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

Abstract

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.

I claim: 
     
         1 . A method comprising:
 screening a first sample of gut microbiota obtained from a subject   dividing the screened first sample of gut microbiota into a first portion and a second portion;   determining a first set of relative proportions and identities of the microbiota and metabolites in the first portion;   culturing the second portion to expand it; and   storing the expanded second portion.   
     
     
         2 . The method of  claim 1 , wherein culturing the second portion is performed by preferentially expanding microbiota based on the first set of relative proportions and identities of microbes and microbial metabolites. 
     
     
         3 . The method of  claim 2 , wherein culturing the second portion comprises:
 culturing the second portion within a cartridge, wherein the cartridge is in fluid communication with a anaerobic, ex vivo culture network comprising a nutrient medium and coated with a matrix for promoting adhesion of gut microbiota.   
     
     
         4 . The method of  claim 3 , wherein the matrix comprises at least one of cell extracts, adhesion proteins, mucus, and commensal colonizing factors. 
     
     
         5 . The method of  claim 1 , wherein determining the first set of relative proportions and identities of the microbiota and metabolites in the first portion comprises sequencing the first portion. 
     
     
         6 . The method of  claim 1 , wherein determining the first set of relative proportions and identities of the microbiota and metabolites in the first portion comprises biochemical analysis of the first portion. 
     
     
         7 . The method of  claim 1 , further comprising:
 administering the expanded second portion to a human subject.   
     
     
         8 . The method of  claim 1 , further comprising:
 determining a second set of relative proportions and identities of microbes and microbial metabolites from a second sample from the subject; and   comparing the second set of relative proportions and identities to the first set of relative proportions and identities to determine temporal microbiome changes.   
     
     
         9 . The method of  claim 8 , further comprising:
 recommending dietary or health-care preventative interventions based on the temporal microbiome changes.   
     
     
         10 . The method of  claim 1 , wherein storing the storing the expanded second portion comprises cryopreserving the first portion. 
     
     
         11 . The method of  claim 10 , wherein storing the storing the expanded second portion comprises maintaining the first portion at between −80° C. and −176° C. 
     
     
         12 . The method of  claim 1 , wherein screening comprises removing endotoxins or pathogenic microbes. 
     
     
         13 . The method of  claim 1 , wherein screening comprises performing stool culture tests. 
     
     
         14 . The method of  claim 1 , wherein screening comprises testing for  Salmonella, Shigella, Escherichia coli , O157:H7,  Yersinia enterocolitica, Campylobacter, Clostridium difficile  toxins A and B, the  Cryptosporidium  antigen, or the  Giardia  antigen. 
     
     
         15 . A system comprising:
 a microbiota processing unit configured to receive a sample of microbiota, screen the sample, and divide the sample into a first portion and a second portion;   a microbiota culturing unit configured to expand the second portion; and   a cryo-microbiota storage unit configured to store the expanded second portion.   
     
     
         16 . The system of  claim 15 , wherein the microbiota culturing unit comprises:
 an anaerobic, ex vivo culture network comprising inner and outer surfaces and a nutrient medium for culturing microbiota, wherein the inner surface is coated with a matrix for promoting adhesion of microbiota to the inner surface, and   hollow cartridges for culturing microbiota, wherein the hollow cartridges are in fluid communication and removably attached to the ex vivo culture network.   
     
     
         17 . The system of  claim 16 , wherein the microbiota culturing unit further comprises:
 a humidifying system in fluid communication with the ex vivo culture network to maintain physiological humidity inside the ex vivo culture network.   
     
     
         18 . The system of  claim 17 , wherein the microbiota culturing unit further comprises:
 a temperature regulation system in contact with the ex vivo culture network to regulate the temperature inside the ex vivo culture network to physiological temperature.   
     
     
         19 . The system of  claim 18 , wherein the microbiota culturing unit further comprises:
 a hollow functional screening portal comprising extracellular matrix proteins, cells, and a port for receiving metabolites generated by microbiota in the ex vivo culture network, wherein the screening portal receives oxygen and other gases for culturing the cells from a gas system in fluid communication with the ex vivo culture network.   
     
     
         20 . A method for banking humanized personal microbiota from human subjects, the method comprising:
 dividing a sample of microbiota into a first portion and a second portion;   determining a first set of relative proportions and identities of the microbiota and metabolites in the first portion;   culturing the second portion to expand it, and   storing the expanded second portion.