Estimating relative biomasses of organisms in microbiota using "phylopeptidomics"

Microbiome
Olivier PibleJean Armengaud

Abstract

There is an important need for the development of fast and robust methods to quantify the diversity and temporal dynamics of microbial communities in complex environmental samples. Because tandem mass spectrometry allows rapid inspection of protein content, metaproteomics is increasingly used for the phenotypic analysis of microbiota across many fields, including biotechnology, environmental ecology, and medicine. Here, we present a new method for identifying the biomass contribution of any given organism based on a signature describing the number of peptide sequences shared with all other organisms, calculated by mathematical modeling and phylogenetic relationships. This so-called "phylopeptidomics" principle allows for the calculation of the relative ratios of peptide-specified taxa by the linear combination of such signatures applied to an experimental metaproteomic dataset. We illustrate its efficiency using artificial mixtures of two closely related pathogens of clinical interest, and with more complex microbiota models. This approach paves the way to a new vision of taxonomic changes and accurate label-free quantitative metaproteomics for fine-tuned functional characterization. Video abstract.

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Citations

Jul 2, 2021·Frontiers in Genetics·Susana Martínez ArbasShaman Narayanasamy
Oct 1, 2021·Microbiome·Virginie JouffretJean Armengaud

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Methods Mentioned

BETA
tandem spectrometry
protein extraction

Software Mentioned

optimize
MinGW
Matrix Science msparser
Mascot Science
CLUSTAL W
Fido
SEQUEST
Gblocks
DIAMOND
Phylopeptidomics

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