Table 1 Current tools available for lactic acid bacteria genome editing

Plasmids-based allelic exchange

Lc. lactis, S. thermophilus, E. faecalis

Homologous recombination-dependent; marker free; time-consuming

[19, 20]

DsDNA recombineering

Lb. plantarum, Lb. casei

Recombinase-mediated; high efficiencies for both deletion and insertion; marker-dependent

[29, 30]

SsDNA recombineering

Lb. reuteri, Lc. lactis, Lb. plantarum, Lb. gasseri

Mutation efficiency 0.4–19%; applicable to genomic mutagenesis; marker free

[31]

CRISPR–Cas-assisted recombineering

Lb. reuteri, Lc. Lactis

High efficiency (up to 100%) for small deletions (< 1.0 kb in Lb. reuteri, < 100 bp in Lc. lactis); marker free

[35, 36]

CRISPR–Cas9D10A

Lb. casei

Used for both gene deletion and insertion (25–65%); simplified editing procedure; marker free

[39]

CRISPRi

Lb. plantarum, Lc. lactis

Used to repress multiple target genes simultaneously; reversible effects; precise targeting; marker free

[40,41,42,43]