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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 | Cyclophotocoagulation: a report by the American Academy of Ophthalmology 显示文摘 | Paster SA Singh K Lee Da | 2001 | Ophthalmologica2001，108，11： | 2 |
| 3 | Molecular analysis of bac- terial species associated with childhood caries显示文摘 | Becker MR Paster BJ Leys EJ | 2002 | J Clin Microbiol2002，40，3： | 1 |
| 4 | Proliferative vitreoretinopathy:an overview显示文摘 | Paster JC | 1998 | Sur Ophthalmology1998，43，： | 1 |
| 5 | Behavioral inhibition and activation dimensions:relationship to MMPI-2 indices of personality disorder显示文摘 | Paster MC Ross SR Segarra P | | 0，，： | 1 |
| 6 | Bacterial diversity in human subgingival plaque显示文摘 | Paster B J Boches SK Galvin JL | 2001 | J Bacteriol2001，183，12： | 1 |
| 7 | Phylogenetic analyses of some extremely halophilic archaea isolated from Dead Sea water, determined on the basis of their 16S rRNA sequences 显示文摘 | ARAHAL D R DEWHIRST F E PASTER B J etal | 1996 | Applied Environ Microbiology1996，62，10： | 1 |
| 8 | Phylogeny of the defined murine microbiota: altered Schaedler flora 显示文摘 | Dewhirst F E Chien C C Paster B J et ol | 1999 | Appl Environ Microbiol1999，65，： | 1 |
| 9 | 查看详情显示文摘 | Paster SA | | 0，，： | 1 |
| 10 | Molecular analysis of oral and respiratory bacterial species associated with ventilator-associated pneumonia 显示文摘 | tMhrani-Mongeot FK Paster BJ Coleman S | 2007 | J Clin Muicrobiol2007，45，15： | 1 |
| 11 | Defining the nor- mal bacterial flora of the oral cavity 显示文摘 | AASJ A PASTER B J STOKES L N | 2005 | Journal of Clinical Mi- crobiology2005，43，11： | 1 |
| 12 | Defining the normal bacte- rial flora of the oral cavity显示文摘 | Aas JA Paster B J Stokes LN | 2005 | Clin Microbiol2005，43，11： | 1 |
| 13 | A poroelastie finite element model with application to the intervertebral disc 显示文摘 | Laible JP Paster DS Krag MH | 1993 | Spine1993，18，5： | 1 |
| 14 | Modeling and design of arrayed waveguide gratings 显示文摘 | MUNOZ P PASTER D CAPMANY J | 2002 | Journal of Lightwave Technology IEEE2002，20，4： | 1 |
| 15 | Opportunities in the industrial biobased products industry显示文摘 | Carole T M Pellegrino J Paster M D | | 0，，04： | 1 |
| 16 | In vitro postanibiotic effect of sparfloxacin and ciprofloxacin against Pseudomonas aeruginosa and Enterococcus faecalis显示文摘 | Paster A Peman J Canton E | 1994 | J Antimicrob Chemother1994，34，： | 1 |
| 17 | Fumigant toxicity of essential oils against four stored -- product insects 显示文摘 | Shaaya E Ravid U Paster N | 1991 | Journal of Chemical- Ecology1991，17，： | 1 |
| 18 | Bacterial diversity in human subgingival plaque 显示文摘 | Paster BJ Boches SK Galvin JL | 2001 | J Bacteriol2001，183，12： | 1 |
| 19 | Cross-reactive adaptive immune responsse to oral commensal bacteria results in an induction of RANKL-dependent periodontal bone resorption in a mouse显示文摘 | Kawai T Paster BJ Komatsuzawa H | 2007 | Oral Microbiol Immunol2007，22，3： | 1 |
| 20 | The phylogeny of the purple bacteria:the beta subdivision显示文摘 | Woese C R Weisburg W G Paster B J | 1984 | Syst Appl Microbiol1984，5，： | 1 |
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