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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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2022
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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. |
format | Online Article Text |
id | pubmed-8932309 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
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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