Skip to main content
SpringerLink
Log in

123 of Metagenomics

  • Living reference work entry
  • First Online:
Encyclopedia of Metagenomics

Introduction

Microbial ecology aims to comprehensively describe the diversity and function of microorganisms in the environment. Culturing, microscopy, and chemical or biological assays were not too long ago the main tools in this field. Molecular methods, such as 16S rRNA gene sequencing, were applied to environmental systems in the 1990s and started to uncover a remarkable diversity of organisms (Barns et al. 1994). Soon, the thirst for describing microbial systems was no longer satisfied by the knowledge of the diversity of just one or a few genes. Thus, approaches were developed to describe the total genetic diversity of a given environment (Riesenfeld et al. 2004). One such approach is metagenomics, which involves sequencing the total DNA extracted from environmental samples. Arguably, metagenomics has been the fastest growing field of microbiology in the last few years and has almost become a routine practice. The learning curve in the field has been steep, and many obstacles...

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

References

  • Barberan A, Bates ST, et al. Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J. 2012;6(2):343–51.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Barns SM, Fundyga RE, et al. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc Natl Acad Sci U S A. 1994;91(5):1609–13.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bates ST, Berg-Lyons D, et al. Examining the global distribution of dominant archaeal populations in soil. ISME J. 2011;5(5):908–17.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bazinet AL, Cummings MP. A comparative evaluation of sequence classification programs. BMC Bioinforma. 2012;13(1):92.

    Article  Google Scholar 

  • Bentley DR, Balasubramanian S, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008;456(7218):53–9.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bergmann GT, Bates ST, et al. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol Biochem. 2011;43(7):1450–5.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Brown MV, Lauro FM, et al. Global biogeography of SAR11 marine bacteria. Mol Syst Biol. 2012;8:595.

    Article  PubMed Central  PubMed  Google Scholar 

  • Caporaso JG, Kuczynski J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335–6.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • de la Bastide M, McCombie WR. Assembling genomic DNA sequences with PHRAP. Curr Protoc Bioinforma. 2007. Chapter 11: Unit11 14.

    Google Scholar 

  • Delmont TO, Malandain C, et al. Metagenomic mining for microbiologists. ISME J. 2011;5(12):1837–43.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Delmont TO, Prestat E, et al. Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME J. 2012;6(9):1677–87.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • DeLong EF, Preston CM, et al. Community genomics among stratified microbial assemblages in the ocean’s interior. Science. 2006;311(5760):496–503.

    Article  CAS  PubMed  Google Scholar 

  • Dinsdale EA, Edwards RA, et al. Functional metagenomic profiling of nine biomes. Nature. 2008;452(7187):629–32.

    Article  CAS  PubMed  Google Scholar 

  • Droge J, McHardy AC. Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. Brief Bioinform. 2012;13(6):646–55.

    Article  PubMed  Google Scholar 

  • Dutilh BE, Huynen MA, et al. Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. Bioinformatics. 2009;25(21):2878–81.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Eid J, Fehr A, et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009;323(5910):133–8.

    Article  CAS  PubMed  Google Scholar 

  • Fan L, Reynolds D, et al. Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts. Proc Natl Acad Sci U S A. 2012;109(27):E1878–87.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Field D, Amaral-Zettler L, et al. The genomic standards consortium. PLoS Bio. 2011;9(6):e1001088.

    Article  CAS  Google Scholar 

  • Fuhrman JA. Microbial community structure and its functional implications. Nature. 2009;459(7244):193–9.

    Article  CAS  PubMed  Google Scholar 

  • Fuhrman JA, Hewson I, et al. Annually reoccurring bacterial communities are predictable from ocean conditions. Proc Natl Acad Sci U S A. 2006;A103(35):13104–9.

    Article  Google Scholar 

  • Fuhrman JA, Steele JA, et al. A latitudinal diversity gradient in planktonic marine bacteria. Proc Natl Acad Sci U S A. 2008;A105(22):7774–8.

    Article  Google Scholar 

  • Gilbert JA, Field D, et al. The taxonomic and functional diversity of microbes at a temperate coastal site: a ‘multi-omic’ study of seasonal and diel temporal variation. PLoS One. 2010a;5(11):e15545.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Gilbert JA, Meyer F, et al. The earth microbiome project: meeting report of the “1 EMP meeting on sample selection and acquisition at Argonne National Laboratory October 6 2010”. Stand Genomic Sci. 2010b;3(3):249–53.

    Article  PubMed Central  PubMed  Google Scholar 

  • Gilbert JA, Bailey M, et al. The earth microbiome project: the Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2010. Stand Genomic Sci. 2011;5(2):243–7.

    Article  PubMed Central  Google Scholar 

  • Gilbert JA, Steele JA, et al. Defining seasonal marine microbial community dynamics. ISME J. 2012;6:298–308.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Gill SR, Pop M, et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312(5778):1355–9.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hess M, Sczyrba A, et al. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science. 2011;331(6016):463–7.

    Article  CAS  PubMed  Google Scholar 

  • Iverson V, Morris RM, et al. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science. 2012;335(6068):587–90.

    Article  CAS  PubMed  Google Scholar 

  • Kanehisa M. The KEGG database. Novartis Found Symp. 2002;247:91–101. discussion 101–103, 119–128, 244–152.

    Article  CAS  PubMed  Google Scholar 

  • Knight R, Jansson J, et al. Designing better metagenomic surveys: the role of experimental design and metadata capture in making useful metagenomic datasets for ecology and biotechnology. Nat Biotechnol. 2012;30(6):513–2.

    Article  CAS  PubMed  Google Scholar 

  • Koren S, Schatz MC, et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol. 2012;30(7):693–700.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Li R, Li Y, et al. SOAP: short oligonucleotide alignment program. Bioinformatics. 2008;24(5):713–4.

    Article  CAS  PubMed  Google Scholar 

  • Liu MY, Kjelleberg S, et al. Functional genomic analysis of an uncultured delta-proteobacterium in the sponge Cymbastela concentrica. ISME J. 2011;5(3):427–35.

    Article  PubMed Central  PubMed  Google Scholar 

  • Loman NJ, Misra RV, et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol. 2012;30(5):434–9.

    Article  CAS  PubMed  Google Scholar 

  • Mackelprang R, Waldrop MP, et al. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature. 2011;480(7377):368–71.

    Article  CAS  PubMed  Google Scholar 

  • Margulies M, Egholm M, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005;437(7057):376–80.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Markowitz VM, Ivanova NN, et al. IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res. 2008;36(Database issue):D534–8.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Martiny JB, Bohannan BJ, et al. Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol. 2006;4(2):102–12.

    Article  CAS  PubMed  Google Scholar 

  • Mavromatis K, Ivanova N, et al. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods. 2007;4(6):495–500.

    Article  CAS  PubMed  Google Scholar 

  • McDonald D, Clemente JC, et al. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience. 2012;1(1):7.

    Article  PubMed Central  PubMed  Google Scholar 

  • McElroy KE, Luciani F, et al. GemSIM: general, error-model based simulator of next-generation sequencing data. BMC Genomics. 2012;13:74.

    Article  PubMed Central  PubMed  Google Scholar 

  • Metzker ML. Sequencing technologies – the next generation. Nat Rev Genet. 2010;11(1):31–46.

    Article  CAS  PubMed  Google Scholar 

  • Meyer F, Paarmann D, et al. The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinforma. 2008;9:386.

    Article  CAS  Google Scholar 

  • Miller JR, Delcher AL, et al. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics. 2008;24(24):2818–24.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Miller JR, Koren S, et al. Assembly algorithms for next-generation sequencing data. Genomics. 2010;95(6):315–27.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Morgan JL, Darling AE, et al. Metagenomic sequencing of an in vitro-simulated microbial community. PLoS One. 2010;5(4):e10209.

    Article  PubMed Central  PubMed  Google Scholar 

  • Namiki T, Hachiya T, et al. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res. 2012;40(20):e155.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Nemergut DR, Costello EK, et al. Global patterns in the biogeography of bacterial taxa. Environ Microbiol. 2011;13(1):135–44.

    Article  PubMed  Google Scholar 

  • Ottesen EA, Marin R, et al. Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton. ISME J. 2011;5(12):1881–95.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Overbeek R, Begley T, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005;33(17):5691–702.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Peng Y, Leung HC, et al. Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics. 2011;27(13):i94–101.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Prabakaran P, Streaker E, et al. 454 antibody sequencing – error characterization and correction. BMC Res Notes. 2011;4:404.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Prosser JI. Replicate or lie. Environ Microbiol. 2010;12(7):1806–10.

    Article  CAS  PubMed  Google Scholar 

  • Quail M, Smith ME, et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics. 2012;13(1):341.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Rho M, Tang H, et al. FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res. 2010;38(20):e191.

    Article  PubMed Central  PubMed  Google Scholar 

  • Riesenfeld CS, Schloss PD, et al. Metagenomics: genomic analysis of microbial communities. Annu Rev Genet. 2004;38:525–52.

    Article  CAS  PubMed  Google Scholar 

  • Rothberg JM, Hinz W, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature. 2011;475(7356):348–52.

    Article  CAS  PubMed  Google Scholar 

  • Rusch DB, Halpern AL, et al. The Sorcerer II global ocean sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol. 2007;5(3):e77.

    Article  PubMed Central  PubMed  Google Scholar 

  • Schneider GF, Dekker C. DNA sequencing with nanopores. Nat Biotechnol. 2012;30(4):326–8. doi: 10.1038/nbt.2181.

    Google Scholar 

  • Salmela L. Correction of sequencing errors in a mixed set of reads. Bioinformatics. 2010;26(10):1284–90.

    Article  CAS  PubMed  Google Scholar 

  • Seshadri R, Kravitz SA, et al. CAMERA: a community resource for metagenomics. PLoS Biol. 2007;5(3):e75.

    Article  PubMed Central  PubMed  Google Scholar 

  • Simpson JT, Wong K, et al. ABySS: a parallel assembler for short read sequence data. Genome Res. 2009;19(6):1117–23.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Trimble WL, Keegan KP, et al. Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. BMC Bioinforma. 2012;13(1):183.

    Article  Google Scholar 

  • Tringe SG, von Mering C, et al. Comparative metagenomics of microbial communities. Science. 2005;308(5721):554–7.

    Article  CAS  PubMed  Google Scholar 

  • Tyson GW, Chapman J, et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004;428(6978):37–43.

    Article  CAS  PubMed  Google Scholar 

  • Venter JC, Remington K, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004;304(5667):66–74.

    Article  CAS  PubMed  Google Scholar 

  • Warnecke F, Luginbuhl P, et al. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature. 2007;450(7169):560–5.

    Article  CAS  PubMed  Google Scholar 

  • Whiteley AS, Jenkins S, et al. Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) platform. J Microbiol Methods. 2012;91(1):80–8.

    Article  CAS  PubMed  Google Scholar 

  • Wilke A, Harrison T, et al. The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinforma. 2012;13:141.

    Article  CAS  Google Scholar 

  • Wilkening J, Wilke A, et al. Using clouds for metagenomics: a case study. IEEE Cluster 2009. 2009

    Google Scholar 

  • Wommack KE, Bhavsar J, et al. Metagenomics: read length matters. Appl Environ Microbiol. 2008;74(5):1453–63.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Yilmaz P, Kottmann R, et al. The “Minimum Information about an ENvironmental Sequence” (MIENS) specification. Nat Biotechnol. 2010. in print.

    Google Scholar 

  • Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18(5):821–9.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Zhou R, Ling S, et al. Population genetics in nonmodel organisms: II. Natural selection in marginal habitats revealed by deep sequencing on dual platforms. Mol Biol Evol. 2011;28(10):2833–42.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Biotechnology and Biomolecular Sciences & Centre for Marine Bio-Innovation, University of New South Wales, 2052, Sydney, NSW, Australia

    Torsten Thomas

  2. Department of Ecology & Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL, 60637, USA

    Jack Gilbert

  3. Institute of Genomic and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA

    Folker Meyer

Authors
  1. Torsten Thomas
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jack Gilbert
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Folker Meyer
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Torsten Thomas .

Editor information

Editors and Affiliations

  1. J. Craig Venter Institute (JCVI), Rockville, Maryland, USA

    Karen E. Nelson

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this entry

Cite this entry

Thomas, T., Gilbert, J., Meyer, F. (2013). 123 of Metagenomics. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_728-4

Download citation

  • DOI: https://doi.org/10.1007/978-1-4614-6418-1_728-4

  • 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

Publish with us

Policies and ethics

Search

Navigation