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Safety and robustness aspects analysis of Lactobacillus delbrueckii ssp. bulgaricus LDB-C1 based on the genome analysis and biological tests

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Abstract

Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) is a microaerophylic anaerobe, which is widely used in the production of yogurt, cheese, and other fermented dairy products. L. bulgaricus and its partner Streptococcus thermophilus were used as starter cultures of yogurt in the world for thousands of years. In our previous study, L. bulgaricus LDB-C1 was obtained from traditional fermented milk, and possessed some characteristics like high exopolysaccharide yield and good fermentation performance. The analysis of its CRISPR–Cas system, antibiotic resistance, virulence factors, and mobile elements, was performed to reveal the stability of the strain LDB-C1. It was found that LDB-C1 contains a plenty of spacers in the CRISPR region, indicating it might have better performance against the infection of phages and plasmids. Furthermore, the acquired or transmittable antibiotic resistance/virulence factor genes were absent in the tested L. bulgaricus strain LDB-C1.

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References

  • Abdel-Bar NM, Harris ND (1984) Inhibitory effect of Lactobacillus bulgaricus on psychrotrophic bacteria in associative cultures and in refrigerated foods. J Food Prot 47(1):61–64

    Article  PubMed  Google Scholar 

  • Abriouel H, Casado Muñoz MDC, Lavilla Lerma L, Pérez Montoro B, Bockelmann W, Pichner R et al (2015) New insights in antibiotic resistance of Lactobacillus species from fermented foods. Food Res Int 78:465–481

    Article  CAS  PubMed  Google Scholar 

  • Accolas J-P, Spillmann H (1979) Morphology of bacteriophages of Lactobacillus bulgaricus, L. lactis and L. helveticus. J Appl Bacteriol 47(2):309–319

    Article  Google Scholar 

  • Adhikari P, Berish SA, Nowalk AJ, Veraldi KL, Morse SA, Mietzner TA (1996) The fbpABC locus of Neisseria gonorrhoeae functions in the periplasm-to-cytosol transport of iron. J Bacteriol 178(7):2145–2149

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ammor MS, Flórez AB, Mayo B (2007) Antibiotic resistance in non-enterococcal lactic acid bacteria and bifidobacteria. Food Microbiol 24(6):559–570

    Article  CAS  PubMed  Google Scholar 

  • Anisimova EA, Yarullina DR (2019) Antibiotic resistance of Lactobacillus strains. Curr Microbiol 76(12):1407–1416

    Article  CAS  PubMed  Google Scholar 

  • Auad L, Räisänen L, Raya RR, Alatossava T (1999) Physical mapping and partial genetic characterization of the Lactobacillus delbrueckii subsp. bulgaricus bacteriophage lb539. Arch Virol 144(8):1503–1512

    Article  CAS  PubMed  Google Scholar 

  • Barcus VA, Ghanekar K, Yeo M, Coffey TJ, Dowson CG (1995) Genetics of high-level penicillin resistance in clinical isolates of Streptococcus pneumoniae. FEMS Microbiol Lett 126(3):299–303

    Article  CAS  PubMed  Google Scholar 

  • Barrangou R, Coûté-Monvoisin AC, Stahl B, Chavichvily I, Damange F, Romero DA et al (2013) Genomic impact of CRISPR immunization against bacteriophages. Biochem Soc T 41(6):1383–1391

    Article  CAS  Google Scholar 

  • Bisicchia P, Bui NK, Aldridge C, Vollmer W, Devine KM (2011) Acquisition of VanB-Type vancomycin resistance by Bacillus subtilis: the impact on gene expression, cell wall composition and morphology. Mol Microbiol 81(1):157–178

    Article  CAS  PubMed  Google Scholar 

  • Bolotin A, Quinquis B, Sorokin A, Ehrlich SD (2005) Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151(8):2551–2561

    Article  CAS  PubMed  Google Scholar 

  • Cabanes D, Dussurget O, Dehoux P, Cossart P (2004) Auto, a surface associated autolysin of Listeria monocytogenes required for entry into eukaryotic cells and virulence. Mol Microbiol 51(6):1601–1614

    Article  CAS  PubMed  Google Scholar 

  • Casey E, Mahony J, O’Connell-Motherway M, Bottacini F, Cornelissen A, Neve H et al (2014) Molecular characterization of three Lactobacillus delbrueckii subsp. bulgaricus phages. Appl Environ Microbiol 80(18):5623–5635

    Article  PubMed  PubMed Central  Google Scholar 

  • Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y et al (2005) VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 33(Dsatabase issue):D325–D328

    CAS  PubMed  Google Scholar 

  • Cheng Y, Promadej N, Kim JW, Kathariou S (2008) Teichoic acid glycosylation mediated by gtcA is required for phage adsorption and susceptibility of Listeria monocytogenes Serotype 4b. Appl Environ Microbiol 74(5):1653–1655

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chylinski K, Makarova KS, Charpentier E, Koonin EV (2014) Classification and evolution of type II CRISPR–Cas systems. Nucleic Acids Res 42(10):6091–6105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Drago L, Mattina R, Nicola L, Rodighiero V, de Vecchi E (2011) Macrolide resistance and in vitro selection of resistance to antibiotics in Lactobacillus isolates. J Microbiol 49(4):651–656

    Article  CAS  PubMed  Google Scholar 

  • Dupont L, Boizet-Bonhoure B, Coddeville M, Auvray F, Ritzenthaler P (1995) Characterization of genetic elements required for site-specific integration of Lactobacillus delbrueckii subsp. bulgaricus bacteriophage mv4 and construction of an integration-proficient vector for Lactobacillus plantarum. J Bacteriol 177(3):586–595

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dussurget O, Cabanes D, Dehoux P, Lecuit M, Buchrieser C, Glaser P et al (2002) Listeria monocytogenes bile salt hydrolase is a PrfA-regulated virulence factor involved in the intestinal and hepatic phases of listeriosis. Mol Microbiol 45(4):1095–1106

    Article  CAS  PubMed  Google Scholar 

  • Frost LS, Leplae R, Summers AO, Toussaint A (2005) Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 3(9):722–732

    Article  CAS  PubMed  Google Scholar 

  • Gaillot O, Pellegrini E, Bregenholt S, Nair S, Berche P (2002) The ClpP serine protease is essential for the intracellular parasitism and virulence of Listeria monocytogenes. Mol Microbiol 35(6):1286–1294

    Article  Google Scholar 

  • Garneau JE, Dupuis MÈ, Villion M, Romero DA, Barrangou R, Boyaval P et al (2010) The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468(7320):67–71

    Article  CAS  PubMed  Google Scholar 

  • Germond JE, Lapierre L, Delley M, Mollet B (1995) A new mobile genetic element in Lactobacillus delbrueckii subsp. bulgaricus. Mol Gen Genet 248(4):407–416

    Article  CAS  PubMed  Google Scholar 

  • Goldin BR (1998) Health benefits of probiotics. Br J Nutr 80(S2):S203–S207

    Article  CAS  PubMed  Google Scholar 

  • Gomez M, Doukhan L, Nair G, Smith I (1998) sigA is an essential gene in Mycobacterium smegmatis. Mol Microbiol 29(2):617–628

    Article  CAS  PubMed  Google Scholar 

  • Guo T, Zhang C, Xin Y, Xin M, Kong J (2016) A novel chimeric prophage vB_LdeS-phiJB from commercial Lactobacillus delbrueckii subsp. bulgaricus. J Ind Microbiol Biotechnol 43(5):681–689

    Article  CAS  PubMed  Google Scholar 

  • Hancock LE, Gilmore MS (2002) The capsular polysaccharide of Enterococcus faecalis and its relationship to other polysaccharides in the cell wall. P Natl Acad Sci USA 99(3):1574–1579

    Article  CAS  Google Scholar 

  • Healy VL, Lessard IAD, Roper DI, Knox JR, Walsh CT (2000) Vancomycin resistance in enterococci: reprogramming of the D-Ala–D-Ala ligases in bacterial peptidoglycan biosynthesis. Chem Biol 7:R109–R119

    Article  CAS  PubMed  Google Scholar 

  • Heikens E, Singh KV, Jacques-Palaz KD, van Luit-Asbroek M, Oostdijk EAN, Bonten MJM et al (2011) Contribution of the enterococcal surface protein Esp to pathogenesis of Enterococcus faecium endocarditis. Microbes Infect 13(14–15):1185–1190

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327(5962):167–170

    Article  CAS  PubMed  Google Scholar 

  • Horvath P, Coûté-Monvoisin AC, Romero DA, Boyaval P, Fremaux C, Barrangou R (2009) Comparative analysis of CRISPR loci in lactic acid bacteria genomes. Int J Food Microbiol 131(1):62–70

    Article  CAS  PubMed  Google Scholar 

  • Hu T, Cui Y, Qu X (2020a) Characterization and comparison of CRISPR loci in Streptococcus thermophilus. Arch Microbiol 202:695–710

    Article  CAS  PubMed  Google Scholar 

  • Hu T, Cui YH, Zhang YS, Qu XJ, Zhao CY (2020b) Genome analysis and physiological characterization of four Streptococcus thermophilus strains isolated from Chinese traditional fermented milk. Front Microbiol 11:84

    Article  Google Scholar 

  • Hummel AS, Hertel C, Holzapfel WH, Franz CMAP (2007) Antibiotic resistances of starter and probiotic strains of lactic acid bacteria. Appl Environ Microb 73(3):730–739

    Article  CAS  Google Scholar 

  • Jagadeesan B, Koo OK, Kim KP, Burkholder KM, Mishra KK, Aroonnual A et al (2010) LAP, an alcohol acetaldehyde dehydrogenase enzyme in Listeria, promotes bacterial adhesion to enterocyte-like Caco-2 cells only in pathogenic species. Microbiology 156(9):2782–2795

    Article  CAS  PubMed  Google Scholar 

  • Jana S, Deb JK (2006) Molecular understanding of aminoglycoside action and resistance. Appl Microbiol Biotechnol 70:140–150

    Article  CAS  PubMed  Google Scholar 

  • Kim K, Lee S, Lee Y (1996) Norfloxacin resistance mechanism of E. coli 11 and E. coli 101-clinical isolates of Escherichia coli in Korea. Arch Pharm Res 19(5):353–358

  • King DT, Sobhanifar S, Strynadka NCJ (2014) The Mechanisms of Resistance to β-Lactam Antibiotics. In: Gotte M, Berghuis A, Matlashewski G, Wainberg M, Sheppard D (eds) Handbook of antimicrobial resistance. Springer, New York, pp 1–22

    Google Scholar 

  • Kitazawa H, Ishii Y, Uemura J, Kawai Y, Saito T, Kaneko T et al (2000) Augmentation of macrophage functions by an extracellular phosphopolysaccharide from Lactobacillus delbrueckii ssp. bulgaricus. Food Microbiol 17(1): 109–118

  • Kotra LP, Haddad J, Mobashery S (2000) Aminoglycosides: perspectives on mechanisms of action and resistance and strategies to counter resistance. Antimicrob Agents Chemother 44(12):3249–3256

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Krauss J, van der Linden M, Grebe T, Hakenbeck R (1996) Penicillin-binding proteins 2x and 2b as primary PBP targets in Streptococcus pneumoniae. Microb Drug Resist 2(2):183–186

    Article  CAS  PubMed  Google Scholar 

  • Li Y, Li L, Kromann S, Chen M, Shi L, Meng H (2019) Antibiotic resistance of Lactobacillus spp. and Streptococcus thermophilus isolated from Chinese fermented milk products. Foodborne Pathog Dis 16(3):221–228

    Article  CAS  PubMed  Google Scholar 

  • Liu B, Zheng D, Jin Q, Che L, Yang J (2018) VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res 47(D1):D687–D692

    Article  PubMed Central  Google Scholar 

  • Magnet S, Blanchard JS (2005) Molecular insights into aminoglycoside action and resistance. Chem Rev 105:477–497

    Article  CAS  PubMed  Google Scholar 

  • Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV (2006) A putative RNA-interference-based immune system in prokaryotes: computation analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct 1(1):7

    Article  PubMed  PubMed Central  Google Scholar 

  • Makarova KS, Haft DH, Barrangou R, Brouns SJJ, Charpentier E, Horvath P et al (2011) Evolution and classification of the CRISPR–Cas systems. Nat Rev Microbiol 9(6):467–477

    Article  CAS  PubMed  Google Scholar 

  • Mathur S, Singh R (2005) Antibiotic resistance in food lactic acid bacteria—a review. Int J Food Microbiol 105(3):281–295

    Article  CAS  PubMed  Google Scholar 

  • Moro-García MA, Alonso-Arias R, Baltadjieva M, Fernández Benítez C, Fernández Barrial MA, Díaz Ruisánchez E et al (2012) Oral supplementation with Lactobacillus delbrueckii subsp. bulgaricus 8481 enhances systemic immunity in elderly subjects. AGE 35(4): 1311–1326

  • Munita JM, Arias CA (2016) Mechanisms of antibiotic resistance. Microbiol Spectr 4(2):1–37

    Article  CAS  Google Scholar 

  • Nagai K, Davies TA, Jacobs MR, Appelbaum PC (2002) Effects of amino acid alterations in penicillin-binding proteins (PBPs) 1a, 2b, and 2x on PBP affinities of penicillin, ampicillin, amoxicillin, cefditoren, cefuroxime, cefprozil, and cefaclor in 18 clinical isolates of penicillin-susceptible, -intermediate, and -resistant Pneumococci. Antimicrob Agents Chemother 46(5):1273–1280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nair S, Frehel C, Nguyen L, Escuyer V, Berche P (1999) ClpE, a novel member of the HSP100 family, is involved in cell division and virulence of Listeria monocytogenes. Mol Microbiol 31(1):185–196

    Article  CAS  PubMed  Google Scholar 

  • Nozawa T, Furukawa N, Aikawa C, Watanabe T, Haobam B, Kurokawa K et al (2011) CRISPR inhibition of prophage acquisition in Streptococcus pyogenes. PLoS ONE 6(5):e19543

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Primm TP, Andersen SJ, Mizrahi V, Avarbock D, Rubin H, Barry CE (2000) The stringent response of Mycobacterium tuberculosis is required for long-term survival. J Bacteriol 182(17):4889–4898

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rabaan AA, Gryllos I, Tomas JM, Shaw JG (2001) Motility and the polar flagellum are required for Aeromonas caviae adherence to HEp-2 cells. Infect Immun 69(7):4257–4267

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Riipinen KA, Forsman P, Alatossava T (2011) The genomes and comparative genomics of Lactobacillus delbrueckii phages. Arch Virol 156(7):1217–1233

    Article  CAS  PubMed  Google Scholar 

  • Roberts MC (2005) Update on acquired tetracycline resistance genes. FEMS Microbiol Lett 245(2):195–203

    Article  CAS  PubMed  Google Scholar 

  • Rouquette C, de Chastellier C, Nair S, Berche P (1998) The ClpC ATPase of Listeria monocytogenesis a general stress protein required for virulence and promoting early bacterial escape from the phagosome of macrophages. Mol Microbiol 27(6):1235–1245

    Article  CAS  PubMed  Google Scholar 

  • Sheikh J, Czeczulin JR, Harrington S, Hicks S, Henderson IR, Bouguénec CL et al (2002) A novel dispersin protein in enteroaggregative Escherichia coli. J Clin Invest 110(9):1329–1337

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Smith AM, Klugman KP (1998) Alterations in PBP 1A Essential for high-level penicillin resistance in Streptococcus pneumoniae. Antimicrob Agents Chemother 42(6):1329–1333

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tok E, Aslim B (2010) Cholesterol removal by some lactic acid bacteria that can be used as probiotic. Microbiol Immunol 54:257–264

    CAS  PubMed  Google Scholar 

  • Touchon M, Rocha EPC (2010) The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PLoS ONE 5(6):e11126

    Article  PubMed  PubMed Central  Google Scholar 

  • Urshev Z, Ishlimova D (2015) Distribution of clustered regularly interspaced palindrome repeats CRISPR2 and CRISPR3 in Lactobacillus delbrueckii ssp. bulgaricus strains. Biotechnol Biotech Eq 29(3):541–546

  • Vachkova-Petrova R, Donchev N, Borov B, Dinoeva S, Vassileva L (1997) Study of the anticarcinogenic activity of Lactobacillus bulgaricus in diethylnitrosamine induced cancerogenesis in white rats. Biotechnol Biotech Eq 11(1–2):66–70

    Article  Google Scholar 

  • Van de Guchte M, Penaud S, Grimaldi C, Barbe V, Bryson K, Nicolas P et al (2006) The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proc Natl Acad Sci USA 103(24):9274–9279

    Article  PubMed  PubMed Central  Google Scholar 

  • Walsh CT (1993) Vancomycin resistance: decoding the molecular logic. Science 261:308–309

    Article  CAS  PubMed  Google Scholar 

  • Westra ER, van Erp PBG, Künne T, Wong SP, Staals RHJ, Seegers CLC et al (2012) CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. Mol Cell 46:595–605

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJJ, van der Oost J et al (2011) Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature 477:486–489

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zago M, Scaltriti E, Rossetti L, Guffanti A, Armiento A, Fornasari M et al (2013) Characterization of the genome of the dairy Lactobacillus helveticus bacteriophage ΦAQ113. Appl Environ Microbiol 79(15):4712–4718

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang S, Oh J, Alexander LM, Özçam M, van Pijkeren JP (2018) D-alanyl–D-alanine ligase as a broad-host-range counterselection marker in vancomycin-resistant lactic acid bacteria. J Bacteriol 200(13):e00607–e00617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was supported by the National Natural Science Foundation of China [Grant numbers 31471712, 31371827].

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  1. Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150090, People’s Republic of China

    Yuxuan Guan, Yanhua Cui & Kai Jing

  2. Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, 150010, People’s Republic of China

    Xiaojun Qu

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  1. Yuxuan Guan
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  2. Yanhua Cui
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Correspondence to Yanhua Cui.

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Guan, Y., Cui, Y., Qu, X. et al. Safety and robustness aspects analysis of Lactobacillus delbrueckii ssp. bulgaricus LDB-C1 based on the genome analysis and biological tests. Arch Microbiol 203, 3955–3964 (2021). https://doi.org/10.1007/s00203-021-02383-7

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