Encyclopedia of Metagenomics

2015 Edition
| Editors: Karen E. Nelson

PhyloPythia(S)

Reference work entry
DOI: https://doi.org/10.1007/978-1-4899-7478-5_736

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),...

This is a preview of subscription content, log in to check access

References

  1. Droge J, McHardy AC. Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. Brief Bioinforma. 2012;13(6):646–55.Google Scholar
  2. 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.Google Scholar
  3. 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.PubMedGoogle Scholar
  4. Hugenholtz P. Exploring prokaryotic diversity in the genomic era. Genome Biol. 2002;3(2):REVIEWS0003.Google Scholar
  5. 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.PubMedGoogle Scholar
  6. 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.Google Scholar
  7. 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.PubMedGoogle Scholar
  8. Metzker ML. Sequencing technologies – the next generation. Nat Rev Genet. 2010;11(1):31–46.PubMedGoogle Scholar
  9. 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.PubMedCentralPubMedGoogle Scholar
  10. 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.PubMedCentralPubMedGoogle Scholar
  11. 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.PubMedCentralPubMedGoogle Scholar
  12. 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.PubMedCentralPubMedGoogle Scholar
  13. 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.PubMedCentralPubMedGoogle Scholar
  14. 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.Google Scholar
  15. 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.Google Scholar
  16. Wu M, Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 2008;9(10):R151.PubMedCentralPubMedGoogle Scholar
  17. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics. 2012;28(7):1033–4.PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Algorithmic BioinformaticsHeinrich Heine University DüsseldorfDüsseldorfGermany