메뉴 건너뛰기




Volumn 13, Issue 1, 2013, Pages

Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods

Author keywords

[No Author keywords available]

Indexed keywords

ARABINOSE; ARGININE; MELIBIOSE;

EID: 84875307995     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-13-68     Document Type: Article
Times cited : (28)

References (40)
  • 2
    • 0035021812 scopus 로고    scopus 로고
    • The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403
    • 10.1101/gr.GR-1697R 11337471
    • The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Bolotin A, Wincker P, Mauger S, Jaillon O, Malarme K, Weissenbach J, Ehrlich SD, Sorokin A, Genome Res 2001 11 5 731 753 10.1101/gr.GR-1697R 11337471
    • (2001) Genome Res , vol.11 , Issue.5 , pp. 731-753
    • Bolotin, A.1    Wincker, P.2    Mauger, S.3    Jaillon, O.4    Malarme, K.5    Weissenbach, J.6    Ehrlich, S.D.7    Sorokin, A.8
  • 5
    • 33745967483 scopus 로고    scopus 로고
    • Phenotypic and molecular characterization of Lactococcus lactis from milk and plants
    • 10.1111/j.1365-2672.2006.02949.x 16882147
    • Phenotypic and molecular characterization of Lactococcus lactis from milk and plants. Nomura M, Kobayashi M, Narita T, Kimoto-Nira H, Okamoto T, J Appl Microbiol 2006 101 2 396 405 10.1111/j.1365-2672.2006.02949.x 16882147
    • (2006) J Appl Microbiol , vol.101 , Issue.2 , pp. 396-405
    • Nomura, M.1    Kobayashi, M.2    Narita, T.3    Kimoto-Nira, H.4    Okamoto, T.5
  • 7
    • 77958505533 scopus 로고    scopus 로고
    • Chromosomal diversity in Lactococcus lactis and the origin of dairy starter cultures
    • 20847124
    • Chromosomal diversity in Lactococcus lactis and the origin of dairy starter cultures. Kelly WJ, Ward LJ, Leahy SC, Genome Biol Evol 2010 2 729 744 20847124
    • (2010) Genome Biol Evol , vol.2 , pp. 729-744
    • Kelly, W.J.1    Ward, L.J.2    Leahy, S.C.3
  • 8
    • 77952072288 scopus 로고    scopus 로고
    • Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium
    • 10.1128/JB.00276-10
    • Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium. Siezen RJ, Bayjanov J, Renckens B, Wels M, Van Hijum SA, Molenaar D, Van Hylckama Vlieg JE, J Bacterio 2010 192 10 2649 2650 10.1128/JB.00276-10
    • (2010) J Bacterio , vol.192 , Issue.10 , pp. 2649-2650
    • Siezen, R.J.1    Bayjanov, J.2    Renckens, B.3    Wels, M.4    Van Hijum, S.A.5    Molenaar, D.6    Van Hylckama Vlieg, J.E.7
  • 9
    • 38349106435 scopus 로고    scopus 로고
    • Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche
    • 10.1128/AEM.01850-07 18039825
    • Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche. Siezen RJ, Starrenburg MJ, Boekhorst J, Renckens B, Molenaar D, van Hylckama Vlieg JE, Appl Environ Microbiol 2008 74 2 424 436 10.1128/AEM.01850-07 18039825
    • (2008) Appl Environ Microbiol , vol.74 , Issue.2 , pp. 424-436
    • Siezen, R.J.1    Starrenburg, M.J.2    Boekhorst, J.3    Renckens, B.4    Molenaar, D.5    Van Hylckama Vlieg, J.E.6
  • 10
    • 79958100336 scopus 로고    scopus 로고
    • Complete genome sequence of Lactococcus lactis subsp. lactis CV56, a probiotic strain isolated from the vaginas of healthy women
    • 10.1128/JB.00358-11 21460077
    • Complete genome sequence of Lactococcus lactis subsp. lactis CV56, a probiotic strain isolated from the vaginas of healthy women. Gao Y, Lu Y, Teng KL, Chen ML, Zheng HJ, Zhu YQ, Zhong J, J Bacteriol 2011 193 11 2886 2887 10.1128/JB.00358-11 21460077
    • (2011) J Bacteriol , vol.193 , Issue.11 , pp. 2886-2887
    • Gao, Y.1    Lu, Y.2    Teng, K.L.3    Chen, M.L.4    Zheng, H.J.5    Zhu, Y.Q.6    Zhong, J.7
  • 11
    • 84857877926 scopus 로고    scopus 로고
    • Complete genome sequence of Lactococcus lactis subsp. cremoris A76
    • 10.1128/JB.06629-11 22328746
    • Complete genome sequence of Lactococcus lactis subsp. cremoris A76. Bolotin A, Quinquis B, Ehrlich SD, Sorokin A, J Bacteriol 2012 194 5 1241 1242 10.1128/JB.06629-11 22328746
    • (2012) J Bacteriol , vol.194 , Issue.5 , pp. 1241-1242
    • Bolotin, A.1    Quinquis, B.2    Ehrlich, S.D.3    Sorokin, A.4
  • 12
    • 84861209407 scopus 로고    scopus 로고
    • Complete genome sequence of Lactococcus lactis IO-1, a lactic acid bacterium that utilizes xylose and produces high levels of L-lactic acid
    • 10.1128/JB.00074-12 22461545
    • Complete genome sequence of Lactococcus lactis IO-1, a lactic acid bacterium that utilizes xylose and produces high levels of L-lactic acid. Kato H, Shiwa Y, Oshima K, Machii M, Araya-Kojima T, Zendo T, Shimizu-Kadota M, Hattori M, Sonomoto K, Yoshikawa H, J Bacteriol 2012 194 8 2102 2103 10.1128/JB.00074-12 22461545
    • (2012) J Bacteriol , vol.194 , Issue.8 , pp. 2102-2103
    • Kato, H.1    Shiwa, Y.2    Oshima, K.3    Machii, M.4    Araya-Kojima, T.5    Zendo, T.6    Shimizu-Kadota, M.7    Hattori, M.8    Sonomoto, K.9    Yoshikawa, H.10
  • 13
    • 84876940203 scopus 로고    scopus 로고
    • Complete Genome of Lactococcus lactis subsp. cremoris UC509.9, Host for a Model Lactococcal P335 Bacteriophage
    • pii: e00119-12. doi: 10.1128/genomeA.00119-12. Epub 2013 Jan 31
    • Complete Genome of Lactococcus lactis subsp. cremoris UC509.9, Host for a Model Lactococcal P335 Bacteriophage. Ainsworth S, Zomer A, De Jager V, Bottacini F, Van Hijum SA, Mahony J, Van Sinderen D, Genome Announc 2013 1 1 pii: e00119-12. doi: 10.1128/genomeA.00119-12. Epub 2013 Jan 31
    • (2013) Genome Announc , vol.1 , Issue.1
    • Ainsworth, S.1    Zomer, A.2    De Jager, V.3    Bottacini, F.4    Van Hijum, S.A.5    Mahony, J.6    Van Sinderen, D.7
  • 14
    • 29144536283 scopus 로고    scopus 로고
    • Complete sequences of four plasmids of Lactococcus lactis subsp. cremoris SK11 reveal extensive adaptation to the dairy environment
    • 10.1128/AEM.71.12.8371-8382.2005 16332824
    • Complete sequences of four plasmids of Lactococcus lactis subsp. cremoris SK11 reveal extensive adaptation to the dairy environment. Siezen RJ, Renckens B, VanSwam I, Peters S, Van Kranenburg R, Kleerebezem M, DeVos WM, Appl Environ Microbiol 2005 71 12 8371 8382 10.1128/AEM.71.12.8371-8382.2005 16332824
    • (2005) Appl Environ Microbiol , vol.71 , Issue.12 , pp. 8371-8382
    • Siezen, R.J.1    Renckens, B.2    Vanswam, I.3    Peters, S.4    Van Kranenburg, R.5    Kleerebezem, M.6    Devos, W.M.7
  • 15
    • 36649035092 scopus 로고    scopus 로고
    • Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting
    • 10.1128/AEM.01017-07 17890345
    • Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting. Rademaker JL, Herbet H, Starrenburg MJ, Naser SM, Gevers D, Kelly WJ, Hugenholtz J, Swings J, van Hylckama Vlieg JE, Appl Environ Microbiol 2007 73 22 7128 7137 10.1128/AEM.01017-07 17890345
    • (2007) Appl Environ Microbiol , vol.73 , Issue.22 , pp. 7128-7137
    • Rademaker, J.L.1    Herbet, H.2    Starrenburg, M.J.3    Naser, S.M.4    Gevers, D.5    Kelly, W.J.6    Hugenholtz, J.7    Swings, J.8    Van Hylckama Vlieg, J.E.9
  • 17
    • 77958497076 scopus 로고    scopus 로고
    • Evaluation of the genetic polymorphism among Lactococcus lactis subsp. cremoris strains using comparative genomic hybridization and multilocus sequence analysis
    • 10.1016/j.ijfoodmicro.2010.02.020 20233634
    • Evaluation of the genetic polymorphism among Lactococcus lactis subsp. cremoris strains using comparative genomic hybridization and multilocus sequence analysis. Taibi A, Dabour N, Lamoureux M, Roy D, LaPointe G, Int J Food Microbiol 2010 144 1 20 28 10.1016/j.ijfoodmicro.2010.02.020 20233634
    • (2010) Int J Food Microbiol , vol.144 , Issue.1 , pp. 20-28
    • Taibi, A.1    Dabour, N.2    Lamoureux, M.3    Roy, D.4    Lapointe, G.5
  • 19
    • 70349961675 scopus 로고    scopus 로고
    • Genotypic and technological characterization of Lactococcus lactis isolates involved in processing of artisanal Manchego cheese
    • 10.1111/j.1365-2672.2009.04334.x 19426262
    • Genotypic and technological characterization of Lactococcus lactis isolates involved in processing of artisanal Manchego cheese. Nieto-Arribas P, Sesena S, Poveda JM, Palop L, Cabezas L, J Appl Microbiol 2009 107 5 1505 1517 10.1111/j.1365-2672.2009.04334.x 19426262
    • (2009) J Appl Microbiol , vol.107 , Issue.5 , pp. 1505-1517
    • Nieto-Arribas, P.1    Sesena, S.2    Poveda, J.M.3    Palop, L.4    Cabezas, L.5
  • 20
    • 33847332962 scopus 로고    scopus 로고
    • Genotypic and phenotypic diversity of Lactococcus lactis isolates from Batzos, a Greek PDO raw goat milk cheese
    • 10.1016/j.ijfoodmicro.2006.09.020 17241681
    • Genotypic and phenotypic diversity of Lactococcus lactis isolates from Batzos, a Greek PDO raw goat milk cheese. Psoni L, Kotzamanidis C, Yiangou M, Tzanetakis N, Litopoulou-Tzanetaki E, Int J Food Microbiol 2007 114 2 211 220 10.1016/j.ijfoodmicro.2006.09.020 17241681
    • (2007) Int J Food Microbiol , vol.114 , Issue.2 , pp. 211-220
    • Psoni, L.1    Kotzamanidis, C.2    Yiangou, M.3    Tzanetakis, N.4    Litopoulou-Tzanetaki, E.5
  • 21
    • 79551491386 scopus 로고    scopus 로고
    • Assessment of the diversity of dairy Lactococcus lactis subsp. lactis isolates by an integrated approach combining phenotypic, genomic, and transcriptomic analyses
    • 10.1128/AEM.01657-10 21131529
    • Assessment of the diversity of dairy Lactococcus lactis subsp. lactis isolates by an integrated approach combining phenotypic, genomic, and transcriptomic analyses. Tan-a-ram P, Cardoso T, Daveran-Mingot ML, Kanchanatawee S, Loubiere P, Girbal L, Cocaign-Bousquet M, Appl Environ Microbiol 2011 77 3 739 748 10.1128/AEM.01657-10 21131529
    • (2011) Appl Environ Microbiol , vol.77 , Issue.3 , pp. 739-748
    • Tan-A-Ram, P.1    Cardoso, T.2    Daveran-Mingot, M.L.3    Kanchanatawee, S.4    Loubiere, P.5    Girbal, L.6    Cocaign-Bousquet, M.7
  • 22
    • 84860543260 scopus 로고    scopus 로고
    • PhenoLink - A web-tool for linking phenotype to omics data for bacteria: Application to gene-trait matching for Lactobacillus plantarum strains
    • 10.1186/1471-2164-13-170 22559291
    • PhenoLink-a web-tool for linking phenotype to omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains. Bayjanov JR, Molenaar D, Tzeneva V, Siezen RJ, van Hijum SA, BMC Genomics 2012 13 170 10.1186/1471-2164-13-170 22559291
    • (2012) BMC Genomics , vol.13 , pp. 170
    • Bayjanov, J.R.1    Molenaar, D.2    Tzeneva, V.3    Siezen, R.J.4    Van Hijum, S.A.5
  • 23
    • 0026573214 scopus 로고
    • Characterization of the novel nisin-sucrose conjugative transposon Tn5276 and its insertion in Lactococcus lactis
    • 1310502
    • Characterization of the novel nisin-sucrose conjugative transposon Tn5276 and its insertion in Lactococcus lactis. Rauch PJ, De Vos WM, J Bacteriol 1992 174 4 1280 1287 1310502
    • (1992) J Bacteriol , vol.174 , Issue.4 , pp. 1280-1287
    • Rauch, P.J.1    De Vos, W.M.2
  • 24
    • 0028290145 scopus 로고
    • Distribution and evolution of nisin-sucrose elements in Lactococcus lactis
    • 8031080
    • Distribution and evolution of nisin-sucrose elements in Lactococcus lactis. Rauch PJ, Beerthuyzen MM, de Vos WM, Appl Environ Microbiol 1994 60 6 1798 1804 8031080
    • (1994) Appl Environ Microbiol , vol.60 , Issue.6 , pp. 1798-1804
    • Rauch, P.J.1    Beerthuyzen, M.M.2    De Vos, W.M.3
  • 25
    • 0032497959 scopus 로고    scopus 로고
    • Characterization of lactococci isolated from minimally processed fresh fruit and vegetables
    • 10.1016/S0168-1605(98)00135-4 9924939
    • Characterization of lactococci isolated from minimally processed fresh fruit and vegetables. Kelly WJ, Davey GP, Ward LJ, Int J Food Microbiol 1998 45 2 85 92 10.1016/S0168-1605(98)00135-4 9924939
    • (1998) Int J Food Microbiol , vol.45 , Issue.2 , pp. 85-92
    • Kelly, W.J.1    Davey, G.P.2    Ward, L.J.3
  • 26
    • 84855320124 scopus 로고    scopus 로고
    • Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution
    • 10.1101/gr.121285.111 22080491
    • Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution. Bachmann H, Starrenburg MJ, Molenaar D, Kleerebezem M, van Hylckama Vlieg JE, Genome Res 2012 22 1 115 124 10.1101/gr.121285.111 22080491
    • (2012) Genome Res , vol.22 , Issue.1 , pp. 115-124
    • Bachmann, H.1    Starrenburg, M.J.2    Molenaar, D.3    Kleerebezem, M.4    Van Hylckama Vlieg, J.E.5
  • 27
    • 0026687972 scopus 로고
    • A binding protein-dependent transport system in Streptococcus mutans responsible for multiple sugar metabolism
    • 1537846
    • A binding protein-dependent transport system in Streptococcus mutans responsible for multiple sugar metabolism. Russell RR, Aduse-Opoku J, Sutcliffe IC, Tao L, Ferretti JJ, J Biol Chem 1992 267 7 4631 4637 1537846
    • (1992) J Biol Chem , vol.267 , Issue.7 , pp. 4631-4637
    • Russell, R.R.1    Aduse-Opoku, J.2    Sutcliffe, I.C.3    Tao, L.4    Ferretti, J.J.5
  • 28
    • 0026246686 scopus 로고
    • Chromosomal deletions in melibiose-negative isolates of Streptococcus mutans
    • 10.1177/00220345910700110501 1835726
    • Chromosomal deletions in melibiose-negative isolates of Streptococcus mutans. Ushiro I, Lumb SM, Aduse-Opoku J, Ferretti JJ, Russell RR, J Dent Res 1991 70 11 1422 1426 10.1177/00220345910700110501 1835726
    • (1991) J Dent Res , vol.70 , Issue.11 , pp. 1422-1426
    • Ushiro, I.1    Lumb, S.M.2    Aduse-Opoku, J.3    Ferretti, J.J.4    Russell, R.R.5
  • 29
    • 0017371715 scopus 로고
    • Inorganic salts resistance associated with a lactose-fermenting plasmid in Streptococcus lactis
    • 404284
    • Inorganic salts resistance associated with a lactose-fermenting plasmid in Streptococcus lactis. Efstathiou JD, McKay LL, J Bacteriol 1977 130 1 257 265 404284
    • (1977) J Bacteriol , vol.130 , Issue.1 , pp. 257-265
    • Efstathiou, J.D.1    McKay, L.L.2
  • 30
    • 0033956060 scopus 로고    scopus 로고
    • The COG database: A tool for genome-scale analysis of protein functions and evolution
    • 10.1093/nar/28.1.33 10592175
    • The COG database: a tool for genome-scale analysis of protein functions and evolution. Tatusov RL, Galperin MY, Natale DA, Koonin EV, Nucleic Acids Res 2000 28 1 33 36 10.1093/nar/28.1.33 10592175
    • (2000) Nucleic Acids Res , vol.28 , Issue.1 , pp. 33-36
    • Tatusov, R.L.1    Galperin, M.Y.2    Natale, D.A.3    Koonin, E.V.4
  • 31
    • 79961037696 scopus 로고    scopus 로고
    • High-resolution AFLP Typing of Lactococcus lactis Strains Enables Identification of Genetic Markers for Subspecies Related Phenotypes
    • 10.1128/AEM.00518-11 21666014
    • High-resolution AFLP Typing of Lactococcus lactis Strains Enables Identification of Genetic Markers for Subspecies Related Phenotypes. Kutahya OE, Starrenburg MJ, Rademaker JL, Klaassen CH, Van Hylckama Vlieg JE, Smid EJ, Kleerebezem M, Appl Environ Microbiol 2011 77 15 5192 5198 10.1128/AEM.00518-11 21666014
    • (2011) Appl Environ Microbiol , vol.77 , Issue.15 , pp. 5192-5198
    • Kutahya, O.E.1    Starrenburg, M.J.2    Rademaker, J.L.3    Klaassen, C.H.4    Van Hylckama Vlieg, J.E.5    Smid, E.J.6    Kleerebezem, M.7
  • 33
    • 70749158609 scopus 로고    scopus 로고
    • A high-throughput cheese manufacturing model for effective cheese starter culture screening
    • 10.3168/jds.2009-2372 19923591
    • A high-throughput cheese manufacturing model for effective cheese starter culture screening. Bachmann H, Kruijswijk Z, Molenaar D, Kleerebezem M, van Hylckama Vlieg JE, J Dairy Sci 2009 92 12 5868 5882 10.3168/jds.2009-2372 19923591
    • (2009) J Dairy Sci , vol.92 , Issue.12 , pp. 5868-5882
    • Bachmann, H.1    Kruijswijk, Z.2    Molenaar, D.3    Kleerebezem, M.4    Van Hylckama Vlieg, J.E.5
  • 36
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • 10.1006/jmbi.2000.5197 11743721
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Remm M, Storm CE, Sonnhammer EL, J Mol Biol 2001 314 5 1041 1052 10.1006/jmbi.2000.5197 11743721
    • (2001) J Mol Biol , vol.314 , Issue.5 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.2    Sonnhammer, E.L.3
  • 37
    • 77952858385 scopus 로고    scopus 로고
    • PanCGHweb: A web tool for genotype calling in pangenome CGH data
    • 10.1093/bioinformatics/btq103 20219865
    • PanCGHweb: a web tool for genotype calling in pangenome CGH data. Bayjanov JR, Siezen RJ, van Hijum SA, Bioinformatics 2010 26 9 1256 1257 10.1093/bioinformatics/btq103 20219865
    • (2010) Bioinformatics , vol.26 , Issue.9 , pp. 1256-1257
    • Bayjanov, J.R.1    Siezen, R.J.2    Van Hijum, S.A.3
  • 38
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • 10.1023/A:1010933404324
    • Random forests. Breiman L, Machine Learning 2001 45 1 5 32 10.1023/A:1010933404324
    • (2001) Machine Learning , vol.45 , Issue.1 , pp. 5-32
    • Breiman, L.1
  • 40
    • 0036489046 scopus 로고    scopus 로고
    • Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data
    • 10.1198/016214502753479248
    • Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data. Dudoit S, Fridlyand J, Speed TP, J Am Stat Assoc 2002 97 457 77 87 10.1198/016214502753479248
    • (2002) J Am Stat Assoc , vol.97 , Issue.457 , pp. 77-87
    • Dudoit, S.1    Fridlyand, J.2    Speed, T.P.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.