Fecal sample and/or breath sample analysis for treating inflammatory bowel disease and related conditions

Abstract

The invention is related to a system for treating irritable bowel syndrome, Crohn's disease, ulcerative colitis (collectively, inflammatory bowel disease, or “IBD”) by determining a number of indicators, including genetic markers, gene expression levels, levels of certain compounds in the gut or feces, hydrogen and/or methane levels, and concentrations of particular bacteria in the gut or feces, and correlating one or more such indicators with symptoms in test subjects with IBD; and correlating diet, drugs, supplements or other therapy, with alleviation of IBD symptoms. The correlations established in the test subjects are confirmed or refuted for individuals suffering IBD, and the treatments established as reducing symptoms are supported through messaging and compliance is verified by monitoring the indicators.

1 - 20 . (canceled) 
     
     
         21 . A method of treating one or more of the conditions of IBS, IBD, frequent diarrhea, high frequency flatulence or high frequency bowel movements by finding an avoidance diet eliminating non-preferred foods to minimize at least one symptom of said conditions and instructing adherence to the avoidance diet by an individual, the method comprising:
 a) finding an avoidance diet by:
 A) assaying breath or fecal samples from the test subjects wherein the assaying determines one or more of: methane levels designated BrM and hydrogen levels designated BrH, wherein BrH and BrM are transmitted to a server when determined from the subjects' breath; 
 B) identifying a correlation between BrM or BrH and the at least one symptom in the test subjects; 
 C) identifying any foods associated with generating or worsening of the at least one symptom in the test subjects, and designating such foods as non-preferred foods; and 
 D) identifying a correlation between avoidance of certain of the non-preferred foods by the test subjects and BrM or BrH; and 
   b) determining in the individual if there is a correlation in the individual between avoidance of said certain of the non-preferred foods by the individual and alleviating the at least one symptom in the individual and, if said correlation is established, instructing adherence to the avoidance diet by sending the individual instructions to avoid said certain of the non-preferred foods.   
     
     
         22 . The method of  claim 21  further including:
 A) assaying fecal samples from the group of test subjects for one or more of: (i) DNA and/or RNA markers associated with the test subjects having the at least one symptom, but not in wild-type, designated Markers1-x; (ii) gene expression of any candidate genes whose expression is elevated or decreased in the test subjects but not in a population which does not exhibit the at least one symptom, designated GeneExp1-x; (iii) concentrations, in samples taken from a subset of the test subjects of a first set of volatile organic compounds, designated VOCsLvL; (iv) concentrations, in samples taken from the subset of test subjects, of a second set of volatile organic compounds, designated B-VOCsLvL; and (v) gut concentrations, in samples taken from the subset of test subjects of one or more of the bacteria:  Bifidobacteria, Lactobacillus, Faecalibacterium prausnitzii , Propionibacteriaceae,  Bacteroides fragilis , Ruminococcaceae and  Clostridium;    
 B) identifying a correlation between one or more of: Markers1-x, GeneExp1-x, VOCsLvL and gut concentrations of one or more of said bacteria; with the at least one symptom in the test subjects; and 
 C) identifying a correlation between avoidance of certain of the non-preferred foods by the test subjects and one or more of: Markers1-x, GeneExp1-x, VOCsLvL and gut concentrations of one or more of said bacteria. 
 
     
     
         23 . The method of  claim 21  wherein BrM or BrH are determined from analysis of breath gas samples taken while the test subjects are exhibiting the at least one symptom. 
     
     
         24 . The method of  claim 22  wherein one or more of BrM, BrH, Markers1-x, GeneExp1-x, VOCsLvL, B-VOCsLvL and gut concentrations of said bacteria are taken from fecal samples while the test subjects are exhibiting the at least one symptom. 
     
     
         25 . The method of  claim 22  further including determining in said individual if there is a correlation between alleviating or worsening of the at least one symptom and one or more of: Markers1-x, GeneExp1-x, VOCsLvL, B-VOCsLvL, BrM, BrH, and gut concentrations of one or more of said bacteria. 
     
     
         26 . The method of  claim 22  wherein if one or more of GeneExp1-x, VOCsLvL, B-VOCsLvL, BrM, BrH, and gut concentrations of one or more of the bacteria don't correlate with avoidance of said certain of the non-preferred foods by the individual as in the test subjects, thereby indicating food entry errors by the individual, then the individual is immediately again sent the instructions. 
     
     
         27 . The method of  claim 26  wherein the individual is sent an instruction to input all food items and quantity consumed. 
     
     
         28 . The method of  claim 21  further including instructing the individual, when the individual has worsening of the at least one symptom, to sequentially eliminate consumption of particular foods to identify consumed foods which result in failure to alleviate the at least one symptom. 
     
     
         29 . The method of  claim 26  further including sending the individual a message relating to the importance of consistently avoiding said certain of the non-preferred foods. 
     
     
         30 . The method of  claim 26  further including sending the individual a message about how to conform the individual's food intake to avoid said certain of the non-preferred foods, based on the food intake reported by the individual during periods when there was lack of alleviation of the at least one symptom. 
     
     
         31 . The method of claim  1  wherein said non-preferred foods are low in fermentable sugars. 
     
     
         32 . The method of  claim 22  wherein the VOCsLvL are selected from the group consisting of: Butanoic acid, ethyl ester; Propanoic acid, methyl ester; 1-Methyl-2-(1-methylethyl)-benzene; Butanoic acid, butyl ester; Butanoic acid, propyl ester; Hexanoic acid, methyl ester; Propanoic acid, propyl ester; Acetic acid, butyl ester; Butanoic acid, 3-methyl-, butyl ester; Propanoic acid, butyl ester; Cyclohexanecarboxylic acid, ethyl ester; Butanoic acid, 2-methyl-, propyl ester; Ethanoic acid, ethyl ester; Pentanoic acid, 4-methyl; Acetic acid, pentyl ester; Pentanoic acid, butyl ester; Butanoic acid, 3-methyl-, propyl ester; Cyclohexanecarboxylic acid, propyl ester; 6-Methyl-5-hepten-2-one; Propanoic acid, 3-methyl-butyl ester; Ethanoic acid, 3-methyl-1-butyl ester; Cyclohexanecarboxylic acid, butyl ester; Benzoic acid, 2-hydroxy-, methyl ester; Pentanoic acid, 4-methyl-, pentyl ester; Butanoic acid, 3-methyl-, methyl ester; Thiopivalic acid; 5-Methyl-2-(1-methylethyl)-cyclohexanone; and 4-Methyl-1-Indole. 
     
     
         33 . The method of  claim 22  wherein the B-VOCsLvL are selected from the group consisting of: 2-Heptanone; 2-Methylpropanal; 3-Methylbutanoic acid; Undecane; 3-Methylbutanal; 2-Methylpropanoic acid; 2-Methyl-1-propanol; 1R-a-Pinene; 2-Penhifizran; Methoxy-phenyl-oxime; and 2-Methylfuran. 
     
     
         34 . The method of  claim 22  wherein the VOCsLvL and B-VOCsLvL are determined in gas from the fecal sample. 
     
     
         35 . A method of treating one or more of the conditions of IBS, IBD, frequent diarrhea, high frequency flatulence or high frequency bowel movements by finding an avoidance diet eliminating non-preferred foods to minimize at least one symptom of said conditions and instructing adherence to the avoidance diet by an individual, the method comprising:
 a) finding an avoidance diet by:
 A) assaying fecal samples from a group of test subjects exhibiting the at least one symptom, for one or more of: (i) concentrations of a first set of volatile organic compounds designated VOCsLvL; (ii) concentrations of a second set of volatile organic compounds designated B-VOCsLvL; and (iii) gut concentrations of one or more of the bacteria:  Bifidobacteria, Lactobacillus, Faecalibacterium prausnitzii , Propionibacteriaceae,  Bacteroides fragilis , Ruminococcaceae and  Clostridium;    
 B) identifying a correlation between one or more of VOCsLvL, B-VOCsLvL, gut concentrations of one or more of said bacteria and the at least one symptom in the test subjects; 
 C) identifying any foods associated with the at least one symptom in the test subjects and designating such foods as non-preferred foods; and 
 D) identifying a correlation between avoidance of certain of the non-preferred foods by the test subjects and one or more of VOCsLvL, B-VOCsLvL and gut concentrations of one or more of said bacteria; and 
   b) determining in the individual if there is a first correlation in the individual between avoidance of said certain of the non-preferred foods by the individual and alleviating the at least one symptom in the individual and, determining in said individual, if there is a second correlation between alleviating or worsening of the at least one symptom and one or more of: VOCsLvL, B-VOCsLvL and gut concentrations of one or more of the bacteria; and if said first or second correlation is established, instructing adherence to the avoidance diet by sending the individual instructions to avoid said certain of the non-preferred foods.   
     
     
         36 . The method of  claim 35  further including:
 assaying breath samples from the test subjects exhibiting the at least one symptom, wherein the assaying determines one or more of: methane levels designated BrM and hydrogen levels designated BrH, wherein BrH and BrM are transmitted to a server; 
 identifying a correlation between BrH or BrM and the at least one symptom in the test subjects; 
 identifying a correlation between avoidance of certain of the non-preferred foods by the test subjects and BrH or BrM; 
 determining in the individual if there is a third correlation between alleviating or worsening of the at least one symptom and BrH or BrM; and if said third correlation is established, instructing adherence to the avoidance diet by sending the individual instructions to avoid said certain of the non-preferred foods. 
 
     
     
         37 . The method of  claim 36  wherein if one or more of VOCsLvL, B-VOCsLvL, BrM, BrH and gut concentrations of one or more of the bacteria don't correlate with avoidance of said certain of the non-preferred foods by the individual as in the test subjects, thereby indicating food entry errors by the individual, then the individual is immediately again sent the instructions. 
     
     
         38 . The method of  claim 35  wherein the individual is sent an instruction to input all food items and quantity consumed. 
     
     
         39 . The method of  claim 35  further including instructing the individual, when the individual has worsening of at least one symptom, to sequentially eliminate consumption of particular foods to identify consumed foods which result in failure to alleviate the at least one symptom. 
     
     
         40 . The method of  claim 36  wherein one or more of BrM, BrH, Markers1-x, GeneExp1-x, VOCsLvL, B-VOCsLvL and gut concentrations of said bacteria are taken while the test subjects are exhibiting the at least one symptom.