Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics.
bioinformatics
mass spectrometry
metagenomics
metaproteomics
microbial ecology
Journal
Frontiers in microbiology
ISSN: 1664-302X
Titre abrégé: Front Microbiol
Pays: Switzerland
ID NLM: 101548977
Informations de publication
Date de publication:
2019
2019
Historique:
received:
15
07
2019
accepted:
03
10
2019
entrez:
12
11
2019
pubmed:
12
11
2019
medline:
12
11
2019
Statut:
epublish
Résumé
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
Identifiants
pubmed: 31708885
doi: 10.3389/fmicb.2019.02395
pmc: PMC6821674
doi:
Types de publication
Journal Article
Langues
eng
Pagination
2395Informations de copyright
Copyright © 2019 Géron, Werner, Wattiez, Lebaron and Matallana-Surget.
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