Differences in rDNA libraries of faecal bacteria derived from 10- and 25-cycle PCRs
R. Bonnet, A. Suau, J. Dore, G. R. Gibson and M. D. Collins Laboratoire d'Ecologie et Physiologie du Systeme Digestif, Institut National de la Recherche Agronomique, 78352 Jouy-en-Josas cedex, France In spite of its shortcoming, analysis of PCR-derived rDNA libraries is being employed increasin...
Saved in:
Published in | International journal of systematic and evolutionary microbiology Vol. 52; no. 3; pp. 757 - 763 |
---|---|
Main Authors | , , , , |
Format | Journal Article |
Language | English |
Published |
England
Soc General Microbiol
01.05.2002
Microbiology Society |
Subjects | |
Online Access | Get full text |
Cover
Loading…
Summary: | R. Bonnet, A. Suau, J. Dore, G. R. Gibson and M. D. Collins
Laboratoire d'Ecologie et Physiologie du Systeme Digestif, Institut National de la Recherche Agronomique, 78352 Jouy-en-Josas cedex, France
In spite of its shortcoming, analysis of PCR-derived rDNA libraries is
being employed increasingly to investigate microbial diversity within many
ecosystems. In the present investigation, the effects of the number of PCR
cycles (10 vs 25 cycles) on the inferred structure of a 16S rDNA library
have been examined. Seventy-five 25-cycle sequences were retrieved and
analysed in comparison with 284 10-cycle sequences already described in a
previous study. The 359 clones obtained were classified into 94 molecular
species (at least 98% sequence similarity). At the level of large
phylogenetic groups, the two cloned rDNA libraries were not different. A
mathematical model was developed in order to estimate the number of
molecular species expected if further sequencing was performed.
Coverage-based computing, projections and statistical analysis demonstrated
that the structures of the two PCR-derived rDNA libraries were different
and that the 25-cycle rDNA library displayed reduced diversity. It is
suggested that the number of PCR cycles used for amplification of 16S rDNA
genes for phylogenetic diversity studies must therefore be kept as small as
possible. |
---|---|
Bibliography: | ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23 |
ISSN: | 1466-5026 1466-5034 |
DOI: | 10.1099/ijs.0.01755-0 |