Genome sequences and comparative genomics of two Lactobacillus ruminis strains from the bovine and human intestinal tracts

Microbial Cell Factories

Volumn 10, Issue SUPPL. 1, 2011, Pages

  Forde, Brian M ^a   Neville, B A ^a   O'Donnell, Michelle M ^a,b   Riboulet Bisson, E ^a   Claesson, M J ^a   Coghlan, Avril ^a   Ross, R P ^b   O'Toole, Paul W ^a  

^a UNIVERSITY COLLEGE CORK   (Ireland)

^b TEAGASC FOOD RESEARCH CENTRE   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOCIN; EXOPOLYSACCHARIDE; SORTASE;

ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATION; COMPARATIVE STUDY; COMPUTER MODEL; COW; GENE IDENTIFICATION; GENE SEQUENCE; GENOME; GENOMICS; HUMAN; IN VITRO STUDY; INTESTINE; LACTOBACILLUS; LACTOBACILLUS RUMINIS; NONHUMAN; PHYLOGENY; PSEUDOGENE; SYNTENY; AMINO ACID SEQUENCE; ANIMAL; BACTERIAL GENOME; CARBOHYDRATE METABOLISM; CATTLE; GENETICS; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

BOVINAE; LACTOBACILLUS; LACTOBACILLUS RUMINIS; LACTOBACILLUS SALIVARIUS;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CARBOHYDRATE METABOLISM; CATTLE; GENOME, BACTERIAL; GENOMICS; HUMANS; INTESTINES; LACTOBACILLUS; MOLECULAR SEQUENCE DATA;

EID: 80052211950     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-10-S1-S13     Document Type: Article

References (83)

1. Wood BJB, Holzapfel WH. The Lactic Acid Bacteria: The genera of lactic acid bacteria. 1995, -398. Springer.
2. LPSN: List of Prokaryotic names with Standing in Nomenclature. , http://www.bacterio.cict.fr/l/lactobacillus.html
3. Klaenhammer TR. Probiotic bacteria: today and tomorrow. The Journal of Nutrition 2000, 130:415S-416S.
4. Schleifer K, Ludwig V. Phylogeny of the genus Lactobacillus and related genera. System. Appl. Microbiol 1995, 461-467.
5. Felis GE, Dellaglio F. Taxonomy of Lactobacilli and Bifidobacteria. Curr Issues Intest Microbiol 2007, 8:44-61.
6. Claesson MJ, van Sinderen D, O'Toole PW. Lactobacillus phylogenomics--towards a reclassification of the genus. International Journal of Systematic and Evolutionary Microbiology 2008, 58:2945-54. 10.1099/ijs.0.65848-0, 19060088.
7. Hamilton-Miller J. Probiotics and prebiotics: scientific aspects * G. W. Tannock, Ed. Caister Academic Press, Wymondham, UK, 2005. * ISBN 1-904455-01-8. 99, 230 pp. Journal of Antimicrobial Chemotherapy 2006, 58:232-233.
8. Hammes W, Hertel C. The Genera Lactobacillus and Carnobacterium. The Prokaryotes 2006, 320-403. Springer New York, Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E.
9. Zhang ZG, Ye ZQ, Yu L, Shi P. Phylogenomic reconstruction of lactic acid bacteria: an update. BMC Evolutionary Biology 2011, 11:1. 10.1186/1471-2148-11-1, 3024227, 21194491.
10. Canchaya C, Claesson MJ, Fitzgerald GF, van Sinderen D, O'Toole PW. Diversity of the genus Lactobacillus revealed by comparative genomics of five species. Microbiology 2006, 152:3185-3196. 10.1099/mic.0.29140-0, 17074890.
11. Collins MD, Wallbanks S, Lane DJ, et al. Phylogenetic analysis of the genus Listeria based on reverse transcriptase sequencing of 16S rRNA. International Journal of Systematic Bacteriology 1991, 41:240-6. 10.1099/00207713-41-2-240, 1713054.
12. Bergey's Manual of Systematic Bacteriology. 2009, 3:393. Williams and amp, Wilkinns 1984, 2.
13. Fujisawa T, Benno Y, Yaeshima T, Mitsuoka T. Taxonomic study of the Lactobacillus acidophilus group, with recognition of Lactobacillus gallinarum sp. nov. and Lactobacillus johnsonii sp. nov. and synonymy of Lactobacillus acidophilus group A3 (Johnson et al: 1980) with the type strain of Lactobacill. International Journal of Systematic Bacteriology 1992, 42:487-91. 10.1099/00207713-42-3-487, 1503977.
14. Berger B, Pridmore RD, Barretto C, et al. Similarity and differences in the Lactobacillus acidophilus group identified by polyphasic analysis and comparative genomics. Journal of Bacteriology 2007, 189:1311-21. 10.1128/JB.01393-06, 1797336, 17142402.
15. JOHNSON JL, PHELPS CF, CUMMINS CS, LONDON J, GASSER F. Taxonomy of the Lactobacillus acidophilus Group. International Journal of Systematic Bacteriology 1980, 30:53-68.
16. Neville BA, O'Toole PW. Probiotic properties of Lactobacillus salivarius and closely related Lactobacillus species. Future Microbiology 2010, 5:759-74. 10.2217/fmb.10.35, 20441548.
17. Sharpe ME, Latham MJ, Garvie EI, Zirngibl J, Kandler O. Two new species of Lactobacillus isolated from the bovine rumen, Lactobacillus ruminis sp.nov. and Lactobacillus vitulinus sp.nov. J Gen Microbiol 1973, 77:37-49.
18. Reuter G. The Lactobacillus and Bifidobacterium microflora of the human intestine: composition and succession. Current Issues in Intestinal Microbiology 2001, 2:43-53.
19. Tannock GW, Munro K, Harmsen HJ, et al. Analysis of the fecal microflora of human subjects consuming a probiotic product containing Lactobacillus rhamnosus DR20. Applied and Environmental Microbiology 2000, 66:2578-88. 10.1128/AEM.66.6.2578-2588.2000, 110584, 10831441.
20. Ventura M, O'Flaherty S, Claesson MJ, et al. Genome-scale analyses of health-promoting bacteria: probiogenomics. Nature reviews. Microbiology 2009, 7:61-71. 10.1038/nrmicro2047, 19029955.
21. Pridmore RD, Berger B, Desiere F, et al. The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533. Proceedings of the National Academy of Sciences of the United States of America 2004, 101:2512-7. 10.1073/pnas.0307327101, 356981, 14983040.
22. Wegmann U, Overweg K, Horn N, et al. Complete genome sequence of Lactobacillus johnsonii FI9785, a competitive exclusion agent against pathogens in poultry. Journal of Bacteriology 2009, 191:7142-3. 10.1128/JB.01182-09, 2772503, 19767436.
23. Callanan M, Kaleta P, O'Callaghan J, et al. Genome sequence of Lactobacillus helveticus, an organism distinguished by selective gene loss and insertion sequence element expansion. Journal of Bacteriology 2008, 190:727-35. 10.1128/JB.01295-07, 2223680, 17993529.
24. Morita H, Toh H, Fukuda S, et al. Comparative genome analysis of Lactobacillus reuteri and Lactobacillus fermentum reveal a genomic island for reuterin and cobalamin production. DNA research : an international journal for rapid publication of reports on genes and genomes 2008, 15:151-61.
25. van de Guchte M, Penaud S, Grimaldi C, et al. The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proceedings of the National Academy of Sciences of the United States of America 2006, 103:9274-9. 10.1073/pnas.0603024103, 1482600, 16754859.
26. Ojala T, Kuparinen V, Koskinen JP, et al. Genome Sequence of Lactobacillus crispatus ST1. Journal of Bacteriology 2010, 192:3547-3548. 10.1128/JB.00399-10, 2897677, 20435723.
27. Zhang W, Yu D, Sun Z, et al. Complete genome sequence of Lactobacillus casei Zhang, a new probiotic strain isolated from traditional home-made koumiss in Inner Mongolia of China. Journal of Bacteriology 2010,
28. Mazé A, Boël G, Zúñiga M, et al. Complete genome sequence of the probiotic Lactobacillus casei strain BL23. Journal of bacteriology 2010, 192:2647-8. 10.1128/JB.00076-10, 2863562, 20348264.
29. Altermann E, Russell WM, Azcarate-Peril MA, et al. Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:3906-12. 10.1073/pnas.0409188102, 554803, 15671160.
30. Claesson MJ, Li Y, Leahy S, et al. Multireplicon genome architecture of Lactobacillus salivarius. Proc Natl Acad Sci U S A 2006, 103:6718-6723. 10.1073/pnas.0511060103, 1436024, 16617113.
31. Kleerebezem M, Boekhorst J, van Kranenburg R, et al. Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci U S A 2003, 100:1990-1995. 10.1073/pnas.0337704100, 149946, 12566566.
32. Genomes online Database. , http://www.genomesonline.org
33. Lerche M, Reuter G. [A contribution to the method of isolation and differentiation of aerobic " lactobacilli" (Genus " Lactobacillus Beijerinck" ).]. Zentralblatt für Bakteriologie : international journal of medical microbiology 1960, 179:354-70.
34. Krause DO, Smith WJM, Conlan LL, et al. Diet influences the ecology of lactic acid bacteria and Escherichia coli along the digestive tract of cattle: neural networks and 16S rDNA. Microbiology (Reading, England) 2003, 149:57-65.
35. Al Jassim RAM. Lactobacillus ruminis is a predominant lactic acid producing bacterium in the caecum and rectum of the pig. Letters in Applied Microbiology 2003, 37:213-7. 10.1046/j.1472-765X.2003.01380.x, 12904222.
36. Neville BA, Forde B, Cleasson M, et al. Flagella of motile commensal lactobacilli elicit an inflammatory response in human epithelial cells. preparation 2011,
37. Taweechotipatr M, Iyer C, Spinler JK, Versalovic J, Tumwasorn S. Lactobacillus saerimneri and Lactobacillus ruminis: novel human-derived probiotic strains with immunomodulatory activities. FEMS Microbiology Letters 2009, 293:65-72. 10.1111/j.1574-6968.2009.01506.x, 19222575.
38. Chain PSG, Grafham DV, Fulton RS, et al. Genomics. Genome project standards in a new era of sequencing. Science (New York, N.Y.) 2009, 326:236-7.
39. Mahillon J, Chandler M. Insertion sequences. Microbiology and Molecular Biology Reviews : MMBR 1998, 62:725-74. 98933, 9729608.
40. O'Donnell M, Forde B, Neville B, Ross P, OToole P. Carbohydrate catabolic flexibility in the mammalian intestinal commensal Lactobacillus ruminis revealed by fermentation studies aligned to genome annotation. Microbial Cell Factories 2011, 10(Suppl 1):S12.
41. Rajagopala SV, Titz B, Goll J, et al. The protein network of bacterial motility. Molecular Systems Biology 2007, 3:128. 1943423, 17667950.
42. Canchaya C, Claesson MJ, Fitzgerald GF, van Sinderen D, O'Toole PW. Diversity of the genus Lactobacillus revealed by comparative genomics of five species. Microbiology 2006, 152:3185-3196. 10.1099/mic.0.29140-0, 17074890.
43. Knappe J, Sawers G. A radical-chemical route to acetyl-CoA: the anaerobically induced pyruvate formate-lyase system of Escherichia coli. FEMS microbiology reviews 1990, 6:383-98.
44. Altermann E, Russell WM, Azcarate-Peril MA, et al. Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. Proc Natl Acad Sci U S A 2005, 102:3906-3912. 10.1073/pnas.0409188102, 554803, 15671160.
45. Cotter PD, Hill C, Ross RP. Bacteriocins: developing innate immunity for food. Nature reviews. Microbiology 2005, 3:777-88. 10.1038/nrmicro1273, 16205711.
46. Nissen-Meyer J, Oppegård C, Rogne P, Haugen HS, Kristiansen PE. Structure and Mode-of-Action of the Two-Peptide (Class-IIb) Bacteriocins. Probiotics and Antimicrobial Proteins 2010, 2:52-60. 10.1007/s12602-009-9021-z, 2850506, 20383320.
47. Eijsink VG, Skeie M, Middelhoven PH, Brurberg MB, Nes IF. Comparative studies of class IIa bacteriocins of lactic acid bacteria. Applied and Environmental Microbiology 1998, 64:3275-81. 106721, 9726871.
48. Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science (New York, N.Y.) 2010, 327:167-70.
49. Krüger E, Witt E, Ohlmeier S, Hanschke R, Hecker M. The clp proteases of Bacillus subtilis are directly involved in degradation of misfolded proteins. Journal of Bacteriology 2000, 182:3259-65. 10.1128/JB.182.11.3259-3265.2000, 94515, 10809708.
50. Serrano LM, Molenaar D, Wels M, et al. Thioredoxin reductase is a key factor in the oxidative stress response of Lactobacillus plantarum WCFS1. Microbial Cell Factories 2007, 6:29. 10.1186/1475-2859-6-29, 2174512, 17725816.
51. Kleerebezem M, Hols P, Bernard E, et al. The extracellular biology of the lactobacilli. FEMS microbiology reviews 2010, 34:199-230. 10.1111/j.1574-6976.2009.00208.x, 20088967.
52. Marraffini LA, Dedent AC, Schneewind O. Sortases and the art of anchoring proteins to the envelopes of gram-positive bacteria. Microbiology and Molecular Biology Reviews : MMBR 2006, 70:192-221. 10.1128/MMBR.70.1.192-221.2006, 1393253, 16524923.
53. Pallen MJ, Lam AC, Antonio M, Dunbar K. An embarrassment of sortases - a richness of substrates?. Trends in Microbiology 2001, 9:97-102. 10.1016/S0966-842X(01)01956-4, 11239768.
54. Kankainen M, Paulin L, Tynkkynen S, et al. Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:17193-8. 10.1073/pnas.0908876106, 2746127, 19805152.
55. Boekhorst J, Siezen RJ, Zwahlen MC, et al. The complete genomes of Lactobacillus plantarum and Lactobacillus johnsonii reveal extensive differences in chromosome organization and gene content. Microbiology 2004, 150:3601-3611. 10.1099/mic.0.27392-0, 15528649.
56. van Pijkeren JP, Canchaya C, Ryan KA, et al. Comparative and functional analysis of sortase-dependent proteins in the predicted secretome of Lactobacillus salivarius UCC118. Applied and Environmental Microbiology 2006, 72:4143-53. 10.1128/AEM.03023-05, 1489637, 16751526.
57. Buck BL, Altermann E, Svingerud T, Klaenhammer TR. Functional analysis of putative adhesion factors in Lactobacillus acidophilus NCFM. Applied and Environmental Microbiology 2005, 71:8344-51. 10.1128/AEM.71.12.8344-8351.2005, 1317474, 16332821.
58. Raftis EJ, Salvetti E, Torriani S, Felis GE, O'Toole PW. Genomic diversity of Lactobacillus salivarius. Applied and Environmental Microbiology 2010, 77:954-65. 3028724, 21131523.
59. Péant B, LaPointe G, Gilbert C, et al. Comparative analysis of the exopolysaccharide biosynthesis gene clusters from four strains of Lactobacillus rhamnosus. Microbiology (Reading, England) 2005, 151:1839-51.
60. Li Y, Canchaya C, Fang F, et al. Distribution of megaplasmids in Lactobacillus salivarius and other lactobacilli. Journal of Bacteriology 2007, 189:6128-39. 10.1128/JB.00447-07, 1951925, 17586640.
61. van der Veen B, O'Toole P, Cleasson M. METAPHORE-Automated bidirectional best hit homology analyses. preparation 2011,
62. Kant R, Blom J, Palva A, Siezen RJ, De Vos WM. Comparative genomics of Lactobacillus. Microbial Biotechnology 2010,
63. OCallaghan J, OToole PW. Lactobacillus: Host-Microbe Relationships. Current Topics in Microbiology & Immunology 2011, Submitted.
64. Margulies M, Egholm M, Altman WE, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-80. 1464427, 16056220.
65. Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 2008, 9:387-402. 10.1146/annurev.genom.9.081307.164359, 18576944.
66. Chevreux B, Wetter T, Suhai S. Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 1999, 45-56.
67. Green P. PHRAP version 1.080812. 1999, , http://phrap.org
68. Milne I, Bayer M, Cardle L, et al. Tablet--next generation sequence assembly visualization. Bioinformatics (Oxford, England) 2010, 26:401-2.
69. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Oxford, England) 2007, 23:673-9.
70. Lukashin AV, Borodovsky M. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Research 1998, 26:1107-15. 10.1093/nar/26.4.1107, 147337, 9461475.
71. Claesson MJ, van Sinderen D. BlastXtract--a new way of exploring translated searches. Bioinformatics (Oxford, England) 2005, 21:3667-8.
72. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 1997, 25:955-64. 10.1093/nar/25.5.955, 146525, 9023104.
73. Suzek BE, Ermolaeva MD, Schreiber M, Salzberg SL. A probabilistic method for identifying start codons in bacterial genomes. Bioinformatics (Oxford, England) 2001, 17:1123-30.
74. Quevillon E, Silventoinen V, Pillai S, et al. InterProScan: protein domains identifier. Nucleic acids research 2005, 33:W116-20. 10.1093/nar/gki442, 1160203, 15980438.
75. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of Molecular Biology 2001, 305:567-80. 10.1006/jmbi.2000.4315, 11152613.
76. Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. Journal of molecular biology 2004, 340:783-95. 10.1016/j.jmb.2004.05.028, 15223320.
77. Rutherford K, Parkhill J, Crook J, et al. Artemis: sequence visualization and annotation. Bioinformatics (Oxford, England) 2000, 16:944-5.
78. Wellcome Trust Sanger Institute. , http://www.sanger.ac.uk
79. Carver TJ, Rutherford KM, Berriman M, et al. ACT: the Artemis Comparison Tool. Bioinformatics (Oxford, England) 2005, 21:3422-3.
80. Kurtz S, Phillippy A, Delcher AL, et al. Versatile and open software for comparing large genomes. Genome Biology 2004, 5:R12. 10.1186/gb-2004-5-2-r12, 395750, 14759262.
81. Grubbs F. Procedures for detecting outlying observations in samples. Technometrics 1969, 11:1-21.
82. Long AD, Mangalam HJ, Chan BY, et al. Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. The Journal of Biological Chemistry 2001, 276:19937-44. 10.1074/jbc.M010192200, 11259426.
83. Rea M. Investigating bacteriocins as potential therapeutics for the control of Clostridium difficile. Ph.D thesis 2011,