A method of forming an ensemble of active microorganism strains, comprising: obtaining at least two samples sharing at least one common characteristic and having at least one different characteristic, wherein the at least one different characteristic includes a collection time at which each of the at least two samples was collected, such that the collection time for a first sample is different from the collection time of a second sample, or a collection location at which each of the at least two samples was collected, such that the collection location for a first sample is different from the collection location of a second sample, and the at least one common characteristic includes a sample source type, such that the sample source type for a first sample is the same as the sample source type of a second sample; for each sample, detecting the presence of one or more microorganism types in each sample; determining a number of cells of each detected microorganism type of the one or more microorganism types in each sample; measuring a number of occurrences of each unique first marker of a set of unique first markers in each sample, each unique first marker being a marker of a microorganism strain; representing the number of occurrences of each unique first marker, from the set of unique first markers, as a percentage of total unique first markers, to give a percentage of each microorganism strain of each microorganism type; multiplying the number of cells of each microorganism type by the percentage of each microorganism strain to yield the absolute cell count of each microorganism strain present in each sample; measuring at least one unique second marker for each microorganism strain based on a specified threshold to determine an activity level for that microorganism strain in each sample, each unique second marker for each microorganism strain being different than the unique first marker for that microorganism strain; filtering the absolute cell count by the determined activity to provide a list of active microorganisms strains and their respective absolute cell counts for each of the at least two samples; comparing the filtered absolute cell counts of active microorganisms strains for each of the at least two samples with at least one measured metadata for each of the at least two samples and categorizing the active microorganism strains into at least two groups based on network analysis; selecting at least one microorganism strain from the at least two groups; and combining the selected at least one microorganism strain from the at least two groups to form a ensemble of microorganisms configured to alter a property corresponding to the at least one metadata. obtaining at least two samples sharing at least one common characteristic and having at least one different characteristic, wherein the at least one different characteristic includes a collection time at which each of the at least two samples was collected, such that the collection time for a first sample is different from the collection time of a second sample, or a collection location at which each of the at least two samples was collected, such that the collection location for a first sample is different from the collection location of a second sample, and the at least one common characteristic includes a sample source type, such that the sample source type for a first sample is the same as the sample source type of a second sample; for each sample, detecting the presence of one or more microorganism types in each sample; determining a number of cells of each detected microorganism type of the one or more microorganism types in each sample; measuring a number of occurrences of each unique first marker of a set of unique first markers in each sample, each unique first marker being a marker of a microorganism strain; representing the number of occurrences of each unique first marker, from the set of unique first markers, as a percentage of total unique first markers, to give a percentage of each microorganism strain of each microorganism type; multiplying the number of cells of each microorganism type by the percentage of each microorganism strain to yield the absolute cell count of each microorganism strain present in each sample; measuring at least one unique second marker for each microorganism strain based on a specified threshold to determine an activity level for that microorganism strain in each sample, each unique second marker for each microorganism strain being different than the unique first marker for that microorganism strain; filtering the absolute cell count by the determined activity to provide a list of active microorganisms strains and their respective absolute cell counts for each of the at least two samples; comparing the filtered absolute cell counts of active microorganisms strains for each of the at least two samples with at least one measured metadata for each of the at least two samples and categorizing the active microorganism strains into at least two groups based on network analysis; selecting at least one microorganism strain from the at least two groups; and combining the selected at least one microorganism strain from the at least two groups to form a ensemble of microorganisms configured to alter a property corresponding to the at least one metadata.