16S rRNA gene-based sequencing of cucumber (Cucumis sativus L.) microbiota cultivated in South Korea |
Seo, Dong Woo
(Department of Food Science and Technology, Chungnam National University)
Kim, Seung Min (Division of Human Ecology, Korea National Open University) Lee, Heoun Reoul (Department of Food Science and Technology, Chungnam National University) Yum, Su-jin (Department of Food Science and Technology, Chungnam National University) Jeong, Hee Gon (Department of Food Science and Technology, Chungnam National University) |
1 | Young G, Turner S, Davies JK, Sundqvist G, Figdor D. Bacterial DNA persists for extended periods after cell death. J. Endod. 33: 1417-1420 (2007) DOI |
2 | Yanagida F, Chen Y, Onda T, Shinohara T. Durancin L28-1A, a new bacteriocin from Enterococcus durans L28-1, isolated from soil. Lett. Appl. Microbiol. 40: 430-435 (2005) DOI |
3 | Yu YC, Yum SJ, Jeon DY, Jeong HG. Analysis of the microbiota on lettuce (Lactuca sativa L.) cultivated in South Korea to identify foodborne pathogens. J. Microbiol. Biotechnol. 28: 1318-1331 (2018) DOI |
4 | Zhang X, Wei H, Chen Q, Han X. The counteractive effects of nitrogen addition and watering on soil bacterial communities in a steppe ecosystem. Soil Biol. Biochem. 72: 26-34 (2014) DOI |
5 | Yabuuchi E, Wang L, Arakawa M, Yano I. Survival of Pseudomonas pseudomallei strains at 5 degrees. Kansenshogaku zasshi 67: 331- 335 (1993) DOI |
6 | Gaastra W, Svennerholm AM. Colonization factors of human enterotoxigenic Escherichia coli (ETEC). Trends Microbiol. 4: 444-452 (1996) DOI |
7 | Cruz AT, Cazacu AC, Allen CH. Pantoea agglomerans, a plant pathogen causing human disease. J. Clin. Microbiol. 45: 1989- 1992 (2007) DOI |
8 | Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinform. 27: 2194-2200 (2011) DOI |
9 | Murray BE. The life and times of the Enterococcus. Clin. Microbiol. Rev. 3: 46-65 (1990) DOI |
10 | McCabe-Sellers BJ, Beattie SE. Food safety: emerging trends in foodborne illness surveillance and prevention. J. Am. Diet. Assoc. 104: 1708-1717 (2004) DOI |
11 | MFDS. Food safety information portal. Available from: https://www.foodsafetykorea.go.kr/portal/healthyfoodlife/foodPoisoningStat.do?menu_no=3724&menu_grp=MENU_NEW02. Accessed Dec. 7, 2020. |
12 | Naravaneni R, Jamil K. Rapid detection of food-borne pathogens by using molecular techniques. J. Med. Microbiol. 54: 51-54 (2005) DOI |
13 | Perez-Diaz IM, Hayes JS, Medina E, Webber AM, Butz N, Dickey AN, Lu Z, Azcarate-Peril MA. Assessment of the non-lactic acid bacteria microbiota in fresh cucumbers and commercially fermented cucumber pickles brined with 6% NaCl. Food Microbiol. 77: 10-20 (2019) DOI |
14 | Perez-Garcia A, Romero E, De Vicente A. Plant protection and growth stimulation by microorganisms: biotechnological applications of Bacilli in agriculture. Curr. Opin. Biotech. 22: 187-193 (2011) DOI |
15 | Rathinavelu S, Zavros Y, Merchant JL. Acinetobacter lwoffii infection and gastritis. Microbes Infect. 5: 651-657 (2003) DOI |
16 | Schrottner P, Rudolph WW, Taube F, Gunzer F. First report on the isolation of Aureimonas altamirensis from a patient with peritonitis. Int. J. Infect. Dis. 29: 71-73 (2014) DOI |
17 | CDC. National Outbreak Reporting System (NORS). Available from: https://wwwn.cdc.gov/norsdashboard. Accessed Dec. 7, 2020. |
18 | Hanshew AS, Mason CJ, Raffa KF, Currie CR. Minimization of chloroplast contamination in 16S rRNA gene pyrosequencing of insect herbivore bacterial communities. J. Microbiol. Methods 95: 149-155 (2013) DOI |
19 | Panoff JM, Corroler D, Thammavongs B, Boutibonnes P. Differentiation between cold shock proteins and cold acclimation proteins in a mesophilic gram-positive bacterium, Enterococcus faecalis JH2-2. J. Bacteriol. 179: 4451-4454 (1997) DOI |
20 | CDC. Annual Summaries of Foodborne Outbreaks. Available from: https://www.cdc.gov/fdoss/annual-reports/index.html. Accessed Nov. 11, 2019. |
21 | Fonseca P, Moreno R, Rojo F. Growth of Pseudomonas putida at low temperature: global transcriptomic and proteomic analyses. Environ. Microbiol. Rep. 3: 329-339 (2011) DOI |
22 | Dutkiewicz J, Mackiewicz B, Lemieszek MK, Golec M, Milanowski J. Pantoea agglomerans: a mysterious bacterium of evil and good. Part III. Deleterious effects: infections of humans, animals and plants. Ann. Agric. Environ. Med. 23: 197-205 (2016) DOI |
23 | Eshaghi A, Shahinas D, Patel SN, Kus JV. First draft genome sequence of Aureimonas altamirensis, isolated from patient blood culture. FEMS Microbiol. Lett. 362: (2015) |
24 | Filip Z, Hermann S. An attempt to differentiate Pseudomonas spp. and other soil bacteria by FT-IR spectroscopy. Eur. J. Soil Biol. 37: 137-143 (2001) DOI |
25 | Freiberg C, Fellay R, Bairoch A, Broughton WJ, Rosenthal A, Perret X. Molecular basis of symbiosis between Rhizobium and legumes. Nature 387: 394-401 (1997) DOI |
26 | Frenk S, Hadar Y, Minz D. Resilience of soil bacterial community to irrigation with water of different qualities under M editerranean climate. Environ. Microbiol. 16: 559-569 (2014) DOI |
27 | Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68: 669-685 (2004) DOI |
28 | Geornaras I, Kunene NF, von Holy A, Hastings JW. Amplified fragment length polymorphism fingerprinting of Pseudomonas strains from a poultry processing plant. Appl. Environ. Microbiol. 65: 3828-3833 (1999) DOI |
29 | Chen TR, Wei QK, Chen YJ. Pseudomonas spp. and Hafnia alvei growth in UHT milk at cold storage. Food Control 22: 697-701 (2011) DOI |
30 | Innerebner G, Knief C, Vorholt JA. Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system. Appl. Environ. Microbiol. 77: 3202-3210 (2011) DOI |
31 | Antunes L, Visca P, Towner KJ. Acinetobacter baumannii: evolution of a global pathogen. Pathog. Dis. 71: 292-301 (2014) DOI |
32 | Aydogan EL, Busse HJ, Moser G, Muller C, Kampfer P, Glaeser SP. Aureimonas galii sp. nov. and Aureimonas pseudogalii sp. nov. isolated from the phyllosphere of Galium album. Int. J. Syst. Evol. Microbiol. 66: 3345-3354 (2016) DOI |
33 | Berger CN, Shaw RK, Brown DJ, Mather H, Clare S, Dougan G, Pallen MJ, Frankel G. Interaction of Salmonella enterica with basil and other salad leaves. ISME J. 3: 261-265 (2009) DOI |
34 | Bergholz TM, Switt AIM, Wiedmann M. Omics approaches in food safety: fulfilling the promise? Trends Microbiol. 22: 275-281 (2014) DOI |
35 | Cruz-Martinez K, Suttle KB, Brodie EL, Power ME, Andersen GL, Banfield JF. Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland. ISME J. 3: 738-744 (2009) DOI |
36 | Davin-Regli A. Enterobacter aerogenes and Enterobacter cloacae; versatile bacterial pathogens confronting antibiotic treatment. Front. Microbiol. 6: 392-401 (2015) DOI |
37 | Jo MJ, Jeong AR, Kim HJ, Lee NR, Oh SW, Kim YJ, Chun HS, Koo MS. Microbiological quality of fresh-cut produce and organic vegetables. Korean J. Food Sci. Technol. 43: 91-97 (2011) DOI |
38 | Iversen C, Forsythe S. Risk profile of Enterobacter sakazakii, an emergent pathogen associated with infant milk formula. Trends Food Sci. Technol. 14: 443-454 (2003) DOI |
39 | Jang JH, Hur HG, Sadowsky MJ, Byappanahalli MN, Yan T, Ishii S. Environmental Escherichia coli: ecology and public health implications-a review. J. Appl. Microbiol. 123: 570-581 (2017) DOI |
40 | Jeon DY, Yum SJ, Seo DW, Kim SM, Jeong HG. Leaf-associated microbiota on perilla (Perilla frutescens var. frutescens) cultivated in South Korea to detect the potential risk of food poisoning. Food Res. Int. 126: 108664 (2019) DOI |
41 | KAMIS. Cool and delicious summer vegetables (Cucumber). Available from: https://www.kamis.or.kr/customer/trend/product/product.do?action=detail&brdctsno=426245&pagenum=1&search_option=SUBJECT&search_keyword=%EC%98%A4%EC%9D%B4&. Accessed Jun. 21, 2018. |
42 | Kim BR, Shin JW, Guevarra RB, Lee JH, Kim DW, Seol KH, Lee JH, Kim HB, Isaacson RE. Deciphering diversity indices for a better understanding of microbial communities. J. Microbiol. Biotechnol. 27: 2089-2093 (2017) DOI |
43 | Kirschbaum MU. The temperature dependence of soil organic matter decomposition, and the effect of global warming on soil organic C storage. Soil Biol. Biochem. 27: 753-760 (1995) DOI |
44 | Ingraham JL. Growth of psychrophilic bacteria. J. Bacteriol. 76: 75- 80 (1958) DOI |
45 | Lu L, Ku KM, Palma-Salgado SP, Storm AP, Feng H, Juvik JA, Nguyen TH. Influence of epicuticular physicochemical properties on porcine rotavirus adsorption to 24 leafy green vegetables and tomatoes. PLoS One 10: e0132841 (2015) DOI |
46 | Compant S, Mitter B, Colli-Mull JG, Gangl H, Sessitsch A. 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 (2011) DOI |
47 | Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FSL, Hufnagle WO, Kowalik DJ, Lagrou M. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406: 959-964 (2000) DOI |
48 | Thukral AK. A review on measurement of Alpha diversity in Biology. Agric. Res. 54: 1-10 (2017) |
49 | Williams TR, Marco ML. Phyllosphere microbiota composition and microbial community transplantation on lettuce plants grown indoors. mBio. 5: e01564-14 (2014) |
50 | Shim WB, Lee CW, Jeong MJ, Kim JS, Ryu JG, Chung DH. An investigation of the hazards associated with cucumber and hot pepper cultivation areas to establish a good agricultural practices (GAP) model. Korean J. Food Sci. Technol. 46: 108-114 (2014) DOI |
51 | Shah N, Tang H, Doak TG, Ye Y. Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics. Biocomput. 16: 165-176 (2011) |
52 | Cordovez V, Schop S, Hordijk K, de Boulois HD, Coppens F, Hanssen I, Raaijmakers JM, Carrion VJ. Priming of plant growth promotion by volatiles of root-associated Microbacterium spp. Appl. Environ. Microbiol. 84: e01865-18 (2018) |
53 | Lopez-Velasco G, Welbaum GE, Boyer RR, Mane SP, Ponder MA. Changes in spinach phylloepiphytic bacteria communities following minimal processing and refrigerated storage described using pyrosequencing of 16S rRNA amplicons. J. Appl. Microbiol. 110: 1203-1214 (2011) DOI |
54 | Kim DH, Hong SH, Kim YT, Ryu SY, Kim HB, Lee JH. Metagenomic approach to identifying foodborne pathogens on Chinese cabbage. J. Microbiol. Biotechnol. 28: 227-235 (2018) DOI |
55 | Bronikowski AM, Bennett AF, Lenski RE. Evolutionary adaptation to temperature. VIII. Effects of temperature on growth rate in natural isolates of Escherichia coli and Salmonella enterica from different thermal environments. Evolution 55: 33-40 (2001) DOI |
56 | Mahmood A, Takagi K, Ito K, Kataoka R. Changes in endophytic bacterial communities during different growth stages of cucumber (Cucumis sativus L.). World J. Microbiol. Biotechnol. 35: 1-13 (2019) DOI |
57 | Chang YH, Choo JH, Lee SY, Kim TY, Jin MH, Chang MY, Lee SH, Lee CK, Park SG. Inhibition of melanogenesis by cucurbitacin B from Cucumis sativus L. J. Soc. Cosmet. Scientists Korea 40: 403-412 (2014) DOI |
58 | Kisluk G, Yaron S. Presence and persistence of Salmonella enterica serotype Typhimurium in the phyllosphere and rhizosphere of spray-irrigated parsley. Appl. Environ. Microbiol. 78: 4030-4036 (2012) DOI |
59 | Madhaiyan M, Reddy BV, Anandham R, Senthilkumar M, Poonguzhali S, Sundaram SP, Sa T. Plant growth-promoting Methylobacterium induces defense responses in groundnu (Arachis hypogaea L.) compared with rot pathogens. Curr. Microbiol. 75: 988-996 (2007) DOI |
60 | Shaw RK, Lasa I, Garcia BM, Pallen MJ, Hinton JC, Berger CN, Frankel G. Cellulose mediates attachment of Salmonella enterica Serovar Typhimurium to tomatoes. Environ. Microbiol. Rep. 3: 569-573 (2011) DOI |
61 | Le Loir Y, Baron F, Gautier M. Staphylococcus aureus and food poisoning. Genet. Mol. Res. 2: 63-76 (2003) |
62 | Abadias M, Usall J, Anguera M, Solsona C, Vinas I. Microbiological quality of fresh, minimally-processed fruit and vegetables, and sprouts from retail establishments. Int. J. Food Microbiol. 123: 121-129 (2008) DOI |
63 | Kumar PS, Brooker MR, Dowd SE, Camerlengo T. Target region selection is a critical determinant of community fingerprints generated by 16S pyrosequencing. PLoS One 6: e20956 (2011) DOI |
64 | Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Thurber RLV, Knight R, Beiko RG, Huttenhower C. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31: 814-821 (2013) DOI |
65 | Miller RR, Montoya V, Gardy JL, Patrick DM, Tang P. Metagenomics for pathogen detection in public health. Genome Med. 5: 1-14 (2013) DOI |
66 | Nakata K. High resistance to oxygen radicals and heat is caused by a galactoglycerolipid in Microbacterium sp. M874. J. Biochem. 127: 731-737 (2000) DOI |
67 | Nordmann P, Naas T, Poirel L. Global spread of carbapenemase-producing Enterobacteriaceae. Emerg. Infect. Dis. 17: 1791-1798 (2011) DOI |
68 | Park SH, Park WS, Kim MR. Quality characteristics of commercial Oiji, Korean cucumber pickle. Korean J. Food Sci. Technol. 36: 385-392 (2004) |
69 | Sperandio V, Nguyen Y. Enterohemorrhagic E. coli (EHEC) pathogenesis. Front. Cell. Infect. Microbiol. 2: 91-97 (2012) |
70 | de Quadros Rodrigues R, Loiko MR, de Paula CMD, Hessel CT, Jacxsens L, Uyttendaele M, Bender RJ, Tondo EC. Microbiological contamination linked to implementation of good agricultural practices in the production of organic lettuce in Southern Brazil. Food Control 42: 152-164 (2014) DOI |
71 | Rasmussen M. Aerococcus: an increasingly acknowledged human pathogen. Clin. Microbiol. Infect. 22: 22-27 (2016) DOI |
72 | Xu Z, Xie J, Soteyome T, Peters BM, Shirtliff ME, Liu J, Harro JM. Polymicrobial interaction and biofilms between Staphylococcus aureus and Pseudomonas aeruginosa: an underestimated concern in food safety. Curr. Opin. Food. Sci. 26: 57-64 (2019) DOI |
73 | Lozupone CA, Hamady M, Kelley ST, Knight R. Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities. J. Appl. Environ. Microbiol. 73: 1576-1585 (2007) DOI |
74 | MAFRA. 2018 Facility vegetables greenhouse status and vetegable production performance. Available from: https://www.mafra.go.kr/mafra/366/subview.do?enc=Zm5jdDF8QEB8JTJGYmJzJTJGbWFmcmElMkY3MSUyRjMyMTY2OCUyRmFydGNsVmlldy5kbyUzRg%3D%3D. Accessed Oct. 15, 2019. |
75 | Vetrovsky T, Baldrian P. The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS One 8: e57923 (2013) DOI |
76 | Turner TR, James EK, Poole PS. The plant microbiome. Genome Biol. 14: 1-10 (2013) |
77 | Xicohtencatl-Cortes J, Chacon ES, Saldana Z, Freer E, Giron JA. Interaction of Escherichia coli O157: H7 with leafy green produce. J. Food. Prot. 72: 1531-1537 (2009) DOI |
78 | Kralik P, Ricchi M. A basic guide to real time PCR in microbial diagnostics: definitions, parameters, and everything. Front. Microbiol. 8: 108-117 (2017) |
79 | Drouin P, Prevost D, Antoun H. Physiological adaptation to low temperatures of strains of Rhizobium leguminosarum bv. viciae associated with Lathyrus spp. FEMS Microbiol. Ecol. 32: 111-120 (2000) DOI |
80 | Kim BY, Weon HY, Park IC, Lee SY, Kim WG, Song JK. Microbial diversity and community analysis in lettuce or cucumber cultivated greenhouse soil in Korea. K.J.S.S.F. 44: 1169-1175 (2011) |
81 | Liu YU, Geng JC, Sha XY, Zhao YX, Hu TM, Yang PZ. Effect of Rhizobium Symbiosis on Low-Temperature Tolerance and Antioxidant Response in Alfalfa (Medicago sativa L.) Front. Plant Sci. 10: 538-551 (2019) |