Sample preservation and storage significantly impact taxonomic and functional profiles in metaproteomics studies of the human gut microbiome

Please always quote using this URN: urn:nbn:de:bvb:20-opus-195976
  • 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 aWith 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.show moreshow less

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Metadaten
Author: Oskar Hickl, Anna Heintz-Buschart, Anke Trautwein-Schult, Rajna Hercog, Peer Bork, Paul Wilmes, Dörte Becher
URN:urn:nbn:de:bvb:20-opus-195976
Document Type:Journal article
Faculties:Fakultät für Biologie
Language:English
Parent Title (English):Microorganisms
ISSN:2076-2607
Year of Completion:2019
Volume:7
Issue:9
Article Number:367
Source:Microorganisms (2019) 7:9, 367. https://doi.org/10.3390/microorganisms7090367
DOI:https://doi.org/10.3390/microorganisms7090367
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Tag:RNAlater; flash freezing; metagenomics; metaproteomics; microbiome; microbiota; proteomics; sample storage
Release Date:2022/04/29
Date of first Publication:2019/09/19
Licence (German):License LogoCC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International