Improved template representation in cpn 60 polymerase chain reaction (PCR) product libraries generated from complex templates by application of a specific mixture of PCR primers

Environmental Microbiology

Volumn 8, Issue 4, 2006, Pages 741-746

  Hill, Janet E ^a   Town, Jennifer R ^a   Hemmingsen, Sean M ^a  

^a NATIONAL RESEARCH COUNCIL CANADA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; CHAPERONIN; PRIMER DNA; RIBOSOME DNA; RNA 16S;

ARTICLE; BACTERIUM; CLASSIFICATION; ENZYMOLOGY; GENE LIBRARY; GENETICS; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION;

BACTERIA; BASE SEQUENCE; CHAPERONIN 60; DNA PRIMERS; DNA, RIBOSOMAL; GENE LIBRARY; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S;

ACTINOBACTERIA;

EID: 33644840902     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2005.00944.x     Document Type: Article

References (19)

1. Benno Y. Endo K. Suzuki K. Mitsuoka T. Namioka S. 1985 Use of nonprotein nitrogen in pigs: effects of dietary urea on the intestinal microflora Am J Vet Res 46 959 962
2. 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 4833
3. Dumonceaux TJ. Hill JE. Briggs SA. Amoako KK. Hemmingsen SM. Van Kessel AG. 2005 Enumeration of specific bacterial populations in complex intestinal communities using quantitative PCR based on the chaperonin-60 target J Microbiol Methods in press ). Aug 18 [Epub ahead of print].
4. Goh SH. Potter S. Wood JO. Hemmingsen SM. Reynolds RP. Chow AW. 1996 HSP60 gene sequences as universal targets for microbial species identification: studies with coagulase-negative staphylococci J Clin Microbiol 34 818 823
5. Goh SH. Santucci Z. Kloos WE. Faltyn M. George CG. Driedger D. Hemmingsen SM. 1997 Identification of Staphylococcus species and subspecies by the chaperonin 60 gene identification method and reverse checkerboard hybridization J Clin Microbiol 35 3116 3121
6. Goh SH. Facklam RR. Chang M. Hill JE. Tyrrell GJ. Burns EC. et al. 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 3959
7. Hartemink R. Rombouts FM. 1999 Comparison of media for the detection of bifidobacteria, lactobacilli and total anaerobes from faecal samples J Microbiol Methods 36 181 192
8. 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 3066
9. Hill JE. Penny SL. Crowell KG. Goh SH. Hemmingsen SM. 2004 cpnDB: a chaperonin sequence database Genome Res 14 1669 1675
10. Hill JE. Goh SH. Money DM. Doyle M. Li A. Crosby WL. et al. 2005a Characterization of vaginal microflora of healthy, non-pregnant women by chaperonin-60 sequence-based methods Am J Obstet Gynecol 193 682 692
11. Hill JE. Hemmingsen SM. Goldade BG. Dumonceaux TJ. Klassen J. Zijlstra RT. et al. 2005b Comparison of ileum microflora of pigs fed corn-, wheat-, or barley-based diets by chaperonin-60 sequencing and quantitative PCR Appl Environ Microbiol 71 867 875
12. 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 1638
13. Kawase Y. Iwai S. Inoue H. Miura K. Ohtsuka E. 1986 Studies on nucleic acid interactions. I. Stabilities of mini-duplexes (dG2A4XA4G2-dC2T4YT4C2) and self-complementary d (GGGAAXYTTCCC) containing deoxyinosine and other mismatched bases Nucleic Acids Res 14 7727 7736
14. Martin FH. Castro MM. boul-ela F. Tinoco I. Jr 1985 Base pairing involving deoxyinosine: implications for probe design Nucleic Acids Res 13 8927 8938
15. Staley JT. Konopka A. 1985 Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats Annu Rev Microbiol 39 321 346
16. Suau A. Bonnet R. Sutren M. Godon JJ. Gibson GR. Collins MD. Dore J. 1999 Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut Appl Environ Microbiol 65 4799 4807
17. Thompson JR. Pacocha S. Pharino C. Klepac-Ceraj V. Hunt DE. Benoit J. et al. 2005 Genotypic diversity within a natural coastal bacterioplankton population Science 307 1311 1313
18. Varadaraj K. Skinner DM. 1994 Denaturants or cosolvents improve the specificity of PCR amplification of a G+C-rich DNA using genetically engineered DNA polymerases Gene 140 1 5
19. Wilson KH. Blitchington RB. 1996 Human colonic biota studied by ribosomal DNA sequence analysis Appl Environ Microbiol 62 2273 2278