Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/30428
Appears in Collections:Biological and Environmental Sciences Journal Articles
Peer Review Status: Refereed
Title: Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics
Author(s): Géron, Augustin
Werner, Johannes
Wattiez, Ruddy
Lebaron, Philippe
Matallana-Surget, Sabine
Keywords: metaproteomics
metagenomics
bioinformatics
mass spectrometry
microbial ecology
Issue Date: 24-Oct-2019
Citation: Géron A, Werner J, Wattiez R, Lebaron P & Matallana-Surget S (2019) Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics. Frontiers in Microbiology, 10, Art. No.: 2395. https://doi.org/10.3389/fmicb.2019.02395
Abstract: Unraveling the complex structure and functioning of microbial communities is essential to accurately predict the impact of perturbations and/or environmental changes. From all molecular tools available today to resolve the dynamics of microbial communities, metaproteomics stands out, allowing the establishment of phenotype–genotype linkages. Despite its rapid development, this technology has faced many technical challenges that still hamper its potential power. How to maximize the number of protein identification, improve quality of protein annotation, and provide reliable ecological interpretation are questions of immediate urgency. In our study, we used a robust metaproteomic workflow combining two protein fractionation approaches (gel-based versus gel-free) and four protein search databases derived from the same metagenome to analyze the same seawater sample. The resulting eight metaproteomes provided different outcomes in terms of (i) total protein numbers, (ii) taxonomic structures, and (iii) protein functions. The characterization and/or representativeness of numerous proteins from ecologically relevant taxa such as Pelagibacterales, Rhodobacterales, and Synechococcales, as well as crucial environmental processes, such as nutrient uptake, nitrogen assimilation, light harvesting, and oxidative stress response, were found to be particularly affected by the methodology. Our results provide clear evidences that the use of different protein search databases significantly alters the biological conclusions in both gel-free and gel-based approaches. Our findings emphasize the importance of diversifying the experimental workflow for a comprehensive metaproteomic study.
DOI Link: 10.3389/fmicb.2019.02395
Rights: © 2019 Géron, Werner, Wattiez, Lebaron and Matallana-Surget. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY - https://creativecommons.org/licenses/by/4.0/). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Licence URL(s): http://creativecommons.org/licenses/by/4.0/

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