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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 | Development of surface area and pore structure for activation of anthracite coal 显示文摘 | JOHN W Z MICHAEL R V | 2007 | Fuel Processing Technology2007，88，： | 1 |
| 3 | Genetic Analysis of Pre-harvest Sprouting Resistance in a Wheat显示文摘 | Silvia Z Michael W Martin K | 2000 | Spelt2000，40，： | 1 |
| 4 | Processing color and complex data using mathematical morphology 显示文摘 | MATT W MICHAEL A Z | 2000 | IEEE2000，，10： | 1 |
| 5 | Intertfirm networks and entrepreneurial behavior:A structural embeddedness perspective显示文摘 | Simsek Z Michael H Lubatkin Steven W Floyd | 2003 | Journal of Management2003，29，3： | 1 |
| 6 | 显示文摘 | Michael J Z | 1992 | J Chem Soc Chem Commun1992，，13： | 1 |
| 7 | Extented-aperture Underwa-ter Acoustic Multisource Azimuth/elevation Direction-fioding Using Uniformly but Sparsely Spaced Vector Hy-drophones显示文摘 | Kainam T W Michaell D Z | 1997 | IEEE Oceanic Engineering1997，22，4： | 1 |
| 8 | Risk-sensitive dynamic pricing for a single perishable product 显示文摘 | Li Michael Z F Zhuang W F | 2009 | Operations Research Letters2009，37，5： | 1 |
| 9 | Soil health and sustainability: managing the biotic component of soil quality显示文摘 | John W D Michael R Z | 2000 | Applied Soil Ecology2000，15，1： | 1 |
| 10 | Proaetive planning for catastrophic events in supply chains 显示文摘 | KNEMEYER A MICHAEL W Z CUNEYT E | 2009 | Jour- nal of Operations Management2009，27，2： | 1 |
| 11 | An Injectable Calcium Phosphate-alginate Hydrogel-umbilical Cord Mesenchymal Stem Cell Paste for Bone Tissue Engineering显示文摘 | Liang Z Michael D W Hockin H K | | 0，，25： | 1 |
| 12 | New molecular insights into the mechanisms of cholestasis显示文摘 | Martin W Gernot Z Michael T | 2009 | Hepato2009，51，3： | 1 |
| 13 | et al Genetic susceptibility to diabetic nephropathy in IDDM is related to polymorphism in the endothelial nitric oxide synthase (eNOS) gene显示文摘 | Anne Z Michael W Dariusz KM | 1998 | Diabetes1998，47，1： | 1 |
| 14 | The value of washers in cannulated screw fixation of femoral neck fractures显示文摘 | Michael Z Brad W Brad P | 2005 | J Trauma2005，59，4： | 1 |
| 15 | Market transition, government policies, and interprovincial migration in China: 1983--1988显示文摘 | Liang Z Michael J W | 1997 | Economic Development and Cultural Change1997，，7： | 1 |
| 16 | Synthesis of micro or nanoerystalline diamond films on WC-Co substrates withvarious pretreatments by hot ilia-ment chemical vapor deposition 显示文摘 | Qiu P W Yu Z M Michael N R Ashfold Ye J Ma L | 2010 | Applied Surface Science2010，256，13： | 1 |
| 17 | Hypoxic enchanement of exosome release by breast cancer cells 显示文摘 | KING H W MICHAEL M Z GLEADLE J M | 2012 | BMC Cancer2012，12，： | 1 |
| 18 | On the formation of very large WC crystals during sintering of ultrafine WC-Co alloys显示文摘 | MICHAEL S SCHUBERT W D ERICH Z | 2002 | International Journal of Refractory Metals and Hard Materials2002，20，1： | 1 |
| 19 | The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus ) 显示文摘 | MING R HOU S B FENG Y YU Q Y DIONNE-LAPORTE A SAW J H SENIN P WANG W LY B V LEWIS K L T SALZBERG S L FENG L JONES M R SKELTON R L MURRAY J E CHEN C X QIAN W B SHEN J G DU P EUSTICE M TONG E TANG H B LYONS E PAULL R E MICHAEL T P WALL K RICE D W AL- BERT H WANG M L ZHU Y J SCHATZ M NAGARAJAN N A- COB R A GUAN P Z BLAS A WAI C M ACKERMAN C M REN Y LIU C WANG J M WANG J P NA J K SHAKIROV E V HAAS B THIMMAPURAM J NELSON D WANG X Y BOWERS J E GSCHWEND A R DELCHER A L SINGH R SUZUKI J Y TRI- PATHI S NEUPANE K WEI H R IRIKURA B PAIDI M JIANG N ZHANG W L PRESTING G WINDSOR A NAVAJAS-P?REZ R TORRES M J FELTUS F A PORTER B LI Y J BURROUGHS A M LUO M C LIU L CHRISTOPHER D A MOUNT S M MOORE P H SUGIMURA T JIANG J M SCHULER M A FRIEDMAN V MITCHELL-OLDS T SHIPPEN D E DEPAMPHILIS C W PALMER J D FREELING M PATERSON A H GONSALVES D WANG L ALAM M | 2008 | Nature2008，452，7190： | 1 |
| 20 | Integration of the Global Positioning System and Geographical Information Systems for Traffic Congestion Studies显示文摘 | Michael A P Jeremy E W Rocco Z | 2000 | Transportation Research Part C:Emerging Technologies2000，8，6： | 1 |
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