1. A method for rehabilitating and improving the phenotypic performance of a production microbial strain, comprising the steps of: a. providing a parental lineage microbial strain and a production microbial strain derived therefrom, wherein the production microbial strain comprises a plurality of identified genetic variations selected from single nucleotide polymorphisms, DNA insertions, and DNA deletions, not present in the parental lineage microbial strain; b. perturbing the genome of either the parental lineage microbial strain, or the production microbial strain, to create an initial library of microbial strains, wherein each strain in the initial library comprises a unique genetic variation from the plurality of identified genetic variations between the parental lineage microbial strain and the production microbial strain; c. screening and selecting individual strains of the initial library for phenotypic performance improvements over a reference microbial strain, thereby identifying unique genetic variations that confer phenotypic performance improvements; d. providing a subsequent plurality of microbes that each comprise a combination of unique genetic variations from the genetic variations present in at least two individual microbial strains screened in the preceding step, to thereby create a subsequent library of microbial strains; e. screening and selecting individual strains of the subsequent library for phenotypic performance improvements over the reference microbial strain, thereby identifying unique combinations of genetic variation that confer additional phenotypic performance improvements; and f. repeating steps d)-e) one or more times, in a linear or non-linear fashion; until a microbial strain exhibits a desired level of improved phenotypic performance compared to the phenotypic performance of the production microbial strain, wherein each subsequent iteration creates a new library of microbial strains, where each strain in the new library comprises genetic variations that are a combination of genetic variations selected from amongst at least two individual microbial strains of a preceding library.