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Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples

BACKGROUND: The transport and storage of samples in temperatures of minus 80 °C is commonly considered as the gold standard for microbiome studies. However, studies conducting sample collection at remote sites without a reliable cold-chain would benefit from a sample preservation method that allows...

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Autores principales: Bensch, Hanna M., Tolf, Conny, Waldenström, Jonas, Lundin, Daniel, Zöttl, Markus
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8932309/
https://www.ncbi.nlm.nih.gov/pubmed/35310158
http://dx.doi.org/10.7717/peerj.13095
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author Bensch, Hanna M.
Tolf, Conny
Waldenström, Jonas
Lundin, Daniel
Zöttl, Markus
author_facet Bensch, Hanna M.
Tolf, Conny
Waldenström, Jonas
Lundin, Daniel
Zöttl, Markus
author_sort Bensch, Hanna M.
collection PubMed
description BACKGROUND: The transport and storage of samples in temperatures of minus 80 °C is commonly considered as the gold standard for microbiome studies. However, studies conducting sample collection at remote sites without a reliable cold-chain would benefit from a sample preservation method that allows transport and storage at ambient temperature. METHODS: In this study we compare alpha diversity and 16S microbiome composition of 20 fecal sample replicates from Damaraland mole-rats (Fukomys damarensis) preserved in a minus 80 °C freezer and transported on dry ice to freeze-dried samples that were stored and transported in ambient temperature until DNA extraction. RESULTS: We found strong correlations between relative abundances of Amplicon Sequence Variants (ASVs) between preservation treatments of the sample, no differences in alpha diversity measures between the two preservation treatments and minor effects of the preservation treatment on beta diversity measures. Our results show that freeze-drying samples can be a useful method for cost-effective transportation and storage of microbiome samples that yields quantitatively almost indistinguishable results in 16S microbiome analyses as those stored in minus 80 °C.
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spelling pubmed-89323092022-03-19 Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples Bensch, Hanna M. Tolf, Conny Waldenström, Jonas Lundin, Daniel Zöttl, Markus PeerJ Biodiversity BACKGROUND: The transport and storage of samples in temperatures of minus 80 °C is commonly considered as the gold standard for microbiome studies. However, studies conducting sample collection at remote sites without a reliable cold-chain would benefit from a sample preservation method that allows transport and storage at ambient temperature. METHODS: In this study we compare alpha diversity and 16S microbiome composition of 20 fecal sample replicates from Damaraland mole-rats (Fukomys damarensis) preserved in a minus 80 °C freezer and transported on dry ice to freeze-dried samples that were stored and transported in ambient temperature until DNA extraction. RESULTS: We found strong correlations between relative abundances of Amplicon Sequence Variants (ASVs) between preservation treatments of the sample, no differences in alpha diversity measures between the two preservation treatments and minor effects of the preservation treatment on beta diversity measures. Our results show that freeze-drying samples can be a useful method for cost-effective transportation and storage of microbiome samples that yields quantitatively almost indistinguishable results in 16S microbiome analyses as those stored in minus 80 °C. PeerJ Inc. 2022-03-15 /pmc/articles/PMC8932309/ /pubmed/35310158 http://dx.doi.org/10.7717/peerj.13095 Text en ©2022 Bensch et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Biodiversity
Bensch, Hanna M.
Tolf, Conny
Waldenström, Jonas
Lundin, Daniel
Zöttl, Markus
Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples
title Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples
title_full Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples
title_fullStr Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples
title_full_unstemmed Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples
title_short Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples
title_sort freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples
topic Biodiversity
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8932309/
https://www.ncbi.nlm.nih.gov/pubmed/35310158
http://dx.doi.org/10.7717/peerj.13095
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