Whole-genome sequence assembly of Pediococcus pentosaceus LI05 (CGMCC 7049) from the human gastrointestinal tract and comparative analysis with representative sequences from three food-borne strains

Gut Pathogens

Volumn 6, Issue 1, 2014, Pages

  Lv, Long Xian ^a   Li, Yu Dong ^b   Hu, Xin Jun ^a   Shi, Hai Yan ^a   Li, Lan Juan ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b ZHEJIANG GONGSHANG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84939196594     PISSN: None     EISSN: 17574749     Source Type: Journal    
DOI: 10.1186/s13099-014-0036-y     Document Type: Article

References (33)

1. Wieme A, Cleenwerck I, Van Landschoot A, Vandamme P: Pediococcus lolii DSM 19927 T and JCM 15055 T are strains of Pediococcus acidilactici. Int J Syst Evol Microbiol 2012, 62:3105-3108.
2. Leroy F, Verluyten J, De Vuyst L: Functional meat starter cultures for improved sausage fermentation. Int J Food Microbiol 2006, 106:270-285.
3. Martino ME, Maifreni M, Marino M, Bartolomeoli I, Carraro L, Fasolato L, Cardazzo B: Genotypic and phenotypic diversity of Pediococcus pentosaceus strains isolated from food matrices and characterisation of the penocin operon. Antonie Van Leeuwenhoek 2013, 103:1149-1163.
4. Bengmark S: Bio-ecological control of chronic liver disease and encephalopathy. Metab Brain Dis 2009, 24:223-236.
5. Zhao X, Higashikawa F, Noda M, Kawamura Y, Matoba Y, Kumagai T, Sugiyama M: The obesity and fatty liver are reduced by plant-derived Pediococcus pentosaceus LP28 in high fat diet-induced obese mice. PLoS One 2012, 7:e30696.
6. Varsha KK, Priya S, Devendra L, Nampoothiri KM: Control of Spoilage Fungi by Protective Lactic Acid Bacteria Displaying Probiotic Properties. Appl Biochem Biotechnol 2014, 172:3402-3413.
7. Lv LX, Hu XJ, Qian GR, Zhang H, Lu HF, Zheng BW, Jiang L, Li LJ: Administration of Lactobacillus salivarius LI01 or Pediococcus pentosaceus LI05 improves acute liver injury induced by D-galactosamine in rats. Appl Microbiol Biotechnol 2014, 98:5619-5632.
8. Dantoft SH, Bielak EM, Seo JG, Chung MJ, Jensen PR: Complete genome sequence of Pediococcus pentosaceus strain SL4. Genome Announc 2013, 26:e01106-e01113.
9. Midha S, Ranjan M, Sharma V, Kumari A, Singh PK, Korpole S, Patil PB: Genome sequence of Pediococcus pentosaceus strain IE-3. J Bacteriol 2012, 194:4468.
10. Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin E, Pavlov A, Pavlova N, Karamychev V, Polouchine N, Shakhova V, Grigoriev I, Lou Y, Rohksar D, Lucas S, Huang K, Goodstein DM, Hawkins T, Plengvidhya V, Welker D, Hughes J, Goh Y, Benson A, Baldwin K, Lee JH, Díaz-Muñiz I, Dosti B, Smeianov V, Wechter W, Barabote R, et al: Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci U S A 2006, 103:15611-15616.
11. Smibert RM, Krieg NR: Phenotypic Characterization. In Methods for General and Molecular Bacteriology. Washington, DC, USA: American Society for Microbiology Press; 1994:607-654.
12. Tamura K, Dudley J, Nei M, Kumar S: MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007, 24:1596-1599.
13. Luo R, Liu BH, Xie YL: SOAPdenovo2: an empirically improved memory-efficient short-read de novoassembler. GigaScience 2012, 1:18.
14. Delcher AL, Bratke KA, Powers EC, Salzberg SL: Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007, 23:673-679.
15. Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNAgenes in genomic sequence. Nucleic Acids Res 1997, 25:955-964.
16. Benson G: Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 1999, 27:573-580.
17. Petersen TN, Brunak S, von Heijne G, Nielsen H: SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011, 8:785-786.
18. Krogh A, Larsson B, von Heijne G, Sonnhammer EL: Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001, 305:567-580.
19. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Pillay M, Ratner A, Huang J, Woyke T, Huntemann M, Anderson I, Billis K, Varghese N, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC: IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res 2014, 42:D560-D567.
20. Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA: BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011, 12:402.
21. Senan S, Prajapati JB, Joshi CG: Whole-genome based validation of the adaptive properties of Indian origin probiotic Lactobacillus helveticus MTCC 5463. J Sci Food Agric 2014, doi:10.1002/jsfa.6721.
22. Grover S, Rashmi HM, Srivastava AK, Batish VK: Probiotics for human health -new innovations and emerging trends. Gut Pathog 2012, 4:15.
23. Kim YC, Tarr AW, Penfold CN: Colicin import into E. coli cells: a model system for insights into the import mechanisms of bacteriocins. Biochim Biophys Acta 1843, 2014:1717-1731.
24. Pastagia M, Schuch R, Fischetti VA, Huang DB: Lysins: the arrival of pathogen-directed anti-infectives. J Med Microbiol 2013, 62:1506-1516.
25. Capozzi V, Russo P, Duenas MT, Lopez P, Spano G: Lactic acid bacteria producing B-group vitamins: a great potential for functional cereals products. Appl Microbiol Biotechnol 2012, 96:1383-1394.
26. Kanmani P, Satish Kumar R, Yuvaraj N, Paari KA, Pattukumar V, Arul V: Probiotics and its functionally valuable products-a review. Crit Rev Food Sci Nutr 2013, 53:641-658.
27. Nadkarni MA, Chen Z, Wilkins MR, Hunter N: Comparative genome analysis of Lactobacillus rhamnosus clinical isolates from initial stages of dental pulp infection: identification of a new exopolysaccharide cluster. PLoS One 2014, 9:e90643.
28. Smith JL: The physiological role of ferritin-like compounds in bacteria. Crit Rev Microbiol 2004, 30:173-185.
29. Zhan D, Han W, Feng Y: Experimental and computational studies indicate the mutation of Glu12 to increase the thermostability of oligomeric protease from Pyrococcus horikoshii. J Mol Model 2011, 17:1241-1249.
30. Canchaya C, Proux C, Fournous G, Bruttin A, Brussow H: Prophage genomics. Microbiol Mol Biol Rev 2003, 67:238-276.
31. Hooper LV, Gordon JI: Commensal host-bacterial relationships in the gut. Science 2001, 292:1115-1118.
32. Loenen WA, Raleigh EA: The other face of restriction: modification-dependent enzymes. Nucleic Acids Res 2014, 42:56-69.
33. Saad R, Rizkallah MR, Aziz RK: Gut Pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes. Gut Pathog 2012, 4:16.