Europe PMC

This website requires cookies, and the limited processing of your personal data in order to function. By using the site you are agreeing to this as outlined in our privacy notice and cookie policy.

16S ribosomal DNA amplification for phylogenetic study.

Author information

Affiliations

  • 1. GENE-TRAK Systems, Framingham, Massachusetts 01701.
      Authors
    • Weisburg WG 1
    (1 author)

ORCIDs linked to this article

Journal of Bacteriology, 01 Jan 1991, 173(2):697-703
https://doi.org/10.1128/jb.173.2.697-703.1991 PMID: 1987160 PMCID: PMC207061

Free full text in Europe PMC

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.

Free full text 

Logo of jbacterLink to Publisher's site
J Bacteriol. 1991 Jan; 173(2): 697–703.
PMCID: PMC207061
PMID: 1987160

16S ribosomal DNA amplification for phylogenetic study.

W G Weisburg, S M Barns, D A Pelletier, and D J Lane
Author information Copyright and License information Disclaimer

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.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.3M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.
 
icon of scanned page 697
697
icon of scanned page 698
698
icon of scanned page 699
699
icon of scanned page 700
700
icon of scanned page 701
701
icon of scanned page 702
702
icon of scanned page 703
703
 

Images in this article

Image
Image
on p.701
Click on the image to see a larger version.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Biggin MD, Gibson TJ, Hong GF. Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci U S A. 1983 Jul;80(13):3963–3965. [Europe PMC free article] [Abstract] [Google Scholar]
  • Birnboim HC, Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. [Europe PMC free article] [Abstract] [Google Scholar]
  • Brosius J, Palmer ML, Kennedy PJ, Noller HF. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A. 1978 Oct;75(10):4801–4805. [Europe PMC free article] [Abstract] [Google Scholar]
  • Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res. 1989 Oct 11;17(19):7843–7853. [Europe PMC free article] [Abstract] [Google Scholar]
  • Fox GE, Stackebrandt E, Hespell RB, Gibson J, Maniloff J, Dyer TA, Wolfe RS, Balch WE, Tanner RS, Magrum LJ, et al. The phylogeny of prokaryotes. Science. 1980 Jul 25;209(4455):457–463. [Abstract] [Google Scholar]
  • Gutell RR, Weiser B, Woese CR, Noller HF. Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol. 1985;32:155–216. [Abstract] [Google Scholar]
  • Kenerley ME, Morgan EA, Post L, Lindahl L, Nomura M. Characterization of hybrid plasmids carrying individual ribosomal ribonucleic acid transcription units of Escherichia coli. J Bacteriol. 1977 Dec;132(3):931–949. [Europe PMC free article] [Abstract] [Google Scholar]
  • Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985 Oct;82(20):6955–6959. [Europe PMC free article] [Abstract] [Google Scholar]
  • Medlin L, Elwood HJ, Stickel S, Sogin ML. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene. 1988 Nov 30;71(2):491–499. [Abstract] [Google Scholar]
  • Rossau R, Heyndrickx L, Van Heuverswyn H. Nucleotide sequence of a 16S ribosomal RNA gene from Neisseria gonorrhoeae. Nucleic Acids Res. 1988 Jul 11;16(13):6227–6227. [Europe PMC free article] [Abstract] [Google Scholar]
  • Weisburg WG, Dobson ME, Samuel JE, Dasch GA, Mallavia LP, Baca O, Mandelco L, Sechrest JE, Weiss E, Woese CR. Phylogenetic diversity of the Rickettsiae. J Bacteriol. 1989 Aug;171(8):4202–4206. [Europe PMC free article] [Abstract] [Google Scholar]
  • Weisburg WG, Oyaizu Y, Oyaizu H, Woese CR. Natural relationship between bacteroides and flavobacteria. J Bacteriol. 1985 Oct;164(1):230–236. [Europe PMC free article] [Abstract] [Google Scholar]
  • Weisburg WG, Woese CR, Dobson ME, Weiss E. A common origin of rickettsiae and certain plant pathogens. Science. 1985 Nov 1;230(4725):556–558. [Abstract] [Google Scholar]
  • Weiss E, Williams JC, Dasch GA, Kang YH. Energy metabolism of monocytic Ehrlichia. Proc Natl Acad Sci U S A. 1989 Mar;86(5):1674–1678. [Europe PMC free article] [Abstract] [Google Scholar]
  • Woese CR. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221–271. [Europe PMC free article] [Abstract] [Google Scholar]
  • Woese CR, Gutell R, Gupta R, Noller HF. Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol Rev. 1983 Dec;47(4):621–669. [Europe PMC free article] [Abstract] [Google Scholar]
Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

Full text links 

Read article at publisher's site: https://doi.org/10.1128/jb.173.2.697-703.1991

Read article for free, from open access legal sources, via Unpaywall: https://europepmc.org/articles/pmc207061?pdf=renderUnpaywall

Free to read at jb.asm.org
http://jb.asm.org/cgi/content/abstract/173/2/697

Free after 4 months at jb.asm.org
http://jb.asm.org/cgi/reprint/173/2/697

Citations & impact 

Impact metrics

5,144
Citations
Jump to Citations
2
Data citations
Jump to Data

Citations of article over time

Alternative metrics

Altmetric item for https://www.altmetric.com/details/1344468
Altmetric
Discover the attention surrounding your research
https://www.altmetric.com/details/1344468

Smart citations by scite.ai
Smart citations by scite.ai include citation statements extracted from the full text of the citing article. The number of the statements may be higher than the number of citations provided by EuropePMC if one paper cites another multiple times or lower if scite has not yet processed some of the citing articles.
Explore citation contexts and check if this article has been supported or disputed.
https://scite.ai/reports/10.1128/jb.173.2.697-703.1991

Supporting
Mentioning
Contrasting
21
5998
0

Article citations

Go to all (5,144) article citations

Other citations

Data 

Similar Articles 

To arrive at the top five similar articles we use a word-weighted algorithm to compare words from the Title and Abstract of each citation.