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PhyloSift: phylogenetic analysis of genomes and metagenomes
Open accessAbstract
Like all organisms on the planet, environmental microbes are subject to the forces of molecular evolution. Metagenomic sequencing provides a means to access the DNA sequence of uncultured microbes. By combining DNA sequencing of microbial communities with evolutionary modeling and phylogenetic analysis we might obtain new insights into microbiology and also provide a basis for practical tools such as forensic pathogen detection. In this work we present an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct several types of analysis. First, we present a method to conduct phylogeny-driven Bayesian hypothesis tests for the presence of an organism in a sample. Second, we present a means to compare community structure across a collection of many samples and develop direct associations between the abundance of certain organisms and sample metadata. Third, we apply new tools to analyze the phylogenetic diversity of microbial communities and again demonstrate how this can be associated to sample metadata. These analyses are implemented in an open source software pipeline called PhyloSift. As a pipeline, PhyloSift incorporates several other programs including LAST, HMMER, and pplacer to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by modern sequencing platforms (e.g., Illumina, 454).
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Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00062-07 · Cited by 19,885
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 19,549
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227
Human gut microbiome viewed across age and geography
Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975
Conservation evaluation and phylogenetic diversity
Faith, D. P. (1992) · Biological Conservation · doi:10.1016/0006-3207(92)91201-3 · Cited by 5,693
Environmental genome shotgun sequencing of the sargasso sea
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., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376
Self-citationMeyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-386 · Cited by 3,565
MEGAN analysis of metagenomic data
Huson, D. H., Auch, A. F., Qi, J., & Schuster, S. C. (2007) · Genome Research · doi:10.1101/gr.5969107 · Cited by 3,312
Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity
Hugenholtz, P., Goebel, B. M., & Pace, N. R. (1998) · Journal of Bacteriology · doi:10.1128/jb.180.18.4765-4774.1998 · Cited by 2,428
Community structure and metabolism through reconstruction of microbial genomes from the environment
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. (2004) · Nature · doi:10.1038/nature02340 · Cited by 2,417
Insights into the phylogeny and coding potential of microbial dark matter
Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson, I. J., Cheng, J.-F., Darling, A., Malfatti, S., Swan, B. K., Gies, E. A., et al. (2013) · Nature · doi:10.1038/nature12352 · Cited by 2,394
Self-citationInteractive metagenomic visualization in a Web browser
Ondov, B. D., Bergman, N. H., & Phillippy, A. M. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-385 · Cited by 2,144
Metagenomic microbial community profiling using unique clade-specific marker genes
Segata, N., Waldron, L., Ballarini, A., Narasimhan, V., Jousson, O., & Huttenhower, C. (2012) · Nature Methods · doi:10.1038/nmeth.2066 · Cited by 1,776
Comparative Metagenomics of Microbial Communities
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., et al. (2005) · Science · doi:10.1126/science.1107851 · Cited by 1,689
Bacterial Rhodopsin: Evidence for a New Type of Phototrophy in the Sea
Béjà, O., Aravind, L., Koonin, E. V., Suzuki, M. T., Hadd, A., Nguyen, L. P., Jovanovich, S. B., Gates, C. M., Feldman, R. A., Spudich, J. L., et al. (2000) · Science · doi:10.1126/science.289.5486.1902 · Cited by 1,532
Adaptive seeds tame genomic sequence comparison
Kiełbasa, S. M., Wan, R., Sato, K., Horton, P., & Frith, M. C. (2011) · Genome Research · doi:10.1101/gr.113985.110 · Cited by 1,281
Matsen, F. A., Kodner, R. B., & Armbrust, E. V. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-538 · Cited by 1,050
Self-citationMetagenomics - a guide from sampling to data analysis
Thomas, T., Gilbert, J., & Meyer, F. (2012) · Microbial Informatics and Experimentation · doi:10.1186/2042-5783-2-3 · Cited by 1,029
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N. N., Kunin, V., Goodwin, L., Wu, M., Tindall, B. J., et al. (2009) · Nature · doi:10.1038/nature08656 · Cited by 993
Self-citationImproving the coverage of the cyanobacterial phylum using diversity driven genome sequencing
Shih, P. M., Wu, D., Latifi, A., Axen, S. D., Fewer, D. P., Talla, E., Calteau, A., Cai, F., Tandeau de Marsac, N., Rippka, R., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1217107110 · Cited by 800
Self-citationRibosomal multilocus sequence typing: universal characterization of bacteria from domain to strain
Jolley, K. A., Bliss, C. M., Bennett, J. S., Bratcher, H. B., Brehony, C., Colles, F. M., Wimalarathna, H., Harrison, O. B., Sheppard, S. K., Cody, A. J., et al. (2012) · Microbiology · doi:10.1099/mic.0.055459-0 · Cited by 663
Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis
Eisen, J. A. (1998) · Genome Research · doi:10.1101/gr.8.3.163 · Cited by 640
Self-citationAdey, A., Morrison, H. G., Asan, Xun, X., Kitzman, J. O., Turner, E. H., Stackhouse, B., MacKenzie, A. P., Caruccio, N. C., Zhang, X., et al. (2010) · Genome Biology · doi:10.1186/gb-2010-11-12-r119 · Cited by 583
Accurate phylogenetic classification of variable-length DNA fragments
McHardy, A. C., Martín, H. G., Tsirigos, A., Hugenholtz, P., & Rigoutsos, I. (2007) · Nature Methods · doi:10.1038/nmeth976 · Cited by 564
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
Brady, A., & Salzberg, S. L. (2009) · Nature Methods · doi:10.1038/nmeth.1358 · Cited by 537
Community-wide analysis of microbial genome sequence signatures
Dick, G. J., Andersson, A. F., Baker, B. J., Simmons, S. L., Thomas, B. C., Yelton, A. P., & Banfield, J. F. (2009) · Genome Biology · doi:10.1186/gb-2009-10-8-r85 · Cited by 536
Metagenomic species profiling using universal phylogenetic marker genes
Sunagawa, S., Mende, D. R., Zeller, G., Izquierdo-Carrasco, F., Berger, S. A., Kultima, J. R., Coelho, L. P., Arumugam, M., Tap, J., Nielsen, H. B., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2693 · Cited by 516
A simple, fast, and accurate method of phylogenomic inference
Wu, M., & Eisen, J. A. (2008) · Genome Biology · doi:10.1186/gb-2008-9-10-r151 · Cited by 507
Self-citationSequencing our way towards understanding global eukaryotic biodiversity
Bik, H. M., Porazinska, D. L., Creer, S., Caporaso, J. G., Knight, R., & Thomas, W. K. (2012) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2011.11.010 · Cited by 491
Self-citationA Bioinformatician's Guide to Metagenomics
Kunin, V., Copeland, A., Lapidus, A., Mavromatis, K., & Hugenholtz, P. (2008) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00009-08 · Cited by 490
Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2
Wu, M., & Scott, A. J. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts079 · Cited by 452
Zhao, Y., Tang, H., & Ye, Y. (2012) · Bioinformatics · doi:10.1093/bioinformatics/btr595 · Cited by 418
Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities
Chen, K., & Pachter, L. (2005) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0010024 · Cited by 391
Miller, C. S., Baker, B. J., Thomas, B. C., Singer, S. W., & Banfield, J. F. (2011) · Genome Biology · doi:10.1186/gb-2011-12-5-r44 · Cited by 347
The future is now: single-cell genomics of bacteria and archaea
Blainey, P. C. (2013) · FEMS Microbiology Reviews · doi:10.1111/1574-6976.12015 · Cited by 299
Eisen, J. A. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050082 · Cited by 268
Self-citationGenome-scale coestimation of species and gene trees
Boussau, B., Szöllősi, G. J., Duret, L., Gouy, M., Tannier, E., & Daubin, V. (2013) · Genome Research · doi:10.1101/gr.141978.112 · Cited by 258
Metagenomic Sequencing of an In Vitro-Simulated Microbial Community
Morgan, J. L., Darling, A. E., & Eisen, J. A. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010209 · Cited by 248
Self-citationOne Bacterial Cell, One Complete Genome
Woyke, T., Tighe, D., Mavromatis, K., Clum, A., Copeland, A., Schackwitz, W., Lapidus, A., Wu, D., McCutcheon, J. P., McDonald, B. R., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010314 · Cited by 233
NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads
Rosen, G. L., Reichenberger, E. R., & Rosenfeld, A. M. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btq619 · Cited by 223
Genomic sequencing of uncultured microorganisms from single cells
Lasken, R. S. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2857 · Cited by 219
Diaz, N. N., Krause, L., Goesmann, A., Niehaus, K., & Nattkemper, T. W. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-56 · Cited by 196
Szöllősi, G. J., Boussau, B., Abby, S. S., Tannier, E., & Daubin, V. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1202997109 · Cited by 194
Wu, D., Jospin, G., & Eisen, J. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077033 · Cited by 186
Self-citationTaxonomic metagenome sequence assignment with structured output models
Patil, K. R., Haider, P., Pope, P. B., Turnbaugh, P. J., Morrison, M., Scheffer, T., & McHardy, A. C. (2011) · Nature Methods · doi:10.1038/nmeth0311-191 · Cited by 155
Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices
Lang, J., Darling, A. E., & Eisen, J. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062510 · Cited by 146
Self-citationThe Phylogenetic Kantorovich–Rubinstein Metric for Environmental Sequence Samples
Evans, S. N., & Matsen, F. A., IV (2012) · Journal of the Royal Statistical Society Series B (Statistical Methodology) · doi:10.1111/j.1467-9868.2011.01018.x · Cited by 146
Haque, M. M., Ghosh, T. S., Komanduri, D., & Mande, S. S. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp317 · Cited by 140
Lateral gene transfer as a support for the tree of life
Abby, S. S., Tannier, E., Gouy, M., & Daubin, V. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1116871109 · Cited by 133
PhymmBL expanded: confidence scores, custom databases, parallelization and more
Brady, A., & Salzberg, S. L. (2011) · Nature Methods · doi:10.1038/nmeth0511-367 · Cited by 124
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm
Löytynoja, A., Vilella, A. J., & Goldman, N. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts198 · Cited by 123
Stark, M., Berger, S. A., Stamatakis, A., & von Mering, C. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-461 · Cited by 119
The Phylogenetic Diversity of Metagenomes
Kembel, S. W., Eisen, J. A., Pollard, K. S., & Green, J. L. (2011) · PLoS ONE · doi:10.1371/journal.pone.0023214 · Cited by 104
Self-citationMatsen, F. A., IV, & Evans, S. N. (2013) · PLoS ONE · doi:10.1371/journal.pone.0056859 · Cited by 99
Sharpton, T. J., Riesenfeld, S. J., Kembel, S. W., Ladau, J., O’Dwyer, J. P., Green, J. L., Eisen, J. A., & Pollard, K. S. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1001061 · Cited by 87
Self-citationA Format for Phylogenetic Placements
Matsen, F. A., IV, Hoffman, N. G., Gallagher, A., & Stamatakis, A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0031009 · Cited by 76
MetaPhyler: Taxonomic profiling for metagenomic sequences
Liu, B., Gibbons, T., Ghodsi, M., & Pop, M. (2010) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2010.5706544 · Cited by 76
McCoy, C. O., & Matsen, F. A., IV (2013) · PeerJ · doi:10.7717/peerj.157 · Cited by 65
MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks
Gori, F., Folino, G., Jetten, M. S. M., & Marchiori, E. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq649 · Cited by 59
ProViDE: A software tool for accurate estimation of viral diversity in metagenomic samples
Ghosh, T. S., Mohammed, M. H., Komanduri, D., & Mande, S. S. (2011) · Bioinformation · doi:10.6026/97320630006091 · Cited by 28
Eu-Detect: An algorithm for detecting eukaryotic sequences in metagenomic data sets
Mohammed, M. H., Chadaram, S., Komanduri, D., Ghosh, T. S., & Mande, S. S. (2011) · Journal of Biosciences · doi:10.1007/s12038-011-9105-2 · Cited by 11
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Metadata
- Authors
- Darling, A. E., Jospin, G., Lowe, E., Matsen, F. A., Bik, H. M., & Eisen, J. A.
- Venue
- PeerJ
- Publisher
- PeerJ
- Published
- 2014-01-09
- Volume
- 2
- Pages
- e243
- ISSN
- 2167-8359 (ISSN-L)
- OpenAlex
- W2045449780
- Cited by
- 631
- References
- 67
- FWCI
- 27.99
- Type
- journal article
- Language
- en
- Open access
- gold
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