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J Bacteriol. 1991 January; 173(2): 697-703

research-article

16S ribosomal DNA amplification for phylogenetic study.

W G Weisburg, S M Barns, D A Pelletier and D J Lane

GENE-TRAK Systems, Framingham, Massachusetts 01701.

ABSTRACT

A set of oligonucleotide primers capable of initiating enzymatic amplification (polymerase chain reaction) on a phylogenetically and taxonomically wide range of bacteria is described along with methods for their use and examples. One pair of primers is capable of amplifying nearly full-length 16S ribosomal DNA (rDNA) from many bacterial genera; the additional primers are useful for various exceptional sequences. Methods for purification of amplified material, direct sequencing, cloning, sequencing, and transcription are outlined. An obligate intracellular parasite of bovine erythrocytes, Anaplasma marginale, is used as an example; its 16S rDNA was amplified, cloned, sequenced, and phylogenetically placed. Anaplasmas are related to the genera Rickettsia and Ehrlichia. In addition, 16S rDNAs from several species were readily amplified from material found in lyophilized ampoules from the American Type Culture Collection. By use of this method, the phylogenetic study of extremely fastidious or highly pathogenic bacterial species can be carried out without the need to culture them. In theory, any gene segment for which polymerase chain reaction primer design is possible can be derived from a readily obtainable lyophilized bacterial culture.

J Bacteriol. 1991 January; 173(2): 697-703




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  • Manh, H. D., Matsuo, Y., Katsuta, A., Matsuda, S., Shizuri, Y., Kasai, H. (2008). Robiginitalea myxolifaciens sp. nov., a novel myxol-producing bacterium isolated from marine sediment, and emended description of the genus Robiginitalea. Int. J. Syst. Evol. Microbiol. 58: 1660-1664 [Abstract] [Full Text]  
  • Scott, K. P., Martin, J. C., Mrazek, J., Flint, H. J. (2008). Transfer of Conjugative Elements from Rumen and Human Firmicutes Bacteria to Roseburia inulinivorans. Appl. Environ. Microbiol. 74: 3915-3917 [Abstract] [Full Text]  
  • Mazzon, L., Piscedda, A., Simonato, M., Martinez-Sanudo, I., Squartini, A., Girolami, V. (2008). Presence of specific symbiotic bacteria in flies of the subfamily Tephritinae (Diptera Tephritidae) and their phylogenetic relationships: proposal of 'Candidatus Stammerula tephritidis'. Int. J. Syst. Evol. Microbiol. 58: 1277-1287 [Abstract] [Full Text]  
  • Weon, H.-Y., Kim, B.-Y., Son, J.-A, Jang, H. B., Hong, S. K., Go, S.-J., Kwon, S.-W. (2008). Massilia aerilata sp. nov., isolated from an air sample. Int. J. Syst. Evol. Microbiol. 58: 1422-1425 [Abstract] [Full Text]  
  • Kim, M. K., Kim, Y.-A., Park, M.-J., Yang, D.-C. (2008). Paenibacillus ginsengihumi sp. nov., a bacterium isolated from soil in a ginseng field. Int. J. Syst. Evol. Microbiol. 58: 1164-1168 [Abstract] [Full Text]  
  • Kulichevskaya, I. S., Ivanova, A. O., Baulina, O. I., Bodelier, P. L. E., Damste, J. S. S., Dedysh, S. N. (2008). Singulisphaera acidiphila gen. nov., sp. nov., a non-filamentous, Isosphaera-like planctomycete from acidic northern wetlands. Int. J. Syst. Evol. Microbiol. 58: 1186-1193 [Abstract] [Full Text]  
  • Chhour, K.-L., Hinds, L. A., Deane, E. M., Jacques, N. A. (2008). The microbiome of the cloacal openings of the urogenital and anal tracts of the tammar wallaby, Macropus eugenii. Microbiology 154: 1535-1543 [Abstract] [Full Text]  
  • Coudeyras, S., Marchandin, H., Fajon, C., Forestier, C. (2008). Taxonomic and Strain-Specific Identification of the Probiotic Strain Lactobacillus rhamnosus 35 within the Lactobacillus casei Group. Appl. Environ. Microbiol. 74: 2679-2689 [Abstract] [Full Text]  
  • Frank, J. A., Reich, C. I., Sharma, S., Weisbaum, J. S., Wilson, B. A., Olsen, G. J. (2008). Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes. Appl. Environ. Microbiol. 74: 2461-2470 [Abstract] [Full Text]  
  • Bouchet, V., Huot, H., Goldstein, R. (2008). Molecular Genetic Basis of Ribotyping. Clin. Microbiol. Rev. 21: 262-273 [Abstract] [Full Text]  
  • Leclerque, A., Kleespies, R. G. (2008). 16S rRNA-, GroEL- and MucZ-based assessment of the taxonomic position of 'Rickettsiella melolonthae' and its implications for the organization of the genus Rickettsiella. Int. J. Syst. Evol. Microbiol. 58: 749-755 [Abstract] [Full Text]  
  • Merhej, V., Adekambi, T., Pagnier, I., Raoult, D., Drancourt, M. (2008). Yersinia massiliensis sp. nov., isolated from fresh water. Int. J. Syst. Evol. Microbiol. 58: 779-784 [Abstract] [Full Text]  
  • Sakai, S., Imachi, H., Hanada, S., Ohashi, A., Harada, H., Kamagata, Y. (2008). Methanocella paludicola gen. nov., sp. nov., a methane-producing archaeon, the first isolate of the lineage 'Rice Cluster I', and proposal of the new archaeal order Methanocellales ord. nov.. Int. J. Syst. Evol. Microbiol. 58: 929-936 [Abstract] [Full Text]  
  • Yoon, J., Matsuo, Y., Kasai, H., Yokota, A. (2008). Limibacter armeniacum gen. nov., sp. nov., a novel representative of the family 'Flammeovirgaceae' isolated from marine sediment. Int. J. Syst. Evol. Microbiol. 58: 982-986 [Abstract] [Full Text]  
  • Yoon, J., Matsuo, Y., Matsuda, S., Adachi, K., Kasai, H., Yokota, A. (2008). Rubritalea sabuli sp. nov., a carotenoid- and squalene-producing member of the family Verrucomicrobiaceae, isolated from marine sediment. Int. J. Syst. Evol. Microbiol. 58: 992-997 [Abstract] [Full Text]  
  • Yoon, J., Matsuo, Y., Adachi, K., Nozawa, M., Matsuda, S., Kasai, H., Yokota, A. (2008). Description of Persicirhabdus sediminis gen. nov., sp. nov., Roseibacillus ishigakijimensis gen. nov., sp. nov., Roseibacillus ponti sp. nov., Roseibacillus persicicus sp. nov., Luteolibacter pohnpeiensis gen. nov., sp. nov. and Luteolibacter algae sp. nov., six marine members of the phylum 'Verrucomicrobia', and emended descriptions of the class Verrucomicrobiae, the order Verrucomicrobiales and the family Verrucomicrobiaceae. Int. J. Syst. Evol. Microbiol. 58: 998-1007 [Abstract] [Full Text]  
  • Qiu, Y.-L., Hanada, S., Ohashi, A., Harada, H., Kamagata, Y., Sekiguchi, Y. (2008). Syntrophorhabdus aromaticivorans gen. nov., sp. nov., the First Cultured Anaerobe Capable of Degrading Phenol to Acetate in Obligate Syntrophic Associations with a Hydrogenotrophic Methanogen. Appl. Environ. Microbiol. 74: 2051-2058 [Abstract] [Full Text]  
  • Kim, M. K., Pulla, R. K., Kim, S.-Y., Yi, T.-H., Soung, N.-K., Yang, D.-C. (2008). Sanguibacter soli sp. nov., isolated from soil of a ginseng field. Int. J. Syst. Evol. Microbiol. 58: 538-541 [Abstract] [Full Text]  
  • Lim, J. H., Baek, S.-H., Lee, S.-T. (2008). Burkholderia sediminicola sp. nov., isolated from freshwater sediment. Int. J. Syst. Evol. Microbiol. 58: 565-569 [Abstract] [Full Text]  
  • Roux, V., Fenner, L., Raoult, D. (2008). Paenibacillus provencensis sp. nov., isolated from human cerebrospinal fluid, and Paenibacillus urinalis sp. nov., isolated from human urine. Int. J. Syst. Evol. Microbiol. 58: 682-687 [Abstract] [Full Text]  
  • Rodrigues, J. L. M., Duffy, M. A., Tessier, A. J., Ebert, D., Mouton, L., Schmidt, T. M. (2008). Phylogenetic Characterization and Prevalence of "Spirobacillus cienkowskii," a Red-Pigmented, Spiral-Shaped Bacterial Pathogen of Freshwater Daphnia Species. Appl. Environ. Microbiol. 74: 1575-1582 [Abstract] [Full Text]  
  • Kim, M. K., Kim, Y.-A., Kim, Y.-J., Soung, N.-K., Yi, T.-H., Kim, S.-Y., Yang, D.-C. (2008). Parapedobacter soli sp. nov., isolated from soil of a ginseng field. Int. J. Syst. Evol. Microbiol. 58: 337-340 [Abstract] [Full Text]  


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