Complex Human Gut Microbiome Cultured In An Anaerobic Human Gut-On-A-Chip

Abstract

A microfluidic device is directed to sustaining a complex microbial community in direct and indirect contact with living human intestinal cells in vitro. The device includes a first microchannel having cultured cells of a human intestinal epithelium and microbiota, the first microchannel further having a first level of oxygen. The device further includes a second microchannel having cultured cells of a vascular endothelium, the second microchannel further having a second level of oxygen. The device also includes a membrane located at an interface region between the first microchannel and the second microchannel, the membrane being composed of an oxygen-permeable material or further having pores via which oxygen flows between the first microchannel and the second microchannel to form a physiologically-relevant oxygen gradient.

1 - 147 . (canceled) 
     
     
         148 . A method, comprising:
 a) providing a microfluidic device, a source of microbes comprising living obligate anaerobes and living parenchyma cells; and   b) culturing the obligate anaerobes and the parenchyma cells in the microfluidic device such that at least a portion of the obligate anaerobes and at least a portion of the parenchyma cells are in direct contact.   
     
     
         149 . The method of  claim 148 , wherein the living obligate anaerobes are from the surface or contents of a body, orifice or cavity. 
     
     
         150 . The method of  claim 148 , wherein the parenchyma cells are human intestinal epithelial cells. 
     
     
         151 . The method of  claim 148 , wherein, after the culturing, unknown microbes are identified. 
     
     
         152 . The method of  claim 148 , wherein the culturing comprises flowing media at a flow rate. 
     
     
         153 . The method of  claim 148 , wherein the microfluidic device comprises a second microchannel positioned below a first microchannel and separated from the first microchannel by a membrane. 
     
     
         154 . The method of  claim 153 , wherein oxygenated medium flows through the second microchannel from external oxygenated medium reservoirs. 
     
     
         155 . The method of  claim 154 , wherein parenchyma cells in the first microchannel get oxygen from the second microchannel. 
     
     
         156 . The method of  claim 148 , wherein the culturing takes place for at least 2 days. 
     
     
         157 . The method of  claim 148 , wherein the culturing takes place for at least 3 days. 
     
     
         158 . The method of  claim 148 , wherein the culturing takes place for at least 5 days. 
     
     
         159 . The method of  claim 157 , wherein cultured microbiome comprises both anaerobic bacteria and aerobic bacteria. 
     
     
         160 . The method of  claim 157 , wherein the cultured microbiome comprises at least 2 anaerobic species found in the fecal sample. 
     
     
         161 . The method of  claim 157 , wherein the cultured microbiome comprises microbes from at least 2 genera found in the fecal sample.