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
First Claim
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1. A method of making a synthetic microbial ensemble to improve at least one target biological property in a target biological environment, comprising:
- selecting at least two active microorganism strains including at least one active fungus strain and a least one active bacterium strain, the at least two active microorganism strains being at least two active microorganism strains identified by processing a plurality of samples collected from a sample population, the processing including;
for each sample of the plurality of samples;
detecting the presence of one or more microorganism types and determining an absolute number of each detected microorganism type;
measuring a quantity of unique first markers, each unique first marker being a marker of a microorganism strain of a detected microorganism type;
determining an absolute cell count of each microorganism strain based on multiplying the number of each detected microorganism type and relative quantity of unique first markers for that microorganism type;
determining an activity level for each microorganism strain based on measuring at least one unique second marker;
filtering each microorganism strain by the determined activity level to provide a set of active microorganism strains and respective absolute cell counts;
measuring at least one biological property for each sample of the plurality of samples collected from the sample population; and
analyzing the set of active microorganism strains and respective absolute cell counts of each sample of the plurality of samples with the at least one measured biological property of each sample of the plurality of samples via network analysis to identify relationships between each active microorganism strain from the set of active microorganism strains and between each active microorganism strain from the set of active microorganism strains and the at least one measured biological property, categorizing active microorganism strains based on the identified relationships between active microorganism strains and the at least one measure biological property according to at least one of predicted function and chemistry, and identifying at least two active microorganism strains based on the categorization;
preparing the at least one active fungus strain and preparing the at least one active bacterium strain for inclusion in a synthetic microbial ensemble configured to improve at least one target biological property in a target biological environment when the synthetic microbial ensemble is introduced into the target biological environment, the at least one target biological property associated with the at least one measured biological property; and
forming the synthetic microbial ensemble from the prepared at least one active fungus strain, the prepared at least one active bacterium strain, and at least one stabilizing carrier.
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Abstract
Methods, apparatuses, and systems for screening, analyzing and selecting microorganisms from complex heterogeneous communities, predicting and identifying functional relationships and interactions thereof, and synthesizing microbial ensembles based thereon are disclosed. Methods for identifying and determining the absolute cell count of microorganism types and strains, along with identifying the network relationships between active microorganisms and environmental parameters, are also disclosed.
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Citations
19 Claims
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1. A method of making a synthetic microbial ensemble to improve at least one target biological property in a target biological environment, comprising:
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selecting at least two active microorganism strains including at least one active fungus strain and a least one active bacterium strain, the at least two active microorganism strains being at least two active microorganism strains identified by processing a plurality of samples collected from a sample population, the processing including; for each sample of the plurality of samples;
detecting the presence of one or more microorganism types and determining an absolute number of each detected microorganism type;
measuring a quantity of unique first markers, each unique first marker being a marker of a microorganism strain of a detected microorganism type;
determining an absolute cell count of each microorganism strain based on multiplying the number of each detected microorganism type and relative quantity of unique first markers for that microorganism type;
determining an activity level for each microorganism strain based on measuring at least one unique second marker;
filtering each microorganism strain by the determined activity level to provide a set of active microorganism strains and respective absolute cell counts;measuring at least one biological property for each sample of the plurality of samples collected from the sample population; and analyzing the set of active microorganism strains and respective absolute cell counts of each sample of the plurality of samples with the at least one measured biological property of each sample of the plurality of samples via network analysis to identify relationships between each active microorganism strain from the set of active microorganism strains and between each active microorganism strain from the set of active microorganism strains and the at least one measured biological property, categorizing active microorganism strains based on the identified relationships between active microorganism strains and the at least one measure biological property according to at least one of predicted function and chemistry, and identifying at least two active microorganism strains based on the categorization; preparing the at least one active fungus strain and preparing the at least one active bacterium strain for inclusion in a synthetic microbial ensemble configured to improve at least one target biological property in a target biological environment when the synthetic microbial ensemble is introduced into the target biological environment, the at least one target biological property associated with the at least one measured biological property; and forming the synthetic microbial ensemble from the prepared at least one active fungus strain, the prepared at least one active bacterium strain, and at least one stabilizing carrier. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9)
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10. A synthetic microbial ensemble feed supplement of active microorganism strains to improve at least one target biological property in a rumen of a ruminant when the synthetic microbial ensemble feed supplement of active microorganism strains administered thereto, comprising:
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at least one preserved active Pichia fungus strain having a colony-forming unit (CFU) value of at least 10̂
7 per gram of synthetic microbial ensemble feed supplement;at least one active Clostridium bacterium strain having a CFU value of at least 10̂
6 per gram of synthetic microbial ensemble feed supplement, the at least one active Clostridium bacterium strain composed of dried spores of the at least one active Clostridium bacterium strain;
the at least one active Pichia fungus strain and the at least one active Clostridium bacterium strain corresponding to active microorganism strains identified by network analysis of a plurality of rumen samples collected from a sample population of ruminants, the network analysis including;for each rumen sample of the plurality of rumen samples;
detecting the presence of one or more microorganism types and determining an absolute number of each detected microorganism type;
measuring a quantity of unique first markers, each unique first marker being a marker of a microorganism strain of a detected microorganism type;
determining the absolute cell count of each microorganism strain from the absolute number of each detected microorganism type and relative quantity of unique first markers of that microorganism type;
determining an activity level for each microorganism strain based on at least one unique second marker;
filtering each microorganism strain by the determined activity level to provide a list of active microorganism strains and their respective absolute cell counts;measuring at least one biological property for each of the plurality of rumen samples collected from the sample population of ruminants and analyzing the active microorganisms strains and respective absolute cell counts of each rumen sample of the plurality of rumen samples with the at least one measured biological property to identify relationships between each microorganism strain and between each active microorganism strain and the at least one measured biological property, categorizing active microorganism strains based on the identified relationships between active microorganism strains and the at least one measure biological property according to at least one of predicted function and chemistry, and identifying at least two active microorganism strains based on the categorization; and at least one stabilizing carrier for the at least one preserved active Pichia fungus strain and the at least one active Clostridium bacterium strain.
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11. A method to improve rumen function in a ruminant with a synthetic microbial ensemble supplement, comprising:
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selecting at least two active microorganism strains, including at least one active Pichia fungus strain and a least one active Clostridium bacterium strain, the selected at least two active microorganism strains corresponding to at least two active microorganism strains identified by network analysis of a plurality of rumen samples collected from a sample population of ruminants, the network analysis including; for each rumen sample of the plurality of rumen samples;
detecting the presence of one or more microorganism types and determining a number of each detected microorganism type;
measuring unique first markers and quantity thereof, each unique first marker being a marker of a microorganism strain;
determining the absolute cell count of each microorganism strain based on the number of each detected microorganism type and relative quantity of unique first markers;
determining an activity level for each microorganism strain based on at least one unique second marker;
generating a list of active microorganism strains and their respective absolute cell counts;measuring at least one biological property for each rumen sample of the plurality of rumen samples collected from the sample population of ruminants; analyzing the absolute cell counts of active microorganisms strains of each of the rumen samples of the plurality of rumen samples with the at least one measured biological property to identify relationships between each active microorganism strain and between each active microorganism strain the at least one measured biological property and categorizing active microorganism strains based on the identified relationships between active microorganism strains and the at least one measured biological property; identifying at least two active microorganism strains based on the categorization; preparing the at least one active Pichia fungus strain and preparing the at least one active Clostridium bacterium strain for inclusion in a synthetic microbial ensemble supplement configured to improve rumen function when administered to a ruminant as a feed supplement; forming the synthetic microbial ensemble supplement from the prepared at least one active Pichia fungus strain and at least one active Clostridium bacterium strain, and at least one stabilizing carrier; and administering the synthetic microbial ensemble supplement to at least one ruminant as a feed supplement to improve rumen function of the at least one ruminant. - View Dependent Claims (12, 13, 14, 15, 16, 17, 18, 19)
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Specification