Methods, apparatuses, and systems for analyzing microorganism strains from complex heterogeneous communities, predicting and identifying functional relationships and interactions thereof, and selecting and synthesizing microbial ensembles based thereon

A method of making a synthetic microbial ensemble, comprising:

• measuring an absolute cell count of a microorganism strain in a plurality of samples;
• measuring an activity level associated with the microorganism strain, based on the absolute cell count;
• and
• preparing the synthetic microbial ensemble by contacting the microorganism strain with a stabilizing carrier.

A method of administering the synthetic microbial ensemble to an animal, wherein the ensemble is prepared by:

• measuring an absolute cell count of a microorganism strains in a plurality of samples;
• measuring a metadata for each sample of the plurality of samples, wherein the at least one metadata is positively associated with the absolute cell count of the at least two microorganism strains;
• and
• contacting the microorganism strain with a stabilizing carrier.