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Profiling of Active Microorganisms by Stable Isotope Probing—Metagenomics

  • Eileen Kröber
  • Özge EyiceEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2046)

Abstract

Stable isotope probing (SIP) provides researchers a culture-independent method to retrieve nucleic acids from active microbial populations performing a specific metabolic activity in complex ecosystems. In recent years, the use of the SIP method in microbial ecology studies has been accelerated. This is partly due to the advances in sequencing and bioinformatics tools, which enable fast and reliable analysis of DNA and RNA from the SIP experiments. One of these sequencing tools, metagenomics, has contributed significantly to the body of knowledge by providing data not only on taxonomy but also on the key functional genes in specific metabolic pathways and their relative abundances. In this chapter, we provide a general background on the application of the SIP-metagenomics approach in microbial ecology and a workflow for the analysis of metagenomic datasets using the most up-to-date bioinformatics tools.

Key words

Microbial diversity Stable isotope probing Metagenomics Bioinformatics 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Microbial Biogeochemistry, RA Landscape FunctioningZALF Leibniz Centre for Landscape ResearchMünchebergGermany
  2. 2.School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK

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