Methods, apparatuses, and systems for microorganism strain analysis of complex heterogeneous communities, predicting and identifying functional relationships and interactions thereof, and selecting and synthesizing microbial ensembles based thereon

A processor-implemented method, comprising:

• obtaining data for at least two samples sharing at least one common environmental parameter, each sample of the at least two samples including a heterogeneous microbial community including a plurality of microorganism types;
• determining an absolute number of cells of each microorganism type of the plurality of microorganism types for each sample;
• determining relative quantity of unique first markers for each microorganism type, each unique first marker being a marker of a microorganism strain of a microorganism type;
• measuring a value of one or more unique second markers, a unique second marker indicative of metabolic activity of a particular microorganism strain of a microorganism type;
• determining an activity of each microorganism strain based on the measured value of the one or more unique second markers exceeding a specified threshold;
• determining respective ratios of the absolute number of cells of active microorganism strains for each microorganism type in each sample;
• analyzing each of the active microorganism strains of the at least two samples via a processor, the analysis including identifying relationships between (i) each active microorganism strain and every other active microorganism strain, and (ii) each active microorganism strain and at least one measured metadata;
• displaying, on a graphical interface, identified relationships between active microorganism strains and the at least one measured metadata;
• and
• formulating a bioensemble comprising a carrier and one or more active microorganism strains based on identified relationships.

A method, comprising:

• forming a bioensemble of active microorganism strains which is able to alter feed efficiency of a target animal, the forming including:
• obtaining a plurality of gastrointestinal tract samples;
• obtaining at least one measured metadata from a sample animal population, the measured metadata indicating a feature of at least one of the plurality of gastrointestinal tract samples;
• analyzing the plurality of gastrointestinal tract samples to identify a plurality of microorganism types present and an absolute number of cells for each identified microorganism type for each sample of the plurality of gastrointestinal tract samples;
• measuring unique first markers and relative quantity thereof for each gastrointestinal tract sample of the plurality of gastrointestinal tract samples;
• a unique first marker being a marker of a microorganism strain of a particular identified microorganism type;
• determining the absolute cell count of each microorganism strain present in each sample as a function of the absolute number of each detected microorganism type in that sample and the relative quantity of unique first markers in that sample;
• measuring at least one unique second marker to determine an activity value for microorganism strains in each gastrointestinal tract sample of the plurality of gastrointestinal tract samples;
• generating a set of active microorganisms strains and their respective absolute cell counts for each gastrointestinal tract sample of the plurality of gastrointestinal tract samples;
• analyzing the active microorganisms strains, respective absolute cell counts, and the at least one measured metadata to identify relationships between active microorganism strains and the at least one measured metadata;
• selecting a plurality of active microorganism strains from the set of active microorganism strains based on the analysis;
• and
• combining the selected plurality of active microorganism strains with a carrier medium to form a bioensemble of active microorganisms which is able to alter feed efficiency when the bioensemble of active microorganisms is administered to a target animal.