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Metaproteomics: together to be stronger!

Metaproteomics provides valuable snapshots of the functional state of microbiota. But the protocols used are still very diverse and the results not always easily comparable. The actors of the discipline, including Jean Armengaud's team (LI2D, Marcoule), are organizing themselves to be able to make the technique even more powerful.

Published on 31 January 2022

The French press recently echoed the interest of the scientific and oyster farming communities in oyster microbiota (original paper: Seaweeds influence oyster microbiota and disease susceptibility - Journal of Animal Ecology - Wiley Online Library). A link has been established between the good health of oysters and the influence of certain algae on their microbiota. This example illustrates the importance of understanding how the microorganisms of a microbiota function and interact with each other and with their environment over time. Above all, it shows that the interest in the study of microbiota goes far beyond the medical applications to which it is often confined for the general public. Microbiota analysis techniques are used for applications in many industrial sectors (agri-food, environmental...). 

What are the available means of analysis?

Metagenomics is the most widely used approach to study microbiota. However, knowing the genomic heritage does not provide reliable information on microbial functional traits that actually change rapidly in response to stimuli from host metabolism, immunity, neurobiology, diet or other environmental factors that induce substrate change.

Metaproteomics offers broader perspectives: by identifying and measuring the proteins that make up a microbiota, it provides "snapshots" of the functional state of a microbiota. But while metagenomics is relatively standardized, experimental protocols for proteomics are still very diverse and in full development.

A structuring of the community is necessary

Under the impetus of European leaders in the field of metaproteomics, such as Jean Armengaud, researcher at Li2D and head of the ProGénomix platform (MTS department of CEA-Joliot, Marcoule), the international metaproteomics community initiated a network in 2021 in order to federate expertise to give added value to the functional characterizations of microbiota. The Metaproteomics Initiative[1], which includes 62 laboratories, is working to:

  • make the most advanced methodologies in this field available to all researchers exploring microbiota,
  • compare these methodologies and refine their limits and fields of application,
  • standardize them for cross-platform analysis of cohorts of samples of medical interest,
  • exploit these data by integrating all the modern tools of the microbiologist,
  • undertake large-scale projects.

An example: international cross-platform comparison

LI2D's ProGénoMix platform has participated in the first international benchmarking exercise in proteomic analysis. The objective of this comparative study, whose results were published in Nature Communications[2], was to evaluate the best practices for research on microbiota, with a focus on their functioning.

The study compared the performance of the participating platforms for the analysis of two test samples: an artificial assembly of microorganisms and microbiota directly extracted from human feces. The results reveal a high variability in the peptides identified and quantified during the measurements. This variability is due to the different protocols of sample preparation and measurement settings, and the great diversity of peptides present in the samples leading to a sampling effect. However, the differences disappear when the data are analyzed at a higher level of interpretation: the analysis of proteins or their functions erases this variability. Thus, metaproteomics provides a reliable picture of the microbial composition and functional profiles of each sample


Contact CEA Joliot's institute: 

Jean Armengaud

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