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

Abstract

Methods, apparatuses, and systems the screening, analyzing and selecting microorganisms from complex heterogeneous communities, predicting and identifying functional relationships and interactions thereof, synthesizing microbial ensembles based thereon, and forming and administering endomicrobial feed supplements are disclosed. Methods for identifying and determining the absolute cell count of microorganism types and strains, along identifying the network relationships between active microorganisms and environmental parameters, are also disclosed.

1 - 3 . (canceled) 
     
     
         4 . A method of making a synthetic microbial ensemble, comprising:
 measuring an absolute cell count of a microorganism strain in a plurality of samples;   measuring at least one metadata for each sample from the plurality of samples, wherein the at least one metadata is positively associated with the absolute cell count of the microorganism strain; and   preparing, based on the measure of absolute cell count and the measure of the at least one metadata, the synthetic microbial ensemble by contacting the microorganism strain with a stabilizing carrier.   
     
     
         5 . The method of  claim 4 , wherein the metadata includes an indication of an parameter associated with a surrounding environment associated with a sample from the plurality of samples. 
     
     
         6 . The method of  claim 4 , wherein the metadata includes an indication of a parameter associated with a surrounding environment associated with a sample including at least one of nutrient acquisition, plant diversity, pH, temperature, expression of a specified protein or mRNA, level and/or identity of one or more nutrients included in the surrounding environment associated with the sample. 
     
     
         7 . The method of  claim 4 , wherein the metadata includes an indication of a parameter associated with a surrounding environment associated with a sample including at least one of an indication of susceptibility or resistance to disease of a surrounding environment associated with a sample, an indication of onset or progression of disease associated with a sample, an indication of susceptibility or resistance to toxins associated with a sample, an indication of efficacy of xenobiotic compounds associated with a sample, or an indication of biosynthesis of natural products associated with a sample. 
     
     
         8 . The method of  claim 4 , wherein the metadata includes an indication of a parameter associated with a surrounding environment associated with a sample including at least one of a genomic information related to a host from which a sample is obtained, a parameter that affects a change in an identity of a microbial community associated with a sample, or a parameter that is affected by a change in the identity of a microbial community associated with a sample. 
     
     
         9 . The method of  claim 4 , wherein the microorganism strain is a first microorganism strain and the metadata include an indication of a presence of a second microorganism strain, different from the first microorganism strain, that is active. 
     
     
         10 . The method of  claim 4 , further comprising:
 calculating a maximal information coefficient (MIC) score associating the at least one metadata with the absolute cell count of the microorganism strain; and   determining, based on the MIC score being at or above a predefined threshold value, a relevance associated with the microorganism strain, the preparing the synthetic microbial ensemble being based on the determination of relevance associated with the microorganism strain.   
     
     
         11 . The method of  claim 4 , further comprising:
 measuring a quantity of a set of unique markers, each unique marker from the set of unique markers indicating a presence of a unique microorganism strain from a plurality of microorganism strains; and   calculating a number of each microorganism type from a plurality of microorganism types from each microorganism strain from a plurality of microorganism strains and the number of the first markers is integrated to yield the absolute cell count of each microorganism strain present in each sample.   
     
     
         12 . 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, based on the measure of absolute cell count and the measure of the activity level, the synthetic microbial ensemble by contacting the microorganism strain with a stabilizing carrier.   
     
     
         13 . The method of  claim 12 , further comprising:
 measuring a level of expression of a set of unique markers, each unique marker from the set of unique markers indicating an activity level associated with a unique microorganism strain;   comparing the level of expression of each unique marker from the set of unique markers against a predefined threshold value associated with that unique marker; and   selecting the microorganism strain, based on the comparison, for preparing the synthetic microbial ensemble.   
     
     
         14 . The method of  claim 12 , further comprising:
 measuring a level of expression of a set of unique markers, each unique marker from the set of unique markers indicating an activity level associated with a microorganism strain, the unique marker including at least one of a protein or an RNA; and   selecting the microorganism, based on the level of expression of the set of unique markers, to prepare the synthetic microbial ensemble.   
     
     
         15 . The method of  claim 12 , further comprising:
 quantifying a strength of a relationship between the absolute cell count of the microorganism strain and the activity level associated with the microorganism strain; and   selecting the microorganism, based on the strength of the relationship being greater than a predefined threshold value, to prepare the synthetic microbial ensemble.   
     
     
         16 . The method of  claim 12 , wherein the measuring the activity level includes measuring a level of expression of a set of unique markers, each unique marker from the set of unique markers indicating an activity level associated with a microorganism strain, the unique marker including at least one of a nucleic acid-based marker, a peptide-based marker, a protein-based marker, a metabolite marker, or a small molecule marker. 
     
     
         17 . The method of  claim 12 , further comprising:
 measuring a quantity of a set of first unique markers, each first unique marker from the set of first unique markers indicating a presence of the a microorganism, the measure of absolute cell count of the microorganism being based on the quantity of at least one first unique marker indicating a presence of the microorganism; and   
       measuring a level of expression of a set of second unique markers, each second unique marker from the set of second unique markers indicating an activity level associated with the microorganism strain, the measure of activity level associated with the microorganism being based on a level of expression of at least one second unique marker indicating an activity level associated with the microorganism. 
     
     
         18 . The method of  claim 12 , further comprising:
 measuring a normalized quantity of a set of first unique markers, each first unique marker from the set of first unique markers indicating a presence of the unique microorganism;   
       measuring a normalized level of expression of a set of second unique markers, each second unique marker from the set of second unique markers indicating an activity level associated with the microorganism strain; and 
       selecting the microorganism, based on the normalized level of expression of a second unique marker indicating an activity level associated with the microorganism strain being greater than the normalized quantity of a first unique marker indicating the presence of the microorganism being, to prepare the synthetic microbial ensemble. 
     
     
         19 . A method of administering a synthetic microbial ensemble, comprising administering the synthetic microbial ensemble to an environment, wherein the synthetic microbial ensemble is prepared by:
 measuring an absolute cell count of a microorganism strain in a plurality of samples;   measuring a metadata for each sample of from the plurality of samples, wherein the at least one metadata is positively associated with the absolute cell count of the microorganism strain; and   preparing, based on the measure of absolute cell count and the measure of the at least one metadata for each sample from the plurality of samples, the microorganism strain with a stabilizing carrier.   
     
     
         20 . The method of  claim 19 , wherein the microorganism strain is an active microorganism strain and the synthetic microbial ensemble is configured to alter a predefined property associated with the environment. 
     
     
         21 . The method of  claim 19 , wherein the synthetic microbial ensemble is further prepared by:
 quantifying a strength of a relationship between the absolute cell count of the microorganism strain and the metadata for each sample of the plurality of samples; and   selecting the microorganism, based on the strength of the relationship, the preparing the microorganism strain being based on the selection.   
     
     
         22 . The method of  claim 19 , wherein the environment comprises at least one of animal, sediment, oil, plant, agricultural product, water sample, or an extreme environmental sample. 
     
     
         23 . The method of  claim 19 , wherein the synthetic microbial ensemble is further prepared by:
 isolating the microorganism strain to generate an isolated microorganism strain, the isolated microorganism strain being in the form of at least one of a biologically pure culture, or a spore, and the preparing the microorganism strain including contacting the isolated microorganism strain with the stabilizing carrier.