Hamady, M. and Knight, R. (2009) Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Research (19). pp. 1141-1152.
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Abstract
High-throughput sequencing studies and new software tools are revolutionizing microbial community analyses, yet the variety of experimental and computational methods can be daunting. In this review, we discuss some of the different approaches to community profiling, highlighting strengths and weaknesses of various experimental approaches, sequencing methodologies, and analytical methods. We also address one key question emerging from various Human Microbiome Projects: Is there a substantial core of abundant organisms or lineages that we all share? It appears that in some human body habitats, such as the hand and the gut, the diversity among individuals is so great that we can rule out the possibility that any species is at high abundance in all individuals: It is possible that the focus should instead be on higher-level taxa or on functional genes instead.
| Item Type: | Article |
|---|---|
| Additional Information: | M.H. was supported by an NSF EAPSI fellowship (OISE0812861) and the NIH Molecular Biophysics Training Grant (T32GM065103). The ideas in this review arose from work in the Knight and Gordon laboratories supported by the NIH (P01DK078669), the Crohn’s and Colitis Foundation of America, the Bill and Melinda Gates Foundation, and from discussion at the Banbury Center Conference ‘‘Living on Human Beings: Metagenomic Approaches and Challenges,’’ March 2–5, 2008. |
| Author Affiliation: | Department of Computer Science, University of Colorado, Boulder, Colorado 80309, USA |
| Subjects: | Soil Science and Microbiology > Microbiology |
| Divisions: | General |
| Depositing User: | Mr Siva Shankar |
| Date Deposited: | 14 Nov 2012 09:42 |
| Last Modified: | 14 Nov 2012 09:42 |
| Official URL: | http://www.genome.org/cgi/doi/10.1101/gr.085464.10... |
| URI: | http://eprints.icrisat.ac.in/id/eprint/8780 |
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