In silico genomic insights into aspects of food safety and defense mechanisms of a potentially probiotic Lactobacillus pentosus MP-10 isolated from brines of naturally fermented Aloreña green table olives

PLoS ONE

Volumn 12, Issue 6, 2017, Pages

  Abriouel, Hikmate ^a   Montoro, Beatriz Pérez ^a   Casado Muñoz, María Del Carmen ^a   Knapp, Charles W ^b   Gálvez, Antonio ^a   Benomar, Nabil ^a  

^a UNIVERSITY OF JAÉN   (Spain)

^b UNIVERSITY OF STRATHCLYDE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC AGENT; PROBIOTIC AGENT; TRANSPOSASE; CRISPR ASSOCIATED PROTEIN;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENOME; BACTERIAL VIRULENCE; COMPUTER MODEL; CONTROLLED STUDY; CRISPR CAS SYSTEM; FOOD PROCESSING; FOOD SAFETY; GENE SEQUENCE; GENOMICS; LACTOBACILLUS PENTOSUS; NONHUMAN; OLIVE; PROPHAGE; TRANSPOSON; CHEMISTRY; FOOD CONTROL; GENETICS; ISOLATION AND PURIFICATION; OLIVE TREE;

CRISPR-ASSOCIATED PROTEINS; DRUG RESISTANCE, BACTERIAL; FOOD MICROBIOLOGY; FOOD SAFETY; GENOME, BACTERIAL; LACTOBACILLUS PENTOSUS; OLEA; PROBIOTICS;

EID: 85021256187     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0176801     Document Type: Article

References (47)

1. Wacher C, Díaz-Ruiz G, Tamang JP. Fermented Vegetable Products. In: Tamang JP, Kailasapathy K, editors. Fermented foods and beverages of the world. Boca Raton, USA: CRC Press; 2010. pp. 149–190.
2. Venema K, Meijerink M. Lactobacilli as probiotics: discovering new functional aspects and target sites. In: Venema K, do Carmo AP, editors. Probiotics and Prebiotics: Current Research and Future Trends. UK: Caister Academic Press; 2015. pp. 29–42.
3. Food and Agricultural Organization of the United Nations and World Health Organization, editor. Report of a Joint FAO/WHO working group report on drafting guidelines for the evaluation of probiotics in food; 2002. April 30, May 1; Ontario, Canada.
4. Granato D, Branco GF, Nazzaro F, Cruz AG, Faria JAF. Functional foods and non dairy probiotic food development: trends, concepts, and products. Compr Rev Food Sci Food Saf. 2010; 9: 292–302.
5. Peres CM, Hernandez-Mendoza A, Peres C, Malcata FX. Review on fermented plant materials as carriers and sources of potentially probiotic lactic acid bacteria with an emphasis on table olives. Trends Food Sci Technol. 2012; 26(1): 31–42.
6. Ranadheera RDCS, Baines SK, Adams MC. Importance of food in probiotic efficacy. Food Res Int. 2010; 43: 1–7.
7. Cammarota M, De Rosa M, Stellavato A, Lamberti M, Marzaioli I, Giuliano M. In vitro evaluation of Lactobacillus plantarum DSMZ 12028 as a probiotic: emphasis on innate immunity. Int J Food Microbiol. 2009; 135: 90–98. https://doi.org/10.1016/j.ijfoodmicro.2009.08.022 PMID: 19748696
8. Chang J-H, Shim YY, Cha S-K, Chee KM. Probiotic characteristics of lactic acid bacteria isolated from kimchi. J Appl Microbiol. 2010; 109: 220–230. https://doi.org/10.1111/j.1365-2672.2009.04648.xPMID: 20102423
9. Spurr HW. The microbial ecology of fruit and vegetable surfaces, its relationship to postharvest biocon-trol. In: Wilson C, Wisniewski M, editors. Biological Control of Postharvest Diseases: Theory and Practice. Boca Raton, FL: CRC Press; 1994. pp. 11–23.
10. Di Cagno R, Cardinali G, Minervini G, Antonielli L, Rizzello CG, Ricciuti P, et al. Taxonomic structure of the yeasts and lactic acid bacteria microbiota of pineapple (Ananas comosus L. Merr.) and use of autochthonous starters for minimally processing. Food Microbiol. 2010; 27: 381–389. https://doi.org/10.1016/j.fm.2009.11.012 PMID: 20227603
11. Bartkiene E, Vidmantiene D, Juodeikiene G, Viskelis P, Urbonaviciene D. Lactic acid fermentation of tomato: effects on cis/trans lycopene isomer and β-carotene concentration and formation of L(+) and D (-)-lactic acid. Food Techn Biotechnol. 2013; 51(4): 471–478.
12. Swain MR, Anandharaj M, Ray RC, Rani RP. Fermented fruits and vegetables of Asia: A potential source of probiotics. Biotechnol Res Int. 2012; 2014: 250424.
13. Shanahan F. A commentary on the safety of probiotics. Gastroenterol Clin North Am. 2012; 41(4): 869–76. https://doi.org/10.1016/j.gtc.2012.08.006 PMID: 23101692
14. EFSA (European Food Safety Authority). Scientific Opinion of the Panel on Biological Hazards on the maintenance of the list of QPS microorganisms intentionally added to food or feed. The EFSA J. 2008; 923: 1–48.
15. Ventura M, O’Flaherty S, Claesson MJ, Turroni F, Klaenhammer TR, van Sinderen D, et al. Genome-scale analyses of health-promoting bacteria: probiogenomics. Nat Rev Microbiol. 2009; 7: 61–71. https://doi.org/10.1038/nrmicro2047 PMID: 19029955
16. Abriouel H, Benomar N, Pérez Pulido R, Martínez Cañamero M, Gálvez A. Annotated genome sequence of Lactobacillus pentosus MP-10 with probiotic potential from naturally-fermented Alorena green table olives. J Bacteriol. 2011; 193: 4559–4560. https://doi.org/10.1128/JB.05171-11 PMID: 21705590
17. Abriouel H, Pérez Montoro B, Casado Muñoz MC, Lavilla Lerma L, Hidalgo Pestaña M, Caballero Gómez N, et al. Complete genome sequence of a potentially probiotic Lactobacillus pentosus MP-10 isolated from fermented Aloreña table olives. Genome Announc. 2016; 4(5): e00854–16. https://doi.org/10.1128/genomeA.00854-16 PMID: 27634988
18. Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin E, et al. Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci U S A. 2006; 103: 15611–15616. https://doi.org/10.1073/pnas. 0607117103 PMID: 17030793
19. Maldonado-Barragán A, Caballero-Guerrero B, Lucena-Padrós H, Ruiz-Barba JL. Genome Sequence of Lactobacillus pentosus IG1, a strain isolated from Spanish-style green olive fermentations. J Bacteriol. 2011; 193(19): 5605. https://doi.org/10.1128/JB.05736-11 PMID: 21914902
20. Anukam KC, Macklaim JM, Gloor GB, Reid G, Boekhorst J. Genome sequence of Lactobacillus pentosus KCA1: vaginal isolate from a healthy premenopausal woman. PLoS ONE. 2013; 8(3): E59239. https://doi.org/10.1371/journal.pone.0059239 PMID: 23527145
21. O’Sullivan O, O’Callaghan J, Sangrador-Vegas A, McAuliffe O, Slattery L, Kaleta P, et al. Comparative genomics of lactic acid bacteria reveals a niche-specific gene set. BMC Microbiol. 2009; 9: 50. https://doi.org/10.1186/1471-2180-9-50 PMID: 19265535
22. Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science. 2010; 327: 167–170. https://doi.org/10.1126/science.1179555 PMID: 20056882
23. Al-Attar S, Westra ER, van der Oost J, Brouns SJ. Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes. Biol Chem. 2011; 392: 277–289. https://doi.org/10.1515/BC.2011.042 PMID: 21294681
24. Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008; 321: 960–964. https://doi.org/10.1126/science. 1159689 PMID: 18703739
25. Young JC, Dill BD, Pan C, Hettich RL, Banfield JF, Shah M, et al. Phage-induced expression of CRISPR-associated proteins is revealed by shotgun proteomics in Streptococcus thermophilus. PLoS ONE. 2012; 7: e38077 10. https://doi.org/10.1371/journal.pone.0038077 PMID: 22666452
26. Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, et al. Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol. 2011; 9: 467–477. https://doi.org/10.1038/ nrmicro2577 PMID: 21552286
27. Wei Y, Terns RM, Terns MP. Cas9 function and host genome sampling in Type II-A CRISPR–Cas adaptation. Genes Dev. 2015; 29(4): 356–361. https://doi.org/10.1101/gad.257550.114 PMID: 25691466
28. Altermann E, Russell WM, Azcarate-Peril MA, Barrangou R, Buck BL, McAuliffe O, et al. Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. Proc Natl Acad Sci U S A. 2005; 102(11): 3906–3912. https://doi.org/10.1073/pnas.0409188102 PMID: 15671160
29. Yoon BH, Jang SH, Chang HI. Sequence analysis of the Lactobacillus temperate phage Sha1. Arch Virol. 2011; 156: 1681–1684. https://doi.org/10.1007/s00705-011-1048-2 PMID: 21701917
30. Jaomanjaka F, Ballestra P, Dols-lafargue M, Le Marrec C. Expanding the diversity of oenococcal bacteriophages: insights into a novel group based on the integrase sequence. Int J Food Microbiol. 2013; 166(2): 331–40. https://doi.org/10.1016/j.ijfoodmicro.2013.06.032 PMID: 23994162
31. Dorscht J, Klumpp J, Bielmann R, Schmelcher M, Born Y, Zimmer M, et al. Comparative genome analysis of Listeria bacteriophages reveals extensive mosaicism, programmed translational frameshifting, and a novel prophage insertion site. J Bacteriol. 2009; 191: 7206–7215. https://doi.org/10.1128/JB. 01041-09 PMID: 19783628
32. Mercanti DJ, Rousseau GM, Capra ML, Quiberoni A, Tremblay DM, Labrie SJ, et al. Genomic diversity of phages infecting probiotic strains of Lactobacillus paracasei. Appl Environ Microbiol. 2016; 82(1): 95–105.
33. Lang AS, Zhaxybayeva O, Beatty JT. Gene transfer agents: phage-like elements of genetic exchange. Nat Rev Microbiol. 2012; 10: 472–482. https://doi.org/10.1038/nrmicro2802 PMID: 22683880
34. Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 2017; 45: D566–D573. https://doi.org/10.1093/nar/gkw1004 PMID: 27789705
35. Yoshida K, Ohki Y-H, Murata M, Kinehara M, Matsuoka H, Satomura T, et al. Bacillus subtilis LmrA is a repressor of the lmrAB and yxaGH operons: identification of its binding site and functional analysis of lmrB and yxaGH. J Bacteriol. 2004; 186(17): 5640–5648. https://doi.org/10.1128/JB.186.17.56405648.2004 PMID: 15317768
36. Florez AB, de los Reyes-Gavilán CG, Wind A, Mayo B, Margolles AA. Ubiquity and diversity of multidrug resistance genes in Lactococcus lactis strains isolated between 1936 and 1995. FEMS Microbiol. Lett. 2006; 263(1): 21–25. https://doi.org/10.1111/j.1574-6968.2006.00371.x PMID: 16958846
37. Fournier B, Aras R, Hooper DC. Expression of the multidrug resistance transporter NorA from Staphylococcus aureus is modified by a two-component regulatory system. J Bacteriol. 2000; 182: 664–671. PMID: 10633099
38. Casado Muñoz MC, Benomar N, Ennahar S, Horvatovich P, Lavilla Lerma L, Knapp CW, et al. Comparative proteomic analysis of a potentially probiotic Lactobacillus pentosus MP-10 for the identification of key proteins involved in antibiotic resistance and biocide tolerance. Int J Food Microbiol. 2016; 222: 8–15. https://doi.org/10.1016/j.ijfoodmicro.2016.01.012 PMID: 26827291
39. Van Hemert S, Meijerink M, Molenaar D, Bron PA, de Vos P, Kleerebezem M, et al. Identification of Lactobacillus plantarum genes modulating the cytokine response of human peripheral blood mononuclear cells. BMC Microbiol. 2010; 10: 293. https://doi.org/10.1186/1471-2180-10-293 PMID: 21080958
40. Siezen RJ, Francke C, Renckens B, Boekhorst J, Wels M, Kleerebezem M, et al. Complete resequen-cing and reannotation of the Lactobacillus plantarum WCFS1 genome. J Bacteriol. 2012; 194(1): 195–6. https://doi.org/10.1128/JB.06275-11 PMID: 22156394
41. Zhang W-Y, Yu D-L, Sun Z-H, Chen W, Hu S-N, Meng H, et al. The comparative analysis of a prophage remnant Lcazh in relation to other Lactobacillus prophages, particularly Lp3. Int J Dairy Technol. 2010; 63: 1–5.
42. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014; 30(14): 2068–9. https://doi.org/10.1093/bioinformatics/btu153 PMID: 24642063
43. Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser L. Prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010; 11: 119. https://doi.org/10.1186/ 1471-2105-11-119 PMID: 20211023
44. Lagesen K, Hallin P, Rødland EA, Stærfeldt H-H, Rognes T. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007; 35: 3100–31008. https://doi.org/10.1093/nar/ gkm160 PMID: 17452365
45. Laslett D, Canback B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32: 11–16. https://doi.org/10.1093/nar/gkh152 PMID: 14704338
46. Zhou Y, Liang Y, Lynch K, Dennis JJ, Wishart DS (2011) “PHAST: A Fast Phage Search Tool” Nucl. Acids Res. 2004; 39(suppl 2): W347–W352.
47. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012; 67(11): 2640–2644. https://doi.org/10.1093/jac/dks261 PMID: 22782487