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Related Concept Videos

Labeling DNA Probes03:31

Labeling DNA Probes

DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
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Updated: Jun 6, 2026

DNA Stable-Isotope Probing (DNA-SIP)
14:57

DNA Stable-Isotope Probing (DNA-SIP)

Published on: August 2, 2010

Protein-based stable isotope probing.

Nico Jehmlich1, Frank Schmidt, Martin Taubert

  • 1Department of Proteomics, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.

Nature Protocols
|December 4, 2010
PubMed
Summary
This summary is machine-generated.

Stable isotope probing (SIP) links microbial metabolism to identity. This protein-SIP method uses labeled substrates to track which microbes consume specific nutrients, revealing their function in ecosystems.

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Workflow Based on the Combination of Isotopic Tracer Experiments to Investigate Microbial Metabolism of Multiple Nutrient Sources
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Identification of Metabolically Active Bacteria in the Gut of the Generalist Spodoptera littoralis via DNA Stable Isotope Probing Using 13C-Glucose
12:11

Identification of Metabolically Active Bacteria in the Gut of the Generalist Spodoptera littoralis via DNA Stable Isotope Probing Using 13C-Glucose

Published on: November 13, 2013

Area of Science:

  • Microbiology
  • Metagenomics
  • Proteomics
  • Stable Isotope Probing

Background:

  • Linking microbial metabolic activity to specific organisms is crucial for understanding ecosystem functions.
  • Traditional methods often struggle to directly connect phylogenetic information with in-situ metabolic functions.
  • Stable isotope probing (SIP) offers a powerful approach to trace nutrient assimilation by microorganisms.

Purpose of the Study:

  • To present a detailed protocol for protein-based stable isotope probing (protein-SIP).
  • To enable the direct linkage of microbe-specific metabolic function with phylogenetic information.
  • To provide a comprehensive guide for researchers utilizing SIP in cultivation experiments.

Main Methods:

  • Utilized carbon ((13)C) or nitrogen ((15)N)-labeled substrates (>98% heavy label) in microbial cultivation.
  • Determined heavy isotope incorporation into proteins (protein-SIP) to quantify substrate assimilation.
  • Employed mass spectrometry-based peptide analysis for phylogenetic identification of metabolizing microorganisms.

Main Results:

  • Developed a robust protein-SIP protocol covering protein extraction, separation, and mass spectrometric analysis.
  • Demonstrated that isotope incorporation levels directly correlate with substrate assimilation by specific microbes.
  • Successfully linked substrate metabolism to microbial phylogeny through peptide sequence analysis.

Conclusions:

  • Protein-SIP is an effective technique for assigning metabolic functions to specific microbial taxa.
  • The protocol facilitates the integration of proteomics and phylogenetic analyses for microbial ecology studies.
  • This method allows for rapid (2-3 days for extraction and mass fingerprinting) insights into microbial processes.