- About this Journal ·
- Abstracting and Indexing ·
- Aims and Scope ·
- Annual Issues ·
- Article Processing Charges ·
- Articles in Press ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
BioMed Research International
Volume 2014 (2014), Article ID 325340, 10 pages
Comparative Metagenomic Analysis of Human Gut Microbiome Composition Using Two Different Bioinformatic Pipelines
1CEINGE-Biotecnologie Avanzate, Via G. Salvatore, 80145 Naples, Italy
2Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via S. Pansini, 80131 Naples, Italy
3IRCCS-Fondazione SDN, Via Gianturco, 80143 Naples, Italy
Received 5 October 2013; Accepted 30 December 2013; Published 25 February 2014
Academic Editor: Qaisar Mahmood
Copyright © 2014 Valeria D’Argenio et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- B. J. Baker, C. S. Sheik, C. A. Taylor et al., “Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling,” The ISME Journal, vol. 7, pp. 1962–1973, 2013.
- L. Philippot, J. M. Raaijmakers, P. Lemanceau, and W. H. van der Putten, “Going back to the roots: the microbial ecology of the rhizosphere,” Nature Reviews Microbiology, vol. 11, pp. 789–799, 2013.
- P. L. Zeeuwen, M. Kleerebezem, H. M. Timmerman, and J. Schalkwijk, “Microbiome and skin diseases,” Current Opinion in Allergy and Clinical Immunology, vol. 13, pp. 514–520, 2013.
- I. Cho and M. J. Blaser, “The human microbiome: at the interface of health and disease,” Nature Reviews Genetics, vol. 13, no. 4, pp. 260–270, 2012.
- S. Fang and R. M. Evans, “Microbiology: wealth management in the gut,” Nature, vol. 500, pp. 538–539, 2013.
- D. Knights, K. G. Lassen, and R. J. Xavier, “Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome,” Gut, vol. 62, pp. 1505–1510, 2013.
- N. Wu, X. Yang, R. Zhang, et al., “Dysbiosis signature of fecal microbiota in colorectal cancer patients,” Microbial Ecology, vol. 66, pp. 462–470, 2013.
- V. D'Argenio, V. Precone, G. Casaburi et al., “An altered gut microbiome profile in a child affected by Crohn's disease normalized after nutritional therapy,” American Journal of Gastroenterology, vol. 108, pp. 851–852, 2013.
- E. S. Gollwitzer and B. J. Marsland, “Microbiota abnormalities in inflammatory airway diseases—potential for therapy,” Pharmacology & Therapeutics, vol. 141, no. 1, pp. 32–39, 2014.
- B. S. Kim, Y. S. Jeon, and J. Chun, “Current status and future promise of the human microbiome,” Pediatric Gastroenterology, Hepatology & Nutrition, vol. 16, pp. 71–79, 2013.
- P. Ribeca and G. Valiente, “Computational challenges of sequence classification in microbiomic data,” Briefings in Bioinformatics, vol. 12, no. 6, pp. 614–625, 2011.
- C. De Filippo, M. Ramazzotti, P. Fontana, and D. Cavalieri, “Bioinformatic approaches for functional annotation and pathway inference in metagenomics data,” Briefings in Bioinformatics, vol. 13, pp. 696–710, 2012.
- F. Meyer, D. Paarmann, M. D'Souza et al., “The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes,” BMC Bioinformatics, vol. 9, article 386, 2008.
- J. G. Caporaso, J. Kuczynski, J. Stombaugh et al., “QIIME allows analysis of high-throughput community sequencing data,” Nature Methods, vol. 7, no. 5, pp. 335–336, 2010.
- H. Teeling and F. O. Glöckner, “Current opportunities and challenges in microbial metagenome analysis: a bioinformatic perspective,” Briefings in Bioinformatics, vol. 13, pp. 728–742, 2012.
- J. A. Navas-Molina, J. M. Peralta-Sánchez, A. González, et al., “Advancing our understanding of the human microbiome using QIIME,” Methods in Enzymology, vol. 531, pp. 371–444, 2013.
- W. J. Kent, “BLAT—the BLAST-like alignment tool,” Genome Research, vol. 12, no. 4, pp. 656–664, 2002.
- E. Pruesse, C. Quast, K. Knittel et al., “SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB,” Nucleic Acids Research, vol. 35, no. 21, pp. 7188–7196, 2007.
- R. C. Edgar, “Search and clustering orders of magnitude faster than BLAST,” Bioinformatics, vol. 26, no. 19, pp. 2460–2461, 2010.
- D. McDonald, M. N. Price, J. Goodrich et al., “An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea,” The ISME Journal, vol. 6, no. 3, pp. 610–618, 2012.
- D. McDonald, J. C. Clemente, J. Kuczynski, et al., “The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome,” GigaScience, vol. 1, no. 1, article 7, 2012.
- S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, no. 3, pp. 403–410, 1990.
- Q. Wang, G. M. Garrity, J. M. Tiedje, and J. R. Cole, “Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy,” Applied and Environmental Microbiology, vol. 73, no. 16, pp. 5261–5267, 2007.
- T. C. J. Hill, K. A. Walsh, J. A. Harris, and B. F. Moffett, “Using ecological diversity measures with bacterial communities,” FEMS Microbiology Ecology, vol. 43, no. 1, pp. 1–11, 2003.
- I. F. Spellerberg and P. J. Fedor, “A tribute to Claude-Shannon (1916-2001) and a plea for more rigorous use of species richness, species diversity and the “Shannon-Wiener” Index,” Global Ecology & Biogeography, vol. 12, no. 3, pp. 177–179, 2003.
- E. W. Beals, “Bray-Curtis ordination: an effective strategy for analysis of multivariate ecological data,” Advances in Ecological Research, vol. 14, pp. 1–55, 1984.
- A. Field, “Analysis of variance (ANOVA),” in Encyclopedia of Measurement and Statistics, N. Salkind, Ed., SAGE Publications, Thousand Oaks, Calif, USA, 2007.
- R. R. Sokal and F. J. Rohlf, Biometry: The Principles and Practice of Statistics in Biological Research, Freeman, New York, NY, USA, 1981.
- H. Abdi, “Bonferroni and Šidák corrections for multiple comparisons,” in Encyclopedia of Measurement and Statistics, N. J. Salkind, Ed., SAGE Publications, Thousand Oaks, Calif, USA, 2007.
- V. Bagdonavicius, J. Kruopis, and M. S. Nikulin, Non-Parametric Tests for Complete Data, John Wiley & Sons, London, UK, 2011.
- P. G. N. Digby and R. A. Kempton, Multivariate Analysis of Ecological Communities, Chapman & Hall, London, UK, 1987.
- M. J. Anderson, “A new method for non-parametric multivariate analysis of variance,” Austral Ecology, vol. 26, no. 1, pp. 32–46, 2001.
- M. J. Crawley, Statistical Computing: An Introduction to Data Analysis Using S-PLUS, John Wiley & Sons, 2002.
- P. D. Schloss, S. L. Westcott, T. Ryabin et al., “Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities,” Applied and Environmental Microbiology, vol. 75, no. 23, pp. 7537–7541, 2009.
- D. A. W. Soergel, N. Dey, R. Knight, and S. E. Brenner, “Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences,” The ISME Journal, vol. 6, pp. 1440–1444, 2012.
- C. Quast, E. Pruesse, P. Yilmaz et al., “The SILVA ribosomal RNA gene database project: improved data processing and web-based tools,” Nucleic Acids Research, vol. 41, pp. D590–D596, 2013.
- R. H. Whittaker, “Evolution and measurement of species diversity,” Taxon, vol. 21, pp. 213–251, 1972.