Defined therapeutic microbiota and methods of use thereof

A method of predicting recurrence of C. difficile infection in a subject, the method comprising:

• (a) determining the relative abundance of all operational taxonomic units (OTUs) in a sample of the subject's stool that are ≥90% identical to a reference sequence of C. scindens;
• (b) determining the relative abundance of all operational taxonomic units (OTUs) in a sample of the subject's stool that are ≥90% identical to a reference sequence of C. hylemonae;
• and
• (c) summing the relative abundances determined in steps (a) and (b), wherein a sum of relative abundances less than or equal to 1% indicates an increased risk of C. difficile recurrence relative to a subject in which the sum of relative abundances is greater than 1%.

A method of determining the therapeutic efficacy of a bacterial organism for treatment of a pathology involving expression of a toxin, produced by a Gram-positive spore-forming bacterium, the method comprising measuring in a biological sample obtained from an individual administered the bacterial organism one or more of:

• a) the amount and/or activity of a secreted proteolytic enzyme;
• b) the amount and/or activity of bacterial proline reductase;
• c) the amount or concentration of one or more branched short-chain fatty acids;
• d) the amount or concentration of one or more branched keto acids;
• and
• e) the amount or concentration of Stickland donor and/or Stickland acceptor amino acids and/or 5-aminovalerate;
• wherein measurement of an increased amount, concentration or activity of one or more of (a)-(e) relative to the amount measured in a sample taken prior to administration the bacterial organism indicates that the bacterial organism is effective for the treatment.

A method to predict the risk of developing a disease involving a toxin produced by a Gram positive, spore-forming bacterium, the method comprising measuring in a biological sample obtained from an individual one or more of the following:

• a) the amount and/or activity of a secreted proteolytic enzyme;
• b) the amount and/or activity of bacterial proline reductase;
• c) the amount or concentration of one or more branched short-chain fatty acids;
• d) the amount or concentration of one or more branched keto acids;
• and
• e) the amount or concentration of Stickland donor and/or Stickland acceptor amino acids;
• and
• comparing the amount, concentration or activity measured in one or more of (a)-(d) to a reference, wherein an amount, concentration or activity in one or more of (a)-(d) below the reference indicates increased risk of developing a disease involving a toxin produced by a Gram positive, spore-forming bacterium.

A method of identifying a candidate bacterial organism that is likely to suppress the expression of a toxin by a Gram-positive, spore-forming bacterial pathogen, the method comprising:

• a) identifying from a database of bacterial genetic information a candidate bacterial organism having in its genome:
• i) one or more genes encoding a secreted protease enzyme;
• and/or
• ii) a gene encoding a proline reductase enzyme;
• and
• b) assaying a sample comprising the candidate bacterial organism for the expression of a secreted protease enzyme and/or the proline reductase enzyme;
• wherein the detection of expression of the secreted protease enzyme and/or the expression of the proline reductase enzyme indicates that the candidate bacterial organism is likely to suppress expression of a toxin by a Gram-positive, spore-forming bacterial pathogen.

A method to predict the risk of developing a spore-forming, toxin-producing Gram-positive bacterial pathogen in the gut or other location, or its recurrence, comprising measuring in a biological sample

• (a) amounts or unit activity of proteolytic activity;
• (b) concentrations of branched short chain fatty acids;
• (c) concentrations of branched keto acids;
• and/or
• (d) concentrations of Stickland donor and Stickland acceptor amino acids,
• wherein an increase in the amount or activity of at least one of (a)-(d) relative to a biological sample obtained prior to administration identifies a risk of developing a spore-forming, toxin-producing Gram-positive bacterial pathogen in the gut or other location.