The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences

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• 作者：Kevin Riehle (1)
  Cristian Coarfa (1)
  Andrew Jackson (1)
  Jun Ma (2)
  Arpit Tandon (1)
  Sameer Paithankar (1)
  Sriram Raghuraman (1)
  Toni-Ann Mistretta (3)
  Delphine Saulnier (4)
  Sabeen Raza (3)
  Maria Alejandra Diaz (3)
  Robert Shulman (5)
  Kjersti Aagaard (2)
  James Versalovic (3)
  Aleksandar Milosavljevic (1)
  
• 刊名：BMC Bioinformatics
• 出版年：2012
• 出版时间：August 2012
• 年：2012
• 卷：13
• 期：13-supp
• 全文大小：1299KB
• 参考文献：1. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI: The human microbiome project. / Nature 2007, 449:804鈥?10. CrossRef
  2. Zoetendal EG, Akkermans AD, De Vos WM: Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. / Applied and environmental microbiology 1998, 64:3854鈥?859.
  3. Hamady M, Knight R: Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. / Genome research 2009, 19:1141鈥?152. CrossRef
  4. Caporaso G, Kuczynski J, Stombaugh J, Bittinger K, Bushman F, Costello E, Fierer N, Pena A, Goodrich J, Gordon J, / et al.: QIIME allows analysis of high-throughput community sequencing data. / Nature Methods 2010, 7:335鈥?36. CrossRef
  5. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, / et al.: Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. / Applied and environmental microbiology 2009, 75:7537鈥?541. CrossRef
  6. Genboree [http://www.genboree.org/]
  7. Fielding RT: Architectural styles and the design of network-based software architectures. In / Thesis (Ph D , Information and Computer Science). / Volume 2000. University of California, Irvine; 2000.
  8. Richardson L, Ruby S: RESTful web services. / O'Reilly Media 2007.
  9. Whittaker RH: Evolution and measurement of species diversity. / Taxon 1972, 213鈥?51.
  10. Wang Q, Garrity GM, Tiedje JM, Cole JR: Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. / Applied and environmental microbiology 2007, 73:5261鈥?267. CrossRef
  11. Li W, Godzik A: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. / Bioinformatics 2006, 22:1658鈥?659. CrossRef
  12. Edgar RC: Search and clustering orders of magnitude faster than BLAST. / Bioinformatics 2010, 26:2460鈥?461. CrossRef
  13. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, / et al.: Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. / Genome Research 2011, 21:494鈥?04. CrossRef
  14. Lozupone C, Knight R: UniFrac: a new phylogenetic method for comparing microbial communities. / Applied and environmental microbiology 2005, 71:8228鈥?235. CrossRef
  15. Letunic I, Bork P: Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. / Bioinformatics 2007, 23:127鈥?28. CrossRef
  16. Gavin DG, Oswald WW, Wahl ER, Williams JW: A statistical approach to evaluating distance metrics and analog assignments for pollen records. / Quaternary Research 2003, 60:356鈥?67. CrossRef
  17. Oswald WW, Brubaker LB, Hu FS, Gavin DG: Pollen-Vegetation Calibration for Tundra Communities in the Arctic Foothills, Northern Alaska. / Journal of Ecology 2003, 91:1022鈥?033. CrossRef
  18. Lozupone CA, Hamady M, Kelley ST, Knight R: Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. / Applied and environmental microbiology 2007, 73:1576鈥?585. CrossRef
  19. Fierer N, Lauber CL, Zhou N, McDonald D, Costello EK, Knight R: Forensic identification using skin bacterial communities. / Proceedings of the National Academy of Sciences of the United States of America 2010, 107:6477鈥?481. CrossRef
  20. Liaw A, Wiener M: Classification and Regression by randomForest. / R news 2002, 2:18鈥?2.
  21. Kursa MB, Rudnicki WR: Feature selection with the Boruta package.
  22. Knights D, Costello EK, Knight R: Supervised classification of human microbiota. / FEMS Microbiology Reviews 2010, no-no.
  23. Wilcoxon F: Individual comparisons by ranking methods. / Biometrics Bulletin 1945, 1:80鈥?3. CrossRef
  24. Qin J, Li R, Raes J, Arumugam M, Burgdorf K, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, / et al.: A human gut microbial gene catalogue established by metagenomic sequencing. / Nature 2010, 464:59鈥?5. CrossRef
  25. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, / et al.: A core gut microbiome in obese and lean twins. / Nature 2009, 457:480鈥?84. CrossRef
  26. Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, / et al.: Gastrointestinal Microbiome Signatures Of Pediatric Patients With Irritable Bowel Syndrome. / Gastroenterology 2011.
  27. The Gordon Lab [http://gordonlab.wustl.edu/SuppData.html]
  28. Li M, Wang B, Zhang M, Rantalainen M, Wang S, Zhou H, Zhang Y, Shen J, Pang X, Wei H, / et al.: Symbiotic gut microbes modulate human metabolic phenotypes. / Proceedings of the National Academy of Sciences of the United States of America 2008, 105:2117鈥?122. CrossRef
  29. Magurran AE: / Measuring biological diversity. Wiley-Blackwell; 2004.
  
• 作者单位：Kevin Riehle (1)
  Cristian Coarfa (1)
  Andrew Jackson (1)
  Jun Ma (2)
  Arpit Tandon (1)
  Sameer Paithankar (1)
  Sriram Raghuraman (1)
  Toni-Ann Mistretta (3)
  Delphine Saulnier (4)
  Sabeen Raza (3)
  Maria Alejandra Diaz (3)
  Robert Shulman (5)
  Kjersti Aagaard (2)
  James Versalovic (3)
  Aleksandar Milosavljevic (1)
  
  1. Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
  2. Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, 77030, USA
  3. Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
  4. Nizo Food Research, Ede, 6710 BA, The Netherlands
  5. Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
  
• ISSN：1471-2105

文摘

Background Microbial metagenomic analyses rely on an increasing number of publicly available tools. Installation, integration, and maintenance of the tools poses significant burden on many researchers and creates a barrier to adoption of microbiome analysis, particularly in translational settings. Methods To address this need we have integrated a rich collection of microbiome analysis tools into the Genboree Microbiome Toolset and exposed them to the scientific community using the Software-as-a-Service model via the Genboree Workbench. The Genboree Microbiome Toolset provides an interactive environment for users at all bioinformatic experience levels in which to conduct microbiome analysis. The Toolset drives hypothesis generation by providing a wide range of analyses including alpha diversity and beta diversity, phylogenetic profiling, supervised machine learning, and feature selection. Results We validate the Toolset in two studies of the gut microbiota, one involving obese and lean twins, and the other involving children suffering from the irritable bowel syndrome. Conclusions By lowering the barrier to performing a comprehensive set of microbiome analyses, the Toolset empowers investigators to translate high-volume sequencing data into valuable biomedical discoveries.