Estimating Bacterial Diversity from Environmental DNA: A Maximum Likelihood Approach
The ability to measure bacterial diversity is a prerequisite for the systematic study of bacterial biogeography and ecology. In this paper we describe a method of estimating diversity from an environmental sample of DNA and apply it to data taken from samples from the Sargasso Sea. Our approach combines the coverage depth method of Venter et al.  and the contig spectrum approach of Angly et al. , but uses maximum likelihood to recover the diversity rather than using hand-fit models as in . We assume four species abundance distributions, then maximize the likelihood of fitting the coverage depth at different positions of the consensus sequence provided in the Sargasso Sea sample. The resulting estimates match well with those obtained using less mathematically rigorous approaches.
Unable to display preview. Download preview PDF.
- 3.Angly, F., et al.: PHACCS, an Online Tool for Estimating the Structure and Diversity of Uncultured Viral Communities Using Metagenomic Information. BMC Bioinformatics 6(41) (2005), http://www.biomedcentral.com/147-2105/6/41
- 5.Myers, G.: Whole-Genome DNA Seqencing. Computing in Science and Engineering, 33–43 (May-June 1999)Google Scholar
- 8.Hubbell, S.: The Unified Neutral Theroy of Biodiversity and Biogeography. Princeton University Press, Princeton (2001)Google Scholar
- 15.Krebs, C.: Ecological Methodology. Harper and Row, New York (1989)Google Scholar
- 18.Reysenbach, A., et al.: Differential Amplification of rRNA Genes by Polymerase Chain Reaction. Appl. Environ. Microbiol. 58, 3417–3418 (1992)Google Scholar
- 19.Suzuki, M., Giovannoni, S.: Bias caused by Template Annealing in the Amplification of Mixutures of 16S rRNA Genes by PCR. Appl. Environ. Microbiol. 62, 625–630 (1996)Google Scholar
- 23.Travis, J.M., Larsen, D.R.: Meaures of Diversity. Natural Resource biometrics (1995)Google Scholar