Hundreds of circular novel plasmids and DNA elements identified in a rat cecum metamobilome

PLoS ONE

Volumn 9, Issue 2, 2014, Pages

  Jørgensen, Tue Sparholt ^a   Xu, Zhuofei ^a   Hansen, Martin Asser ^a   Sørensen, Søren Johannes ^a   Hansen, Lars Hestbjerg ^a,b  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b AARHUS UNIVERSITY   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; CIRCULAR DNA;

ANIMAL TISSUE; ARTICLE; CECUM; COMPUTER MODEL; GENE SEQUENCE; METAGENOMICS; METAMOBILOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; RAT; SEQUENCE HOMOLOGY; UNINDEXED SEQUENCE; ANIMAL; BIOLOGY; HIGH THROUGHPUT SEQUENCING; METABOLISM; PHYLOGENY; PROCEDURES; REPLICON; REPRODUCIBILITY;

ANIMALS; CECUM; COMPUTATIONAL BIOLOGY; DNA, CIRCULAR; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOMICS; PHYLOGENY; PLASMIDS; RATS; REPLICON; REPRODUCIBILITY OF RESULTS;

EID: 84895153034     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0087924     Document Type: Article

References (44)

1. Lederberg J (1952) Cell genetics and hereditary symbiosis. Physiol Rev 32: 403-430.
2. Sørensen SJ, Bailey M, Hansen LH, Kroer N, Wuertz S (2005) Studying plasmid horizontal transfer in situ: a critical review. Nature Reviews Microbiology 3: 700-710. (Pubitemid 41195086)
3. Harshey RM, Jayaram M (2006) The Mu Transpososome Through a Topological Lens. Critical Reviews in Biochemistry and Molecular Biology 41: 387-405. doi: 10.1080/10409230600946015. (Pubitemid 44724881)
4. Mullany P, Roberts AP (2012) Identification of Mobile Genetic Elements in Metagenomes. In: Francino MP, editors. Horizontal Gene Transfer in Microorganisms. Horizon Scientific Press. pp. 155-164.
5. Van Elsas JD, Costa R, Jansson J, Sjöling S, Bailey M et al. (2008) The metagenomics of disease-suppressive soils -experiences from the METACONTROL project. Trends in biotechnology 26: 591-601.
6. Barkay T, Smets BF (2005) Horizontal gene flow in microbial communities. ASM NEWS-AMERICAN SOCIETY FOR MICROBIOLOGY 71: 412.
7. Li LL, Norman A, Hansen LH, Sørensen SJ (2012) Metamobilomics-expanding our knowledge on the pool of plasmid encoded traits in natural environments using high-throughput sequencing. Clinical Microbiology and Infection 18: 5-7.
8. Del Solar G, Giraldo R, Ruiz-Echevarría MJ, Espinosa M, Díaz-Orejas R (1998) Replication and control of circular bacterial plasmids. Microbiology and molecular biology reviews 62: 434-464. (Pubitemid 28270281)
9. Klevens RM, Morrison MA, Nadle J, Petit S, Gershman K et al. (2007) Invasive methicillin-resistant Staphylococcus aureus infections in the United States. JAMA: the journal of the American Medical Association 298: 1763-1771.
10. 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.
11. Ma Y, Paulsen IT, Palenik B (2012) Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments. Environmental Microbiology 14: 453-466.
12. Novick RP, Clowes RC, Cohen SN, Curtiss RIII (1976) Uniform nomenclature for bacterial plasmids: a proposal. Bacteriological reviews 40: 168-189.
13. Guglielmetti S, Mayo B, Álvarez-Martín P (2013) Mobilome and genetic modification of bifidobacteria. Beneficial microbes 4: 143-166.
14. Sentchilo V, Mayer AP, Guy L, Miyazaki R et al. (2013) Community-wide plasmid gene mobilization and selection. The ISME journal 7: 1173-1186.
15. Kav AB, Sasson G, Jami E, Doron-Faigenboim A, Benhar I et al. (2012) Insights into the bovine rumen plasmidome. Proceedings of the National Academy of Sciences 109: 5452-5457.
16. Krupovic M, Gonnet M, Hania WB, Forterre P, Erauso GI (2013) Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new thermococcus plasmids. PloS one 8: e49044.
17. Palenik B, Ren Q, Tai V, Paulsen IT (2008) Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity. Environmental Microbiology 11: 349-359.
18. Sentchilo V, Mayer AP, Guy L, Miyazaki R, Tringe SG et al. (2013) Community-wide plasmid gene mobilization and selection. The ISME journal 7: 1173-1186.
19. Peng Y, Leung H, Yiu SM, Chin FYL (2012) IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28: 1420-1428.
20. Miller JR, Koren S, Sutton G (2010) Assembly algorithms for next-generation sequencing data. Genomics 95: 315-327.
21. Siefert JL (2009) Defining the mobilome. In: Walker JM, editors. Horizontal Gene Transfer. Hatfield: Springer. pp. 13-27.
22. Earl D, Bradnam K, John JS, Darling A, Lin D et al. (2011) Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research 21: 2224-2241.
23. Fredskilde JWL, Nielsen U (2008) Måleprogram på rigshospitalet: målinger for udvalgte spildevandsparametre og lægemidler samt undersøgelse af antibiotikaresistens i spildevand og kloakrotter. Copenhagen: DHI.
24. Yang MG, Manoharan K, Young AK (1969) Influence and degradation of dietary cellulose in cecum of rats. The Journal of nutrition 97: 260-264.
25. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M, editors. Singapore: Wiley. pp. 115-145.
26. Brown Kav A, Benhar I, Mizrahi I (2013) A method for purifying high quality and high yield plasmid DNA for metagenomic and deep sequencing approaches. Journal of microbiological methods 95: 272-279.
27. Lindgreen S (2012) AdapterRemoval: Easy Cleaning of Next Generation Sequencing Reads. BMC Research Notes 5: 337-344.
28. Schmieder R, Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27: 863-864.
29. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW et al. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119-130.
30. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J et al. (2012) The Pfam protein families database. Nucleic Acids Research 40: D290-D301.
31. Schlüter A, Krause L, Szczepanowski R, Goesmann A, Pühler A (2008) Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant. Journal of biotechnology 136: 65-76.
32. Morariu VI, Srinivasan BV, Raykar VC, Duraiswami R, Davis LS (2008) Automatic online tuning for fast Gaussian summation. Advances in Neural Information Processing Systems 1113-1120.
33. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular biology and evolution 28: 2731-2739.
34. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386.
35. Soki J, Wareham DW, Rátkai C, Aduse-Opoku J, Urbán E et al. (2010) Prevalence, nucleotide sequence and expression studies of two proteins of a 5.6 kb, Class III, Bacteroides plasmid frequently found in clinical isolates from European countries. Plasmid 63: 86-97.
36. Yang F, Yang J, Zhang X, Chen L, Jiang Y et al. (2005) Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Research 33: 6445-6458. (Pubitemid 41742581)
37. Shkoporov AN, Efimov BA, Khokhlova EV, Steele JL, Kafarskaia LI et al. (2008) Characterization of plasmids from human infant 〈i〉 Bifidobacterium〈/i〉 strains: Sequence analysis and construction of 〈i. E. coliΓÇôBifidobacterium〈/i〉 shuttle vectors. Plasmid 60: 136-148.
38. Zaleski P, Wolinowska R, Strzezek K, Lakomy A, Plucienniczak A (2006) The complete sequence and segregational stability analysis of a new cryptic plasmid pIGWZ12 from a clinical strain of Escherichia coli. Plasmid 56: 228-232. (Pubitemid 44646648)
39. Carattoli A (2009) Resistance plasmid families in Enterobacteriaceae. Antimicrobial agents and chemotherapy 53: 2227-2238.
40. Petersen J (2011) Phylogeny and compatibility: plasmid classification in the genomics era. Archives of microbiology 193: 313-321.
41. Polisky B (1988) ColE1 replication control circuitry: sense from antisense. Cell 55: 929-932.
42. Salyers AA, Shoemaker NB, Stevens AM, Li LY (1995) Conjugative transposons: an unusual and diverse set of integrated gene transfer elements. Microbiological reviews 59: 579-590.
43. Ochman H, Gerber AS, Hartl DL (1988) Genetic applications of an inverse polymerase chain reaction. Genetics 120: 621-623. (Pubitemid 18260496)
44. Minot S, Bryson A, Chehoud C, Wu GD, Lewis JD et al. (2013) Rapid evolution of the human gut virome. Proceedings of the National Academy of Sciences 110: 12450-12455.