Abstract: A phage defense rotation strategy for use in the successive fermentations of a substrate in a fermentation plant is disclosed. The strategy comprises (a) fermenting substrate with a first bacterial culture comprising a bacterial strain capable of fermenting the substrate and, preferably, carrying a first phage defense mechanism; and then (b) fermenting the substrate with a second bacterial culture comprising a second bacterial strain isogenic with the first bacterial strain, wherein the second strain carries a second phage defense mechanism different from the first phage defense mechanism.Also disclosed is a mixed bacterial culture capable of fermenting a substrate. The mixed culture comprises (a) a first bacterial strain carrying a first phage defense mechanism; and (b) a second bacterial strain isogenic with the first strain, wherein the second strain carries a phage defense mechanism different from the phage defense mechanism carried by the first strain.

Abstract: Recombinant bacteria containing phage-encoded resistance ("Per") and methods of making and using the same are disclosed. Such bacteria are made by (a) conducting a fermentation of a substrate in a medium containing a defined bacterial culture until bacteriophage are detected in the medium, the bacteriophage being specific to at least one bacteria in the medium; (b) isolating the bacteriophage; (c) digesting DNA of the bacteriophage to produce a library of DNA fragments; (d) transforming the bacteria susceptible to said bacteriophage with the library of DNA fragments to provide transformed bacteria; (e) selecting from among the transformed bacteria, a bacteriophage-resistant transformed bacteria; (f) adding bacteriophage resistant transformed bacteria to the medium; and (g) recommencing step (a).