[1] ISHINO Y, SHINAGAWA H, MAKINO K, et al.Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product[J].Journal of Bacteriology, 1987, 169(12):5 429-5 433.
[2] JANSEN R, VAN EMBDEN J D A, GAASTRA W, et al.Identification of genes that are associated with DNA repeats in prokaryotes[J].Molecular Microbiology, 2002, 43(6):1 565-1 575.
[3] KLAENHAMMER T R, BARRANGOU R, BUCK B L, et al.Genomic features of lactic acid bacteria effecting bioprocessing and health[J].FEMS Microbiology Reviews, 2005, 29(3):393-409.
[4] BARRANGOU R, FREMAUX C, DEVEAU H, et al.CRISPR provides acquired resistance against viruses in prokaryotes[J].Science, 2007, 315(5 819):1 709-1 712.
[5] CRAWLEY A B, HENRIKSEN E D, STOUT E, et al.Characterizing the activity of abundant, diverse and active CRISPR-Cas systems in lactobacilli[J].Scientific Reports, 2018, 8(1):1-12.
[6] SANOZKY-DAWES R, SELLE K, O'FLAHERTY S, et al.Occurrence and activity of a type II CRISPR-Cas system in Lactobacillus gasseri[J].Microbiology (Reading, England), 2015, 161(9):1 752-1 761.
[7] BARRANGOU R, MARRAFFINI L A.CRISPR-cas systems:Prokaryotes upgrade to adaptive immunity[J].Molecular Cell, 2014, 54(2):234-244.
[8] DELTCHEVA E, CHYLINSKI K, SHARMA C M, et al.CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III[J].Nature, 2011, 471(7 340):602-607.
[9] ANDERS C, NIEWOEHNER O, DUERST A, et al.Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease[J].Nature, 2014, 513(7 519):569-573.
[10] SONG X, HUANG H, XIONG Z Q, et al.CRISPR-Cas9 D10A nickase-assisted genome editing in Lactobacillus casei[J].Applied and Environmental Microbiology, 2017, 83(22):e01259-e01217.
[11] XIONG Z Q, WEI Y Y, KONG L H, et al.Short communication:An inducible CRISPR/dCas9 gene repression system in Lactococcus lactis[J].Journal of Dairy Science, 2020, 103(1):161-165.
[12] MYRBRÅTEN I S, WIULL K, SALEHIAN Z, et al.CRISPR interference for rapid knockdown of essential cell cycle genes in Lactobacillus plantarum[J].mSphere, 2019, 4(2):e00007-e00019.
[13] MAKAROVA K S, WOLF Y I, IRANZO J, et al.Evolutionary classification of CRISPR-Cas systems:a burst of class 2 and derived variants[J].Nature Reviews Microbiology, 2020, 18(2):67-83.
[14] KOONIN E V, MAKAROVA K S.Origins and evolution of CRISPR-Cas systems[J].Philosophical Transactions of the Royal Society B: Biological Sciences, 2019, 374(1 772):20180087.
[15] BALGIR P P, RANI S.In silico analysis of CRISPR-cas-mediated bacteriophage resistance in lactobacilli[J].Journal of Gastrointestinal Infections, 2019, 9(1):15-22.
[16] MOHANRAJU P, MAKAROVA K S, ZETSCHE B, et al.Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems[J].Science, 2016, 353(6 299):aad5147.
[17] KAZLAUSKIENE M, KOSTIUK G, VENCLOVAS Č, et al.A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems[J].Science, 2017, 357(6 351):605-609.
[18] SCHUSTER J A, VOGEL R F, EHRMANN M A.Characterization and distribution of CRISPR-Cas systems in Lactobacillus sakei[J].Archives of Microbiology, 2019, 201(3):337-347.
[19] HIDALGO-CANTABRANA C, CRAWLEY A B, SANCHEZ B, et al.Characterization and exploitation of CRISPR loci in Bifidobacterium longum[J].Frontiers in Microbiology, 2017, 8:1 851.
[20] KNOTT G J, DOUDNA J A.CRISPR-Cas guides the future of genetic engineering[J].Science, 2018, 361(6 405):866-869.
[21] HIDALGO-CANTABRANA C, GOH Y J, PAN M C, et al.Genome editing using the endogenous type I CRISPR-Cas system in Lactobacillus crispatus[J].Proceedings of the National Academy of Sciences of the United States of America, 2019, 116(32):15 774-15 783.
[22] GOH Y J, BARRANGOU R.Portable CRISPR-Cas9 N system for flexible genome engineering in Lactobacillus acidophilus, Lactobacillus gasseri, and Lactobacillus paracasei[J].Applied and Environmental Microbiology, 2021, 87(6):e02669-e02620.
[23] LELOUP L, EHRLICH S D, ZAGOREC M, et al.Single-crossover integration in the Lactobacillus sake chromosome and insertional inactivation of the ptsI and lacL genes[J].Applied and Environmental Microbiology, 1997, 63(6):2 117-2 123.
[24] GROOT M N, KLAASSENS E, DE VOS W M, et al.Genome-based in silico detection of putative manganese transport systems in Lactobacillus plantarum and their genetic analysis[J].Microbiology, 2005, 151(Pt 4):1 229-1 238.
[25] ORTIZ-VELEZ L, BRITTON R.Genetic Tools for the Enhancement of Probiotic Properties[M]//Bugs as Drugs.Washington, DC, USA:ASM Press, 2018:371-387.
[26] OH J H, VAN PIJKEREN J P.CRISPR-Cas9-assisted recombineering in Lactobacillus reuteri[J].Nucleic Acids Research, 2014, 42(17):e131.
[27] GUO T T, XIN Y P, ZHANG Y, et al.A rapid and versatile tool for genomic engineering in Lactococcus lactis[J].Microbial Cell Factories, 2019, 18(1):22.
[28] ZHOU D, JIANG Z N, PANG Q X, et al.CRISPR/Cas9-assisted seamless genome editing in Lactobacillus plantarum and its application in N-acetylglucosamine production[J].Applied and Environmental Microbiology, 2019, 85(21):e01367-e01319.
[29] HUANG H, SONG X, YANG S.Development of a RecE/T-assisted CRISPR-Cas9 toolbox for Lactobacillus[J].Biotechnology Journal, 2019, 14(7):1800690.
[30] SONG X, LIU L, LIU X X, et al.Single-plasmid systems based on CRISPR-Cas9 for gene editing in Lactococcus lactis[J].Journal of Dairy Science, 2021, 104(10):10 576-10 585.
[31] BRAVO D, LANDETE J M.Genetic engineering as a powerful tool to improve probiotic strains[J].Biotechnology & Genetic Engineering Reviews, 2017, 33(2):173-189.
[32] YANG P, WANG J, QI Q S.Prophage recombinases-mediated genome engineering in Lactobacillus plantarum[J].Microbial Cell Factories, 2015, 14:154.
[33] LEMAY M L, OTTO A, MAAß S, et al.Investigating Lactococcus lactis MG1363 response to phage p2 infection at the proteome level[J].Molecular & Cellular Proteomics, 2019, 18(4):704-714.
[34] WANG G Q, YU H N, FENG X, et al.Specific bile salt hydrolase genes in Lactobacillus plantarum AR113 and relationship with bile salt resistance[J].LWT, 2021, 145:111208.
[35] TIAN X W, LIU X H, ZHANG Y F, et al.Metabolic engineering coupled with adaptive evolution strategies for the efficient production of high-quality L-lactic acid by Lactobacillus paracasei[J].Bioresource Technology, 2021, 323:124549.
[36] VAN DER ELS S, JAMES J K, KLEEREBEZEM M, et al.Versatile Cas9-driven subpopulation selection toolbox for Lactococcus lactis[J].Applied and Environmental Microbiology, 2018, 84(8):e02752-e02717.
[37] PUJATO S, GALLIANI V, IRAZOQUI J M, et al.Analysis of CRISPR systems of types II-A, I-E and I-C in strains of Lacticaseibacillus[J].International Dairy Journal, 2021, 118:105027.
[38] ROGALSKI E, VOGEL R F, EHRMANN M A.Monitoring of Lactobacillus sanfranciscensis strains during wheat and rye sourdough fermentations by CRISPR locus length polymorphism PCR[J].International Journal of Food Microbiology, 2020, 316:108475.
[39] SCALTRITI E, CARMINATI D, CORTIMIGLIA C, et al.Survey on the CRISPR arrays in Lactobacillus helveticus genomes[J].Letters in Applied Microbiology, 2019, 68(5):394-402.
[40] YANG L, LI W X, UJIROGHENE O J, et al.Occurrence and diversity of CRISPR loci in Lactobacillus casei group[J].Frontiers in Microbiology, 2020, 11:624.
[41] STOUT E A, SANOZKY-DAWES R, GOH Y J, et al.Deletion-based escape of CRISPR-Cas9 targeting in Lactobacillus gasseri[J].Microbiology, 2018, 164(9):1 098-1 111.
[42] LEENAY R T, VENTO J M, SHAH M, et al.Genome editing with CRISPR-Cas9 in Lactobacillus plantarum revealed that editing outcomes can vary across strains and between methods[J].Biotechnology Journal, 2019, 14(3):1700583.
