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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 | 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 |
| 3 | Horizontal well IPR calculation显示文摘 | THOMS L K TODD B J EVANS C E | 1998 | SPE Reservoir Evaluation & Engineering1998，1，39： | 1 |
| 4 | Earnings Functions and Rates of Return显示文摘 | Heckman J J L J Lochner and P E Todd | 2008 | Journal of Human Capital2008，，2： | 1 |
| 5 | Evaluation of Salmonella antisera for an optimum enzyme-linked antibody de- tection of Salmonella using hydrophobic grid membrane filters 显示文摘 | Todd E C D Mackenzie J M Parrington L J | 1991 | Food Microbiology1991，8，4： | 1 |
| 6 | A remote irrigation monitoring and control system for continuous move systems显示文摘 | JOSé L C FRANcis J P TODD V E | 2010 | PrecisionAgriculture2010，11，1： | 1 |
| 7 | Application of biological data in cancer risk estimations of chlordane and heptachlor 显示文摘 | ADESHINA F TODD E L | 1991 | Regul Toxicol Pharmacol1991，14，1： | 1 |
| 8 | Influence of wetland networks on bat activity in mixed-use landscapes显示文摘 | Todd R L Andrew J E Katharina A M E | 2010 | Biological Conservation2010，14，4： | 1 |
| 9 | The perception of human growth 显示文摘 | Todd J T Mark L S Shaw R E | 1980 | Scientific American Perception1980，242，： | 1 |
| 10 | Mechanism of Cu sorption onto iron oxides:results from sorption isotherms and spectroscopy显示文摘 | Peacock C L Sherman D M Todd E | 2000 | Journal of Conference Abstract2000，5，： | 1 |
| 11 | Glucose metabolism in the amygdala in depression: Relationship to diagnostic subtype and plasma cortisol levels显示文摘 | Wayne C Drevets Joseph L Price Mark E Bardgett Theodore Reich Richard D Todd Marcus E Raichle | 2002 | Pharmacology Biochemistry and Behavior2002，，3： | 1 |
| 12 | Superparamagnetic iron oxide:Clinical application as a contrast agent for MR imaging of the liver 显示文摘 | Stark D D Weissleder R Elizondo G Hahn P F Saini S Todd L E Wittenberg J Ferrucci J T | 1988 | Radiology1988，168，2： | 1 |
| 13 | Characterization of novel circovirus DNAs associated with wasting syndromes in pigs显示文摘 | Meehan B M McNeilly F Todd D Kennedy S Jewhurst V A Ellis J A Hassard L E Clark E G Haines D M Allan G M | 1998 | J Gen Virol1998，79，9： | 1 |
| 14 | Evidence for variable selective pressures at MCIR显示文摘 | Harding R M Healy E Ray A J Ellis N S Flanagan N Todd C Dixon C Sa]antila A Jackson I J Birch-Machin MA Rees J L | 2000 | Am J Hum Genet2000，66，： | 1 |
| 15 | The perception of human growth显示文摘 | TODD J T MARK L S SHAW R E | 1980 | Scientific American1980，242，2： | 1 |
| 16 | Targeted disruption of the α1,3-galactosytransferase gene in cloned pigs显示文摘 | Todd D V Jeremy B Shu-Hung Chen Carol J P Suyapa B Jeff A M Peter M J Kenneth J M Ashley E Lamborn Jamie L Cowell-Lucero Kevin D W Alan C Irina A P David L A | 2002 | Nat Biotechnology2002，20，3： | 1 |
| 17 | Waterborne nutrient budgets for the riparian zone of an agricultural watershed 显示文摘 | Lowrance R R Todd R L Asmussen L E | 1983 | Agriculture Ecosystems & Environment1983，10，： | 1 |
| 18 | Transfer of Listeria monocytogenes during mechanical slicing of turkey breast, bologna, and salami 显示文摘 | Vorst K L Todd E C D Ryser E T | 2006 | Journal of Food Protection2006，69，3： | 1 |
| 19 | Percutaneous Reduction and Fixation of Displaced Intra-Articular Calcaneus Fractures显示文摘 | Matthew DeWall Christopher E Henderson Todd O McKinley Thomas Phelps Lori Dolan J L Marsh | 2010 | Journal of Orthopaedic Trauma2010，，8： | 1 |
| 20 | Effects of ingestion of a biotin - binding protein on adult and larval honey bees 显示文摘 | Malone L A Tregidga E L Todd J H | 2002 | Apidologie2002，33，： | 1 |
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