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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 | Phase II Trial of Erlotinib and Capecitabine for Patients with Previously Untreated Metastatic Colorectal Cancer显示文摘 | Peter Kozuch Steve Malamud Carrie Wasserman Peter Homel Takhir Mirzoyev Michael Grossbard | 2009 | Clinical Colorectal Cancer2009，，1： | 2 |
| 3 | Inactivation of human immunodeficiency virus type 1 by nonoxynol-9,C31G,or an alkyl sulfate,sodium dodecyl sulfate显示文摘 | Miller SR Malamud D | 1999 | Antiviral Res1999，43，3： | 1 |
| 4 | Indifference pricing for CRRA utilities显示文摘 | MALAMUD S TRUBOWITZ E WUTHRICH M | 2013 | Mathematics and Financial Economics2013，7，3： | 1 |
| 5 | Landslides, forest fires, and earthquakes: examples of self- organizedcritical behavior 显示文摘 | Turcotte D L Malamud B D | 2004 | Physica A2004，340，： | 1 |
| 6 | Controlled syn thesis of the DSF cell cell signal is required for biofilm forma tion and virulence in Xanthomonas campestris显示文摘 | Torres P S Malamud F Rigano L A | 2007 | Environ Mi crobiol2007，9，8： | 1 |
| 7 | Landslide inventories and their statistical proper- ties显示文摘 | Malamud B D Tureotte D L Reichenbach P | 2004 | Earth Surface Processes and Landforms2004，29，6： | 1 |
| 8 | Cellular Automata Models Applied to Natural Hazards显示文摘 | Malamud B Turcotte D | 2000 | Computing In Science & Engineering (S1521-9615)2000，2，4： | 1 |
| 9 | Self-affine time series: measures of weak and strong persistence显示文摘 | Malamud B D and Turcotte D L | 1999 | Journal of Statistical Planning and Inference1999，80，12： | 1 |
| 10 | Forest Fires:An Exampie of Self-Organized Critical Behavior 显示文摘 | Malamud B Morein G Turcotte D | 1998 | Science1998，281，： | 1 |
| 11 | Tryptase activates peripheral blood mononuclear cells causing the synthesis and release of TNF-alpha, IL-6 and IL-1beta: possible relevance to multiple sclerosis显示文摘 | Malamud V Vaaknin A Abramsky O | 2003 | J Neuroimmunol2003，138，： | 1 |
| 12 | Self-affine time series:measures of weak and strong persistence显示文摘 | Malamud B D Turcotte D L | 1999 | Journal of Statistical Planning and Inference1999，，： | 1 |
| 13 | Landslide inventories and their statistical proper- ties显示文摘 | Malamud B D Turcotte D L Reichenbach P | 2004 | Earth Surface Processes and Landforms2004，29，6： | 1 |
| 14 | Tryptase activates peripheral blood mononuclear cells causing the synthesis and release of TNF-alpha, IL-6 and IL-lbeta: possible relevance to multiple sclerosis 显示文摘 | Vaaknin A Abramsky O | 2003 | J Neuroimmunol2003，138，12： | 1 |
| 15 | Self-affine time series: measures of weak and strong persistence显示文摘 | Malamud B D and Turcotte D L | 1999 | Journal of Statistical Planning and Inference1999，80，12： | 1 |
| 16 | Tryptase activates peripheral blood mononuclear cells causing the synthesis and release of TNF-alpha, IL-6 and IL-1 beta:possible relevance to multiple sclerosis显示文摘 | Malamud V Vaaknin A Abramsky O | 2003 | J Neuroimmunol2003，138，12： | 1 |
| 17 | L-Carnitine Supplementation in Patients with Advanced Cancer and Carnitine Deficiency: A Double-Blind, Placebo-Controlled Study显示文摘 | Ricardo A. Cruciani Ella Dvorkin Peter Homel Bruce Culliney Stephen Malamud Jeanne Lapin Russell K. Portenoy Nora Esteban-Cruciani | 2009 | Journal of Pain and Symptom Management2009，，4： | 1 |
| 18 | Forest fires: an example of self-organized critical behavior显示文摘 | Malamud B D Morein G Turcotte D L | 1998 | Science1998，281，5384： | 1 |
| 19 | The problem of multicentrie gliomas显示文摘 | Batzdorf U Malamud U | 1963 | J Neurosurg1963，20，： | 1 |
| 20 | Cellular Automata Models Applied to Natural Hazards显示文摘 | Malamud B Turcotte D | 2000 | Computing Science & Engineering2000，32，4： | 1 |
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