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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 | Medical image matching -- a review of classification 显示文摘 | VANDENELSEN P A POLE J D VIERGEVER M A | 1993 | IEEE Engineering in Medical and Biology1993，12，1： | 1 |
| 3 | Nitrification modelling in biofilms under inhibitory conditions 显示文摘 | Gheewala S H Pole R K Armachhatre A P | 2004 | Water Research2004，38，1415： | 1 |
| 4 | Acylated flavonoids in cullus cultures of Citrus aurantifolia显示文摘 | Berhow M A Nennett R D Poling S M | 1994 | Phytochemistry1994，36，5： | 1 |
| 5 | PTSD symptoms predict waking salivary cortisol levels in police officers 显示文摘 | Neylan T C Brunet A Pole N | 2005 | Psychoneuroendocrinol- ogy2005，30，4： | 1 |
| 6 | Blood Lactate during Exercise:Time Course of Training Adaptation in Humans显示文摘 | GAESSER G A POLE D C | 1988 | Int J Sports Med1988，9，： | 1 |
| 7 | Cesarean section : does it really prevent the development of postpartum stress urinary incontinence? A prospective study of 363 women one year after their first delivery 显示文摘 | Groutz A Rimon E Poled S | 2004 | Neurourol Urodyn2004，23，： | 1 |
| 8 | Phase Ⅱ study of neoadjuvant chemotherapy with paclitaxel and cisplatin given every 2 weeks for patients with a respectable squamous cell carcinoma of the oesophagus显示文摘 | Polee M B Tilanus H W Eskens F A | | 0，，08： | 1 |
| 9 | Function of NKT cells, potential anti-HIV effector cells, are improved by beginning HAART during acute HIV-1 infection 显示文摘 | Vasan S Poles MA Horowitz A Siladji EE Markowitz M Tsuji M | 2007 | Int Irnmunol2007，19，8： | 1 |
| 10 | Synergistic heterozygosity for TGFbeta1 SNPs and BMPR2 mutations modulates the age at diagnosis and penetrance of familial pulmonary arterial hypertension显示文摘 | PHILLIPS J A POLING J S PHILLIPS C A | 2008 | Genet Med2008，10，5： | 1 |
| 11 | Oligomers of the amyloid-beta protein disrupt working memory: confirmation with two behavioral procedures显示文摘 | Poling A Morgan-Paisley K Panos J] | 2008 | Behav Brain Res2008，193，2： | 1 |
| 12 | Prima ry HIV-1 infection is associated with preferential depletion of CD4^+ T lymphocytes from effector sites in the gastrointestinal tract显示文摘 | Mehandru S Poles M A Tenner-Racz K | 2004 | J Exp Med2004，200，： | 1 |
| 13 | Primary HIV-1 infection is associated with preferential depletion of CD4+T lymphocytes from effector sites in the gastrointestinal tract显示文摘 | Mehandru S Poles M A Tenner-Racz K | 2004 | J Exp Med2004，200，6： | 1 |
| 14 | A preponderance ofCCR5 + CXCR4 + mononuclear cells enhances gastrointestinal mu-cosal susceptibility to human immunodeficiency vims type 1 infec-tion显示文摘 | POLES M A ELLIOTT J TAING P | 2001 | J Virol2001，75，18： | 1 |
| 15 | Phase II study of neo-adjuvant chemotherapy with paclitaxel and cisplatin given every 2 weeks for patients with a resectable squamous cell carcinoma of the esophagus显示文摘 | Polee M B Tilanus H W Eskens F A | | 0，，08： | 1 |
| 16 | Enhanced levels offunctional HIV -1 co - receptors on human mucosal T cells dem-onstrated using intestinal biopsy tissue 显示文摘 | ANTON P A ELLIOTT J POLES M A | 2000 | AIDS2000，14，12： | 1 |
| 17 | Medical Image matching? a Review with classification显示文摘 | Van den ELSEN P A POLE J D VIERGEVER M A | 1993 | IEEE Eng Med Biol1993，12，： | 1 |
| 18 | PrimaryHIV - 1 infection is associated with preferential depletion of CD4 +T lymphocytes from effector sites in the gastrointestinal tract显示文摘 | MEHANDRU S POLES M A TENNER RACZ K | 2004 | JExp Med2004，200，6： | 1 |
| 19 | Phase I显示文摘 | Polee M B Eskens F A Vander Burg M E | 2002 | Br J Cancer2002，86，5： | 1 |
| 20 | Medical image matching - a review with classification 显示文摘 | VAN DEN ELSEN P A POLE J D VIERGEVERM A | 1993 | IEEE Eng in Med&Biol1993，12，1： | 1 |
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