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Updated: Jul 7, 2026

DNA Stable-Isotope Probing DNA-SIP
Published on: August 2, 2010
Revealing taxonomy, activity, and substrate assimilation in mixed bacterial communities by GroEL-proteotyping-based
Simon Klaes1,2, Shobhit Madan1,3, Darja Deobald1
1Department of Molecular Environmental Biotechnology, Helmholtz-Centre for Environmental Research - UFZ, 04318 Leipzig, Saxony, Germany.
None:
Protein-based stable isotope probing (protein-SIP) can link microbial taxa to substrate assimilation. Traditionally, protein-SIP requires a sample-specific metagenome-derived database for samples with unknown composition. Here, we describe GroEL-prototyping-based stable isotope probing (GroEL-SIP), that uses GroEL as a taxonomic marker protein to identify bacterial taxa (GroEL-proteotyping) coupled to SIP directly linking identified taxa to substrate consumption. GroEL-SIP's main advantages are that (1) it can be performed with a sample-independent database and (2) sample complexity can be reduced by enriching GroEL proteins, increasing sensitivity and reducing instrument time. We applied GroEL-SIP to pure cultures, synthetic bicultures, and a human gut model using 2H-, 18O-, and 13C-labeled substrates. While 2H and 18O allowed assessing general activity, 13C enabled differentiation of substrate source and utilized metabolic pathways. GroEL-SIP offers fast and straightforward protein-SIP analyses of highly abundant families in mixed bacterial communities, but further work is needed to improve sensitivity, resolution, and database coverage.
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