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| 1 | Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome显示文摘AIM:To design and validate broad-range 16S rRNA primers for use in high throughput sequencing to classify bacteria isolated from the human foregut microbiome.METHODS:A foregut microbiome dataset was constructed using 16S rRNA gene sequences obtained from oral,esophageal,and gastric microbiomes produced by Sanger sequencing in previous studies represented by 219 bacterial species.Candidate primers evaluated were from the European rRNA database.To assess the effect of sequence length on accuracy of classification,16S rRNA genes of various lengths were created by trimming the full length sequences.Sequences spanning various hypervariable regions were selected to simulate the amplicons that would be obtained using possible primer pairs.The sequences were compared with full length 16S rRNA genes for accuracy in taxonomic classification using online software at the Ribosomal Database Project (RDP).The universality of the primer set was evaluated using the RDP 16S rRNA database which is comprised of 433 306 16S rRNA genes,represented by 36 phyla.RESULTS:Truncation to 100 nucleotides(nt)downstream from the position corresponding to base 28 in the Escherichia coli 16S rRNA gene caused misclassification of 87(39.7%)of the 219 sequences,compared with misclassification of only 29(13.2%)sequences with truncation to 350 nt.Among 350-nt sequence reads within various regions of the 16S rRNA gene,the reverse read of an amplicon generated using the 343F/798R primers had the least(8.2%)effect on classification.In comparison,truncation to 900 nt mimicking single pass Sanger reads misclassified 5.0%of the 219 sequences.The 343F/798R amplicon accurately assigned 91.8%of the 219 sequences at the species level.Weighted by abundance of the species in the esophageal dataset,the 343F/798R amplicon yielded similar classification accuracy without a significant loss in species coverage(92%).Modification of the 343F/798R primers to 347F/803R increased their universality among foregut species.Assuming that a typicalpolymerase chain reaction can tolerate 2 mismatches between a primer and a template,the modified 347F and 803R primers should be able to anneal 98%and 99.6%of all 16S rRNA genes in the RDP database.CONCLUSION:347F/803R is the most suitable pair of primers for classification of foregut 16S rRNA genes but also possess universality suitable for analyses of other complex microbiomes. | Carlos W Nossa William E Oberdorf Jφrn A Aas Bruce J Paster Todd Z DeSantis Eoin L Brodie Daniel Malamud Michael A Poles Zhiheng Pei | 2010 | World Journal of Gastroenterology2010，16，33： | 16 |
| 2 | Monitoring surface and subsurface water storage using confined aquifer water levels at the Savannah River Site, USA 显示文摘 | Todd C Rasmussen Thomas L Mote | 2007 | Vadose Zone2007，6，2： | 1 |
| 3 | Extensive neurite out-growth and active synapse formation on self-assembling peptide scaffolds 显示文摘 | Todd C H Sonsoles L Xing S | 2000 | PNAS2000，97，12： | 1 |
| 4 | Delicious poisons: arsenic trioxide for the treatment of leukemia显示文摘 | Kwong Y L Todd D | 1997 | Blood1997，89，9： | 1 |
| 5 | Carbon cycle for rapeseed oil biodiesel fuels显示文摘 | Charles L Peterson Todd Hustrulid | 1998 | Biomass and bioenergy1998，14，： | 1 |
| 6 | Assessing IT usage the role of prior experience 显示文摘 | Taylor S Todd P L | 1995 | Management Information Systems Quarterly1995，19，4： | 1 |
| 7 | Guidelines for Conscious Sedation and Monitoring During Gastrointestinal Endoscopy显示文摘 | J.Patrick Waring Todd H Baron William K Hirota Jay L Goldstein Brian C Jacobson Jonathan A Leighton J.Shawn Mallery Douglas O Faigel | 2003 | Gastrointestinal Endoscopy2003，，3： | 1 |
| 8 | Chemical Characterization of an Antimicrobial Substance Produced by Lactobacillus reuteri 显示文摘 | Todd L Talarico Waiter J Dobrogosz | 1989 | Antimicrobial Agents and Chemotherapy1989，，5： | 1 |
| 9 | Relationship between wear rate,surface pullout and microstructure during abrasive wear of alumina and alumina/SiC nanocomposites显示文摘 | MERINO J O L TODD R I | 2005 | Acta Materialia2005，53，12： | 1 |
| 10 | Molecular basis for the herbicide resistance of roundup ready crops显示文摘 | Todd F Han H J Healy-Fried M L Fischer M Schnbrunn E | 2006 | Proceedings of the National Academy of Sciences of the United States of America2006，，13： | 1 |
| 11 | Evaporation measurements and predictions from soils under crop canopies显示文摘 | Klocke N L Martin D L Todd R W | 1990 | Transactions of the ASAE1990，33，5： | 1 |
| 12 | Network intrusion detection 显示文摘 | Biswanath M Todd L Karl N | 1994 | IEEE Network1994，8，3： | 1 |
| 13 | Regulation of transendothelial neutrophil migration by endogenous interleukin 8 显示文摘 | Huber A R Kunker S L Todd R F | 1991 | Science1991，254，： | 1 |
| 14 | Carbon cycle for rapeseed oil biodiesel fuels显示文摘 | CHARLES L P TODD H | 1998 | Biomass Bioenergy1998，14，2： | 1 |
| 15 | A novel Bragg grating sensor interrogation system utilizing a scanning filter, a Maeh-Zehnder interferometer and a 3 × 3 coupler 显示文摘 | TODD M D JOHNSON G A ALTHOUSE B L | 2001 | Measurement Science and Technology2001，12，7： | 1 |
| 16 | Network Intrusion Detection 显示文摘 | Biswanath M Todd L Karl N | 1994 | IEEE Network1994，8，3： | 1 |
| 17 | Comparative toxicology of monensin sodium in laboratory animals显示文摘 | Todd G C Novilla M N Howard L C | 1984 | J Anim Sci1984，59，6： | 1 |
| 18 | Assessing lake Okeechobee eutrophication with water-quality models 显示文摘 | JIN Kang-ren DANIEL P L TODD S T | 1998 | Journal of water resources planning and management1998，1，： | 1 |
| 19 | 查看详情显示文摘 | L A Overbey C C Olson M D Todd | | 0，，： | 1 |
| 20 | Nitrate Removal in Wetland Microcosms显示文摘 | Todd L Richardson C J Seidel K | 1998 | Water Res1998，32，3： | 1 |
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