Insights into the bovine rumen plasmidome

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 14, 2012, Pages 5452-5457

  Kav, Aya Brown ^a,b   Sasson, Goor ^a   Jami, Elie ^a,b   Doron Faigenboim, Adi ^a   Benhar, Itai ^b   Mizrahi, Itzhak ^a  

^a VOLCANI CENTER   (Israel)

^b TEL AVIV UNIVERSITY   (Israel)

Author keywords

Metagenomics; Microbial ecology; Rumen microbiology

Indexed keywords

PLASMID DNA;

ANIMAL EXPERIMENT; ARTICLE; BACTERIAL FLORA; BACTERIUM ISOLATION; BACTEROIDETES; CONTROLLED STUDY; COW; DNA EXTRACTION; DNA ISOLATION; DNA SEQUENCE; FIRMICUTES; NONHUMAN; PHYLUM; PLASMID; PLASMIDOME; PRIORITY JOURNAL; PROTEOBACTERIA; RUMINANT STOMACH;

ANIMALS; CATTLE; PHYLOGENY; PLASTIDS; RUMEN;

BACTERIA (MICROORGANISMS); BACTEROIDETES; BOVINAE; FIRMICUTES; PROTEOBACTERIA;

EID: 84859474080     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1116410109     Document Type: Article

References (63)

1. Jain R, Rivera MC, Moore JE, Lake JA (2003) Horizontal gene transfer accelerates genome innovation and evolution. Mol Biol Evol 20:1598-1602. (Pubitemid 41070820)
2. Koonin EV, Wolf YI (2008) Genomics of bacteria and archaea: The emerging dynamic view of the prokaryotic world. Nucleic Acids Res 36:6688-6719.
3. Frost LS, Leplae R, Summers AO, Toussaint A (2005) Mobile genetic elements: The agents of open source evolution. Nat Rev Microbiol 3:722-732. (Pubitemid 41195088)
4. Hacker J, Carniel E (2001) Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes. EMBO Rep 2:376-381. (Pubitemid 32509951)
5. Halary S, Leigh JW, Cheaib B, Lopez P, Bapteste E (2010) Network analyses structure genetic diversity in independent genetic worlds. Proc Natl Acad Sci USA 107:127-132.
6. Heuer H, Abdo Z, Smalla K (2008) Patchy distribution of flexible genetic elements in bacterial populations mediates robustness to environmental uncertainty. FEMS Microbiol Ecol 65:361-371.
7. Novick RP (2003) Mobile genetic elements and bacterial toxinoses: The superantigen-encoding pathogenicity islands of Staphylococcus aureus. Plasmid 49:93-105.
8. Crossman LC (2005) Plasmid replicons of Rhizobium. Biochem Soc Trans 33:157-158.
9. van der Meer JR, Sentchilo V (2003) Genomic islands and the evolution of catabolic pathways in bacteria. Curr Opin Biotechnol 14:248-254.
10. Gil R, Sabater-Muñoz B, Perez-Brocal V, Silva FJ, Latorre A (2006) Plasmids in the aphid endosymbiont Buchnera aphidicola with the smallest genomes. A puzzling evolutionary story. Gene 370:17-25. (Pubitemid 43375895)
11. Zhang T, Zhang XX, Ye L (2011) Plasmid metagenome reveals high levels of antibiotic resistance genes and mobile genetic elements in activated sludge. PLoS ONE 6:e26041.
12. Bekele AZ, Koike S, Kobayashi Y (2010) Genetic diversity and diet specificity of ruminal Prevotella revealed by 16S rRNA gene-based analysis. FEMS Microbiol Lett 305:49-57.
13. Smalla K, et al. (2000) Exogenous isolation of antibiotic resistance plasmids from piggery manure slurries reveals a high prevalence and diversity of IncQ-like plasmids. Appl Environ Microbiol 66:4854-4862.
14. Flint HJ (1997) The rumen microbial ecosystem - Some recent developments. Trends Microbiol 5:483-488.
15. Garcia-Vallvé S, Romeu A, Palau J (2000) Horizontal gene transfer of glycosyl hydrolases of the rumen fungi. Mol Biol Evol 17:352-361. (Pubitemid 30123756)
16. Tóthová T, Pristas P, Javorský P (2006) Mercuric reductase gene transfer from soil to rumen bacteria. Folia Microbiol (Praha) 51:317-319.
17. Flint HJ, Thomson AM, Bisset J (1988) Plasmid-associated transfer of tetracycline resistance in Bacteroides ruminicola. Appl Environ Microbiol 54:855-860.
18. Fliegerová K, Benada O, Flint HJ (1998) Large plasmids in ruminal strains of Selenomonas ruminantium. Lett Appl Microbiol 26:243-247. (Pubitemid 28239987)
19. Flint HJ, McPherson CA, Martin J (1991) Expression of two xylanase genes from the rumen cellulolytic bacterium Ruminococcus flavefaciens 17 cloned in pUC13. J Gen Microbiol 137:123-129.
20. Gilmour M, Mitchell WJ, Flint HJ (1996) Genetic transfer of lactate-utilizing ability in the rumen bacterium Selenomonas ruminantium. Lett Appl Microbiol 22:52-56. (Pubitemid 26025502)
21. Kazimierczak KA, Flint HJ, Scott KP (2006) Comparative analysis of sequences flanking tet(W) resistance genes in multiple species of gut bacteria. Antimicrob Agents Chemother 50:2632-2639. (Pubitemid 44198681)
22. Melville CM, Scott KP, Mercer DK, Flint HJ (2001) Novel tetracycline resistance gene, tet(32), in the Clostridium-related human colonic anaerobe K10 and its transmission in vitro to the rumen anaerobe Butyrivibrio fibrisolvens. Antimicrob Agents Chemother 45:3246-3249. (Pubitemid 32988864)
23. Mercer DK, Melville CM, Scott KP, Flint HJ (1999) Natural genetic transformation in the rumen bacterium Streptococcus bovis JB1. FEMS Microbiol Lett 179:485-490. (Pubitemid 29460717)
24. Mercer DK, Patel S, Flint HJ (2001) Sequence analysis of the plasmid pRRI2 from the rumen bacterium Prevotella ruminicola 223/M2/7 and the use of pRRI2 in Prevotella/Bacteroides shuttle vectors. Plasmid 45:227-232. (Pubitemid 32579410)
25. Al-Khaldi SF, Evans JD, Martin SA (1999) Complete nucleotide sequence of a cryptic plasmid from the ruminal bacterium Selenomonas ruminantium HD4 and identification of two predicted open reading frames. Plasmid 42:45-52. (Pubitemid 29364604)
26. May T, Kocherginskaya SA, Mackie RI, Vercoe PE, White BA (1996) Complete nucleotide sequence of a cryptic plasmid, pBAW301, from the ruminal anaerobe Ruminococcus flavefaciens R13e2. FEMS Microbiol Lett 144:221-227. (Pubitemid 26354332)
27. Ohara H, et al. (1998) Structural analysis of a new cryptic plasmid pAR67 isolated from Ruminococcus albus AR67. Plasmid 39:84-88. (Pubitemid 28119702)
28. Ogata K, et al. (1996) Structural organization of pRAM4, a cryptic plasmid from Prevotella ruminicola. Plasmid 35:91-97. (Pubitemid 26117226)
29. Stevenson DM, Weimer PJ (2007) Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantifi- cation real-time PCR. Appl Microbiol Biotechnol 75:165-174. (Pubitemid 46669229)
30. Hansen JB, Olsen RH (1978) Isolation of large bacterial plasmids and characterization of the P2 incompatibility group plasmids pMG1 and pMG5. J Bacteriol 135:227-238. (Pubitemid 8377449)
31. Kado CI, Liu ST (1981) Rapid procedure for detection and isolation of large and small plasmids. J Bacteriol 145:1365-1373. (Pubitemid 11097357)
32. Anderson DG, McKay LL (1983) Simple and rapid method for isolating large plasmid DNA from lactic streptococci. Appl Environ Microbiol 46:549-552. (Pubitemid 13024762)
33. Thurber RV, Haynes M, Breitbart M, Wegley L, Rohwer F (2009) Laboratory procedures to generate viral metagenomes. Nat Protoc 4:470-483.
34. Johne R, Müller H, Rector A, van Ranst M, Stevens H (2009) Rolling-circle amplification of viral DNA genomes using phi29 polymerase. Trends Microbiol 17:205-211.
35. Zerbino DR, Birney E (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821-829. (Pubitemid 351645072)
36. Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: Short oligonucleotide alignment program. Bioinformatics 24:713-714. (Pubitemid 351321217)
37. Leplae R, Hebrant A, Wodak SJ, Toussaint A (2004) ACLAME: A CLAssification of Mobile genetic Elements. Nucleic Acids Res 32(Database issue):D45-D49. (Pubitemid 38081601)
38. Markowitz VM, et al. (2010) The integrated microbial genomes system: An expanding comparative analysis resource. Nucleic Acids Res 38(Database issue):D382-D390.
39. Brulc JM, et al. (2009) Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci USA 106:1948-1953.
40. Hess M, et al. (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331:463-467.
41. Sharon I, et al. (2011) Comparative metagenomics of microbial traits within oceanic viral communities. ISME J 5:1178-1190.
42. Berg Miller ME, et al. (2012) Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome. Environ Microbiol 14:207-227.
43. Reyes A, et al. (2010) Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466:334-338.
44. Rodriguez-Valera F, et al. (2009) Explaining microbial population genomics through phage predation. Nat Rev Microbiol 7:828-836.
45. Frickey T, Lupas AN (2004) PhyloGenie: Automated phylome generation and analysis. Nucleic Acids Res 32:5231-5238. (Pubitemid 39445511)
46. Stamatakis A, Ludwig T, Meier H (2005) RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21:456-463. (Pubitemid 40310232)
47. Fonty G, Gouet P, Jouany J-P, Senaud J (1987) Establishment of the microflora and anaerobic fungi in the rumen of lambs. J Gen Microbiol 133:1835-1843. (Pubitemid 17140469)
48. Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T (2011) Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res 21:599-609.
49. Kloesges T, Popa O, Martin W, Dagan T (2011) Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths. Mol Biol Evol 28:1057-1074.
50. Sorek R, et al. (2007) Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318:1449-1452. (Pubitemid 350208955)
51. Lurie-Weinberger MN, Peeri M, Gophna U (2012) Contribution of lateral gene transfer to the gene repertoire of a gut-adapted methanogen. Genomics 99:52-58.
52. Dinsdale EA, et al. (2008) Functional metagenomic profiling of nine biomes. Nature 452:629-632. (Pubitemid 351483360)
53. Rohwer F, Thurber RV (2009) Viruses manipulate the marine environment. Nature 459:207-212.
54. Jones BV, Marchesi JR (2007) Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat Methods 4:55-61. (Pubitemid 46029477)
55. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
56. Meyer F, et al. (2008) The metagenomics RAST server - A public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386.
57. Overbeek R, et al. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33:5691-5702. (Pubitemid 41548835)
58. Hino T, Russell JB (1985) Effect of reducing-equivalent disposal and NADH/NAD on deamination of amino acids by intact rumen microorganisms and their cell extracts. Appl Environ Microbiol 50:1368-1374. (Pubitemid 16213350)
59. Russell JB, Strobel HJ (1990) ATPase-dependent energy spilling by the ruminal bacterium, Streptococcus bovis. Arch Microbiol 153:378-383. (Pubitemid 20109066)
60. Miwa T, Esaki H, Umemori J, Hino T (1997) Activity of H(+)-ATPase in ruminal bacteria with special reference to acid tolerance. Appl Environ Microbiol 63:2155-2158. (Pubitemid 27232908)
61. Miwa T, Abe T, Fukuda S, Ohkawara S, Hino T (2001) Regulation of H(+)-ATPase synthesis in response to reduced pH in ruminal bacteria. Curr Microbiol 42:106-110. (Pubitemid 32234643)
62. Dowd SE, et al. (2008) Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol 8:125.
63. Caporaso JG, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335-336.