PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample.

@article{citeulike:556231, abstract = {The contribution of PCR artifacts to 16S rRNA gene sequence diversity from a complex bacterioplankton sample was estimated. Taq DNA polymerase errors were found to be the dominant sequence artifact but could be constrained by clustering the sequences into 99\% sequence similarity groups. Other artifacts (chimeras and heteroduplex molecules) were significantly reduced by employing modified amplification protocols. Surprisingly, no skew in sequence types was detected in the two libraries constructed from PCR products amplified for different numbers of cycles. Recommendations for modification of amplification protocols and for reporting diversity estimates at 99\% sequence similarity as a standard are given.}, address = {Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.}, author = {Acinas, S. G. and Sarma-Rupavtarm, R. and Klepac-Ceraj, V. and Polz, M. F. }, citeulike-article-id = {556231}, doi = {http://dx.doi.org/10.1128/AEM.71.12.8966-8969.2005}, issn = {0099-2240}, journal = {Appl Environ Microbiol}, keywords = {16s, indicators, validation}, month = {December}, number = {12}, pages = {8966--8969}, posted-at = {2008-04-30 20:04:53}, priority = {2}, title = {PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample.}, url = {http://dx.doi.org/10.1128/AEM.71.12.8966-8969.2005}, volume = {71}, year = {2005} }

TY - JOUR ID - citeulike:556231 L3 - citeulike-article-id:556231 N2 - The contribution of PCR artifacts to 16S rRNA gene sequence diversity from a complex bacterioplankton sample was estimated. Taq DNA polymerase errors were found to be the dominant sequence artifact but could be constrained by clustering the sequences into 99% sequence similarity groups. Other artifacts (chimeras and heteroduplex molecules) were significantly reduced by employing modified amplification protocols. Surprisingly, no skew in sequence types was detected in the two libraries constructed from PCR products amplified for different numbers of cycles. Recommendations for modification of amplification protocols and for reporting diversity estimates at 99% sequence similarity as a standard are given. IS - 12 JF - Appl Environ Microbiol SN - 0099-2240 AD - Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. EP - 8969 TI - PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. VL - 71 SP - 8966 KW - 16s KW - indicators KW - validation AU - Acinas, SG AU - Sarma-Rupavtarm, R AU - Klepac-Ceraj, V AU - Polz, MF PY - 2005/12// UR - http://dx.doi.org/10.1128/AEM.71.12.8966-8969.2005 ER -