Definition
PhyloPythia and its successor PhyloPythiaS are fast and accurate oligomer signature-based classifiers for the taxonomic assignment of metagenome sequence fragments.
Introduction
Metagenomics uses random shotgun sequencing to recover genome sequence information from microbial communities without the need for cultivation of its member species. It thus gives access to the vast portion of the microbial world that cannot be cultured with standard techniques (Hugenholtz 2002). The sequencing of randomly sheared microbial community DNA initially generates a collection of short sequence fragments called reads. Depending on the sequencing technology used, the amount of generated data and read lengths vary (Metzker 2010; Droge and McHardy 2012): while traditional Sanger sequencing generates reads of around 800 bp, the commercially available “next-generation” sequencing technologies return reads of approximately 50–75 bp (SOLID sequencing by Applied Biosciences/Life Technologies),...
References
Droge J, McHardy AC. Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. Brief Bioinforma. 2012;13(6):646–55.
Glass EM, Wilkening J, Wilke A, Antonopoulos D, Meyer F. Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harb Protoc. 2010; 2010(1):pdb prot5368.
Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, et al. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science. 2011;331(6016):463–7.
Hugenholtz P. Exploring prokaryotic diversity in the genomic era. Genome Biol. 2002;3(2):REVIEWS0003.
Illumina. 2012. Available from: http://www.illumina.com/Documents/systems/hiseq/datasheet_hiseq_systems.pdf.
Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales RL, Armbrust EV. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science. 2012;335(6068):587–90.
Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Grechkin Y, et al. IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res. 2012;40(Database issue):D123–9.
McHardy AC, Garcia-Martin H, Tsirigos A, Hugenholtz P, Rigoutsos I. Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods. 2007;4(1):63–72.
Metzker ML. Sequencing technologies – the next generation. Nat Rev Genet. 2010;11(1):31–46.
Namiki T, Hachiya T, Tanaka H, Sakakibara Y. MetaVelvet: an extension of velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res. 2012;40(20):e155.
Patil KR, Haider P, Pope PB, Turnbaugh PJ, Morrison M, Scheffer T, et al. Taxonomic metagenome sequence assignment with structured output models. Nat Methods. 2011;8(3):191–2.
Pope PB, Denman SE, Jones M, Tringe SG, Barry K, Malfatti SA, et al. Adaptation to herbivory by the tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proc Natl Acad Sci U S A. 2010;107(33):14793–8.
Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods. 2012;9(8):811–4.
Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O’Dwyer JP, Green JL, et al. PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Comput Biol. 2011;7(1):e1001061.
Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, et al. Community cyberinfrastructure for advanced microbial ecology research and analysis: the CAMERA resource. Nucleic Acids Res. 2011;39(Database issue):D546–51.
Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, et al. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature. 2007;450(7169):560–5.
Wu M, Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 2008;9(10):R151.
Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics. 2012;28(7):1033–4.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media New York
About this entry
Cite this entry
McHardy, A.C. (2013). PhyloPythia(S). In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_736-8
Download citation
DOI: https://doi.org/10.1007/978-1-4614-6418-1_736-8
Received:
Accepted:
Published:
Publisher Name: Springer, New York, NY
Online ISBN: 978-1-4614-6418-1
eBook Packages: Springer Reference Biomedicine and Life SciencesReference Module Biomedical and Life Sciences