Microbiome Byproducts and Uses Thereof

A method for treating a microorganism-related condition in a patient, the method comprising:

• detecting microorganisms in a set of samples collected from a population;
• comparing a relative abundance of and co-occurrence between different microbial taxa in the set of samples;
• associating a change in the relative abundance of or the co-occurrence between the microbial taxa with samples from people, among the population, with the microorganism-related condition and samples from people, among the population, without the microorganism-related condition to determine a target taxa;
• identifying a blend of therapeutic microorganisms, the blend being configured to change an abundance of the target taxa in a community of microorganisms;
• and
• administering a therapeutic composition comprising the blend to the patient with the microorganism-related condition.

A method for identifying new bacteria-produced antibacterial compounds, the method comprising:

• generating a database of antibacterial compounds produced by bacteria by screening known antibacterial compounds-producing microorganisms and antibacterial compounds;
• identifying, by a processor, binding regions of the antibacterial compounds from the database that bind other microorganisms by comparing sequence alignment of curated antibacterial compounds with a sequence alignment of reference proteomes;
• and
• identify new bacteria-produced antibacterial compounds based on the identified peptide motifs.

A method of producing a therapeutic composition, the method comprising:

• identifying a protein from bacteria that produce metabolites underlying a microorganism-related condition;
• identifying, by a processor, a first inhibitor for the identified protein and a second inhibitor of a protein orthologous to the identified protein using virtual high-throughput screening;
• and
• producing a therapeutic composition comprising one or both of the first inhibitor and the second inhibitor.