Abstract
A major hindrance to studies of microbial diversity has been that the vast majority of microbes cannot be cultured in the laboratory and thus are not amenable to traditional methods of characterization. Environmental shotgun sequencing (ESS) overcomes this hurdle by sequencing the DNA from the organisms present in a microbial community. The interpretation of this metagenomic data can be greatly facilitated by associating every sequence read with its source organism. We report the development of CompostBin, a DNA composition-based algorithm for analyzing metagenomic sequence reads and distributing them into taxon-specific bins. Unlike previous methods that seek to bin assembled contigs and often require training on known reference genomes, CompostBin has the ability to accurately bin raw sequence reads without need for assembly or training. CompostBin uses a novel weighted PCA algorithm to project the high dimensional DNA composition data into an informative lower-dimensional space, and then uses the normalized cut clustering algorithm on this filtered data set to classify sequences into taxon-specific bins. We demonstrate the algorithm’s accuracy on a variety of low to medium complexity data sets.
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References
Rappe, M.S., Giovannoni, S.J.: The uncultured microbial majority. Annu Rev Microbiol 57, 369–394 (2003)
Lane, D.J., Pace, B., Olsen, G.J., Stahl, D.A., Sogin, M.L., Pace, N.R.: Rapid determination of 16s ribosomal rna sequences for phylogenetic analyses. Proc. Natl Acad. Sci. USA 82(20), 6955–6959 (1985)
Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., Wu, D., Paulsen, I., Nelson, K.E., Nelson, W., Fouts, D.E., Levy, S., Knap, A.H., Lomas, M.W., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., Baden-Tillson, H., Pfannkoch, C., Rogers, Y.H., Smith, H.O.: Environmental genome shotgun sequencing of the sargasso sea. Science 304(5667), 66–74 (2004)
Tyson, G.W., Chapman, J., Hugenholtz, P., Allen, E.E., Ram, R.J., Richardson, P.M., Solovyev, V.V., Rubin, E.M., Rokhsar, D.S., Banfield, J.F.: Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428(6978), 37–43 (2004)
Gill, S.R., Pop, M., Deboy, R.T., Eckburg, P.B., Turnbaugh, P.J., Samuel, B.S., Gordon, J.I., Relman, D.A., Fraser-Liggett, C.M., Nelson, K.E.: Metagenomic analysis of the human distal gut microbiome. Science 312(5778), 1355–1359 (2006)
Wu, D., Daugherty, S.C., Van Aken, S.E., Pai, G.H., Watkins, K.L., Khouri, H., Tallon, L.J., Zaborsky, J.M., Dunbar, H.E., Tran, P.L., Moran, N.A., Eisen, J.A.: Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. PLoS Biol. 4(6), 188 (2006)
Rusch, D.B., Halpern, A.L., Sutton, G., Heidelberg, K.B., Williamson, S., Yooseph, S., Wu, D., Eisen, J.A., Hoffman, J.M., Remington, K., Beeson, K., Tran, B., Smith, H., Baden-Tillson, H., Stewart, C., Thorpe, J., Freeman, J., Andrews-Pfannkoch, C., Venter, J.E., Li, K., Kravitz, S., Heidelberg, J.F., Utterback, T., Rogers, Y.H., Falcon, L.I., Souza, V., Bonilla-Rosso, G., Eguiarte, L.E., Karl, D.M., Sathyendranath, S., Platt, T., Bermingham, E., Gallardo, V., Tamayo-Castillo, G., Ferrari, M.R., Strausberg, R.L., Nealson, K., Friedman, R., Frazier, M., Venter, J.C.: The sorcerer ii global ocean sampling expedition: Northwest atlantic through eastern tropical pacific. PLoS Biol. 5(3), e77 (2007)
Tringe, S.G., von Mering, C., Kobayashi, A., Salamov, A.A., Chen, K., Chang, H.W., Podar, M., Short, J.M., Mathur, E.J., Detter, J.C., Bork, P., Hugenholtz, P., Rubin, E.M.: Comparative metagenomics of microbial communities. Science 308(5721), 554–557 (2005)
von Mering, C., Hugenholtz, P., Raes, J., Tringe, S., Doerks, T., Jensen, L., Ward, N., Bork, P.: Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315(5815), 1126–1130 (2007)
Huson, D.H., Auch, A.F., Qi, J., Schuster, S.C.: Megan analysis of metagenomic data. Genome Research (in press, 2007)
Teeling, H., Waldmann, J., Lombardot, T., Bauer, M., Glockner, F.O.: Tetra: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in dna sequences. BMC Bioinformatics 5(1471–2105 (Electronic)) (2004)
Abe, T., Sugawara, H., Kinouchi, M., Kanaya, S., Ikemura, T.: Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples. DNA Res 12(5), 281–290 (2005)
McHardy, A.C., Martin, H.G., Tsirigos, A., Hugenholtz, P., Rigoutsos, I.: Accurate phylogenetic classification of variable-length dna fragments. Nat Methods 4(1), 63–72 (2007)
Karlin, S., Burge, C.: Dinucleotide relative abundance extremes: a genomic signature. Trends Genet 11(7), 283–290 (1995)
Woyke, T., Teeling, H., Ivanova, N.N., Huntemann, M., Richter, M., Gloeckner, F.O., Boffelli, D., Anderson, I.J., Barry, K.W., Shapiro, H.J., Szeto, E., Kyrpides, N.C., Mussmann, M., Amann, R., Bergin, C., Ruehland, C., Rubin, E.M., Dubilier, N.: Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443(7114), 950–955 (2006)
Delcher, A.L., Bratke, K.A., Powers, E.C., Salzberg, S.L.: Identifying bacterial genes and endosymbiont dna with glimmer. Bioinformatics 23(6), 673–679 (2007)
Jolliffe, I.T.: Principal Component Analysis. Springer, Heidelberg (2002)
Kent, W.J.: Blat-the blast-like alignment tool. Genome Res 12(4), 656–664 (2002)
Lander, E.S., Waterman, M.S.: Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 2(3), 231–239 (1988)
Tenebaum, J.B., Silva, V.D., Langford, J.C.: A global geometric framework for nonlinear dimensionality reduction. Science 190(5500), 2319–2323 (2000)
Wu, M., Eisen, J.: A simple, fast and accurate method for phylogenenomics inference approach (submitted, 2007)
Shi, J., Malik, J.: Normalized cuts and image segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence 22(8), 888–905 (2000)
Schmid, R., Schuster, S.C., Steel, M.A., Huson, D.H.: Readsim- a simulator for sanger and 454 sequencing (in press, 2007)
Markowitz, V.M., Korzeniewski, F., Palaniappan, K., Szeto, E., Werner, G., Padki, A., Zhao, X., Dubchak, I., Hugenholtz, P., Anderson, I., Lykidis, A., Mavromatis, K., Ivanova, N., Kyrpides, N.C.: The integrated microbial genomes (img) system. Nucleic Acids Res. 34(Database issue), D344–348 (2006)
Mavromatis, K., Ivanova, N., Barry, K., Shapiro, H., Goltsman, E., McHardy, A.C., Rigoutsos, I., Salamov, A., Korzeniewski, F., Land, M., Lapidus, A., Grigoriev, I., Richardson, P., Hugenholtz, P., Kyrpides, N.C.: Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat. Methods 4(6), 495–500 (2007)
Gelfand, M.S., Koonin, E.V.: Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes. Nucleic Acids Res. 25(12), 2430–2439 (1997)
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Chatterji, S., Yamazaki, I., Bai, Z., Eisen, J.A. (2008). CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads. In: Vingron, M., Wong, L. (eds) Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science(), vol 4955. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-78839-3_3
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DOI: https://doi.org/10.1007/978-3-540-78839-3_3
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