Fecal fungome and therapeutic efficacy of fecal microbiota transplantation

Abstract

Methods are provided for identifying subjects as suitable donor or recipients for FMT, for assessing the likelihood of FMT treatment success, and for enhancing FMT treatment efficacy. Also provided are kits and compositions for FMT with enhanced efficacy.

1 . A method for assessing likelihood of effective fecal microbiota transplantation (FMT), comprising determining  C. albicans  level in a stool sample obtained from a potential recipient prior to FMT. 
     
     
         2 . The method of  claim 1 , wherein the  C. albicans  level is a percentage relative abundance. 
     
     
         3 . The method of  claim 2 , wherein the  C. albicans  level is greater than 10% and FMT is assessed as unlikely to be effective for the potential recipient. 
     
     
         4 . The method of  claim 3 , wherein the recipient is administered an effective amount of an antifungal agent that suppresses  C. albicans  growth before FMT. 
     
     
         5 . The method of  claim 4 , further comprising determining  C. albicans  level in a stool sample obtained from the recipient after FMT. 
     
     
         6 . The method of  claim 2 , wherein the  C. albicans  level is no greater than 10% and FMT is assessed as likely to be effective for the potential recipient. 
     
     
         7 . The method of  claim 1 , further comprising determining total fungal load in the stool sample. 
     
     
         8 . The method of  claim 7 , further comprising performing FMT on the potential recipient. 
     
     
         9 . The method of  claim 1 , wherein  C. albicans  level is determined in a first stool sample obtained from a first potential recipient prior to FMT and in a second stool sample obtained from a second potential recipient prior to FMT. 
     
     
         10 . The method of  claim 9 , wherein the first potential recipient has a lower  C. albicans  level than the second potential recipient and is assessed to have a higher likelihood of effective FMT than the potential recipient. 
     
     
         11 . The method of  claim 9 , wherein the second potential recipient is administered an effective amount of an antifungal agent that suppresses  C. albicans  growth before FMT. 
     
     
         12 . The method of  claim 1 , wherein the potential recipient has inflammatory bowel disease (IBD) with concurrent  Clostridium difficile  infection (CDI). 
     
     
         13 . The method of  claim 12 , wherein the  C. albicans  level is determined in stool samples taken from the recipient before and after FMT. 
     
     
         14 . A method for identifying a suitable donor for FMT, comprising the step of determining  C. albicans  level in a stool sample obtained from a candidate. 
     
     
         15 . The method of  claim 14 , wherein the  C. albicans  level is a percentage relative abundance. 
     
     
         16 . The method of  claim 15 , wherein the  C. albicans  level is no greater than 0.1% and the candidate is identified as a suitable donor for FMT. 
     
     
         17 . The method of  claim 15 , wherein the  C. albicans  level is greater than 10% and the candidate is identified as an unsuitable donor for FMT. 
     
     
         18 . The method of  claim 14 , further comprising determining  Saccharomyces  level and  Aspergillus  level in the stool sample. 
     
     
         19 . The method of  claim 14 , further comprising determining  Escherichia  level and  Proteus  level in the stool sample. 
     
     
         20 . The method of  claim 14 , further comprising determining total fungal load in the stool sample. 
     
     
         21 . A method for improving FMT efficacy, comprising administering to an FMT recipient prior to FMT an effective amount of an antifungal agent that suppresses  C. albicans  growth. 
     
     
         22 . The method of  claim 21 , wherein  C. albicans  level is determined in a stool sample from the FMT recipient prior to administration of the antifungal agent. 
     
     
         23 . The method of  claim 21 , wherein  C. albicans  level is determined in a stool sample from the FMT recipient after administration of the antifungal agent. 
     
     
         24 . The method of  claim 21 , further comprising administering to the recipient prior to FMT an effective amount of an agent that reduces total fungal load in a stool sample taken from the recipient prior to FMT. 
     
     
         25 . The method of  claim 21 , wherein the recipient has inflammatory bowel disease (IBD) with concurrent  Clostridium difficile  infection (CDI). 
     
     
         26 . A kit comprising (1) a first composition comprising donor stool; and
 (2) a second composition comprising an effective amount of an antifungal agent that suppresses  C. albicans  growth.   
     
     
         27 . The kit of  claim 22 , wherein the first composition comprises donor stool that has been dried, frozen, and placed in a capsule for oral ingestion. 
     
     
         28 . The kit of  claim 22 , further comprising in the second composition or in a third composition an effective amount of an agent that reduces total fungal load. 
     
     
         29 . (canceled)