Guided microbial remodeling, a platform for the rational improvement of microbial species for agriculture

A computationally guided microbial remodeling method for the rational improvement of plant-associated microbes to perform plant-beneficial functions, comprising:

• a. accessing a plurality of microbial whole genome sequences;
• b. identifying a plurality of regulatory gene sequences that actively regulate the transcription of a gene under a metabolically relevant environmental condition;
• c. identifying a plurality of genes associated with a plant-beneficial function;
• d. selecting a regulatory gene sequence and a gene associated with a plant-beneficial function from said pluralities;
• wherein steps a)-d) occur in silico;
• and
• e. manufacturing, in vivo, a remodeled microbial cell that has the selected regulatory gene sequence operably linked to the selected gene associated with a plant-beneficial function, thereby improving the expression of the gene associated with a plant-beneficial function.

A computationally guided microbial remodeling system for the rational improvement of plant-associated microbes to perform plant-beneficial functions, comprising:

• a. one or more processors;
• and
• b. one or more memories operatively coupled to the one or more processors and having instructions stored thereon, that when executed by the one or more processors, cause the system to:
• i. access a plurality of microbial whole genome sequences;
• ii. identify a plurality of regulatory gene sequences that actively regulate the transcription of a gene under a metabolically relevant environmental condition;
• iii. identify a plurality of genes associated with a plant-beneficial function;
• and
• iv. select a regulatory gene sequence and a gene associated with a plant-beneficial function from said pluralities.

A computationally guided microbial remodeling method for the rational improvement of plant-associated microbes to perform plant-beneficial functions, comprising:

• a. activating a computer system having:
• one or more processors and one or more memories operatively coupled to the one or more processors and having instructions stored thereon, thereby causing the one or more processors to execute the instructions, and cause the system to:
• i. access a plurality of microbial whole genome sequences;
• ii. identify a plurality of regulatory gene sequences that actively regulate the transcription of a gene under a metabolically relevant environmental condition;
• iii. identify a plurality of genes associated with a plant-beneficial function;
• iv. select a regulatory gene sequence and a gene associated with a plant-beneficial function from said pluralities;
• and
• b. manufacturing, in vivo, a remodeled microbial cell that has the selected regulatory gene sequence operably linked to the selected gene associated with a plant-beneficial function, thereby improving the expression of the gene associated with a plant-beneficial function.