Optimized individualized prebiotic compositions

A method of treating or ameliorating a condition selected from degraded mucosal lining, intestinal wall inflammation, ulcerative colitis, and a digestive irregularity in a subject, the method comprising:

• obtaining a fecal sample from the subject;
• sequencing nucleic acids from the fecal sample to identify a plurality of microorganisms present in the fecal sample and to obtain genomic sequences of the plurality of microorganisms;
• identifying, from the genomic sequences, for one or more of the plurality of microorganisms, one or more carbohydrate-active enzymes and/or carbohydrate transport proteins encoded by the microorganism;
• identifying, from the plurality of microorganisms, one or more target microorganisms that encode one or more enzymes associated with production of a short-chain fatty acid;
• determining a hierarchy of carbohydrate preferences for the one or more target microorganisms and for one or more non-target microorganisms in the fecal sample, based at least on the identified carbohydrate-active enzymes or carbohydrate transport proteins;
• selecting a carbohydrate formulation comprising at least one carbohydrate substrate that is metabolizable by the one or more target microorganisms, wherein the carbohydrate formulation is selected so as to reduce carbohydrate competition for the one or more target microorganisms by the one or more non-target microorganisms;
• and
• administering the carbohydrate formulation to the subject in an amount effective to increase growth or metabolic activity of the one or more target microorganisms and thereby increase colonic production of the short-chain fatty acid in the subject.

A method of preparing a carbohydrate composition for a subject, the method comprising:

• obtaining a fecal sample from the subject;
• sequencing nucleic acids from the fecal sample to identify a plurality of microorganisms present in the fecal sample and to obtain genomic sequences of the plurality of microorganisms;
• identifying, from the genomic sequences, carbohydrate-active enzymes and/or carbohydrate transport proteins encoded by one or more of the plurality of microorganisms;
• identifying one or more target microorganisms in the fecal sample that encode one or more enzymes associated with production of a short-chain fatty acid;
• determining a hierarchy of carbohydrate preferences for the one or more target microorganisms and for one or more non-target microorganisms in the fecal sample, based at least on the identified carbohydrate-active enzymes or carbohydrate transport proteins;
• selecting, based on the hierarchy of carbohydrate preferences, one or more carbohydrate substrates that are metabolizable by the one or more target microorganisms and that reduce carbohydrate competition for the one or more target microorganisms by the one or more non-target microorganisms;
• and
• preparing a carbohydrate composition comprising the selected one or more carbohydrate substrates.

A method of treating or ameliorating a condition associated with reduced colonic butyrate production in a subject, the condition selected from degraded mucosal lining, intestinal wall inflammation, and ulcerative colitis, the method comprising:

• obtaining a fecal sample from the subject;
• sequencing nucleic acids from the fecal sample to identify a plurality of microorganisms present in the fecal sample and to obtain genomic sequences of the plurality of microorganisms;
• identifying, from the genomic sequences, one or more target microorganisms that encode one or more enzymes associated with butyrate production;
• identifying, from the genomic sequences, carbohydrate-active enzymes and/or carbohydrate transport proteins encoded by the one or more target microorganisms and by one or more non-target microorganisms in the fecal sample;
• selecting a carbohydrate formulation comprising at least one carbohydrate substrate that is metabolizable by the one or more target microorganisms based on the identified carbohydrate-active enzymes or carbohydrate transport proteins, wherein the carbohydrate formulation is selected to reduce carbohydrate competition for the one or more target microorganisms by the one or more non-target microorganisms;
• and
• administering the carbohydrate formulation to the subject in an amount effective to increase colonic butyrate production in the subject.