rifampicin, streptomycin, erythromycin, roxithromycin, DEA-CP, bismuth thiols, bismuth subcitrate; bismuth subsalicylate; a bismuth ethanondiothol, a bismuth dimercaprol, a bismuth dimercapropranol, an antibiotic (for example, a secnidazole, nitazoxanide, furazolidone, a nitroimidazole (for example, metronidazole, tinidazole, nimorazole, dimetridazole, pretomanid, ornidazole, megazol, and / or azanidazole), paromomycin, iodoquinol, doxycycline, norfloxacin, ciprofloxacin, levofloxacin, a P-lactam antibiotic such as penicillin (or penicillin G or penicillin V) and / or neomycin), a vitamin (for example, vitamin C), a nanoparticle (for example, a silver nanoparticle), a micropore particle or any combination thereof.

[0059] In alternative embodiments, antibiotic pre-treatment with one, 2, 3, 4, 5 or more antibiotics, including for example any of the above-described antibiotics, for at least 1 to 2 weeks, or between one week and one month, or between about 2 weeks and 6 months, or longer, are also used to enhance FMT engraftment in an individual in need thereof.FMT materials

[0060] In alternative embodiments, a third component of a triple component therapy as provided herein is the microbiome replacement therapy or in vivo administration (or patient delivery) of FMT material.

[0061] Inventor has found that by using the combination triple therapy as provided herein, mucosal biofilms (for example, colonic biofilms) can be substantially removed and long term FMT engraftment success improved, improving a 6 to 24 weeks period of FMT engraftment success, improving on previous about 50% success of patients treatedand FMT engrafted. By using the combination triple therapy as provided herein a high level of improvement is seen, for example, for patients treated with methods as provided herein, including the combination triple therapy as provided herein, about 90% remain engrafted at 12 months and the majority continue to be engrafted and clinically well for several years.

[0062] In alternative embodiments, an exemplary FMT implantation of new microbiome comprises: a liquid product or an encapsulated product, either or both with one or more or various additions, for example, including sugars such as trehalose.

[0063] In alternative embodiments, an exemplary FMT used in methods and products as provided herein comprise donor-derived microbiota can be used or cultured microbiota in lower numbers. In alternative embodiments, non-donor derived, for example, non-human bacteria, yeast and / or fungi, can also be added to the mix. In alternative embodiments, mixtures of the above can be the cellular or filtered and be acellular human or non-human compositions. In alternative embodiments, the liquid is stored frozen and unfrozen for infusion. In alternative embodiments, the FMT microbiota and / or bacteria are formulated as a solid or powder or lyophilized formulation, which can be formulated into capsules, for example, by freeze-drying an extract, for example, freeze-drying a washed extract, for example, as described in US Patent Nos. 9,901,603; 10,821,138; and 11,123,377.

[0064] In alternative embodiments, the combination triple therapy as provided herein is used to control, or diminish, or substantially remove or disrupt, a mucus layer to permit FMT implantation of a new microbiome that is foreign to the individual in need thereof (a patient), and the combination triple therapy and the FMT implantation of a new microbiome can administered to a gastrointestinal tract, including for example a small bowel (intestine), a large bowel (a colon) or a small and a large bowel.

[0065] In alternative embodiments, the combination triple therapy as provided herein and a microbiota implantation of a new microbiome can also be administered to or implanted in a nasal sinus, or a nasopharyngeal area. In alternative embodiments, the nasal mucosa is washed and flushed with dissolving agents.

[0066] In alternative embodiments, the combination triple therapy as provided herein and a microbiota implantation of a new microbiome can be used to replace an infected or dysfunctional lung microbiome to, for example, relieve and cure presence of asthma and other chronic infections that may be causing idiopathic pulmonary fibrosis.

[0067] In alternative embodiments, the combination triple therapy as provided herein and a microbiota implantation of a new microbiome can be used in a vagina to remove a microbe, for example, a fungi, and then re-implant a normal or non-infected or diseased vaginal microbiome, which optionally comprises various Lactobacilli.

[0068] In alternative embodiments, the combination triple therapy as provided herein and a microbiota implantation of a new microbiome can be used in a bladder for a bladder infection, such as a chronic bladder infection.

[0069] In alternative embodiments, the combination triple therapy as provided herein and a microbiota implantation of a new microbiome can be used in children with autism spectrum disorder (ASD) and / or autism. Pediatric nurses, anesthetists, small anesthetic equipment, and sedation recovery nurses may be required.

[0070] In alternative embodiments, before the biofilm removal process, individuals in need thereof are treated or pre-treated with one or various antibiotics, for example, using poorly absorbable vancomycin and rifaximin are administered.

[0071] In alternative embodiments, children are given a food, for example, a yoghurt, capsule preparation, such a RITE PREP™, then sedated, colonoscoped with the MOTUS PURE-VU EVS SYSTEM™ or equivalent thereof, the biofilm substantially disrupted or removed, and FMT material administered, for example, in the form of a liquid, In alternative embodiments, children are infused with formulation into the terminal ileum, for example, using uniform volumes, then the colonoscope is withdrawn. Carbon dioxide gas (not air) can be used to distend the bowel.

[0072] Oral FMT capsules may then follow (for example, one to ten capsules a day, or once a day, once every other day, twice a week, or once a week) for between about one to 26 weeks, or between about two to 50 weeks.

[0073] In some embodiments Bromelain tablets are admininstered together with the FMT capsules. For example, the Bromealin tablets may be administered together with the FMT capsules for between about one to about twenty days, or for about ten days.Diseases and conditions caused by infected biofilm

[0074] In alternative embodiments, methods and formulations as provided herein, including the triple component therapy as provided herein, can be used to treat, ameliorate and / or prevent any condition or disease or infection caused by or aggravated by an infected or dysfunctional mucosal biofilm, including for example: colitis (optionally collagenous colitis or early onset colitis), Crohn’s disease, irritable bowel syndrome of its various forms, constipation, autism, also a GI infection, Multiple Sclerosis (MS), Parkinson’s disease (PD), any Gl-related condition. Inventor has found that substantially dissolving of the mucous layer or biofilm can markedly prolong the success of FMT implantation.

[0075] In alternative embodiments, methods and formulations as provided herein, including the triple component therapy as provided herein, can be used to treat, ameliorate and / or prevent: a diarrhea (for example, an antibiotic-associated diarrhea), Alzheimer’s disease (AD); Alopecia, Anorexia nervosa; Celiac disease; Chronic intestinal pseudoobstruction (CIPO); Cytomegalovirus (CMV) infection; Chronic obstructive pulmonary disease (COPD); a viral infection (for example, a norovirus, Epstein-Barr virus (EBV) or influenza infection, or COVID-19 infection, Coronavirus disease 2019 or long COVID); a fungal infection; a bacterial infection (for example, Helicobacter pylori infection or sepsis or a multi-drug resistant infection); lung abscess, pyogenic liver abscess, Diversion colitis; Drug-induced hypersensitivity syndrome (DIHS); D-lactic acidosis; Essential tremor; Hepatic encephalopathy; Immune dysregulation polyendocrinopathy enteropathy X-linked syndrome (IPEX syndrome); Immune thrombocytopenia; Multiple organ dysfunction syndrome (MODS); Multiple sclerosis (MS); Nonalcoholic fatty liver disease; Primary sclerosing cholangitis; Severe alcoholichepatitis; Systemic sclerosis;Primary Sclerosing Cholangitis (PSC); radiation enteritis, hypertension, graft versus host disease, Crohn’s disease (CD), intraperitoneal infection, urinary tract infection, cirrhosis, Non-alcoholic fatty liver disease (NAFLD), Subarachnoid Hemorrhage (SAH), chronic fatigue syndrome, depression, anxiety, epilepsy, bipolar disorder, alcoholism (or alcoholuse disorder), Tourette syndrome, atopic dermatitis, a cancer (for example, melanoma, adenocarcinoma, a gastric, intestinal or colon cancer, such as a gastro-esophageal cancer), gut fermentation syndrome, food intolerance, small intestine bacterial overgrowth, nonerosive reflux disease, colitis (optionally collagenous colitis or early onset colitis), metabolic syndrome, diabetes, gout, obesity, and / or trimethylaminuria (TMAU), Good’s syndrome, a chemotherapy induced diarrhea such as a TKI-induced diarrhea, dry eye, alopecia, kidney disease (such as chronic kidney disease), arthropathy, psoriasis, irritable bowel syndrome, constipation, and / or any disease or condition as set forth in FIG. 2.Products of manufacture and Kits

[0076] Provided are products of manufacture and kits for practicing methods as provided herein; and optionally, products of manufacture and kits can further comprise instructions for practicing methods as provided herein.

[0077] Any of the above aspects and embodiments can be combined with any other aspect or embodiment as disclosed here in the Summary, Figures and / or Detailed Description sections.

[0078] As used in this specification and the claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise.

[0079] Unless specifically stated or obvious from context, as used herein, the term “or” is understood to be inclusive and covers both “or” and “and”.

[0080] Unless specifically stated or obvious from context, as used herein, the term “about” is understood as within a range of normal tolerance in the art, for example within 2 standard deviations of the mean. About (use of the term “about”) can be understood as within 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12% 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, or 0.01% of the stated value. Unless otherwise clear from the context, all numerical values provided herein are modified by the term “about.”

[0081] Unless specifically stated or obvious from context, as used herein, the terms “substantially all”, “substantially most of’, “substantially all of’ or “majority of’encompass at least about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 99.5%, or more of a referenced amount of a composition.

[0082] The entirety of each patent, patent application, publication and document referenced herein hereby is incorporated by reference. Citation of the above patents, patent applications, publications and documents is not an admission that any of the foregoing is pertinent prior art, nor does it constitute any admission as to the contents or date of these publications or documents. Incorporation by reference of these documents, standing alone, should not be construed as an assertion or admission that any portion of the contents of any document is considered to be essential material for satisfying any national or regional statutory disclosure requirement for patent applications. Notwithstanding, the right is reserved for relying upon any of such documents, where appropriate, for providing material deemed essential to the claimed subject matter by an examining authority or court.

[0083] Modifications may be made to the foregoing without departing from the basic aspects of the invention. Although the invention has been described in substantial detail with reference to one or more specific embodiments, those of ordinary skill in the art will recognize that changes may be made to the embodiments specifically disclosed in this application, and yet these modifications and improvements are within the scope and spirit of the invention. The invention illustratively described herein suitably may be practiced in the absence of any element(s) not specifically disclosed herein. Thus, for example, in each instance herein any of the terms "comprising", "consisting essentially of", and "consisting of" may be replaced with either of the other two terms. Thus, the terms and expressions which have been employed are used as terms of description and not of limitation, equivalents of the features shown and described, or portions thereof, are not excluded, and it is recognized that various modifications are possible within the scope of the invention. Embodiments of the invention are set forth in the following claims.

[0084] A number of embodiments of the invention have been described. Nevertheless, it can be understood that various modifications may be made without departing from the spirit and scope of the invention. Accordingly, other embodiments are within the scope of the following claims.

[0085] The invention will be further described with reference to the examples described herein; however, it is to be understood that the invention is not limited to such examples.ExamplesExample 1: Treatment of Irritable Bowel Syndrome (IBS)

[0086] Irritable bowel syndrome (IBS) is a functional gastrointestinal disorder characterized by chronic abdominal pain and altered bowel habits which significantly impacts quality of life. FMT has been used for IBS with intermittent success, however a high frequency of disease recurrence often occurs upon cessation of FMT. Either by direct or indirect involvement the intestinal biofilm has been implicated as an influencing factor in sustained FMT response. By mechanical washout involving a mucolytic of the small bowel and colon, and infusion of FMT into both of these areas, the problematic biofilm is eliminated.

[0087] A 31-year-old female patient presented with diarrhoea predominant IBS (IBS-D). Patient’s previous treatments include antibiotic therapy as well as 3 FMT treatments (variations of fresh and frozen by colonoscopy, enema, and nasojejunal (NJ) tube). These treatments were moderately successful however the patient returned to pre-treatment status between 4 to 8 weeks after the last FMT.

[0088] Following an antibiotic preparation the patient underwent FMT treatment via NJ tube and colonoscopic delivery proceeded by a small bowel and colon washout using mucolytic agents (of bromelain and n- acetylcysteine) and isotonic solutions (Hartmann’s lactate). This was followed by FMT capsules along with Bromelain tablets for the next 10 days.

[0089] The patient was monitored for 3 months following the FMT treatment.Table 1. Symptom severity, bowel movements, and condition specific questionnaire results up to 3 months.

[0090] Overall, at the 3 months mark the patient reported her condition to be under control which is confirmed by 9 out of 11 symptoms decreasing in severity or disappearing all together three months post treatment as hown in Table 1.

[0091] Sustained improvements were observed in a single case study of an IBS-D patient receiving FMT via NJ tube and transcolonoscopically which was preceded by a small bowel and colon washout, and followed by 10 days of FMT and Bromelain capsules than with previous FMT treatments.

Claims

CLAIMS:

1. A method for microbiome transplantation and engraftment in a mucosal environment in an individual in need thereof, the method comprising: removing of some (substantially all) or all microbiome from a mucosal environment in the individual in need thereof, wherein optionally the microbiome in the mucosal environment is an infected, diseased or dysfunctional microbiome, or a microbiome causing, aggravating or perpetuating a disease or condition, and optionally the mucosal environment is a gastrointestinal (GI) tract, respiratory tract, stomach, nasal sinus, nasopharyngeal, lung, bladder or vaginal mucosal environment, wherein if the mucosal environment is the colon, removing of some (substantially all) or all colonic fecal material from the colon of the individual in need thereof by washing out colonic fecal material from the colon, and administering a normal or non-diseased microbiome population, or a fecal microbiota transplantation (FMT) material, to the washed mucosal environment in the individual in need thereof, wherein optionally the normal or non-diseased microbiome population, or a fecal microbiota transplantation (FMT) material, is administered or formulated as a liquid, a solution, a freeze-dried or lyophilized formulation, wherein the removing of some (substantially all) or all microbiome from a mucosal environment in the individual in need thereof comprises administration of a formulation comprising a biofilm dissolving or disrupting agent selected from:(a) bromelain and acetylcysteine, or(b) bromelain and acetylcysteine, and any one or several of: a solution of soap in water, N-acetylcysteine, dispersin, ribonucleic-acid-III inhibiting peptide (RIP), Salvadora persica extracts, competence- stimulating peptide (CSP) patulin (PAT), penicillic acid (PA) / EDTA, cathelicidin-derived peptides, small lytic peptide PTP-7, nitric oxide, cys-2-decenoic acid, sodium nitroprusside, s-nitroso- 1-glutathione (GSNfaO), s-nitroso -N-acetylpenicillamine (SNAP), chlorhexidine, povidone-iodine (PI), a nanoemulsion, a lytic bacteriophage, a lactoferrin, a xylitol hydrogel, a synthetic iron chelator, a cranberry component, a curcumin, acetyl- 11-keto-boswellic acid (AKBA), a barley coffee (BC) component, silver nanoparticles, a probiotic (optionally the probiotic comprises a Bacillus), sinefungin, N-acetyl-cysteine, S-adenosylmethionine, S-adenosyl- homocysteine, a Delisea furanone, a N-sulfonyl homoserine lactone, iron salts, ionic silver salts, arsenicals, selenium, titanium dioxide, gallium nitrate, ethanol, hydrogen peroxide, hydrochloric acid, formaldehyde, luminal formalin in low concentrations, ozonated water, super-oxidized aqueous solution, nitrofurantoin, hexamine hippurate, potassium hydroxide, mercuric chloride, an iodine- or iodopovidone-comprising formulation (optionally the iodine- or iodopovidone-comprising formulation comprises povidone-iodine (PVP-I) and / or poly hexamethylene biguanide (PHMB)), disodium EDTA, ozone insufflation, and a combination of selenium and gentamicin; or is selected from the group consisting of azithromycin, clarithromycin, gentamicin, vancomycin, rifaximin, rifabutin, rifampicin, streptomycin, erythromycin, roxithromycin, DEA-CP, bismuth thiols, bismuth subcitrate; bismuth subsalicylate; a bismuth ethanondiothol, a bismuth dimercaprol, a bismuth dimercapropranol, an antibiotic (and optionally the antibiotic comprises a secnidazole, nitazoxanide, furazolidone, a nitroimidazole (for example, metronidazole, tinidazole, nimorazole, dimetridazole, pretomanid, ornidazole, megazol, and / or azanidazole), paromomycin, iodoquinol, doxycycline, norfloxacin, ciprofloxacin, levofloxacin, a P-lactam antibiotic such as penicillin (or penicillin G or penicillin V) and / or neomycin), a vitamin (and optionally the vitamin comprises vitamin C), a nanoparticle (and optionally the nanoparticle comprises a silver nanoparticle), a micropore particle or any combination thereof.

2. The method of claim 1, wherein said removing of some, substantially all or all infected or diseased or dysfunctional microbiome, or colonic fecal material, and / or said administering a normal or non-diseased microbiome, or a fecal microbiota transplantation (FMT), is carried out using a device as described in U.S. PatentApplication Publication serial no. US / 2018 / 0235448 Al; U.S. Patent Application Publication serial no. US / 2018 / 0344907 Al; U.S. Patent no. 10,022,488; U.S. Patent no. 10,080,487; U.S. Patent no. 10,179,202; U.S. Patent no. 10,265,461; U.S. Patent no. 10,322,226; and / or U.S. Patent no. 9,949,618.

3. The method of claim 1, wherein said removing of some, substantially all or all infected or diseased or dysfunctional microbiome, or colonic fecal material, and / or said administering a normal or non-diseased microbiome, or a fecal microbiota transplantation (FMT), is carried out using a colonoscope, optionally, an OLYMPUS EVIS EXERA III GIF-HQ190 VIDEO GASTROSCOPE™ (KenMed Surgical) or equivalents; or an ELUXEO 700 SERIES® colonoscope (Fuji) or equivalents; or a SLIM DEC DUODENOSCOPE™ (Pentax Medical) or equivalents.

4. The method of claim 1, wherein said removing of some, substantially all or all infected or diseased or dysfunctional microbiome, or colonic fecal material, and / or said administering a normal or non-diseased microbiome, or a fecal microbiota transplantation (FMT), is carried out using an AQUANET™ or equivalent thereof, or a MOTUS PURE-VU EVS SYSTEM™ or equivalent thereof.

5. The method of any one of claims 1 to 4, wherein the normal or nondiseased microbiome, or fecal microbiota transplantation (FMT) material, liquid, formulation or solution, is administered to the individual in need thereof immediately after the removing of some, substantially all or all of the infected or diseased or dysfunctional microbiome, or colonic fecal material.

6. The method of any one of claims 1 to 4, wherein the fecal microbiota transplantation (FMT) material, liquid, formulation or solution, or a normal or nondiseased microbiome, is administered to the individual in need thereof less than 1 hour after the removing of some, substantially all or all of the infected or diseased or dysfunctional microbiome, or colonic fecal material.

7. The method of any one of claims 1 to 4, wherein the fecal microbiota transplantation (FMT) material, liquid, formulation or solution, or a normal or nondiseased microbiome, is administered to the individual in need thereof less than 15minutes after the removing of some, substantially all or all of the infected or diseased or dysfunctional microbiome, or colonic fecal material.

8. A method for treating, ameliorating, or preventing a gastrointestinal (GI) disease initiated by or exacerbated by a pathological colonic microbiome in an individual in need thereof, the method comprising carrying out the method of any one of claims 1 to 7.

9. The method of claim 8, wherein the gastrointestinal (GI) disease initiated by or exacerbated by a pathological colonic microbiome is constipation or ulcerative colitis.

10. A method for treating, ameliorating, or preventing: colitis (such as a microscopic colitis or allergic colitis, or pouchitis), Crohn’s disease, irritable bowel syndrome, constipation, autism (optionally, autism spectrum disorder), a GI infection, collagenous colitis, Multiple Sclerosis (MS), Parkinson’s disease (PD), or any Gl-related condition, the method comprising carrying out the method of any one of claims 1 to 7.

11. A method for treating, ameliorating, lessening the severity of or decreasing the symptoms of, or preventing: a diarrhea (and optionally the diarrhea comprises an antibiotic-associated diarrhea), Alzheimer’s disease (AD); Alopecia, Anorexia nervosa; Celiac disease; Chronic intestinal pseudo-obstruction (CIPO); Cytomegalovirus (CMV) infection; Chronic obstructive pulmonary disease (COPD); a viral infection (for example, a norovirus, Epstein-Barr virus (EBV) or influenza infection, or COVID-19 infection, Coronavirus disease 2019 or long COVID); a fungal infection; a bacterial infection (and optionally the bacterial infection comprises Helicobacter pylori infection or sepsis or a multi-drug resistant infection); lung abscess, pyogenic liver abscess, Diversion colitis; Drug-induced hypersensitivity syndrome (DIHS); D-lactic acidosis; Essential tremor; Hepatic encephalopathy; Immune dysregulation polyendocrinopathy enteropathy X- linked syndrome (IPEX syndrome); Immune thrombocytopenia; Multiple organ dysfunction syndrome (MODS); Multiple sclerosis (MS); Nonalcoholic fatty liver disease; Primary sclerosing cholangitis; Severe alcoholichepatitis; Systemic sclerosis; Primary Sclerosing Cholangitis (PSC); radiation enteritis, hypertension, graft versus host disease, Crohn’s disease (CD), intraperitoneal infection, urinary tract infection, cirrhosis,Non-alcoholic fatty liver disease (NAFLD), Subarachnoid Hemorrhage (SAH), chronic fatigue syndrome, depression, anxiety, epilepsy, bipolar disorder, alcoholism (or alcohol use disorder), Tourette syndrome, atopic dermatitis, a cancer (and optionally the cancer is: melanoma, adenocarcinoma, a gastric, intestinal or colon cancer, such as a gastroesophageal cancer), gut fermentation syndrome, food intolerance, small intestine bacterial overgrowth, nonerosive reflux disease, colitis (optionally collagenous colitis or early onset colitis), metabolic syndrome, diabetes, gout, obesity, and / or trimethylaminuria (TMAU), Good’s syndrome, a chemotherapy induced diarrhea such as a TKI-induced diarrhea, dry eye, alopecia, kidney disease (such as chronic kidney disease), arthropathy, psoriasis, irritable bowel syndrome, constipation, and / or any disease or condition as set forth in FIG. 2, the method comprising carrying out the method of any one of claims 1 to 7.

12. A pharmaceutical composition or a formulation comprising:(a) bromelain and acetylcysteine, or(b) bromelain and acetylcysteine, and any one or several of: a solution of soap in water, N-acetylcysteine, dispersin, ribonucleic-acid-III inhibiting peptide (RIP), Salvadora persica extracts, competence-stimulating peptide (CSP) patulin (PAT), penicillic acid (PA) / EDTA, cathelicidin-derived peptides, small lytic peptide PTP-7, nitric oxide, cys-2-decenoic acid, sodium nitroprusside, s-nitroso- 1-glutathione (GSNfaO), s-nitroso -N- acetylpenicillamine (SNAP), chlorhexidine, povidone-iodine (PI), a nanoemulsion, a lytic bacteriophage, a lactoferrin, a xylitol hydrogel, a synthetic iron chelator, a cranberry component, a curcumin, acetyl- 11-keto-boswellic acid (AKBA), a barley coffee (BC) component, silver nanoparticles, a probiotic (and optionally the probiotic comprises a Bacillus), sinefungin, N-acetyl-cysteine, S-adenosylmethionine, S- adenosyl-homocysteine, a Delisea furanone, a N-sulfonyl homoserine lactone, iron salts, ionic silver salts, arsenicals, selenium, titanium dioxide, gallium nitrate, ethanol, hydrogen peroxide, hydrochloric acid, formaldehyde, luminal formalin in low concentrations, ozonated water, super-oxidized aqueous solution, nitrofurantoin, hexamine hippurate, potassium hydroxide, mercuric chloride, iodine or iodopovidone (and optionally the iodine or iodopovidone comprises povidone-iodine (PVP-I) and / or polyhexamethylene biguanide (PHMB)), disodium EDTA, ozone insufflation, and acombination of selenium and gentamicin; or is selected from the group consisting of azithromycin, clarithromycin, gentamicin, vancomycin, rifaximin, rifabutin, rifampicin, streptomycin, erythromycin, roxithromycin, DEA-CP, bismuth thiols, bismuth subcitrate; bismuth subsalicylate; a bismuth ethanondiothol, a bismuth dimercaprol, a bismuth dimercapropranol, an antibiotic (for example, a secnidazole, nitazoxanide, furazolidone, a nitroimidazole (and optionally the nitroimidazole comprises metronidazole, tinidazole, nimorazole, dimetridazole, pretomanid, ornidazole, megazol, and / or azanidazole), paromomycin, iodoquinol, doxycycline, norfloxacin, ciprofloxacin, levofloxacin, a P- lactam antibiotic such as penicillin (or penicillin G or penicillin V) and / or neomycin), a vitamin (and optionally the vitamin comprises vitamin C), a nanoparticle (and optionally the nanoparticle comprses a silver nanoparticle), a micropore particle or any combination thereof.

13. The pharmaceutical composition or formulation of claim 11, formulated into a capsule or a tablet, a solid, a liquid (optionally saline), a powder or an aerosol.

14. Use of a pharmaceutical composition or formulation of claim 12 or claim 13 for treating, ameliorating, lessening the severity of or decreasing the symptoms of, or preventing a disease or condition as set forth in any one of claims 9 to claim 11.

15. A pharmaceutical composition or formulation of claim 12 or claim 13 for use in treating, ameliorating, lessening the severity of or decreasing the symptoms of, or preventing a disease or condition as set forth in any one of claims 9 or claim 11.

16. A trans-colonoscopic device having a lumen having an aspiration port lumen of between about 2 mm and 20 mm, or having an aspiration port lumen between about 3 and 10 mm, or having an aspiration port lumen of about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 4, 15, 16, 17, 18, 19 or 20 or more mm in diameter, wherein the device further comprises or is combined with multiple (or a plurality of) water jets or channels circumferentially positioned or situated around the tip / edge of the device.

17. The trans-colonoscopic device of claim 16, further comprising multiple (or a plurality of) water jets or channels circumferentially positioned or situated within between about 0.5 and 20 cm of the tip or end of the tip / end / or edge of the instrument ordevice, or between about 1 mm and 15 cm of the tip or end of the tip / end / or edge of the instrument or device, or between about 10 mm and 10 cm of the tip or end of the tip / end / or edge of the instrument or device, optionally also being positioned at the tip of the device / instrument.

18. The trans-colonoscopic device of claim 16 or 17, further comprising a removable (or replaceable) external layer or sleeve comprising multiple or a plurality of fluid streaming channels.

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