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Applied and Environmental Microbiology, February 2003, p. 1251-1262, Vol. 69, No. 2
0099-2240/03/$08.00+0     DOI: 10.1128/AEM.69.2.1251-1262.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Application of New Primer-Enzyme Combinations to Terminal Restriction Fragment Length Polymorphism Profiling of Bacterial Populations in Human Feces

Koji Nagashima,1* Takayoshi Hisada,2 Maremi Sato,1 and Jun Mochizuki2

Hokkaido Food Processing Research Center, Ebetsu, Hokkaido 069-0836,1 Research Center, NCIMB Japan Co., Ltd., Orido, Shimizu-shi, Shizuoka 424-8610, Japan2

Received 22 July 2002/ Accepted 28 October 2002

New primer-enzyme combinations for terminal restriction fragment length polymorphism (T-RFLP) targeting of the 16S rRNA gene were constructed by using the T-RFLP analysis program (designated TAP T-RFLP) located at the Ribosomal Database Project website, and their performance was examined empirically. By using the fluorescently labeled 516f primer (Escherichia coli positions 516 to 532) and 1510r primer (positions 1510 to 1492), the 16S rRNA gene was amplified from human fecal DNA. The resulting amplified product was digested with RsaI plus BfaI or with BslI. When the T-RFLP was carried out with fecal DNAs from eight individuals, eight predominant operational taxonomic units (OTUs) were detected with RsaI and BfaI digestion and 14 predominant OTUs were detected with BslI digestion. The distribution of the OTUs was consistent with the results of the computer simulations with TAP T-RFLP. The T-RFLP analyses of the fecal DNAs from individuals gave characteristic profiles, while the variability of the T-RFLP profiles between duplicate DNA preparations from the same samples were minimal. This new T-RFLP method made it easy to predict what kind of intestinal bacterial group corresponded to each OTU on the basis of the terminal restriction fragment length compared with the conventional T-RFLP and, moreover, made it possible to identify the bacterial species that an OTU represents by cloning and sequencing.

* Corresponding author. Mailing address: Hokkaido Food Processing Research Center, 589-4 Bunkyodai Midorimachi, Ebetsu, Hokkaido 069-0836, Japan. Phone: 81-11-387-4125. Fax: 81-11-387-4664. E-mail: knagashima{at}foodhokkaido.gr.jp.

Applied and Environmental Microbiology, February 2003, p. 1251-1262, Vol. 69, No. 2
0099-2240/03/$08.00+0     DOI: 10.1128/AEM.69.2.1251-1262.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.



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