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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 | 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 |
| 3 | 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 |
| 4 | 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 |
| 5 | 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 |
| 6 | Fumigant toxicity of essential oil against four stored-product insects 显示文摘 | Shaaya E Ravid U Paster N | 1991 | Journal of Chemical-Ecology1991，17，： | 1 |
| 7 | Phylogeny of 54 representative strains of species in the family Pasteurel- laceae as determined by comparison of 16S rRNA se- quences显示文摘 | Dewhirst F E Paster B J Olsen I | 1992 | J Bacteriol1992，174，： | 1 |
| 8 | Fumigant toxicity of essential oils against four stored-product insects 显示文摘 | SHAAYA E RAVID U PASTER N | 1991 | Jouronal of Chemical-Ecology1991，，17： | 1 |
| 9 | Molecular analysis of bacterial species associated with childhood caries显示文摘 | Becker MR Paster B J Leys E J | 2002 | J Clin Microbiol2002，40，3： | 1 |
| 10 | In vitro post-anibiotic effect of sparfloxacin and ciprofloxacin against Pseudomonas aeruginosa and Enterococcus faecalis 显示文摘 | Peman J Canton E | 1994 | J Antimicrob Chemother1994，34，5： | 1 |
| 11 | Effects of prenatal stress on development in mice: maturation and learning 显示文摘 | Meek L R Burda K M Paster E | 2000 | Physiol Behav2000，71，5： | 1 |
| 12 | Preservation of agricultural lands through and use planning tools and techniques显示文摘 | PASTER E | 2004 | Natural Resources Journal2004，44，： | 1 |
| 13 | 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 |
| 14 | Bacteria-reactive immune response may induce RANKL-expressing T cells in the mouse periapical bone loss lesion显示文摘 | Silva MJ Kajiya M AlShwaimi E Sasaki H Hong J Ok P Rezende TM Pagonis TC White RR Paster BJ Stashenko P Kawai T | | 0，，： | 1 |
| 15 | Phylogenetic relationships and diversity within the pasteurella haemolytica complex based on 16s rRNA sequence comparison and outer membrane protein and lipopolysaccharide analysis 显示文摘 | Davies R L Paster B J Dewhirst F E | 1996 | Int J Syst Bacteriol1996，46，3： | 1 |
| 16 | Techniques characterizing the coronary atherosclerotic plaque:influence on clinical decsion marking 显示文摘 | Paster G Falk E Woutman H | 2000 | J Am Coil Cardiol2000，36，1： | 1 |
| 17 | Molecular analysis of bacterial species associated with childhood caries显示文摘 | BEEKER M R PASTER B J LEYS E J | 2002 | J Clin Mierobiol2002，40，3： | 1 |
| 18 | Phylogeny of 54 representative strains of species in the family Pasteurellaceae as determined by comparison of 16S rRNA sequences显示文摘 | Dewhirst F E Paster B J Olsen I | 1992 | J Bacterial1992，174，6： | 1 |
| 19 | Phylogenetic analysis of cultivable oral treponemas from the smibert collection显示文摘 | Paster B J Dewhirst F E Coleman B C | 1998 | Syst Bacteriol1998，48，： | 1 |
| 20 | Trends in congenital heart disease in Dallas county births显示文摘 | Fixler MD Patricia Paster MA | 1990 | Circulation1990，81，： | 1 |
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