Draft genome sequences and description of Lactobacillus rhamnosus strains L31, L34, and L35

Standards in Genomic Sciences

Volumn 9, Issue 3, 2015, Pages 744-754

  Boonma, Prapaporn ^a   Spinler, Jennifer K ^b,c   Qin, Xiang ^c   Jittaprasatsin, Chutima ^a   Muzny, Donna M ^c   Doddapaneni, Harsha ^c   Gibbs, Richard ^c   Petrosino, Joe ^c   Tumwasorn, Somying ^a   Versalovic, James ^b,c  

^a CHULALONGKORN UNIVERSITY   (Thailand)

^b TEXAS CHILDREN S HOSPITAL   (United States)

^c BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

Anti inflammatory; Comparative genomics; Lactic acid bacteria; Lactobacillus rhamnosus; Probiotics

Indexed keywords

FECES; GENOME; IN VITRO STUDY; INFANT; LACTOBACILLUS RHAMNOSUS;

EID: 84954183325     PISSN: None     EISSN: 19443277     Source Type: Journal    
DOI: 10.4056/sigs.5048907     Document Type: Article

References (50)

1. Human Microbiome Project Consortium. Struc-ture, function and diversity of the healthy human microbiome. Nature 2012; 486:207-214. PubMed http://dx.doi.org/10.1038/nature11234
2. Bernardeau M, Vernoux JP, Henri-Dubernet S, Guéguen M. Safety assessment of dairy microor-ganisms: the Lactobacillus genus. Int J Food Microbiol 2008; 126:278-285. PubMed http://dx.doi.org/10.1016/j.ijfoodmicro.2007.08.015
3. Spinler JK. Human Microbiome, Lactobacillaceae in the. In: Nelson K, editor. Encyclopedia of Metagenomics. Verlag Berlin Heidelberg: Spring-er; 2013.
4. Schleifer KH. Family I. Lactobacillaceae Winslow, Broadhurst, Buchanan, Krumwiede, Rogers and Smith 1917, familia. In: De Vos PG, G.M.; Jones, D.; Krieg, N.R.; Ludwig, W.; Rainey, F.A.; Schleifer, K.H.; Whitman, W.B., editor. Bergey's Manual of Systematic Bacteriology, Volume Three The Firmicutes. 2nd ed. Volume 3, TheFirmicutes. New York: Springer; 2009. p 465-532.
5. Peña JA, Versalovic J. Lactobacillus rhamnosus GG decreases TNF-alpha production in lipopoly-saccharide-activated murine macrophages by a contact-independent mechanism. Cell Microbiol 2003; 5:277-285. PubMed http://dx.doi.org/10.1046/j.1462-5822.2003.t01-1-00275.x
6. Zhang L, Li N, Caicedo R, Neu J. Alive and dead Lactobacillus rhamnosus GG decrease tumor ne-crosis factor-alpha-induced interleukin-8 produc-tion in Caco-2 cells. J Nutr 2005; 135:1752-1756. PubMed
7. Mack DR, Michail S, Wei S, McDougall L, Hollingsworth MA. Probiotics inhibit enteropathogenic E. coli adherence in vitro by in-ducing intestinal mucin gene expression. Am J Physiol 1999; 276:G941-G950. PubMed
8. Donato KA, Gareau MG, Wang YJ, Sherman PM. Lactobacillus rhamnosus GG attenuates interfer-on-(gamma) and tumour necrosis factor-alpha-induced barrier dysfunction and pro-inflammatory signalling. Microbiology 2010; 156:3288-3297. PubMed http://dx.doi.org/10.1099/mic.0.040139-0
9. Jittaprasatsin C. Quantification and determination of antagonistic activity of bifidobacteria and lac-tobacilli in faeces of breast-fed and mixed-fed in-fants. Bangkok,Thailand: Chulalongkorn Universi-ty; 2008. 113 p.
10. Euzéby JP. List of Bacterial Names with Standing in Nomenclature: a folder available on the Inter-net. Int J Syst Bacteriol 1997; 47:590-592. PubMed http://dx.doi.org/10.1099/00207713-47-2-590
11. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evo-lutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731-2739. PubMed http://dx.doi.org/10.1093/molbev/msr121
12. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the do-mains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576
13. Gibbons NE, Murray RGE. Proposals concerning the higher taxa of bacteria. Int J Syst Bacteriol 1978; 28:1-6. http://dx.doi.org/10.1099/00207713-28-1-1
14. Garrity G, Holt J. The Road Map to the Manual. Bergey's Manual of Systematic Bacteriology. Vol-ume 1. New York: Springer; 2001. p 119-169.
15. Murray RGE. The Higher Taxa, or, a Place for Everything.? In: Holt JG (ed), Bergey's Manual of Systematic Bacteriology, First Edition, Volume 1, The Williams and Wilkins Co., Baltimore, 1984, p. 31-34.
16. Skerman VBD, McGowan V, Sneath PHA. Ap-proved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225-420. http://dx.doi.org/10.1099/00207713-30-1-225
17. Cohn F. Untersuchungen über Bakterien. Beitr Biol Pflanz 1872; 1:127-224.
18. Gibson T, Gordon RE. Genus I. Bacillus Cohn 1872, 174; Nom. gen. cons. Nomencl. Comm. Intern. Soc. Microbiol. 1937, 28; Opin. A. Jud. Comm. 1955, 39. In: Buchanan RE, Gibbons NE (eds), Bergey's Manual of Determinative Bac-teriology, Eighth Edition, The Williams and Wil-kins Co., Baltimore, 1974, p. 529-550.
19. List of new names and new combinations previ-ously effectively, but not validly, published. List no. 132. Int J Syst Evol Microbiol 2010; 60:469-472. http://dx.doi.org/10.1099/ijs.0.022855-0
20. Ludwig W, Schleifer KH, Whitman WB. Order II. Lactobacillales ord. nov. In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds), Bergey's Manu-al of Systematic Bacteriology, Second Edition, Volume 3, Springer-Verlag, New York, 2009, p. 464.
21. Winslow CEA, Broadhurst J, Buchanan RE, Krumwiede C, Rogers LA, Smith GH. The Fami-lies and Genera of the Bacteria: Preliminary Re-port of the Committee of the Society of American Bacteriologists on Characterization and Classifica-tion of Bacterial Types. J Bacteriol 1917; 2:505-566. PubMed
22. Beijerinck MW. Sur les ferments lactiques de l'industrie. Archives Néerlandaises des Sciences Exactes et Naturelles 1901; 6:212-243.
23. Cai Y, Pang H, Kitahara M, Ohkuma M. Lactoba-cillus nasuensis sp. nov., a lactic acid bacterium isolated from silage, and emended description of the genus Lactobacillus. Int J Syst Evol Microbiol 2012; 62:1140-1144. PubMed http://dx.doi.org/10.1099/ijs.0.031781-0
24. Rogosa M. Genus Lactobacillus Beijerinck 1901, 212; Nom. cons. Opin. 38, Jud. Comm. 1971, 104. In: Buchanan RE, Gibbons NE (eds), Bergey's Manual of Determinative Bacteriology, Eighth Edition, The Williams and Wilkins Co., Baltimore, 1974, p. 576-593.
25. Haakensen M, Dobson CM, Hill JE, Ziola B. Re-classification of Pediococcus dextrinicus (Coster and White 1964) Back 1978 (Approved Lists 1980) as Lactobacillus dextrinicus comb. nov., and emended description of the genus Lactobacil-lus. Int J Syst Evol Microbiol 2009; 59:615-621. PubMed http://dx.doi.org/10.1099/ijs.0.65779-0
26. Editorial Secretary (for the Judicial Commission of the International Committee on Systematic Bacteriology). Opinion 38: Conservation of the Generic Name Lactobacillus Beijerinck. Int J Syst Bacteriol 1971; 21:104. http://dx.doi.org/10.1099/00207713-21-1-104
27. Felis GE, Dellaglio F. Taxonomy of Lactobacilli and Bifidobacteria. Curr Issues Intest Microbiol 2007; 8:44-61. PubMed
28. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Con-sortium. Nat Genet 2000; 25:25-29. PubMed http://dx.doi.org/10.1038/75556
29. Boonma P. Role of Lactobacillus in the suppres-sion of Clostridium difficile-induced IL-8 produc-tion in colonic epithelial cells. Bangkok,Thailand: Chulalongkorn University; 2013. 120 p.
30. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic pro-jects and their associated metadata. Nucleic Acids Res 2010; 38:D346-D354. PubMed http://dx.doi.org/10.1093/nar/gkp848
31. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. PubMed http://dx.doi.org/10.1038/nbt1360
32. Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, et al. A catalog of reference genomes from the human microbiome. Science 2010; 328:994-999. PubMed http://dx.doi.org/10.1126/science.1183605
33. Claesson MJ, van Sinderen D, O'Toole PW. Lac-tobacillus phylogenomics-towards a reclassifica-tion of the genus. Int J Syst Evol Microbiol 2008; 58:2945-2954. PubMed http://dx.doi.org/10.1099/ijs.0.65848-0
34. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identifi-cation. BMC Bioinformatics 2010; 11:119. PubMed http://dx.doi.org/10.1186/1471-2105-11-119
35. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455-457. PubMed http://dx.doi.org/10.1038/nmeth.1457
36. Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271-2278. PubMed http://dx.doi.org/10.1093/bioinformatics/btp393
37. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in ge-nomic sequence. Nucleic Acids Res 1997; 25:955-964. PubMed http://dx.doi.org/10.1093/nar/25.5.0955
38. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucle-ic Acids Res 2007; 35:3100-3108. PubMed http://dx.doi.org/10.1093/nar/gkm160
39. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nu-cleic Acids Res 2003; 31:439-441. PubMed http://dx.doi.org/10.1093/nar/gkg006
40. 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. PubMed http://dx.doi.org/10.1006/jmbi.2000.4315
41. Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004; 340:783-795. PubMed http://dx.doi.org/10.1016/j.jmb.2004.05.028
42. Saxelin M, Pessi T, Salminen S. Fecal recovery following oral administration of Lactobacillus strain GG (ATCC 53103) in gelatine capsules to healthy volunteers. Int J Food Microbiol 1995; 25:199-203. PubMed http://dx.doi.org/10.1016/0168-1605(94)00091-J
43. Guarino A, Lo Vecchio A, Canani RB. Probiotics as prevention and treatment for diarrhea. Curr Opin Gastroenterol 2009; 25:18-23. PubMed http://dx.doi.org/10.1097/MOG.0b013e32831b4455
44. Saxelin M, Tynkkynen S, Mattila-Sandholm T, de Vos WM. Probiotic and other functional mi-crobes: from markets to mechanisms. Curr Opin Biotechnol 2005; 16:204-211. PubMed http://dx.doi.org/10.1016/j.copbio.2005.02.003
45. Vanderhoof JA, Mitmesser SH. Probiotics in the management of children with allergy and other disorders of intestinal inflammation. Benef Mi-crobes 2010; 1:351-356. PubMed http://dx.doi.org/10.3920/BM2010.0034
46. Kankainen M, Paulin L, Tynkkynen S, von Ossowski I, Reunanen J, Partanen P, Satokari R, Vesterlund S, Hendrickx AP, Lebeer S, et al. Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human-mucus binding protein. Proc Natl Acad Sci USA 2009; 106:17193-17198. PubMed http://dx.doi.org/10.1073/pnas.0908876106
47. Douillard FP, Ribbera A, Kant R, Pietila TE, Jarvinen HM, Messing M, Randazzo CL, Paulin L, Laine P, Ritari J, et al. Comparative Genomic and Functional Analysis of 100 Lactobacillus rhamnosus Strains and Their Comparison with Strain GG. PLoS Genet 2013; 9:e1003683. PubMed http://dx.doi.org/10.1371/journal.pgen.1003683
48. Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011; 12:402. PubMed http://dx.doi.org/10.1186/1471-2164-12-402
49. Ferain T, Garmyn D, Bernard N, Hols P, Delcour J. Lactobacillus plantarum ldhL gene: overexpres-sion and deletion. J Bacteriol 1994; 176:596-601. PubMed
50. Tsai YK, Lin TH. Sequence, organization, tran-scription and regulation of lactose and galactose operons in Lactobacillus rhamnosus TCELL-1. J Appl Microbiol 2006; 100:446-459. PubMed http://dx.doi.org/10.1111/j.1365-2672.2005.02790.x