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US20180030403A1 - Devices, systems and methods for the production of humanized gut commensal microbiota - Google Patents

Devices, systems and methods for the production of humanized gut commensal microbiota Download PDF

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US20180030403A1
US20180030403A1 US15/221,927 US201615221927A US2018030403A1 US 20180030403 A1 US20180030403 A1 US 20180030403A1 US 201615221927 A US201615221927 A US 201615221927A US 2018030403 A1 US2018030403 A1 US 2018030403A1
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microbiota
gut
commensal
human
microbiome
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Bobban Subhadra
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Individual
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Priority to US15/221,927 priority Critical patent/US20180030403A1/en
Priority to US15/470,214 priority patent/US10119116B2/en
Priority to US15/598,488 priority patent/US10767157B2/en
Priority to PCT/US2017/042130 priority patent/WO2018022327A1/fr
Priority to ES17834968T priority patent/ES2972284T3/es
Priority to EP17834968.4A priority patent/EP3490573B1/fr
Priority to US15/656,539 priority patent/US10138460B2/en
Priority to US15/831,591 priority patent/US20180105792A1/en
Publication of US20180030403A1 publication Critical patent/US20180030403A1/en
Priority to US15/893,028 priority patent/US10246677B2/en
Priority to US16/118,769 priority patent/US20190032004A1/en
Abandoned legal-status Critical Current

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Definitions

  • Dysbiosis of the GI microbiota is associated with many disease susceptibilities, including obesity, steatosis, diabetes, atherosclerosis malignancy, liver disease and GI pathology such as inflammatory bowel disease (IBD). It is clear that there is direct and indirect crosstalk between this microbial community and host immune response. However, the precise mechanism of this microbial influence in disease pathogenesis remains elusive and is now a major research focus.
  • IBD inflammatory bowel disease
  • antibiotics can give transient improvement, but often fail (for example, recurrent CDI), and these failures point-to a need for a fresh approach to treatment.
  • transplantation is also one possible treatment.
  • the infection cannot be demonstrated by culture as the diversity of microbial sub-species level composition is quite enormous, and only a small percentage of these can be cultured.
  • One embodiment provides a commensal gut production platform for ex vivo production of human gut commensal microbiota.
  • Another embodiment provides devices, systems and methods for ex vivo culturing of gut microflora in a system that mimics the human gut environment. The culturing of the commensal microbiota in the disclosed systems produces gut microbiota having defined characteristics and properties that can be exploited to treat various conditions in a subject.
  • An exemplary device and system for culturing humanized commensal gut microbiota includes an airtight gas system equipped with a system to supply and/or monitor gases, a humidifying system to maintain high humidity inside the airtight anaerobic gas system, a column system made from a plurality of columns connected in a tortious manner, a plurality of cartridges to provide substrate for commensal microbiota adhesion, growth and proliferation, and a temperature regulation system to regulate the temperature inside the apparatus.
  • the cartridges are removable.
  • the system contains a functional screening portal.
  • the functional screening portal includes a substrate to grow various live human cell types in monolayer or as tissue scaffold or 3-D printed vascularized tissue scaffolds. Exemplary cells include but are not limited to immune cells, enterocytes, colonocytes, lymphocytes, hepatocytes, glial cells, neurons, and keratinocytes.
  • the functional screening portal has a separate gas line to provide the optimum gaseous mixture for the cell growth.
  • the screening portal 110 is in fluid communication with a column cartridge 104 so that metabolites from the column cartridges can diffuse into the screening portal and the effect of microbiota metabolites on various function of various tissue systems (e.g., cell signaling, cell proliferation, apoptosis and other cellular bioactivity) can be studied.
  • the functional screening portal has a membrane with 0.2-0.4 um pores separating the cells from the microbiota column ( FIG. 7A ).
  • An exemplary method for producing humanized commensal gut microbiota includes screening stool and optionally serum samples from a healthy human donor, collecting, screening, purifying, and selecting microbiota samples from the healthy human donor, mixing the selected microbiota samples with a medium to prepare a seed culture, infusing the seed culture into the cartridge for culturing and further processing in the system.
  • Methods for treating gastrointestinal illnesses are provided in which human commensal microbiota are cultured ex vivo, harvested, and administered to a subject in need thereof.
  • FIG. 1 represents an exemplary commensal microbiota producing system 100 .
  • FIGS. 2A-2D represents the inset of different types of interiors for columns 102 .
  • FIG. 2A shows a column 102 having an interior with villi-like projections on loose glass wool.
  • FIG. 2B shows a column 102 having an interior containing a glass wool substrate.
  • FIG. 2C shows a column 102 having an interior having brush-like cartridges with glass wool.
  • FIG. 2D shows a column having an interior containing a highly porous sponge.
  • FIG. 4 represents an alternative arrangement of the device with cartridge 104 .
  • FIGS. 6A and 6B show a section of the thin layer glass wool sheet and high perforated high surface area rough sponge, respectively.
  • Coupled is defined as connected, whether directly or indirectly through intervening components, and is not necessarily limited to physical connections.
  • the connection can be such that the objects are permanently connected or connected in a releasable manner.
  • inside indicates that at least a portion of a region is partially contained within a boundary formed by the object.
  • microbiota refers to the ecological community of commensal, symbiotic and pathogenic microorganisms that share a host's body space.
  • microbiome refers, collectively, to the collection of microbial genomes in an environment.
  • the term “commensal” refers to organisms that are normally harmless to a host, and can also establish mutualistic relations with the host.
  • the human body contains about 100 trillion commensal organisms, which have been suggested to outnumber human cells by a factor to 10.
  • modulating as used in the phrase “modulating a microbial niche” is to be construed in its broadest interpretation to mean a change in the representation of microbes in a bacterial niche of a subject.
  • the change may be an increase or a decrease in the presence of a particular species, genus, family, order, class, or phylum.
  • the change may also be an increase or a decrease in the activity of an organism or a component of an organism, such as a bacterial enzyme, a bacterial antigen, a bacterial signaling molecule, or a bacterial metabolite.
  • the devices and methods relate to production of humanized gut commensal flora having the characteristics of human gut commensal microbiota produced in vivo.
  • One embodiment provides an apparatus that has predictable and quality controlled flora for the production of humanized gut commensal microbiota.
  • the disclosed devices can be used to determine the antibiotic resistance gene profile of the flora and provide superior microbiota production and adherence properties.
  • the gas control/vacuum control system 105 - 106 controls the flow of gas with respect to quantity and intervals for flow.
  • the gas control/vacuum control system 105 - 106 helps the apparatus 100 to create a suitable environment for the growth and production of the humanized commensal gut microbiota.
  • the system also includes a gas monitor device 114 such as an oxygen monitor, carbon dioxide monitor, nitrogen monitor or a combination thereof.
  • the gas control/vacuum control system 105 - 106 provides a means for supplying and/or monitoring of oxygen, nitrogen, carbon dioxide, and other gases.
  • the gas control/vacuum control system 105 - 106 is capable of supplying the required amount of any particular gas or combination of gases into the system for the growth and production of the humanized commensal gut microbiome.
  • the gas control system 105 - 106 can supply oxygen, carbon dioxide and combinations thereof.
  • the airtight gas system also includes a humidifying system 108 , to maintain high humidity inside the airtight gas system 103 .
  • the systems for creating gas gradients in the current device includes: 1) injecting gas gradients into the cartridge; 2) taking out excess air by anaerobic unit (palladium catalyst unit; and) 3) simultaneous injection of oxic (21% oxygen) or anoxic (0.1%) culture media.
  • These built-in techniques allow the establishment and maintenance of an oxygen gradient representative of the in vivo situation.
  • Oxygen sensors allow continuous monitoring of the dissolved oxygen concentrations in the chamber. The measured dissolved oxygen concentrations in the screening portal chamber is stabilized to 5.5% which is comparable to the actual recorded concentrations in various human tissues, that is, 4.6%.
  • the oxygen concentration in the humanized microbial growing cartridge chamber ranged from 0.8-2.6% of dissolved oxygen.
  • the apparatus further includes a column system, the column system having a plurality of columns 102 connected together in tortious manner, for example a zig zag manner.
  • the plurality of columns 102 are hollow cylindrical tubes made from a durable material such as plastic, polymeric material, or metal. Any suitable material can be used for making the columns.
  • the plurality of columns 102 is detachably connected at the edges with the help of connectors.
  • the hollow column preset in the system plays an important role in production of the humanized commensal gut microbiota in order to provide accurate and required growth.
  • the plurality of columns are packed with growth substrates such as but not limited to glass wool, perforated sponge and the like.
  • the apparatus includes a plurality of cartridges 104 , to provide substrate for the adhesion, growth and proliferation of commensal microorganisms.
  • the pluralities of cartridges 104 as defined in the apparatus have villi like micro projections with crypts that mimic the human inner gut lining.
  • the cartridges 104 are filled with suitable materials which provide required growth environment and media for the human gut. Further, the plurality of cartridges is coated with extracellular matrix proteins to enhance and support the production of the humanized commensal gut microbiome. Subsequent to the filling of suitable materials and covering the cartridges with extracellular matrix proteins, the cartridges are seeded with live cells of the gastrointestinal system. The cells of the gastrointestinal system seeded into the cartridges are the cells which will be used for the production of the humanized commensal gut microbiota. After seeding the cartridges with human gut microbiota, the cartridges are loaded into the column 102 and assembled inside the airtight chamber 103 for production.
  • FIGS. 2A-2D illustrate various non-limiting examples of villi like projections as defined for substrate cartridges 104 , on loose glass wool, glass wool substrate, brush like cartridges with glass wool and highly porous sponge.
  • FIG. 2A shows the cross section of an exemplary cartridge 104 that contains an inner layer 115 in contact with the inner surface of cartridge 104 .
  • First layer 115 contains a layer of extracellular matrix proteins coating the interior surface of cartridge 104 and a layer of human intestine cells covering the layer of extracellular matrix proteins.
  • a secondary substrate is in contact cells.
  • the secondary substrate is loose glass wool with villi-like projections in the lumen 117 .
  • cartridge 104 has a secondary substrate that comply fills the interior of cartridge 104 so there is no lumen 117 .
  • FIG. 2B shows the cross section of another cartridge 104 in which the interior of the cartridge is filled with glass wool substrate 118 .
  • FIG. 2C is another embodiment of cartridge 104 in which the secondary substrate is brush-like glass wool. This cartridge optionally contains a lumen 117 .
  • FIG. 2D shows another embodiment of cartridge 104 in which the secondary substrate is highly porous sponge with an optional lumen 117 .
  • the apparatus for the production of humanized commensal gut microbiota includes an integrated anaerobic atmosphere generating means for generating an anaerobic atmosphere for the apparatus which create an ambient environment for the production of humanized commensal gut microbiota.
  • the anaerobic generating means comprise provisions such as but not limited to gas-pak, oxygen removing catalyst, and gas infusion lines.
  • the anaerobic atmosphere maintenance is aided by the gas control/vacuum control system 105 - 106 which provides nitrogen gas through a Nitrogen gas cylinder 111 , Oxygen and Carbon Dioxide through Oxygen+CO 2 cylinder 109 and several other appropriate means that will be apparent to those skilled in the art for supplying and/or monitoring other gases.
  • the apparatus also includes a functional screening portal 110 designed for real-time screening of specific activity of a metabolite on different cell types ( FIGS. 7A and 7B ).
  • the functional screening portal 110 in the apparatus includes a cell-growing surface 111 with cell culture media, and a semi-permeable membrane 112 that allows diffusion of only metabolites.
  • the functional screening portal 110 can also be used to harvest metabolite on a continuous basis to conduct functional studies.
  • the metabolites are drained through a 0.4 um line 113 and stored for various in-vitro assays and models (T-cell maturation, T cell selection, Keratinocyte maturation, Effects on cancer cell line, Re-aggregate tissue scaffold or culture models of various disease models).
  • FIG. 3 illustrates an exemplary arrangement of the plurality of columns 102 of the column system in a zig zag manner in order to replicate the human gut conditions, prior to loading the cartridges.
  • FIG. 4 illustrates an exemplary arrangement of the plurality of columns 102 of the column system in a zig zag manner in order to replicate the human gut conditions, with the loaded cartridges.
  • FIGS. 5A-5C illustrate the different kinds of substrates that could be used in the apparatus, and can include but not limited to glass wool, perforated sponge and high surface area porous glass wool.
  • FIG. 6A provides a magnified front view of a thin layer glass wool sheet and FIG. 6B provides a magnified front view of a high perforated high surface area rough sponge.
  • One embodiment provides an apparatus for the ex vivo production of humanized commensal gut microbiota; wherein the apparatus includes an airtight anaerobic gas system having, a gas control/vacuum control system, to supply and/or monitor gases; a humidifying system, to maintain high humidity inside the airtight anaerobic gas system; a column system, comprising a plurality of columns connected together in a zig zag manner; a plurality of cartridges, to provide substrate for commensal adhesion, growth and proliferation; and a temperature regulation system to regulate the temperature inside the apparatus.
  • the airtight anaerobic gas system provides the required environment to facilitate growth of obligate anaerobic gut commensals for the production of humanized commensal gut microbiome.
  • the gas control/vacuum control system provides a means for supplying and/or monitoring of oxygen, nitrogen, carbon dioxide, and other gases.
  • the plurality of columns are detachably connected at the edges with the help of connectors.
  • the plurality of columns are packet with growth substrates such as but not limited to glass wool, perforated sponge and the like.
  • cartridges are further seeded with live cells of intestine.
  • the apparatus additionally has an integrated anaerobic generating means.
  • the anaerobic generating means comprises provisions such as but not limited to gas-pak, oxygen removing catalyst, and gas infusion lines.
  • the apparatus additionally has a functional screening portal designed for real-time screening of specific activity of a metabolite on different cell types.
  • the secondary substrate of the packaging layer is a highly porous material such as but not limited to glass wool, rockwool, porous sponge, perforated sponge and the like.
  • the secondary substrate after tight packaging creates a gaseous gradient from aerobic to microaerophilic to anaerobic inside the cartridge.
  • the adhesive molecules are molecules such as but not limited to collagen, fibrinogen, fibronectin, mucin proteins and the like.
  • a synthetic media composition for use in culturing humanized commensal gut microbiome includes: organic nitrogen sources, protein sources, carbohydrate sources, metal salts, intestinal secretions, enzymes, vitamins, and trace minerals maintained at a slightly neutral to acidic pH.
  • the protein source is one or more from peptone and/or amino acids such as L-cysteine and the like.
  • the carbohydrate sources are dextrose and soluble starch.
  • the metal salts are sodium chloride, potassium phosphate, ammonium citrate, magnesium sulfate, and manganese sulfate.
  • the intestinal secretions are primary and secondary bile acids, enzymes, and mucus proteins.
  • the synthetic media composition is additionally provided with nutrients and metabolites normally present in the intestine.
  • the nutrients and metabolites normally present in the intestine are hydrolyzed amino acids, inulin, oligofructosides, galactofructosides, free fatty acids, triglycerides, gastric juice, pancreatic enzymes, bile acids, and entero-endocrine hormones.
  • the disclosed system has a large number of uses.
  • One embodiment provides methods for the ex vivo production of human gut microbiota. Once a healthy donor is identified, the samples of gut microbiota are collected, screened and purified to remove any impurities present therein such as endotoxins and pathogenic microbes. In one embodiment, the gut microbiota is collected from healthy human volunteers through endoscopy and/or from fecal samples.
  • the samples are screened properly to detect any defects in the samples, for example inadequate quantities, sample vial integrity, sample contamination etc.
  • the fecal samples are also screened for ova, parasites and the like through stool culture and sensitivity tests.
  • the screening of fecal samples includes tests for Salmonella, Shigella, Escherichia coli , O157:H7, Yersinia enterocolitica, Campylobacter, Clostridium difficile toxins A and B, Cryptosporidium antigen, Giardia antigen and the like.
  • the serum samples are screened for diseases such as but not limited to HIV-1, HIV-2, Hepatitis A B C, and the like. Further the serum samples are additionally screened for rapid plasma regain, fluorescent treponemal antibody, and absorbed Treponema pallidum and the like. Defective samples are eliminated.
  • Another embodiment provides a method for the production of humanized commensal gut microbiota including screening stool and serum samples from a healthy human donor; collecting, screening, purifying, and selecting microbiome samples from the healthy human donor; preparation and assembly of a plurality of columns each loaded with a cartridge; mixing of the selected microbiota samples with a media to prepare a seed culture; infusion of the seed culture into the cartridge; and culturing and harvesting the commensal microbiota for further processing.
  • Another embodiment provides a method for the preparation and assembly of a plurality of columns each loaded with a cartridge.
  • the cartridges are loaded into the columns, and then the columns are packed with secondary substrates. After packing the columns with secondary substrates, the loaded and packed columns are assembled, for example in a zig-zag manner through connectors at their edges.
  • the next step includes preparation of a synthetic media, and nutrients and metabolites normally present in the intestine which are infused in the cartridge during culturing.
  • the synthetic media which are infused in cartridge during culturing includes organic nitrogen sources, protein sources, carbohydrate sources, metal salts, intestinal secretions, enzymes, vitamins, and trace minerals maintained at a slightly neutral to acidic pH.
  • Synthetic media are used because of their known chemical compositions. Synthetic media are useful for nutritional and metabolic studies.
  • the synthetic media may include but is not limited to Czakek's-Dox Medium (GM-9) and Richard's solution (GM-27).
  • the synthetic media composition used for culturing humanized commensal gut microbiome includes organic nitrogen sources, protein sources, carbohydrate sources, metal salts, intestinal secretions, enzymes, vitamins, and trace minerals maintained at a slightly neutral to acidic pH.
  • the organic nitrogen source in the synthetic media composition is one or more from hydrolyzed fish extract and/or algae extract, and/or yeast extract.
  • the protein source present in the synthetic media composition for culturing humanized commensal gut microbiome includes one or more from peptone and/or amino acids such as L-cysteine and the like.
  • the carbohydrate sources in the synthetic media composition are dextrose and soluble starch.
  • the metal salts in the synthetic media composition are sodium chloride, potassium phosphate, ammonium citrate, magnesium sulfate, and manganese sulfate.
  • the synthetic media composition includes the intestinal secretions which are preferably primary and secondary bile acids, enzymes, and mucus proteins.
  • the synthetic media composition possesses slightly neutral to acidic pH is around 6.8.
  • the synthetic media composition includes additional nutrients and metabolites normally present in intestine.
  • the synthetic media includes nutrients and metabolites that are normally present in intestine are hydrolyzed amino acids, inulin, oligofructosides, galactofructosides, free fatty acids, triglycerides, gastric juice, pancreatic enzymes, bile acids, and entero-endocrine hormones.
  • the organic nitrogen sources in the synthetic media include hydrolyzed fish extract and/or algae extract, and/or yeast extract.
  • the synthetic media includes a protein source which is one or more of peptone and/or amino acids such as L-cysteine and the like.
  • the carbohydrate sources in the synthetic media are dextrose and soluble starch.
  • the synthetic media includes the metal salts preferably sodium chloride, potassium phosphate, ammonium citrate, magnesium sulfate, and manganese sulfate.
  • the intestinal secretions present in the synthetic media are primary and secondary bile acids, enzymes, and mucus proteins.
  • the synthetic media is maintained at a slightly neutral to acidic pH around 6.8.
  • the cartridge is infused with nutrients and metabolites normally present in intestine are hydrolyzed amino acids, inulin, oligofructosides, galactofructosides, free fatty acids, triglycerides, gastric juice, pancreatic enzymes, bile acids, and entero-endocrine hormones.
  • the cartridges are infused with seed culture, the seed culture primarily containing the microorganisms such as but not limited to, human-derived Bacteriodetes, Prevotella, Xylanibacter, Facaelibacterium, Eubacterium, Subdoligranulum, Parabacteriodetes, Clostridium leptum, Clostridium coccoides, Ruminococcus, Collinsella, Roseburia, Akkermansia, Veillonella, Bifidobacterium, Verrucomicrobia, Lactobacillus, Escherichia (from the Enterobacteriaceae family), Desulfovibrio, Saccharomyces boulardiim, Cladosporium, Pentatrichomonas, Chilomastix, Entamoeba dispar, gut microbiome viruses (e.g., phages) and the like.
  • the microorganisms such as but not limited to, human-derived Bacteriodetes, Prevotella, Xy
  • the humanized commensal gut microbiota are harvested. After harvesting, the harvested humanized commensal gut microbiota are formulated as a freeze-dried (lyophilized) stable powder form in therapeutic delivery forms such as but not limited to capsules, sachets, rectal enema, rectal suppositories, creams, gels, oral solutions and the like.
  • the harvested humanized commensal gut microbiota of can be administered via food and beverages such as but not limited to juices, milk, physiological saline, water, food and the like.
  • One embodiment provides a method for the treatment of metabolic disorders.
  • the method includes obtaining a microbiota sample from healthy human donor and scrutinizing and purifying the same. Further the method includes, culturing the microbiota sample obtained from healthy human donor in a zig zag column system packed with cartridges that are designed to mimic the human gut lining, in a synthetic culture media supplemented with nutrients and metabolites normally present in intestine; harvesting and administering the microbiota to a patient in need of metabolic disorder treatment.
  • Ex vivo produced human gut microbiota can be used to treat disorders including but not limited to, crohns disease (CD), inflammatory bowel disease (IBD), type 1 diabetes (T1D), type 2 diabetes (T2D) obesity, colitis, cancers, steatosis, atherosclerosis, Parkinson's disease, Alzheimer's disease, depressive disorders, malignancy, infectious diarrhea, necrotizing enterocolitis, and esophagitis.
  • CD crohns disease
  • IBD inflammatory bowel disease
  • T1D type 1 diabetes
  • T2D type 2 diabetes
  • colitis cancers
  • cancers steatosis
  • atherosclerosis atherosclerosis
  • Parkinson's disease Alzheimer's disease
  • depressive disorders malignancy
  • infectious diarrhea necrotizing enterocolitis
  • necrotizing enterocolitis and esophagitis.
  • Another embodiment provides a method for the production of a designed human gut microbiota expressing a functional bioactive molecule in gut of a patient undergoing a therapy.
  • the microbiota can genetically engineered to secrete a therapeutic protein, peptide, lipid, or small molecule.
  • the method for production of designed microbiota includes obtaining a plurality of microbiota samples from healthy human donors. The human donors are inspected with respect to their health and credibility before taking the samples. Further, configuring a zig zag column system packed with cartridges designed to mimic the human gut lining, provides a metabolic situation for culturing the samples of gut microbiota.
  • the method includes culturing the plurality of microbiota samples obtained from healthy human donors, in a synthetic culture media supplemented with nutrients and metabolites normally present in intestine, under physiological conditions to express functional bioactive molecules. Once the culture is ready, the culture is harvested and administered into the gastrointestinal tract of a patient in need thereof.
  • the functional bioactive molecules produced in the ex vivo produced gut microbiota include, but are not limited to bone morphogenetic protein (BMP), e (EPO), g (G-CSF), g (GM-CSF), interferon alpha, interferon beta, interferon gamma, interleukin 2 (IL-2), interleukin 11 (IL-11), mammary-associated serum amyloid protein (M-SAA) and the like.
  • BMP bone morphogenetic protein
  • EPO e
  • G-CSF g
  • GM-CSF g
  • interferon alpha interferon beta
  • interferon gamma interleukin 2
  • IL-2 interleukin 2
  • IL-11 interleukin 11
  • M-SAA mammary-associated serum amyloid protein
  • Human gut microbiota compositions described herein can be used to treat bone-related conditions, anemia, neutropenia, fungal infections, hepatitis C, multiple sclerosis, cancer, thrombocytopenia, chronic granulomatous disease, osteoporosis and the like.
  • the preparation and assembly of the column includes the steps of: loading the cartridges into the columns; packing the column with secondary substrates; and assembling the loaded and packed columns in a zig-zag manner through connectors from their edges.
  • a synthetic media, and nutrients and metabolites normally present in intestine are infused in the cartridge during culturing.
  • the synthetic media includes: organic nitrogen sources, protein sources, carbohydrate sources, metal salts, intestinal secretions, enzymes, vitamins, and trace minerals maintained at a slightly neutral to acidic pH.
  • the organic nitrogen source is one or more from hydrolyzed fish extract and/or algae extract, and/or yeast extract.
  • the protein source is one or more from peptone and/or amino acids such as L-cysteine and the like.
  • the carbohydrate sources are dextrose and soluble starch.
  • the metal salts are sodium chloride, potassium phosphate, ammonium citrate, magnesium sulfate, and manganese sulfate.
  • the intestinal secretions are primary and secondary bile acids, enzymes, and mucus proteins.
  • the slightly neutral to acidic pH is around 6.8.
  • the nutrients and metabolites normally present in intestine are hydrolyzed amino acids, inulin, oligofructosides, galactofructosides, free fatty acids, triglycerides, gastric juice, pancreatic enzymes, bile acids, and entero-endocrine hormones.
  • the seed culture primarily includes the genus such as but not limited to, Human-derived Bacteriodetes, Prevotella, Xylanibacter, Facaelibacterium, Eubacterium, Subdoligranulum, Parabacteriodetes, Clostridium leptum, Clostridium coccoides, Ruminococcus, Collinsella, Roseburia, Akkermansia, Veillonella, Bifidobacterium, Verrucomicrobia, Lactobacillus, Escherichia (from the Enterobacteriaceae family), Desulfovibrio, Saccharomyces boulardiim, Cladosporium, Pentatrichomonas, Chilomastix, Entamoeba dispar , gut microbiome viruses (e.g. phages) and the like.
  • the genus such as but not limited to, Human-derived Bacteriodetes, Prevotella, Xylanibacter, Facaelibacterium, Eubacterium
  • the harvested humanized commensal gut microbiota are administered in optimally freeze-dried stable powder form via therapeutic delivery forms such as but not limited to capsules, sachets, rectal enema, rectal suppositories, creams, gels, oral solutions and the like.
  • the harvested humanized commensal gut microbiota are administered in food and beverages such as but not limited to juices, milk, physiological saline, water, food and the like.
  • a method for the treatment of metabolic disorders includes obtaining a microbiome/microbiota sample from healthy human donor; culturing the microbiome sample obtained from healthy human donor in a zig zag column system packed with cartridges that are designed to mimic the human gut lining, in a synthetic culture media supplemented with nutrients and metabolites normally present in intestine; harvesting and administering the microbiome to a patient in need of metabolic disorder treatment.
  • the metabolic disorder is Crohns disease (CD), inflammatory bowel disease (IBD), type 1 diabetes (T1D), type 2 diabetes (T2D) obesity, colitis, cancers, steatosis, atherosclerosis, Parkinson's disease, Alzheimer's disease, depressive disorders, malignancy, infectious diarrhea, necrotizing enterocolitis, and esophagitis.
  • CD Crohns disease
  • IBD inflammatory bowel disease
  • T1D type 1 diabetes
  • T2D type 2 diabetes
  • colitis cancers
  • cancers steatosis
  • atherosclerosis atherosclerosis
  • Parkinson's disease Alzheimer's disease
  • depressive disorders malignancy
  • infectious diarrhea necrotizing enterocolitis
  • necrotizing enterocolitis and esophagitis.
  • a method for production of designed microbiota expressing a functional bioactive molecule in gut of a patient undergoing a therapy includes: obtaining a plurality of microbiota samples from healthy human donors; configuring a zig zag column system packed with cartridges designed to mimic the human gut lining, to provide a metabolic situation; culturing the plurality of microbiome samples obtained from healthy human donors, in a synthetic culture media supplemented with nutrients and metabolites normally present in intestine, under the metabolic situation to adapt in expressing the functional bioactive molecules; harvesting and administering the microbiota to the patient undergoing the therapy for expressing the functional bioactive molecule.
  • the functional bioactive molecules are but not limited to Bone morphogenetic protein (BMP), Erythropoietin (EPO), Granulocyte colony-stimulating factor (G-CSF), Granulocyte macrophage colony-stimulating factor (GM-CSF), Interferon alpha, Interferon beta, Interferon gamma, Interleukin 2 (IL-2), Interleukin 11 (IL-11), Mammary-associated serum amyloid protein (M-SAA), Humanin (Alzheimer's Disease preventing peptide) and the like.
  • BMP Bone morphogenetic protein
  • EPO Erythropoietin
  • G-CSF Granulocyte colony-stimulating factor
  • GM-CSF Granulocyte macrophage colony-stimulating factor
  • Interferon alpha Interferon beta
  • Interleukin 2 IL-2
  • IL-11 Interleukin 11
  • M-SAA Mammary-associated serum amyloid protein
  • Humanin
  • the patient is undergoing treatment for an illness that includes but is not limited to bone-related conditions, anemia, neutropenia, fungal infections, hepatitis C, multiple sclerosis, cancer, thrombocytopenia, chronic granulomatous disease, osteoporosis and the like.
  • the disclosed systems and methods can be used for production of designed microbiota expressing functional bioactive molecules in gut.
  • the microbiota can be shaped into a functional organ to do critical bodily metabolic functions.
  • a specific metabolic profile can be mimicked in the microniche and the commensal microbiota can be forced to evolve to better adapt to that profile by optimally switching into that metabolic genomic expression patterns.
  • the commensal microbiota can be designed to perform key metabolic functions for the body.
  • the organ systems might not be doing the intended optimal function because of the chemo-induced cellular damage.
  • microbiota can temporarily make key cellular metabolites, which the patient needs until the patient's organs are revived fully.
  • This can include growth-hormone stimulating peptides, neuroendocrine agents, endorphins, and key enzymes to complement vital functions for the body.
  • Complex glycolysated protein metabolites such as cytokines (IL-2, haemopoietic growth factors, interferons, EGF) can be made by fungal microbiota (mycobiota).
  • Saccharomyces boulardii, Cladosporium, Pentatrichomonas, Chilomastix and Entamoeba dispar are common eukaryotic commensal gut microbiota which can make complex glycolysated proteins.
  • a partial list of bioactive molecules that can be expressed by gut commensal flora include: bone morphogenetic protein (BMP), used to treat bone-related conditions; erythropoietin (EPO), used to treat anemia; granulocyte colony-stimulating factor (G-CSF), used to treat neutropenia in cancer patients; granulocyte macrophage colony-stimulating factor (GM-CSF), used to treat neutropenia and fungal infections in cancer patients; interferon alpha, used to treat hepatitis C and multiple sclerosis; interferon beta, used to treat multiple sclerosis; interleukin 2 (IL-2), used to treat cancer; interleukin 11 (IL-11), used to treat thrombocytopenia in cancer patients; interferon gamma is used to treat chronic granulomatous disease and osteoporosis; and mammary-associated serum amyloid protein (M-SAA).
  • BMP bone morphogenetic protein
  • EPO erythropo
  • the disclosed systems and methods can be used to design high health promoting probiotics.
  • the highly adhesive health promoting probiotic phenotypes can be evolved using this technology.
  • a health promoting probiotic which has less colonizing capacity, can be adapted for better colonizing capacity.
  • Health promoting probiotic consortium can also be humanized with the current technology.
  • a less adherent strain is co-incubated with core microbiota for 1 week and then harvested with the core-microbiota. The strain is forced to adapt to the human adhesive molecule via changes in the selective expression of its genes or by acquiring adhesive genes from the core-microbiome.
  • the disclosed systems and methods can be used to study the specific effect of diet and dietary components on the gut microbiota.
  • the disclosed devices can be used to study the effect of different diet components on the core commensal microbiota of humans.
  • several diet components can be simulated including the following: high fat diet, low fat diet, high sugar diet, low sugar diets, high protein diet, low protein diet, high fiber diet, low fiber diet, and a balanced diet.
  • Microbiomes from lean/obese human subjects can be used to see the dietary effect on the microbiome genomic and diversity signature overtime.
  • Microbiota from a lean human can be used to mass culture in the device as a interventional formulation for metabolic disorders such as type II diabetes, obesity etc.
  • the disclosed systems and methods can be used to design specific diet adapted designer gut commensal microbiota.
  • the effect of the different diet regimes and how it affects the commensal flora can be studied.
  • a better adapted core microbiota for each dietary regimes can be harvested and transplanted to human for better digestion and health benefits.
  • the microbiota can be grown on plant-based diet, fruit-based diet, meat-based diet, milk-based diet, or a balanced diet regime (plant+meat+milk).
  • Hydrolyzed plant or meat protein or other nutrients can be infused into the device and changes in the core commensal flora and microbiome can be monitored to identify different aspects of growth and metabolism, and its effect on the patient.
  • the disclosed systems and methods can be used to design a gut commensal microbiota with specific energy utilization ratio for metabolic disorders.
  • Energy harvest and utilization of intake-food is an essential predictor of metabolic disorders.
  • the device can be used to design an optimum group of bacteria which will metabolize the food in relative proportion which will obviate any metabolic disorders. For example, better enzyme producing groups and better short-chain fatty acid producing groups.
  • the disclosed systems and methods can be used to study the effect of artificial sweetener on the commensal gut flora.
  • artificial sweeteners Aspartame, Cyclamate, Saccharin, Stevia , Sucralose
  • the effects of the artificial sweeteners on the core commensal microbiome can be studied by infusing these into the device and observing the changes.
  • the disclosed systems and methods can be used to study the effect of alcohol on the commensal gut flora.
  • Alcohol induced cirrhosis and non-alcoholic cirrhosis can be affected by the gut microbiome.
  • a tailored synthetic humanized commensal microbiome can be made using the device for the management of cirrhosis.
  • the gut microbiota affect the liver functions in several ways: 1) digesting the components and energy metabolism; 2) the production and synthesis of bile acid physiology; and 3) the diversification of the gut microbiome affected by alcohol.
  • a designer commensal microbiota which can efficiently metabolize without changing the normal commensal microbiota can be designed using adaptive technology of core-microbiome and by mix-match of core commensal seed microbiota.
  • a better alcohol metabolizing commensal flora can be designed.
  • the disclosed systems and methods can be used to study and optimize the metabolites from commensal microbiota and its physiological roles.
  • Commensal microbiota makes several functional metabolites (peptides, hormones, proteins, lipoproteins, glycoproteins, small molecules) which promote several key metabolic and immune functions of the body.
  • the device has specialized design to harvest the bacteria-free metabolites by an inner-chamber separated by 0.22 um membrane.
  • a specialized attachment called functional screening port 110 is also integrated into the apparatus to do cell-screening studies on live cells.
  • the functional screening portal 110 has a cell-growing surface with cell culture media and also has separate gas line for optimal oxygen+CO 2 .
  • the metabolites can be diffused into the screening portal 110 via a semi-permeable membrane which would not allow any bacteria to enter.
  • This set-up can be used to real-time screening of specific activity of the metabolites on different cell types.
  • the harvested substrate and core-commensal microbiome can be a source of metabolites (these can be put in PBS for overnight to release membrane proteins and secreted proteins and can be concentrated).
  • the media used for the growing can also be periodically concentrated for secreted proteins and assayed for various functional studies.
  • Non-limiting examples of different types of activity and screening include: protein fractions which have proliferation of specific T-cells (Th-17 cells) can be assay in T-cell proliferation assays; protein fractions which have T-cell selection can be studied in T-cell selection assays; bioactives with enterocyte differentiation can be assayed in cell-culture studies; bioactives with neuroendocrine functions can be assayed in cell-culture studies; bioactives with natural killer cells proliferation assays can be determined in cell-culture studies; bioactives with commensal quorum sensing molecules can be studied with quorum sensing reporting assays; bioactives with antibacterial and antibiofilm can be assayed using specific pathogens and antibacterial and antibiofilm assays; bioactives with anti-inflammatory can be assayed using cell culture and cytokine assays; bioactives with pro-inflammatory can be assayed using cell culture and cytokine assays; bioactives with barrier and tight junction function and be assayed using 3-D organ models
  • the disclosed systems and methods can be used to study the effect of changing the binding molecule of substrate matrix and its effect on commensal microbiota population.
  • the substrate can be coated with different microbial adherence molecules.
  • the gut bacteria adhere on the gut with different mechanisms.
  • the main adherence proteins are fibronectin binding proteins, fibrinogen-binding proteins, collagen-binding proteins and other tight-junction binding proteins.
  • the bacteria also bind with their pili and flagella to the cells.
  • the mucin proteins can also have different binding molecules to bind commensal bacteria.
  • the binding molecules are important colonizing host factors and are important parameters in defining commensal microbiome structure and evolution.
  • the core inner highly bound microbiome serves as the source from which new populations are derived.
  • Microbial surface component recognizing adhesive matrix molecules are adhesive proteins that mediates initial attachment of bacteria to the host tissue.
  • the adhesion can be mediated by degree hydrophobicity, neutral and hydrophilic or ionic interaction of the attachment between host and bacteria.
  • Several classes of these molecules can be immobilized into the substrates cartridges and studied. The best mix of adherence molecules is used for harvesting the most-adapted substrates.
  • the disclosed systems and methods can be used to study and design synthetic antimicrobial microbiota.
  • An Eco biological Approach Rational design of microbial communities as biologic products can treat, prevent, cure, or mitigate infectious diseases or their squeal.
  • Current approaches harness existing functional constituents of the microbiota and their products to restore health to the host.
  • Physicians and clinician scientists use fecal microbiota transplants to treat infectious diseases such as C. difficile associated diarrhea, and researchers are developing the use of microbial bio therapeutics as adjunct therapy to antibiotic treatment for bacterial vaginosis.
  • Commensal microbiota and microbiome with antimicrobial activity towards several bacteria can be designed by mixing and matching microbiota from several different human subjects.
  • enteric pathogens such as Salmonella, Shigella, Enterotoxigenic E. coli , and Enterpathogenic E. coli (EPEC), Vibrio cholera .
  • enteric pathogens such as Salmonella, Shigella, Enterotoxigenic E. coli , and Enterpathogenic E. coli (EPEC), Vibrio cholera .
  • Specific signature commensal flora which have adapted for a variety of physiological activities; antibacterial production, specific enzyme activity, reduced adherence, anti-aggregate formation, anti-quorum sensing activity, competitive exclusion and other signaling to reduce the load of pathogen can be designed into a single microbiome or group of microbiota.
  • One method to develop this signature core-commensal includes establishing different core-microbiota from different seed cultures including pathogens (for example, 8 log EPEC are added to the different cultures). The growth physiology of the EPEC on various core-microbiome is assessed. Growth reduction or growth promotional effects of core-microbiota are assayed. If a core-microbiota causes a 2-4 log reduction, it is subjected to further mix-match with other core-microbiomes.
  • the disclosed systems and methods can be used for optimizing bacteriophage-treatment to reduce the antimicrobial resistance genes in the microbiome.
  • Commensal flora is a constant source of antibiotic resistant genes (AMR).
  • Bacteriophage can be used to reduce the load specific populations of microbes which harbor antimicrobial resistance genes.
  • CRISP-Cas 9 gene cassettes can be used in specific phages to target populations of antimicrobial resistance flora and lyse those cells. After several rounds of phage-treatment, a specific microbiome can AMR gene-free. The commensal flora which is AMR-gene-free can then be used for several indications.
  • the disclosed systems and methods can be used to study and design humanized commensal microbiota adapted bacteriophages for phage-therapy.
  • Bacteriophages are an important element in the human gut microbiota. The ratio of different phages determines the relative ratio of different microbes in the gut.
  • the device can be used for harvesting humanized commensal microbiota adapted bacteriophages which can maintain the gut commensal flora in a specific relative proportions.
  • the disclosed systems and methods can be used to study relative metabolic functionality proportion of the commensal microflora.
  • the microbiome of the commensal defines key metabolic functions which have important implications in digestion, energy homeostasis, neural and immune functions.
  • the proportion of butyrate producers, short chain fatty acid producers, secondary bile acid metabolizers, mucin producers, mucin degraders and neuro-active peptide producers etc. are important in defining the effect of the commensal microbiota on the host health and metabolism.
  • a typical designer flora includes the relative percentage proportions of various metabolic groups, and can be as follows: butyrate producers—20-25%; short chain fatty acid producers—15-20%; mucin degrading organisms—10-12%; mucin producers—1-5%; digestive enzyme producers—10-15%; neuroendocrine peptide producers—0.5-1.0%; secondary bile acid metabolizers (ursodeoxycholic acid and lithocholic acid)—2-5%; polyphenol and isothiocyanate producers—1-2%; tight junction protein production inducers—1-5%; and epigenetic modulators (histone deacetylase producers, DNA methylase producers etc.)—0.5-4%.
  • the discloses systems and methods can be used for optimizing different methods for delivering the commensal microbiota for the treatment of a specific indication.
  • the harvested commensal flora are intended to be use in several forms.
  • the flora can be optimally freeze-dried into a stable powder form and used in the following forms of therapeutic delivery forms: capsules; sachets; rectal enema; rectal suppositories; creams or gels; sachet in powder form; and oral solution.
  • specific doses can also be delivered via food and beverages including: juices; milk; physiological saline; water; and food.
  • a typical formulation and dosage is: (a) A 250 mg commensal microbiota from a sachet suspended in an 8 oz juice twice daily for 2 weeks; (b) 1 g commensal microbiota formulated with a thickener as a rectal suppository; and (c) 500 mg gelatin capsule for oral delivery.
  • Gut microbiota specific metabolites influence the signaling of various pathways which influences the glucose metabolism and insulin sensitivity in the human body.
  • the optimum expression of incretins (glucose-dependent insulinotropic peptide (GIP) and glucagon-like peptide-1 (GLP-1), xenin, leptin, diacetlyghrelin and ghrelin are all vital components in glucose metabolism.
  • GIP glucose-dependent insulinotropic peptide
  • GLP-1 glucagon-like peptide-1
  • xenin xenin
  • leptin diacetlyghrelin
  • diacetlyghrelin diacetlyghrelin
  • ghrelin diacetlyghrelin
  • the disclosed systems and methods can be used to create humanized gut microbiota ex vivo by optimized production of all these metabolites in specific pre-determined level so as to use as a prophylactic control of pre-diabetic patients.
  • These designer microbiota also increase the intestinal barrier so as to reduce the systemic endotoxemia which is another chronic cause of type II diabetes.
  • the disclosed systems and methods can be used for the production of humanized designer phages that are adapted to the human gut microbiome.
  • humanized designer phages that are adapted to the human gut microbiome.
  • real-time dynamics of microbial symbiosis in the human gut can be studied.
  • phage specifically shape microbiota and microbiome diversity can also be elucidated.
  • Specific phages such as engineer bacteriophage that produces an antimicrobial compound that helps avoid bacteria such as enteroaggregative Escherichia coli or Klebsiella that are developing resistance to the phage, thereby increasing their value for treating associated childhood diseases.
  • Food pathogens are a leading cause of death in children under five years old in the developing world but there are no effective vaccines due in part to the many different forms of the bacterium.
  • the effects of the specific phages on the human gut microbes and its dynamics are evaluated both by sequencing to determine the quantities and types of bacteria in the gut, and by analyzing protein production in the bacteria and the mice, which will also reveal insight into the host immune response.
  • the disclosed systems and methods can be used to develop a bacteriophage to destroy the diarrhea-causing bacterium Shigella or Salmonella or Listeria monocytogenes , and study its effect on microbial populations in the gut. How a unique phage-based editing of the gut microbiome and its functionality can be mimicked in the disclosed systems and methods.
  • the disclosed systems and methods can be used for creating designer humanized phage-edited gut microbiota for various applications.
  • the disclosed systems and methods can be used for studying the effects of various xenobiotics and their effect on the human microbiome/microbiota and thereby to the human body.
  • Specific xenobiotic situations can be re-created in the disclosed system by infusing various drugs and the changes in the metabolomic, proteomic, metatranscriptomics, and metagenomic studies on the gut microbiome can be specifically elucidated.
  • Mechanisms that link the gut microbiota and xenobiotic metabolism include: gut microbiota can directly metabolize xenobiotics into active, inactive or toxic metabolites; xenobiotics may also shape the composition of the gut microbiota through antimicrobial activity or selective growth; gut microbiota can indirectly influence xenobiotics through the modulation of host pathways that are responsible for metabolism and transport; and this can be mediated by microbial metabolites or through the microbial modification of host metabolites.
  • Xenobiotics include antibiotics, therapeutics drugs, diet-derived bioactive molecules, and pollutants.
  • Xenobiotics include antibiotics, therapeutics drugs, diet-derived bioactive molecules, and pollutants.
  • the disclosed systems and methods can be used for creating a humanized microbiome/microbiota for increased human longevity.
  • the study of the extreme limits of human lifespan may allow a better understanding of how human beings can escape, delay, or survive the most frequent age-related causes of morbidity, a peculiarity shown by long-living individuals.
  • Longevity is a complex trait in which genetics, environment, and stochasticity concur to determine the chance to reach 100 or more years of age.
  • the gut microbiota Because of its impact on human metabolism and immunology, the gut microbiota has been proposed as a possible determinant of healthy aging. Indeed, the preservation of host-microbes homeostasis can counteract inflammation, intestinal permeability, and decline in bone and cognitive health.
  • Aging is characterized by an increasing abundance of subdominant species, as well as a rearrangement in their co-occurrence network. These features are maintained in longevity and extreme longevity, but peculiarities emerged, especially in semi-supercentenarians, describing changes that, even accommodating opportunistic and allochthonous bacteria, might possibly support health maintenance during aging, such as an enrichment and/or higher prevalence of health-associated groups (e.g., Akkermansia, Bifidobacterium , and Christensenellaceae). Probiotics have been shown to be effective in restoring the microbiota changes of older subjects, promoting different aspects of health in elderly people as improving immune function and reducing inflammation.
  • health-associated groups e.g., Akkermansia, Bifidobacterium , and Christensenellaceae.
  • GI microbiota composition Whether modulation of GI microbiota composition, with multi-targeted interventions, could have an effect on the prevention of frailty remains to be further investigated in the perspective of improving the health status of frail ‘high risk’ older individuals. Further, recent studies have shown that gut microbial metabolites from pomegranate, berries, and nut produces Urolithin A, a mitophagy preventing natural compound. Urolithin A increases life expectancy by increasing the mitochondria levels in cells. In another embodiment the disclosed systems and methods can be used for creating a humanized microbiome/microbiota for high level of Urolithin A in human body.
  • the active microbial cells can be differentiated from total flora by means of a tagging-technique based on the presence of RNA using pyronin-Y, a fluorescent stain for total RNA.
  • Flow-cytometry cell sorting can be used to isolate active microbial fraction from fecal samples of healthy volunteers.
  • the disclosed systems and methods can be used enrich and isolate bioactive and health promoting gut microbiota (e.g. clostridales) from total gut microbiota.
  • the disclosed systems and methods can be used produce gut microbiota producing excess amounts of trehalose.
  • trehalose a disaccharide molecule—is highly neuroprotective and might have significant benefits in various neural diseases.
  • the trehalose biosynthetic genes, otsBA operon, can be used for creating a signature trehalose expressing microbiome repertoire using the disclosed systems and methods. This humanized signature microbiota can be used for treatment of neural disorders.
  • Example 1 Production of Humanized Commensal Gut Microbiome for Various Treatments
  • Microbiota from healthy human volunteers is collected by endoscopy (rectal or oral) and from fecal samples. Other methods such as samples left after surgical procedures can also be used to procure healthy microbiota and would be apparent for any person skilled in the art.
  • the donors are screened for the presence of ova and parasites in the stool culture.
  • Specific pathogens to be screened for include, but are not limited to the following: Salmonella, Shigella, Escherichia coli , O157:H7, Yersinia enterocolitica; Campylobacter; Clostridium difficile toxins A and B; Cryptosporidium antigen and Giardia antigen.
  • the sample is a serum sample
  • the sample is screened for pathogens includes but not limited to the following: HIV-1 and HIV-2; Hepatitis A, B, and C; rapid plasma regain; fluorescent treponemal antibody; and absorbed Treponema pallidum.
  • This step is necessary in order to ascertain that the commensal microbiota should be devoid of disease causing Blastocystis (IBD) and Candida (leaky gut), Entamoeba histolytica, Cryptosporidium parvurn, Pneumocystis carnii, microsporidia, Giardia intestinalis, Encephalitozoon, Toxoplasma, Naegleria and the like.
  • Donors are excluded, if they matched any alarming condition such as but not limited to, BMI>30, active smoking, known chronic diseases, antibiotic usage in the past 6 months and detection of inflammation and/or infection in blood- and/or fecal assessments.
  • Donor blood is also assessed for full blood count and serological testing for hepatitis A, B and C; HIV-1 and 2 and Treponema pallidum .
  • Donor stools are specifically screened for enteropathogens. Bacterial culture is performed to detect the following enteropathogens: Salmonella spp, Shigella spp, Yersinia enterocolitica and Y. pseudotuberculosis, Campylobacter spp, and Aeromonas spp.
  • C. difficile toxins A and B C. difficile toxins A and B
  • glutamate dehydrogenase C. difficile toxins A and B
  • PCR is performed in case of discordance between results of toxins and glutamate.
  • Patients undergo full ileocolonoscopy with calculation of the Crohn's disease Endoscopic Index of Severity (CDEIS) and Simplified Endoscopic Activity score (SES-CD) and Mayo endoscopy sub score (for UC) at baseline and week 8 after FMT.
  • C—reactive protein (CRP) and clinical disease activity were collected using the Crohn's disease Activity Index (CDAI) for CD and the Mayo score for UC. Patients are followed-up for at least 6 months.
  • the clinician who undertakes the procedure estimates the risk that the donor had recently contracted a transmissible disease, such as HIV or hepatitis, as well as rule out potential exposure to pathogenic agents that are not identified by laboratory methods to a high degree of sensitivity. This can be facilitated by eliminating donors with a history of engaging in high-risk behaviors, such as illicit drug use, sexual encounters with multiple partners, or unprotected sexual activity. Additional potential exclusions include donors with a history of incarceration, tattoo or body piercing in the past 6 months, current or known exposure to a communicable disease, use of immunosuppressant agents, or antibiotics within the last 3 months.
  • a transmissible disease such as HIV or hepatitis
  • SM seed microbiota
  • Seed microbiota can come from a single donor or from multiple donors.
  • the approximate composition of major genus in the seed culture is as follows: human-derived Bacteriodetes; Prevotella; Xylanibacter; Facaelibacterium; Eubacterium; Subdoligranulum; Parabacteriodetes; Clostridium leptum; Clostridium coccoides; Ruminococcus; Collinsella; Roseburia; Akkermansia; Veillonella; Bifidobacterium; Verrucomicrobia; Lactobacillus; Escherichia (from the Enterobacteriaceae family); Desulfovibrio; Saccharomyces boulardii; Cladosporium, Pentatrichomonas, Chilomastix; Entamoeba dispar and various gut viruses (e.g., phages)
  • the cartridges are processed to immobilize human cells such as gastrointestinal cells, adhesive proteins, and mucus proteins.
  • the cartridges are loaded into the column and assembled.
  • the secondary substrates such as glass wool or perforated sponge are tightly packed into the column.
  • the prepared synthetic media also contains bile acids and enzymes and other hydrolyzed nutrients in proportion, which are similar to human gut.
  • the seed microbiota is mixed in the prepared media and infused into the cartridge column. After initial growth of the seed culture, the culture system infused with nutrients and metabolites normally present in intestine to mimic the human intestine physiology.
  • the media composition used for culturing the microbiota is prepared to 1 liter having the following composition and maintained to a pH of 6.8: hydrolyzed fish extract or algae extract: 2.5 g; peptone: 2.5 g; sodium chloride: 1.25 g; dextrose: 1.25 g; yeast extract: 0.5 g; soluble starch: 0.3 g; 1-cysteine: 0.35 g; potassium phosphate: 0.25 g; ammonium citrate: 0.25 g; magnesium sulfate: 0.05 g; manganese sulfate: 0.02 g; bile acid mix (primary and secondary bile acids): 0.3 ml; enzyme mix, digestive enzymes: 0.3; mucus proteins: 0.1 ml; trace mineral and vitamin solution: 1 ml; carbohydrate—10-60 g; resistant starch—40 g; hydrolyzed amino acids—10 g; inulin, oligofructosides, and galactofructosides
  • the culture system is also infused with nutrients and metabolites normally present in the intestine and several bioactive media components are added depending on the specific adaptive need of the commensal flora.
  • the excess liquid media from the column is drained off and the gaseous system is activated to create and maintain a gradient of aerobic to microaerophilic to anaerobic atmosphere inside the column and cartridges.
  • High humidity 70-80%
  • a small quantity of fresh media 100 ml
  • the seed culture is allowed to grow for 24-48 hrs.
  • the core commensal microbiota are established in 48-72 hrs and has the signature adherence expression profile and phenotype of human gut commensals.
  • the cartridges are taken out from the column and immersed in physiological saline or PBS. If necessary, processing is conducted under an anaerobic chamber to safeguard the viability of anaerobic flora.
  • the commensal flora can be detached from the substrate by gently vortexing, sonication or mechanical stirring.
  • the harvested microbes are spun down and stored under ⁇ 80° C. with appropriate cryoprotectants until used.
  • the quantitative and qualitative counts are estimated for the flora via different analytical methods.
  • the diversity, resistance gene profile and percentage representative flora is determined via genomic and sequencing methods.
  • the material after quality control is again gave a batch and lot number and ready to use.
  • Humanized commensal microbiota with high diversity and proportion are produced from a seed culture, and can deliver metabolic benefits when administered to a host.
  • the resistance genes of the microbiome are profiled for the presence of any resistance genes.
  • Increased concentration of clostridial cluster XI and XVI is a feature of designer commensal flora.
  • a typical designer commensal flora includes 500-1000 different species with below relative percentage proportions:
  • Subdoligranulum 0.5-1.0%
  • the human gut microbiota is dominated by five bacterial phyla (Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia) and one Archaea (Euryarchaeota).
  • the less prevalent bacterial groups are distributed among Cyanobacteria, Fusobacteria, Lentisphaerae, Spirochaetes and TM7.
  • the Firmicutes phylum contains relevant genera, including Ruminococcus, Clostridium, Lactobacillus (several strains of which are probiotics), and the butyrate producers Eubacterium, Faecalibacterium and Roseburia .
  • the Actinobacteria phylum includes Collinsella and Bifidobacterium (which contains probiotic strains).
  • Common Proteobacteria are Escherichia (from the Enterobacteriaceae family) and Desulfovibrio (which contains sulphate-reducing bacteria).
  • Verrucomicrobia was recently discovered and includes Akkermansia (which are specialized for mucus degradation).
  • Euryarchaeota contains the prevalent Methanobrevibacter (which is involved in the continuation of intestinal methanogenesis).
  • Complex carbohydrates such as dietary fiber, are metabolized by the colonic microbiota to oligosaccharides and monosaccharides and then fermented to short-chain fatty acid end-products, mainly acetate, propionate and butyrate.
  • Short-chain fatty acids are absorbed in the colon, where butyrate provides energy for colonic epithelial cells, and acetate and propionate reach the liver and peripheral organs, where they are substrates for gluconeogenesis and lipogenesis.
  • short-chain fatty acids control colonic gene expression by inhibiting the enzyme histone deacetylase (HDAC) and metabolic regulation by signaling through G-protein-coupled receptors (GPCRs), such as GPR41 or GPR43.
  • HDAC histone deacetylase
  • GPCRs G-protein-coupled receptors
  • the development of high-throughput sequencing technologies has facilitated metagenomics research in determining the complexity and immense diversity of microbial life in various ecological niches.
  • Metagenomic analysis demonstrated significant interindividual variation in gut microbiota composition, described as continuous gradients or distinct microbiota clusters (“enterotypes” or “co-abundance groups”). At present, there is no clear evidence for a single pathogen causing IBD. On the other hand, marked alterations in microbial communities are observed in IBD patients.
  • Example 3 Treatment for Ulcerative Colitis (UC) and Crohns Disease (CD) Using Commensal Microbiome Therapy
  • the commensal microbiota therapy for Crohns Disease and Ulcerative Colitis includes a highly diversified humanized commensal flora prepared from multiple donors and screened for species diversity and exclusion UC/CD-specific flora.
  • the commensal flora is screened for resistome and other screening criteria as described in Example-1.
  • the lyophilized commensal microbiota is delivered in two formats for the patients.
  • Retention enema 500 mg commensal microbiome in 50 ml PBS
  • a capsule 500 mg capsule, one capsule/day.
  • Patients were scheduled for a flexible sigmoidoscopy and also completed baseline questionnaires to obtain demographic information, Mayo score, and Inflammatory Bowel Disease questionnaire score.
  • Participants were given 50 mL commensal microbiome in PBS as a retention enema once per week for 8 weeks.
  • the enema was administered with the patient in the left lateral position with instructions to retain this for at least 20 minutes.
  • Patients provided stool samples each week before receiving their retention enema and samples were stored at ⁇ 20° C. for fecal microbiota analysis.
  • the primary outcome was UC/CD remission at week 7, defined as a full Mayo score ⁇ 3 and complete healing of the mucosa at flexible sigmoidoscopy (endoscopic Mayo score 1/40). Secondary outcomes included improvement in UC symptoms, as well as change in Mayo, Inflammatory Bowel Disease Questionnaire, and EQ-5D scores.
  • Fecal transplant was used as the comparative treatment for comparison.
  • Example 4 Treatment of Infectious Diarrhea and Necrotizing Enterocolitis by Expression of Mammary-Associated Serum Amyloid Protein (M-SAA3)
  • M-SAA3 Mammary-associated serum amyloid protein
  • a 10-mer peptide derived from the N-terminal region of the 42-mer human M-SAA3 may have a role as an anti-infective, as it prevents enteropathogenic Escherichia coli (EPEC) adherence in vitro, both to human intestinal epithelial cells and small intestinal mucosa.
  • This antiadhesive effect is mediated by enhancement of innate protection through stimulation of production of the intestinal mucin MUC3, a mechanism also demonstrated for the probiotic Lactobacillus GG.
  • the 10-mer peptide, consisting of residues two to 11 of the N-terminal region of the human 42-mer protein contains a TFLK motif. The gene can be transferred to the microbiome by several methods:
  • Conjugative transfer The gene is cloned into a plasmid in a conjugative transfer strain of E. coli -S17-1 (with conjugative plasmids: pARO181 or pARO190). This strain is infused into the mature evolved microbiome in the apparatus with the media and allowed to grow aerobically for 2-3 days. The M-SAA3 gene is transferred to gut commensal flora by this method. The aerobic E. coli -S17-1 were cured of the culture system by repeated washing and anaerobic culturing.
  • SMPP medium (0.3% bovine serum albumin, 5% 2 M sucrose, 25% 4 ⁇ PAB, 50% 2 ⁇ SMM), composition of 2 ⁇ SMM being 1 M sucrose, 0.04 M maleic acid and 0.04 MgCl2 (pH 6.5), and protoplasts are obtained after incubation at 37° C. on a rotary shaker at 100 rpm for 30 min in presence of lysozyme (10 mg/ml) and mutanolysin (75 U/ml). The presence of protoplasts is verified by phase contrast microscopy. Protoplasts are then carefully harvested by centrifugation at 5200 ⁇ g and 4° C.
  • SMMP medium without PAB ice cold washing buffer
  • DNA plasmid DNA or synthetic gene (DNA)
  • SMMP medium without PAB
  • a 2 ml protoplast preparation is mixed with 15 ⁇ g of plasmid DNA or synthetic gene (DNA) in a 15 ml tube. 1.5 ml of 40% polyethylene glycol is immediately added and incubated for 2 minutes at room temperature. Protoplasts are diluted with 5 ml SMMP and harvested by gentle centrifugation and removal of supernatant. After addition of 500 ⁇ l SMMP cells are incubated overnight at 37° C. with gentle shaking. Then cells are added to apparatus and incubated for 2-3 days at 37° C. Confirmation of the gene transfer is continued by sequencing the microbiome.
  • the microbiota XY M-SAA3+ are harvested and lyophilized.
  • the lyophilized XY M-SAA3+ is made into 500 mg gelatin capsules (for adult patients) or oral PBS solution with 500 mg lyophilized powder.
  • Patients with bloody diarrhea or necrotizing enterocolitis are treated with 2 capsules daily for 7 days or oral gavage of the solution once daily for 7 days.
  • the commensal microbiota device can be used to study or model how antimicrobial resistance (AMR) evolves in commensal flora.
  • AMR antimicrobial resistance
  • the commensal flora is a reservoir of AMR genes or resistome.
  • the mechanism of AMR evolution of commensal flora is still unknown. Even without antibiotics, the commensal flora can develop and exhibit resistance phenotypes towards multiple antibiotics. Some of the resistance genes are hidden in the commensal microbiome while others are expressed phenotypically in the GI tract.
  • the flora X is cultured in the microbiota apparatus without any antibiotic selective pressure for 4-15 days as described previously (Example-1). After specific time-intervals the resistome of the flora X can be profiled to real-time changes with respect to the evolution of AMR. Also the phenotypic expression of AMR towards multiple antibiotics can be studied. Information on key groups of bacteria and genes which are susceptible for AMR generation can be identified. Specific phenotypes which are more prone to AMR can be identified (biofilm phenotype, aggregates, adhesive communities, specific consortiums of commensals). The prominent mutations can be used for predictive analytics for AMR resistance
  • AMR studies can be studied with antibiotic selection pressure using single antibiotics or multiple antibiotic.
  • a single antibiotic or multiple antibiotics are mixed with the media and at periodical intervals samples are taken to analyze for species diversity, resistome profiling, identifying AMR vulnerable genus and species, mutations and phenotypic expression etc., and the results have been discussed in the table below:
  • Non-adaptive mutation Adaptive mutations Spontaneous mutation Directed mutations under selective pressure Phenotypic variation, biofilm, Selection is the major force for nutrients drive AMR mutation Slower rate of AMR Phenotypic variation, selection of AMR groups in a commensal community Non-specific towards antibiotics Specific mutations/AMR towards antibiotics or classes of antibiotics Does not change the normal Change the dynamics of dynamics of commensal flora commensal (quantitative and (quantitative and qualitative qualitative change) change)
  • Example 6 Treatment of Anti-Hemorrhoidal Agents Using Metabolites from Commensal Microbiome Device
  • Example 7 Personalized Microbiome Repository and Re-Use for Various Treatments
  • the seed-microbiota of a person is acquired from birth and co-evolves with the host and it becomes and integral modulator of several key metabolic processes. When you are in the best health, your microbiota is also best adapted and optimized for your bodily needs and metabolism. Although there are general similarities among human microbiota, each person's microbiota is highly unique and co-adapted with the host cells with respect to binding nature, gut adaptability to diet, colonizing capacity and functional microbiome-metabolome. As you age or as your metabolism changes, or succumb to disease conditions, the commensal microbiota signature also changes, sometimes a good change otherwise not so.
  • Microbiome/microbiota banking services provide the banking as a long-term proactive health care service for personalized health and well-being.
  • Proprietary technologies were developed to expand and make ‘humanized designer’ version of a person's microbiota based on different parameters such as dietary changes, health supplement-adapted, and other medications adapted (NSAIDS, painkillers etc.). Further, the strength in microbiome is leveraged to design new microbiome therapeutics for various disease conditions and indications.
  • Microbiome/microbiota banking helps people to catalogue their-own microbiome or microbiota on a yearly basis.
  • the bank keeps track of the microbiota changes based on various parameters and sequence information (quantitative and qualitative diversity, gene diversity, ratio of Bacteriodetes, proteobacteria, Firmicute ratio (BPF ratio) over time. Based on this analysis, dietary and health-care preventative interventions can be recommended and reported to a primary care physician.
  • the members have the option to expand and re-infuse their microbiota as additional service. Healthcare providers are consulted to enhance the quality of life based on microbiota science. Further, the members can also opt to expand and donate their microbiome for members or close relatives of their family. BiomSafe allows you to store your microbiome at various time-intervals and use it later for re-infusing for any health or indications. Save and store your highly health-promoting microbiome when you are in superior health.
  • Bacteriophage-based strategies may address many of the challenges above, as they are pathogen-specific and do not directly interact with eukaryotic cells. Furthermore, there may be ways to mitigate the development of bacterial resistance to introduced bacteriophage to the extent that an intervention could be plausible. Yet the majority of research aimed at developing bacteriophage therapeutics ceased with the advent of modern antibiotics.
  • the disclosed systems and methods can be used for the production of humanized designer phages that are adapted to the human gut microbiome dynamics.
  • By co-culturing phages and various microbiota in the disclosed systems and methods one can study the real-time dynamics of microbial symbiosis in the human gut. Further how phage specifically shape microbiota and microbiome diversity can also be elucidated.
  • Specific phages such as engineer bacteriophage that produce an antimicrobial compound that helps avoid bacteria such as enteroaggregative Escherichia coli or Klebsiella that are developing resistance to the phage, thereby increasing their value for treating associated childhood diseases.
  • Food pathogens are a leading cause of death in children under five years old in the developing world but there are no effective vaccines due in part to the many different forms of the bacterium.
  • the effects of the specific phages on the human gut microbes and its dynamics are evaluated both by sequencing to determine the quantities and types of bacteria in the gut, and by analyzing protein production in the bacteria and the mice, which will also reveal insight into the host immune response.
  • one can develop a bacteriophage to destroy the diarrhea-causing bacterium Shigella or Salmonella or Listeria monocytogenes and study its effect on microbial populations in the gut. How a unique phage-based editing of the gut microbiome and its functionality can be mimicked in the disclosed systems and methods. Further the disclosed systems and methods can be used for creating designer humanized phage-edited gut microbiota for various applications.
  • Example 9 Humanized Microbiome for Xenobiotic Metabolism
  • the gut microbiota is a significant component of first-pass metabolism. Prior to entering systemic circulation and reaching the target tissue, orally ingested compounds are subject to metabolism in the intestine and liver, which decreases the eventual systemic drug concentration. The gut microbiota may metabolize compounds prior to absorption, after efflux from the intestinal epithelium or following biliary excretion from the liver.
  • SN-38 a topoisomerase I inhibitor and the active form of the chemotherapeutic drug irinotecan (also known as CPT-11) gets inactivated by the liver to SN-38-G. In this glucoronated and inactive form, it enters the gut lumen where the gut microbiota reactivates it back to the toxic and active SN-38 form through microbial beta glucuronidase activity. This microbial activation causes significant adverse side effects, such as severe diarrhea, weight loss, and suppression of the immune system, which all limit further increases in dosage.
  • Microbial metabolism can be essential for successful therapeutic outcomes, especially in anticancer immunotherapies.
  • B. thetaiotaomicron and B. fragilis to be essential for the efficacy of the antibody Ipilimumab to target the immune checkpoint blocker CTLA-4.
  • Example 10 Creating a Humanized Microbiome for Increased Human Longevity
  • the disclosed systems and methods can be used for creating a humanized microbiome for increased human longevity.
  • the study of the extreme limits of human lifespan may allow a better understanding of how human beings can escape, delay, or survive the most frequent age-related causes of morbidity, a peculiarity shown by long-living individuals.
  • Longevity is a complex trait in which genetics, environment, and stochasticity concur to determine the chance to reach 100 or more years of age.
  • the gut microbiome Because of its impact on human metabolism and immunology, the gut microbiome has been proposed as a possible determinant of healthy aging. Indeed, the preservation of host-microbes homeostasis can counteract inflammation, intestinal permeability, and decline in bone and cognitive health.
  • Aging is characterized by an increasing abundance of subdominant species, as well as a rearrangement in their co-occurrence network. These features are maintained in longevity and extreme longevity, but peculiarities emerged, especially in semi-supercentenarians, describing changes that, even accommodating opportunistic and allochthonous bacteria, might possibly support health maintenance during aging, such as an enrichment and/or higher prevalence of health-associated groups (e.g., Akkermansia, Bifidobacterium , and Christensenellaceae).
  • Probiotics have been shown to be effective in restoring the microbiota changes of older subjects, promoting different aspects of health in elderly people as improving immune function and reducing inflammation. Whether modulation of GI microbiota composition, with multi-targeted interventions, could have an effect on the prevention of frailty remains to be further investigated in the perspective of improving the health status of frail ‘high risk’ older individuals.

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US10246677B2 (en) * 2016-07-28 2019-04-02 Bobban Subhadra Devices, systems and methods for the production of humanized gut commensal microbiota
WO2020197965A1 (fr) * 2019-03-22 2020-10-01 University Of Washington Systèmes, trousses et méthodes associées de transplantation fécale
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JP2024032920A (ja) * 2019-06-25 2024-03-12 日環科学株式会社 閉鎖型３ｄフラクタル培養システムとその培養物

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