Resolution of phenotypically distinct strains of Enterococcus spp. in a complex microbial community using cpn60 universal target sequencing

Microbial Ecology

Volumn 59, Issue 1, 2010, Pages 14-24

  Vermette, Catherine J ^a   Russell, Amanda H ^a   Desai, Atul R ^a   Hill, Janet E ^a  

^a UNIVERSITY OF SASKATCHEWAN   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; CHAPERONIN; RNA 16S;

ANIMAL; ARTICLE; BACTERIAL COUNT; CLASSIFICATION; DNA SEQUENCE; ENTEROCOCCUS; FECES; GENETICS; METABOLISM; MICROBIOLOGY; PHENOTYPE; PHYLOGENY; SWINE;

ANIMALS; CARBON; CHAPERONIN 60; COLONY COUNT, MICROBIAL; ENTEROCOCCUS; FECES; PHENOTYPE; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SWINE;

ANIMALIA; ENTEROCOCCUS; ENTEROCOCCUS FAECALIS; ENTEROCOCCUS HIRAE; SUIDAE;

EID: 74149088531     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-009-9601-1     Document Type: Article

References (40)

1. Aakra A, Nyquist OL, Snipen L, Reiersen TS, Nes IF (2007) Survey of genomic diversity among Enterococcus faecalis strains by microarray-based comparative genomic hybridization. Appl Environ Microbiol 73: 2207.
2. Acinas SG, Klepac-Ceraj V, Hunt DE, Pharino C, Ceraj I, Distel DL, Polz MF (2004) Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430: 551.
3. Acinas SG, Sarma-Rupavtarm R, Klepac-Ceraj V, Polz MF (2005) PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Environ Microbiol 71: 8966.
4. Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997) The complete genome sequence of Escherichia coli K-12. Science 277: 1453.
5. Brousseau R, Hill JE, Prefontaine G, Goh SH, Harel J, Hemmingsen SM (2001) Streptococcus suis serotypes characterized by analysis of chaperonin 60 gene sequences. Appl Environ Microbiol 67: 4828.
6. Cohan FM (2002) What are bacterial species? Annu Rev Microbiol 56: 457.
7. Devriese LA, Hommez J, Pot B, Haesebrouck F (1994) Identification and composition of the streptococcal and enterococcal flora of tonsils, intestines and faeces of pigs. J Appl Bacteriol 77: 31.
8. Devriese LA, Pot B, Collins MD (1993) Phenotypic identification of the genus Enterococcus and differentiation of phylogenetically distinct enterococcal species and species groups. J Appl Bacteriol 75: 399.
9. Dorsch M, Stackebrandt E (1992) Some modifications in the procedure of direct sequencing of PCR amplified 16S rDNA. J Microbiol Methods 16: 271.
10. Dumonceaux TJ, Hill JE, Hemmingsen SM, van Kessel AG (2006) Characterization of intestinal microbiota and response to dietary virginiamycin supplementation in the broiler chicken. Appl Environ Microbiol 72: 2815.
11. Dumonceaux TJ, Hill JE, Pelletier C, Paice MG, van Kessel AG, Hemmingsen SM (2006) Molecular characterization of microbial communities in Canadian pulp and paper activated sludge and quantification of a novel Thiothrix eikelboomii-like bulking filament. Can J Microbiol 52: 494.
12. Felsenstein J (1993) PHYLIP (Phylogeny Infererence Package) version 3. 5c, distributed by the author. Department of Genetics, University of Washington, Seattle.
13. Gans J, Wolinsky M, Dunbar J (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309: 1387.
14. Goh SH, Facklam RR, Chang M, Hill JE, Tyrrell GJ, Burns EC, Chan D, He C, Rahim T, Shaw C, Hemmingsen SM (2000) Identification of Enterococcus species and phenotypically similar Lactococcus and Vagococcus species by reverse checkerboard hybridization to chaperonin 60 gene sequences. J Clin Microbiol 38: 3953.
15. Hill JE, Goh SH, Money DM, Doyle M, Li A, Crosby WL, Links M, Leung A, Chan D, Hemmingsen SM (2005) Characterization of vaginal microflora of healthy, nonpregnant women by chaperonin-60 sequence-based methods. Am J Obstet Gynecol 193: 682.
16. Hill JE, Hemmingsen SM, Goldade BG, Dumonceaux TJ, Klassen J, Zijlstra RT, Goh SH, van Kessel AG (2005) Comparison of ileum microflora of pigs fed corn-, wheat-, or barley-based diets by chaperonin-60 sequencing and quantitative PCR. Appl Environ Microbiol 71: 867.
17. Hill JE, Paccagnella A, Law K, Melito PL, Woodward DL, Price DL, Ng L-K, Hemmingsen SM, Goh SH (2006) Identification of Campylobacter spp. and discrimination from Helicobacter and Arcobacter spp. by direct sequencing of PCR-amplified cpn60 sequences and comparison to cpnDB, a chaperonin reference sequence database. J Med Microbiol 55: 393.
18. Hill JE, Penny SL, Crowell KG, Goh SH, Hemmingsen SM (2004) cpnDB: a chaperonin sequence database. Genome Res 14: 1669.
19. Hill JE, Seipp RP, Betts M, Hawkins L, van Kessel AG, Crosby WL, Hemmingsen SM (2002) Extensive profiling of a complex microbial community by high-throughput sequencing. Appl Environ Microbiol 68: 3055.
20. Inoue R, Tsukahara T, Nakanishi N, Ushida K (2005) Development of the intestinal microbiota in the piglet. J Gen Appl Microbiol 51: 257.
21. Jian W, Zhu L, Dong X (2001) New approach to phylogenetic analysis of the genus Bifidobacterium based on partial HSP60 gene sequences. Int J Syst Evol Microbiol 51: 1633.
22. Jordan IK, Rogozin IB, Wolf YI, Koonin EV (2002) Microevolutionary genomics of bacteria. Theor Popul Biol 61: 435.
23. Kohara T, Hayashi S, Hamatsuka J, Nishitani Y, Masuda Y, Osawa R (2007) Intra-specific composition and succession of Bifidobacterium longum in human feces. Syst Appl Microbiol 30: 165.
24. Mackie RI, Sghir A, Gaskins HR (1999) Developmental microbial ecology of the neonatal gastrointestinal tract. Am J Clin Nutr 69: 1035S.
25. Maidak BL, Cole JR, Lilburn TG, Parker CT Jr, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM, Tiedje JM (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Res 29: 173.
26. Makarova KS, Koonin EV (2007) Evolutionary genomics of lactic acid bacteria. J Bacteriol 189: 1199.
27. McBride SM, Fischetti VA, Leblanc DJ, Moellering RC Jr, Gilmore MS (2007) Genetic diversity among Enterococcus faecalis. PLoS ONE 2: e582.
28. Minana-Galbis D, Urbizu-Serrano A, Farfan M, Fuste MC, Loren JG (2009) Phylogenetic analysis and identification of Aeromonas species based on sequencing of the cpn60 universal target. Int J Syst Evol Microbiol. doi: ijs. 0. 005413-005410.
29. Ott SJ, Musfeldt M, Wenderoth DF, Hampe J, Brant O, Folsch UR, Timmis KN, Schreiber S (2004) Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut 53: 685.
30. Paulsen IT, Banerjei L, Myers GS, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR, Heidelberg JF, Tettelin H, Dodson RJ, Umayam L, Brinkac L, Beanan M, Daugherty S, DeBoy RT, Durkin S, Kolonay J, Madupu R, Nelson W, Vamathevan J, Tran B, Upton J, Hansen T, Shetty J, Khouri H, Utterback T, Radune D, Ketchum KA, Dougherty BA, Fraser CM (2003) Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 299: 2071.
31. Perna NT, Plunkett G 3rd, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA, Posfai G, Hackett J, Klink S, Boutin A, Shao Y, Miller L, Grotbeck EJ, Davis NW, Lim A, Dimalanta ET, Potamousis KD, Apodaca J, Anantharaman TS, Lin J, Yen G, Schwartz DC, Welch RA, Blattner FR (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157: H7. Nature 409: 529.
32. Perriere G, Gouy M (1996) WWW-query: an on-line retrieval system for biological sequence banks. Biochimie 78: 364.
33. Pieper R, Janczyk P, Zeyner A, Smidt H, Guiard V, Souffrant WB (2008) Ecophysiology of the developing total bacterial and Lactobacillus communities in the terminal small intestine of weaning piglets. Microb Ecol 56: 474.
34. Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16: 276.
35. Savage DC (1977) Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol 31: 107.
36. Solheim M, Aakra A, Snipen LG, Brede DA, Nes IF (2009) Comparative genomics of Enterococcus faecalis from healthy Norwegian infants. BMC Genomics 10: 194.
37. Staden R, Beal KF, Bonfield JK (2000) The Staden package, 1998. Methods Mol Biol 132: 115.
38. Swords WE, Wu CC, Champlin FR, Buddington RK (1993) Postnatal changes in selected bacterial groups of the pig colonic microflora. Biol Neonate 63: 191.
39. Wall R, Fitzgerald G, Hussey S, Ryan T, Murphy B, Ross P, Stanton C (2007) Genomic diversity of cultivable Lactobacillus populations residing in the neonatal and adult gastrointestinal tract. FEMS Microbiol Ecol 59: 127.
40. Xu J (2006) Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Mol Ecol 15: 1713.