Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Analysis of the Microbiota on Lettuce (Lactuca sativa L.) Cultivated in South Korea to Identify Foodborne Pathogens

  • Yu, Yeon-Cheol (Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University) ;
  • Yum, Su-Jin (Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University) ;
  • Jeon, Da-Young (Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University) ;
  • Jeong, Hee-Gon (Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University)
  • Received : 2018.03.08
  • Accepted : 2018.06.20
  • Published : 2018.08.28
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Abstract

Lettuce (Lactuca sativa L.) is a major ingredient used in many food recipes in South Korea. Lettuce samples were collected during their maximum production period between April and July in order to investigate the microbiota of lettuce during different seasons. 16S rRNA gene-based sequencing was conducted using Illumina MiSeq, and real-time PCR was performed for quantification. The number of total bacterial was greater in lettuce collected in July than in that collected in April, albeit with reduced diversity. The bacterial compositions varied according to the site and season of sample collection. Potential pathogenic species such as Bacillus spp., Enterococcus casseliflavus, Klebsiella pneumoniae, and Pseudomonas aeruginosa showed season-specific differences. Results of the network co-occurrence analysis with core genera correlations showed characteristics of bacterial species in lettuce, and provided clues regarding the role of different microbes, including potential pathogens, in this microbiota. Although further studies are needed to determine the specific effects of regional and seasonal characteristics on the lettuce microbiota, our results imply that the 16S rRNA gene-based sequencing approach can be used to detect pathogenic bacteria in lettuce.

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References

  1. Jang S, Lee E, Kim W. 2007. Analysis of research and development papers on lettuce in Korea. Korean J. Hortic. Sci. Technol. 25: 295-303.
  2. Oyinlola LA, Obadina AO, Omemu AM, Oyewole OB. 2017. Prevention of microbial hazard on fresh-cut lettuce through adoption of food safety and hygienic practices by lettuce farmers. Food Sci. Nutr. 5: 67-75. https://doi.org/10.1002/fsn3.365
  3. Wachtel MR, Whitehand LC, Mandrell RE. 2002. Association of Escherichia coli O157:H7 with preharvest leaf lettuce upon exposure to contaminated irrigation water. J. Food Prot. 65: 18-25. https://doi.org/10.4315/0362-028X-65.1.18
  4. Ackers M-L, Mahon BE, Leahy E, Goode B, Damrow T, Hayes PS, et al. 1998. An outbreak of Escherichia coli O157:H7 infections associated with leaf lettuce consumption. J. Infect. Dis. 177: 1588-1593. https://doi.org/10.1086/515323
  5. Szabo E, Scurrah K, Burrows J. 2000. Survey for psychrotrophic bacterial pathogens in minimally processed lettuce. Lett. Appl. Microbiol. 30: 456-460. https://doi.org/10.1046/j.1472-765x.2000.00747.x
  6. Kim YJ, Kim HS, Kim KY, Chon JW, Kim DH, Seo KH. 2016. High occurrence rate and contamination level of Bacillus cereus in organic vegetables on sale in retail markets. Foodborne Pathog. Dis. 13: 656-660. https://doi.org/10.1089/fpd.2016.2163
  7. Jackson KA, Stroika S, Katz LS, Beal J, Brandt E, Nadon C, et al. 2016. Use of whole genome sequencing and patient interviews to link a case of sporadic listeriosis to consumption of prepackaged lettuce. J. Food Prot. 79: 806-809. https://doi.org/10.4315/0362-028X.JFP-15-384
  8. Heaton JC, Jones K. 2008. Microbial contamination of fruit and vegetables and the behaviour of enteropathogens in the phyllosphere: a review. J. Appl. Microbiol. 104: 613-626. https://doi.org/10.1111/j.1365-2672.2007.03587.x
  9. Streit WR, Schmitz RA. 2004. Metagenomics - the key to the uncultured microbes. Curr. Opin. Microbiol. 7: 492-498. https://doi.org/10.1016/j.mib.2004.08.002
  10. Turner TR, James EK, Poole PS. 2013. The plant microbiome. Genome Biol. 14: 209. https://doi.org/10.1186/gb-2013-14-6-209
  11. Taghavi S, Garafola C, Monchy S, Newman L, Hoffman A, Weyens N, et al. 2009. Genome survey and characterization of endophytic bacteria exhibiting a beneficial effect on growth and development of poplar trees. Appl. Environ. Microbiol. 75: 748-757. https://doi.org/10.1128/AEM.02239-08
  12. Shade A, McManus PS, Handelsman J. 2013. Unexpected diversity during community succession in the apple flower microbiome. MBio 4: e00602-e00612.
  13. Morris CE, Kinkel LL. 2002. Fifty years of phyllosphere microbiology: significant contributions to research in related fields, pp. 365-375. In Lindow SE, Hecht-Poinar EI, Elliott VJ. (eds), Phyllosphere Microbiology. APS Press, St. Paul, MN.
  14. Atamna-Ismaeel N, Finkel OM, Glaser F, Sharon I, Schneider R, Post AF, et al. 2012. Microbial rhodopsins on leaf surfaces of terrestrial plants. Environ. Microbiol. 14: 140-146. https://doi.org/10.1111/j.1462-2920.2011.02554.x
  15. Badri DV, Zolla G, Bakker MG, Manter DK, Vivanco JM. 2013. Potential impact of soil microbiomes on the leaf metabolome and on herbivore feeding behavior. New Phytol. 198: 264-273. https://doi.org/10.1111/nph.12124
  16. Berg G, Grube M, Schloter M, Smalla K. 2014. Unraveling the plant microbiome: looking back and future perspectives. Front. Microbiol. 5: 148.
  17. van der Heijden MG, Hartmann M. 2016. Networking in the plant microbiome. PLoS Biol. 14: e1002378. https://doi.org/10.1371/journal.pbio.1002378
  18. Naravaneni R, Jamil K. 2005. Rapid detection of food-borne pathogens by using molecular techniques. J. Med. Microbiol. 54: 51-54. https://doi.org/10.1099/jmm.0.45687-0
  19. Miller RA, Jian J, Beno SM, Wiedmann M, Kovac J. 2018. Intraclade variability in toxin production and cytotoxicity of Bacillus cereus group type strains and dairy-associated isolates. Appl. Environ. Microbiol. 84: e02479-17.
  20. Frentzel H, Thanh MD, Krause G, Appel B, Mader A. 2018. Quantification and differentiation of Bacillus cereus group species in spices and herbs by real-time PCR. Food Control 83: 99-108. https://doi.org/10.1016/j.foodcont.2016.11.028
  21. Wang RF, Cao WW, Cerniglia C. 1997. A universal protocol for PCR detection of 13 species of foodborne pathogens in foods. J. Appl. Microbiol. 83: 727-736. https://doi.org/10.1046/j.1365-2672.1997.00300.x
  22. Dutka-Malen S, Evers S, Courvalin P. 1995. Detection of glycopeptide resistance genotypes and identification to the species level of clinically relevant enterococci by PCR. J. Clin. Microbiol. 33: 24-27.
  23. Dong D, Liu W, Li H, Wang Y, Li X, Zou D, et al. 2015. Survey and rapid detection of Klebsiella pneumoniae in clinical samples targeting the rcsA gene in Beijing, China. Front. Microbiol. 6: 519.
  24. Spilker T, Coenye T, Vandamme P, LiPuma JJ. 2004. PCRbased assay for differentiation of Pseudomonas aeruginosa from other Pseudomonas species recovered from cystic fibrosis patients. J. Clin. Microbiol. 42: 2074-2079. https://doi.org/10.1128/JCM.42.5.2074-2079.2004
  25. Hanshew AS, Mason CJ, Raffa KF, Currie CR. 2013. Minimization of chloroplast contamination in 16S rRNA gene pyrosequencing of insect herbivore bacterial communities. J. Microbiol. Methods 95: 149-155. https://doi.org/10.1016/j.mimet.2013.08.007
  26. Kumar PS, Brooker MR, Dowd SE, Camerlengo T. 2011. Target region selection is a critical determinant of community fingerprints generated by 16S pyrosequencing. PLoS One 6: e20956. https://doi.org/10.1371/journal.pone.0020956
  27. Lee M-J, Lee J-J, Chung HY, Choi SH, Kim B-S. 2016. Analysis of microbiota on abalone (Haliotis discus hannai) in South Korea for improved product management. Int. J. Food Microbiol. 234: 45-52. https://doi.org/10.1016/j.ijfoodmicro.2016.06.032
  28. Williams T R, Moy ne A-L, Harris L J, Marco M L. 2 013. Season, irrigation, leaf age, and Escherichia coli inoculation influence the bacterial diversity in the lettuce phyllosphere. PLoS One 8: e68642. https://doi.org/10.1371/journal.pone.0068642
  29. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200. https://doi.org/10.1093/bioinformatics/btr381
  30. Dehingia M, Talukdar NC, Talukdar R, Reddy N, Mande SS, Deka M, et al. 2015. Gut bacterial diversity of the tribes of India and comparison with the worldwide data. Sci. Rep. 5: 18563.
  31. Rastogi G, Sbodio A, Tech JJ, Suslow TV, Coaker GL, Leveau JH. 2012. Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce. ISME J. 6: 1812-1822. https://doi.org/10.1038/ismej.2012.32
  32. Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, et al. 2009. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc. Natl. Acad. Sci. USA 106: 16428-16433. https://doi.org/10.1073/pnas.0905240106
  33. Knief C, Ramette A, Frances L, Alonso-Blanco C, Vorholt JA. 2010. Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere. ISME J. 4: 719-728. https://doi.org/10.1038/ismej.2010.9
  34. Williams TR, Marco ML. 2014. Phyllosphere microbiota composition and microbial community transplantation on lettuce plants grown indoors. Mbio 5: e01564-e01514.
  35. Perez-Garcia A, Romero D, De Vicente A. 2011. Plant protection and growth stimulation by microorganisms: biotechnological applications of Bacilli in agriculture. Curr. Opin. Biotechnol. 22: 187-193. https://doi.org/10.1016/j.copbio.2010.12.003
  36. Compant S, Mitter B, Colli-Mull JG, Gangl H, Sessitsch A. 2011. Endophytes of grapevine flowers, berries, and seeds: identification of cultivable bacteria, comparison with other plant parts, and visualization of niches of colonization. Microb. Ecol. 62: 188-197. https://doi.org/10.1007/s00248-011-9883-y
  37. Ibanez F, Angelini J, Taurian T, Tonelli ML, Fabra A. 2009. Endophytic occupation of peanut root nodules by opportunistic Gammaproteobacteria. Syst. Appl. Microbiol. 32: 49-55. https://doi.org/10.1016/j.syapm.2008.10.001
  38. Gruter D, Schmid B, Brandl H. 2006. Influence of plant diversity and elevated atmospheric carbon dioxide levels on belowground bacterial diversity. BMC Microbiol. 6: 68. https://doi.org/10.1186/1471-2180-6-68
  39. Cardinale M, Grube M, Erlacher A, Quehenberger J, Berg G. 2015. Bacterial networks and co-occurrence relationships in the lettuce root microbiota. Environ. Microbiol. 17: 239-252. https://doi.org/10.1111/1462-2920.12686
  40. Wahab AA. 1975. Phyllosphere microflora of some Egyptian plants. Folia Microbiol. 20: 236. https://doi.org/10.1007/BF02876785
  41. Baldani JI, Rouws L, Cruz LM, Olivares FL, Schmid M, Hartmann A. 2014. The family Oxalobacteraceae, pp. 919-974. In Rosenverg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds.), The Prokaryotes - Alphaproteobacteria and Betaproteobacteria. Springer, Berlin/Heidelberg.
  42. Pearson MD, Noller HF. 2011. The draft genome of Planococcus donghaensis MPA1U2 reveals nonsporulation pathways controlled by a conserved Spo0A regulon. J. Bacteriol. 193: 6106. https://doi.org/10.1128/JB.05983-11
  43. Vishnivetskaya TA, Kathariou S, Tiedje JM. 2009. The Exiguobacterium genus: biodiversity and biogeography. Extremophiles 13: 541-555. https://doi.org/10.1007/s00792-009-0243-5
  44. White RA, Grassa CJ, Suttle CA. 2013. Draft genome sequence of Exiguobacterium pavilionensis strain RW-2, with wide thermal, salinity, and pH tolerance, isolated from modern freshwater microbialites. Genome Announc. 1: e00597-13.
  45. Behrendt U, Ulrich A, Schumann P. 2003. Fluorescent pseudomonads associated with the phyllosphere of grasses; Pseudomonas trivialis sp. nov., Pseudomonas poae sp. nov. and Pseudomonas congelans sp. nov. Int. J. Syst. Evol. Microbiol. 53: 1461-1469. https://doi.org/10.1099/ijs.0.02567-0
  46. Nair J, Singh G, Sekar V. 2002. Isolation and characterization of a novel Bacillus strain from coffee phyllosphere showing antifungal activity. J. Appl. Microbiol. 93: 772-780. https://doi.org/10.1046/j.1365-2672.2002.01756.x
  47. McSpadden Gardener BB. 2004. Ecology of Bacillus and Paenibacillus spp. in agricultural systems. Phytopathology 94: 1252-1258. https://doi.org/10.1094/PHYTO.2004.94.11.1252
  48. Berg G, Eberl L, Hartmann A. 2005. The rhizosphere as a reservoir for opportunistic human pathogenic bacteria. Environ. Microbiol. 7: 1673-1685. https://doi.org/10.1111/j.1462-2920.2005.00891.x
  49. Sutthiwong N, Fouillaud M, Valla A, Caro Y, Dufosse L. 2014. Bacteria belonging to the extremely versatile genus Arthrobacter as novel source of natural pigments with extended hue range. Food Res. Int. 65: 156-162. https://doi.org/10.1016/j.foodres.2014.06.024
  50. Chernin L, Ismailov Z, Haran S, Chet I. 1995. Chitinolytic Enterobacter agglomerans antagonistic to fungal plant pathogens. Appl. Environ. Microbiol. 61: 1720-1726.
  51. Saleem M, Arshad M, Hussain S, Bhatti AS. 2007. Perspective of plant growth promoting rhizobacteria (PGPR) containing ACC deaminase in stress agriculture. J. Ind. Microbiol. Biotechnol. 34: 635-648. https://doi.org/10.1007/s10295-007-0240-6
  52. Karthick Raja Namasivayam S, Sahayaraj K. 1998. Changes in bacterial and actinomycetes diversity of groundnut phyllosphere with reference to plant age, kinds of leaves and seasons adapting culture dependent method. Int. J. Microbiol. 6: 1-6.
  53. Jawad A, Heritage J, Snelling A, Gascoyne-Binzi D, Hawkey P. 1996. Influence of relative humidity and suspending menstrua on survival of Acinetobacter spp. on dry surfaces. J. Clin. Microbiol. 34: 2881-2887.
  54. Granum PE, Lund T. 1997. Bacillus cereus and its food poisoning toxins. FEMS Microbiol. Lett. 157: 223-228. https://doi.org/10.1111/j.1574-6968.1997.tb12776.x
  55. Reid KC, Cockerill III FR, Patel R. 2001. Clinical and epidemiological features of Enterococcus casseliflavus/flavescens and Enterococcus gallinarum bacteremia: a report of 20 cases. Clin. Infect. Dis. 32: 1540-1546. https://doi.org/10.1086/320542
  56. Calbo E, Freixas N, Xercavins M, Riera M, Nicolas C, Monistrol O, et al. 2011. Foodborne nosocomial outbreak of SHV1 and CTX-M-15-producing Klebsiella pneumoniae: epidemiology and control. Clin. Infect. Dis. 52: 743-749. https://doi.org/10.1093/cid/ciq238
  57. Sabota JM, Hoppes WL, Ziegler Jr JR, DuPont H, Mathewson J, Rutecki GW. 1998. A new variant of food poisoning: enteroinvasive Klebsiella pneumoniae and Escherichia coli sepsis from a contaminated hamburger. Am. J. Gastroenterol. 93: 118. https://doi.org/10.1111/j.1572-0241.1998.118_c.x
  58. Hirano SS, Upper CD. 1991. Bacterial community dynamics, pp. 271-294. In Andrews JH, Hirano SS (eds.), Microbial Ecology of Leaves. Springer, New York, NY.
  59. Tauxe RV. 2002. Emerging foodborne pathogens. Int. J. Food Microbiol. 78: 31-41. https://doi.org/10.1016/S0168-1605(02)00232-5

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