Pan-Genomics of Lactobacillus plantarum Revealed Group-Specific Genomic Profiles without Habitat Association |
Choi, Sukjung
(Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University)
Jin, Gwi-Deuk (Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University) Park, Jongbin (Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University) You, Inhwan (Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University) Kim, Eun Bae (Laboratory of Microbial Genomics and Big Data, College of Animal Life Sciences, Kangwon National University) |
1 | Holzapfel W, Wood BJ. 2012. The Genera of Lactic Acid Bacteria. Springer Science & Business Media, Berlin. |
2 | Makarova KS, Koonin EV. 2007. Evolutionary genomics of lactic acid bacteria. J. Bacteriol. 189: 1199-1208. DOI |
3 | De Vries MC, Vaughan EE, Kleerebezem M, de Vos WM. 2006. Lactobacillus plantarum - survival, functional and potential probiotic properties in the human intestinal tract. Int. Dairy J. 16: 1018-1028. DOI |
4 | Aizenman E, Engelberg-Kulka H, Glaser G. 1996. An Escherichia coli chromosomal "addiction module" regulated by guanosine [corrected] 3',5'-bispyrophosphate: a model for programmed bacterial cell death. Proc. Natl. Acad. Sci. USA 93: 6059-6063. DOI |
5 | Mittenhuber G. 1999. Occurence of MazEF-like antitoxin/toxin systems in bacteria. J. Mol. Microbiol. Biotechnol. 1: 295-302. |
6 | Nystrom T. 1998. To be or not to be: the ultimate decision of the growth-arrested bacterial cell. FEMS Microbiol. Rev. 21: 283-290. DOI |
7 | Gormley NA, Watson MA, Halford SE. 2001. Bacterial restriction-modification systems. eLS DOI: 10.1038/npg.els.0001037. DOI |
8 | Kobayashi I. 2001. Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res. 29: 3742-3756. DOI |
9 | Plumed-Ferrer C, Koistinen KM, Tolonen TL, Lehesranta SJ, Karenlampi SO, Makimattila E, et al. 2008. Comparative study of sugar fermentation and protein expression patterns of two Lactobacillus plantarum strains grown in three different media. Appl. Environ. Microbiol. 74: 5349-5358. DOI |
10 | Zago M, Fornasari ME, Carminati D, Burns P, Suarez V, Vinderola G, et al. 2011. Characterization and probiotic potential of Lactobacillus plantarum strains isolated from cheeses. Food Microbiol. 28: 1033-1040. DOI |
11 | Saxelin M, Tynkkynen S, Mattila-Sandholm T, de Vos WM. 2005. Probiotic and other functional microbes: from markets to mechanisms. Curr. Opin. Biotechnol. 16: 204-211. DOI |
12 | Seddik HA, Bendali F, Gancel F, Fliss I, Spano G, Drider D. 2017. Lactobacillus plantarum and its probiotic and food potentialities. Probiotics Antimicrob. Proteins 9: 111-122. DOI |
13 | Molenaar D, Bringel F, Schuren FH, de Vos WM, Siezen RJ, Kleerebezem M. 2005. Exploring Lactobacillus plantarum genome diversity by using microarrays. J. Bacteriol. 187: 6119-6127. DOI |
14 | Siezen RJ, Tzeneva VA, Castioni A, Wels M, Phan HT, Rademaker JL, et al. 2010. Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches. Environ. Microbiol. 12: 758-773. DOI |
15 | Martino ME, Bayjanov JR, Caffrey BE, Wels M, Joncour P, Hughes S, et al. 2016. Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats. Environ. Microbiol. 18: 4974-4989. DOI |
16 | Galloway-Peña J, Roh JH, Latorre M, Qin X, Murray BE. 2012. Genomic and SNP analyses demonstrate a distant separation of the hospital and community-associated clades of Enterococcus faecium. PLoS One 7: e30187. DOI |
17 | Kim EB, Marco ML. 2014. Nonclinical and clinical Enterococcus faecium strains, but not Enterococcus faecalis strains, have distinct structural and functional genomic features. Appl. Environ. Microbiol. 80: 154-165. DOI |
18 | Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9: 75. DOI |
19 | Kopit LM, Kim EB, Siezen RJ, Harris LJ, Marco ML. 2014. Safety of the surrogate microorganism Enterococcus faecium NRRL B-2354 for use in thermal process validation. Appl. Environ. Microbiol. 80: 1899-1909. DOI |
20 | Kim EB, Jin GD, Lee JY, Choi YJ. 2016. Genomic features and niche-adaptation of Enterococcus faecium strains from Korean soybean-fermented foods. PLoS One 11: e0153279. DOI |
21 | Rizk G, Lavenier D. 2010. GASSST: global alignment short sequence search tool. Bioinformatics 26: 2534-2540. DOI |
22 | Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797. DOI |
23 | Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33: 1870-1874. DOI |
24 | Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425. |
25 | Siliakus MF, van der Oost J, Kengen SW. 2017. Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure. Extremophiles 21: 651-670. DOI |
26 | Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791. DOI |
27 | Tamura K, Nei M, Kumar S. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Natl. Acad. Sci. USA 101: 11030-11035. DOI |