Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities

Proc Natl Acad Sci U S A. 2018 Jun 12;115(24):E5576-E5584. doi: 10.1073/pnas.1722325115. Epub 2018 May 29.


Measurements of stable carbon isotope ratios (δ13C) are widely used in biology to address questions regarding food sources and metabolic pathways used by organisms. The analysis of these so-called stable isotope fingerprints (SIFs) for microbes involved in biogeochemical cycling and microbiota of plants and animals has led to major discoveries in environmental microbiology. Currently, obtaining SIFs for microbial communities is challenging as the available methods either only provide low taxonomic resolution, such as the use of lipid biomarkers, or are limited in throughput, such as nanoscale secondary ion MS imaging of single cells. Here we present "direct protein-SIF" and the Calis-p software package (, which enable high-throughput measurements of accurate δ13C values for individual species within a microbial community. We benchmark the method using 20 pure culture microorganisms and show that the method reproducibly provides SIF values consistent with gold-standard bulk measurements performed with an isotope ratio mass spectrometer. Using mock community samples, we demonstrate that SIF values can also be obtained for individual species within a microbial community. Finally, a case study of an obligate bacteria-animal symbiosis shows that direct protein-SIF confirms previous physiological hypotheses and can provide unexpected insights into the symbionts' metabolism. This confirms the usefulness of this approach to accurately determine δ13C values for different species in microbial community samples.

Keywords: Protein-SIP; Q Exactive; metaproteome; microbial ecology; microbiome.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Carbon / metabolism*
  • Carbon Isotopes / metabolism
  • Environmental Microbiology
  • Isotope Labeling / methods
  • Metabolic Networks and Pathways / physiology*
  • Microbiota / physiology*
  • Proteome / metabolism*
  • Proteomics / methods*
  • Software
  • Symbiosis / physiology


  • Carbon Isotopes
  • Proteome
  • Carbon