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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 | The valence change from RE3+ (RE=Eu,Sm,Yb) in SrB4O7:RE prepared in air and the spectral properties of RE2+显示文摘 | PEI Z W SU Q ZHANG J Y | 1993 | Journal of Alloys and Compound1993，198，： | 2 |
| 3 | The reduction of RE3+ in SrB6O2 prepared in air and the luminescence of∶RE2+(RE=Eu,Sm,Tm) 显示文摘 | Zheng Q H Pei Z W WANG S B | 1999 | Spectroscopy Letters1999，32，6： | 2 |
| 4 | The properties of high-resolution range profiles显示文摘 | Xing M D Bao Z Pei B N | 2002 | Optical Engineering2002，41，2： | 2 |
| 5 | Retail services and firm profit in a dualchannel market 显示文摘 | Yan R Pei Z | 2009 | Journal of Retailing and Consumer Services2009，，4： | 1 |
| 6 | Effective Wipe Detection in MPEG Compressed Video Using Macro Block Type Information 显示文摘 | Pei S C Chou Y Z | 2002 | IEEE Trans on Multimedia2002，4，3： | 1 |
| 7 | On the topological properties of fuzzy rough sets显示文摘 | Qin K Pei Z | 2005 | Fuzzy Sets and Systems2005，151，3： | 1 |
| 8 | Conjugate heat and mass transfer in membrane-formed channels in all entry regions显示文摘 | Zhang L Z Liang C H Pei L X | 2010 | International Journal of Heat and Mass Transfer2010，53，56： | 1 |
| 9 | Rotary Ultrasonic Machining of Structural Ceramics-A Review显示文摘 | Pei Z J Khanna N Ferreira P M | 1995 | Ceramic Engineering and Science Proceedings1995，，16： | 1 |
| 10 | Magnetic and electric bulge-test instrument for the determina- tion of coupling mechanical properties of functional free-standing films and flexible electronics显示文摘 | Yu Z Mao W Li F Feng X Pei Y Fang D | 2014 | Review of Scientific Instrument s2014，85，06： | 1 |
| 11 | Preparation of silicon carbide nanotubes by hydrothermal method显示文摘 | Pei L Z Tang Y H Chen Y W | 2006 | J Appl Phys2006，99，11： | 1 |
| 12 | Grinding of Silicon Wafers: a Review from Historical Perspectives 显示文摘 | Pei Z J Fisher G R Liu J | 2008 | International Journal of Machine Tools and Manufacture2008，48，： | 1 |
| 13 | Investigation on the electrical properties and inhomogeneous distribution of ZnO: Al thin films prepared by dc magnetron sputtering at low deposition temperature显示文摘 | Zhang X B Pei Z L Gong J | 2007 | Journal of Applied Physics2007，101，01： | 1 |
| 14 | Low Temperature Growth and Characterizations of Single Crystalline CuGeO3 Nanowires 显示文摘 | Pei L Z Zhao H S Tan W | 2009 | Cost Eng Comm2009，11，7： | 1 |
| 15 | ELID grinding of silicon wa- fers: A literature review 显示文摘 | Liu J H Pei Z J Fisher G R | 2007 | Int J Mach Tools Manuf2007，47，34： | 1 |
| 16 | Plastic flow in rotary ultrasonic machining of ceramics显示文摘 | Pei Z J Ferreira P M Haselkorn M | 1995 | Journal of Materials Processing Technology1995，48，14： | 1 |
| 17 | Alan Strasbaugh, grinding induced subsurface crack in silicon wafers显示文摘 | Z J Pei | | 0，，： | 1 |
| 18 | Efficient MPEG compressed video analysis using macroblock type information 显示文摘 | Pei S C Chou Y Z | 1999 | IEEE Transactions on Multimedia1999，1，4： | 1 |
| 19 | Preparation of copper germanate nanowires with good electrochemical sensing proper ties显示文摘 | PEI L Z WANG J F YANG L J etal | 2011 | Crystal Research and Technology2011，46，1： | 1 |
| 20 | Application of ENVISAT ASAR data in mapping rice crop growth in Southern China显示文摘 | Chen C Lin H Pei Z | 2007 | IEEE Geoscience and Remote Sensing Letters2007，4，： | 1 |
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