Multi-Omics Analysis Unravels the Impact of Stool Sample Logistics on Metabolites and Microbial Composition.

Autor:	Krause JL; German Rheumatism Research Center Berlin, A Leibniz Institute-DRFZ, Schwiete Laboratory for Microbiota and Inflammation, 10117 Berlin, Germany., Engelmann B; Helmholtz-Centre for Environmental Research-UFZ, Department of Molecular Toxicology, 04318 Leipzig, Germany., Lallinger DJD; German Rheumatism Research Center Berlin, A Leibniz Institute-DRFZ, Schwiete Laboratory for Microbiota and Inflammation, 10117 Berlin, Germany., Rolle-Kampczyk U; Helmholtz-Centre for Environmental Research-UFZ, Department of Molecular Toxicology, 04318 Leipzig, Germany., von Bergen M; Helmholtz-Centre for Environmental Research-UFZ, Department of Molecular Toxicology, 04318 Leipzig, Germany.; Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, 04103 Leipzig, Germany.; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany., Chang HD; German Rheumatism Research Center Berlin, A Leibniz Institute-DRFZ, Schwiete Laboratory for Microbiota and Inflammation, 10117 Berlin, Germany.; Department for Cytometry, Institute of Biotechnology, Technical University Berlin, 10115 Berlin, Germany.
Jazyk:	angličtina
Zdroj:	Microorganisms [Microorganisms] 2024 Sep 30; Vol. 12 (10). Date of Electronic Publication: 2024 Sep 30.
DOI:	10.3390/microorganisms12101998
Abstrakt:	Human health and the human microbiome are inevitably intertwined, increasing their relevance in clinical research. However, the collection, transportation and storage of faecal samples may introduce bias due to methodological differences, especially since postal shipping is a common practise in large-scale clinical cohort studies. Using four different Omics layer, we determined the structural (16S rRNA sequencing, cytometric microbiota profiling) and functional integrity (SCFAs, global metabolome) of the microbiota in relation to different easy-to-handle conditions. These conditions were storage at -20 °C, -20 °C as glycerol stock, 4 °C and room temperature with and without oxygen exposure for a maximum of one week. Storage time affected the microbiota on all Omics levels. However, the magnitude was donor-dependent, highlighting the need for purpose-optimized sample collection in clinical multi-donor studies. The effects of oxygen exposure were negligible for all analyses. At ambient temperature, SCFA and compositional profiles were stable for 24 h and 48 h, respectively, while at 4 °C, SCFA profiles were maintained for 48 h. The global metabolome was highly susceptible, already changing at 24 h in non-frozen conditions. Thus, faecal microbiota was best preserved on all levels when transported as a native sample frozen within 24 h, leading to the least biased outcomes in the analysis. We conclude that the immediate freezing of native stool samples for transportation to the lab is best suited for planned multi-Omics analyses that include metabolomics to extend standard sequencing approaches. Competing Interests: The authors declare no conflict of interest.
Databáze:	MEDLINE
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