Chapter 16 : Genetic Tools for the Enhancement of Probiotic Properties

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With renewed interest in the human microbiome and its role in human health, unique opportunities for using microbes as therapeutics have recently emerged. These opportunities range from the traditional probiotics to the engineering of intestinal mutualistic bacteria to deliver therapeutic proteins ( ). However, a more in-depth understanding of how intestinal microbes impact human health and how they function in the complex, dynamic environment of the gastrointestinal tract (GIT) requires advancements in genetic tools for nonmodel strains.

Citation: Ortiz-velez L, Britton R. 2018. Genetic Tools for the Enhancement of Probiotic Properties, p 371-387. In Britton R, Cani P (ed), Bugs as Drugs. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.BAD-0018-2016
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Figure 1

Schematic representation of dsDNA recombineering in . (A) A piece of dsDNA harboring the -- cassette ( and sites, red; Cat/CM marker, yellow) and regions with homology to the genomic insertion site (H1, green; H2, blue) is transformed into expressing an exonuclease (Lp0642), a possible host nuclease inhibitor (Lp0640), and an ssDNA binding protein (Lp0641). (B) Once the dsDNA fragments are integrated into the genome, which renders the cells resistant to CM (CM), bacteria are transformed with a plasmid that induces the expression of the recombinase Cre to recombine the sites. This recombination deletes the CM marker contained inside the sites, rendering the cells CM-sensitive and leaving a modified site (72).

Citation: Ortiz-velez L, Britton R. 2018. Genetic Tools for the Enhancement of Probiotic Properties, p 371-387. In Britton R, Cani P (ed), Bugs as Drugs. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.BAD-0018-2016
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Figure 2

Schematic representation of ssDNA recombineering in . (A) An oligomer harboring the mutation (red) and regions with homology to the genomic insertion site (blue) is transformed into cells expressing RecT. (B) The oligomer is incorporated into the lagging strand being synthesized at the DNA replication fork, generating a mutant with a mixed genotype (GT). (C) Screening of the mutant is done by MAMA-PCR, using two oligomers that amplify from a WT sequence (black) and a third oligomer (red-blue) that only amplifies when the mutation is incorporated. Thus, two amplicons are generated in the case of the mutant (lane 1), whereas only one amplicon is generated in the case of the WT (lanes 2 to 5). After the mixed genotype is identified, single colony purification is done to isolate cells containing only the mutation (pure genotype).

Citation: Ortiz-velez L, Britton R. 2018. Genetic Tools for the Enhancement of Probiotic Properties, p 371-387. In Britton R, Cani P (ed), Bugs as Drugs. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.BAD-0018-2016
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Figure 3

Overview of recombineering/CRISPR-Cas9 genome engineering in . (A) An oligomer harboring the mutation (red) and regions with homology to the genomic insertion site (blue) is transformed into expressing RecT, Cas9, and its tracrRNA. (B) The oligomer targets the lagging strains and is incorporated into one of the DNA strands at the replication fork. When cells divide, a mixed population of WT and mutant cells is generated. (C) A plasmid expressing guide RNA (pgRNA) that targets the WT sequence is introduced into the cell. Cas9 is directed by the gRNA to cleave DNA of cells that did not incorporate the mutations (WT), whereas cells that incorporate the mutation are void of cleavage (mutant).

Citation: Ortiz-velez L, Britton R. 2018. Genetic Tools for the Enhancement of Probiotic Properties, p 371-387. In Britton R, Cani P (ed), Bugs as Drugs. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.BAD-0018-2016
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