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Open AccessArticle

Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome

1
Institute of Microbiology, University of Greifswald, D-17489 Greifswald, Germany
2
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, D-04103 Leipzig, Germany
3
Helmholtz Centre for Environmental Research GmbH – UFZ, D-06120 Halle, Germany
4
Luxembourg Centre for Systems Biomedicine, Université du Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
5
European Molecular Biology Laboratory Heidelberg, D-69117 Heidelberg, Germany
6
Max Delbrück Centre for Molecular Medicine, D-13125 Berlin, Germany
7
Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory and University Hospital Heidelberg, D-69120 Heidelberg, Germany
8
Faculty of Biology, University of Würzburg, D-97074 Würzburg, Germany
*
Author to whom correspondence should be addressed.
Microorganisms 2019, 7(9), 367; https://doi.org/10.3390/microorganisms7090367
Received: 29 August 2019 / Revised: 13 September 2019 / Accepted: 17 September 2019 / Published: 19 September 2019
(This article belongs to the Special Issue Towards Integrated Multi-omics Analyses of Environmental Microbiota)
With the technological advances of the last decade, it is now feasible to analyze microbiome samples, such as human stool specimens, using multi-omic techniques. Given the inherent sample complexity, there exists a need for sample methods which preserve as much information as possible about the biological system at the time of sampling. Here, we analyzed human stool samples preserved and stored using different methods, applying metagenomics as well as metaproteomics. Our results demonstrate that sample preservation and storage have a significant effect on the taxonomic composition of identified proteins. The overall identification rates, as well as the proportion of proteins from Actinobacteria were much higher when samples were flash frozen. Preservation in RNAlater overall led to fewer protein identifications and a considerable increase in the share of Bacteroidetes, as well as Proteobacteria. Additionally, a decrease in the share of metabolism-related proteins and an increase of the relative amount of proteins involved in the processing of genetic information was observed for RNAlater-stored samples. This suggests that great care should be taken in choosing methods for the preservation and storage of microbiome samples, as well as in comparing the results of analyses using different sampling and storage methods. Flash freezing and subsequent storage at −80 °C should be chosen wherever possible. View Full-Text
Keywords: proteomics; metaproteomics; metagenomics; microbiome; microbiota; flash freezing; RNAlater; sample storage proteomics; metaproteomics; metagenomics; microbiome; microbiota; flash freezing; RNAlater; sample storage
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MDPI and ACS Style

Hickl, O.; Heintz-Buschart, A.; Trautwein-Schult, A.; Hercog, R.; Bork, P.; Wilmes, P.; Becher, D. Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome. Microorganisms 2019, 7, 367.

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