Skip to main content
SpringerLink
Log in

Approaches in Metagenome Research: Progress and Challenges

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

Synonyms

Function-based screening, Metagenomic biomolecule, Metagenomic library, Metagenomics, Next-generation sequencing, Sequence-based screening

Definition

Metagenomics comprises the culture-independent and DNA-based analysis of entire microbial communities and complements cultivation-based analysis of microorganisms. Metagenomic approaches allow comprehensive insights into phylogenetic and functional diversity of complex microbial consortia present in moderate as well as extreme environments on Earth. The introduction of next-generation sequencing technologies enabled cost-effective high-throughput sequencing of metagenomic DNA molecules resulting in increased resolution of microbial community analysis. In addition, screening of metagenomic libraries led to the identification of numerous novel biomolecules from various environments such as soil, seawater, or glacial ice.

Introduction

The immensely manifold microbial niches on Earth comprise an extraordinarily high abundance and...

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

  • Alonso Sáez L, Waller AS, Mende DR, et al. Role for urea in nitrification by polar marine Archaea. Proc Natl Acad Sci USA. 2012;109:17989–94.

    Article  PubMed Central  PubMed  Google Scholar 

  • Camacho C, Coulouris G, Avagyan V, et al. BLAST+: architecture and applications. BMC Bioinforma. 2009;10:421.

    Article  Google Scholar 

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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Engel P, Martinson VG, Moran NA. Functional diversity within the simple gut microbiota of the honey bee. Proc Natl Acad Sci USA. 2012;109:11002–7.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Gonzalez A, Knight R. Advancing analytical algorithms and pipelines for billions of microbial sequences. Curr Opin Biotechnol. 2012;23:64–71.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Guazzaroni ME, Morgante V, Mirete S, et al. Novel acid resistance genes from the metagenome of the Tinto River, an extremely acidic environment. Environ Microbiol. 2013;15:1088–1102.

    Google Scholar 

  • Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 2004;68:669–85.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hettich RL, Sharma R, Chourey K, et al. Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities. Curr Opin Microbiol. 2012;15:373–80.

    Google Scholar 

  • Huson DH, Mitra S, Ruscheweyh HJ, et al. Integrative analysis of environmental sequences using MEGAN4. Genome Res. 2011;21:1552–60.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kanehisa M, Araki M, Goto S, et al. KEGG for linking genomes to life and environment. Nucleic Acids Res. 2008;36:D480–4.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kembel SW, Wu M, Eisen JA, et al. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Comput Biol. 2012;8:e1002743.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Li K, Bihan M, Yooseph S, Methé BA. Analyses of the microbial diversity across the human microbiome. PLoS ONE. 2012;7:e32118.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ludwig W, Klenk HP. Overview: a phylogenetic backbone and taxonomic framework for procaryotic systematics. In: Garrity GM, Boone DR, Castenholz RW, editors. Bergey’s manual of systematic bacteriology, Vol. 1. 2nd ed. New York: Springer; 2001. p. 49–65.

    Chapter  Google Scholar 

  • Meyer F, Paarmann D, D’Souza M, 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 

  • Murray AE, Kenig F, Fritsen CH, et al. Microbial life at −13 °C in the brine of an ice-sealed Antarctic lake. Proc Natl Acad Sci USA. 2012;109:20626–31.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Nacke H, Will C, Herzog S, et al. Identification of novel lipolytic genes and gene families by screening of metagenomic libraries derived from soil samples of the German biodiversity exploratories. FEMS Microbiol Ecol. 2011;78:188–201.

    Article  CAS  PubMed  Google Scholar 

  • Nacke H, Engelhaupt M, Brady S, et al. Identification and characterization of novel cellulolytic and hemicellulolytic genes and enzymes derived from German grassland soil metagenomes. Biotechnol Lett. 2012;34:663–75.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Nacke H, Fischer C, Thürmer A, et al. Land use type significantly affects microbial gene transcription in soil. Microb Ecol. 2014;67:919–30.

    Google Scholar 

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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Parachin NS, Gorwa-Grauslund MF. Isolation of xylose isomerases by sequence- and function-based screening from a soil metagenomic library. Biotechnol Biofuels. 2011;4:9.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Patil KR, Haider P, Pope PB, et al. Taxonomic metagenome sequence assignment with structured output models. Nat Methods. 2011;8:191–2.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Patti GJ, Yanes O, Siuzdak G. Innovation: Metabolomics: the apogee of the omics trilogy. Nat Rev Mol Cell Biol. 2012;13:263–69.

    Google Scholar 

  • Piel J. Approaches to capturing and designing biologically active small molecules produced by uncultured microbes. Annu Rev Microbiol. 2011;65:431–53.

    Article  CAS  PubMed  Google Scholar 

  • Simon C, Daniel R. Achievements and new knowledge unraveled by metagenomic approaches. Appl Microbiol Biotechnol. 2009;85:265–76.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Simon C, Daniel R. Metagenomic analyses: past and future trends. Appl Environ Microbiol. 2011;77:1153–61.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Song ZQ, Wang FP, Zhi XY, et al. Bacterial and archaeal diversities in Yunnan and Tibetan hot springs, China. Environ Microbiol. 2013;15:1160–75.

    Google Scholar 

  • Standfuß-Gabisch C, Al-Halbouni D, Hofer B. Characterization of biphenyl dioxygenase sequences and activities encoded by the metagenomes of highly polychlorobiphenyl-contaminated soils. Appl Environ Microbiol. 2012;78:2706–15.

    Article  PubMed Central  PubMed  Google Scholar 

  • Sulaiman S, Yamato S, Kanaya E, et al. Isolation of a novel cutinase homolog wit polyethylene terephthalate-degrading activity from leaf-branch compost by using a metagenomic approach. Appl Environ Microbiol. 2012;78:1556–62.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wang Y, Chen Y, Zhou Q, et al. A culture-independent approach to unravel uncultured bacteria and functional genes in a complex microbial community. PLoS ONE. 2012;7:e47530.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Weinstock GM. Genomic approaches to studying the human microbiota. Nature. 2012;489:250–6.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Georg-August-University Göttingen, Göttingen, Germany

    Heiko Nacke & Rolf Daniel

  2. Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Grisebachstr. 8, Göttingen, D-37077, Germany

    Heiko Nacke & Rolf Daniel

Authors
  1. Heiko Nacke
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rolf Daniel
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Heiko Nacke .

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

© 2014 Springer Science+Business Media New York

About this entry

Cite this entry

Nacke, H., Daniel, R. (2014). Approaches in Metagenome Research: Progress and Challenges. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_790-3

Download citation

  • DOI: https://doi.org/10.1007/978-1-4614-6418-1_790-3

  • 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