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

Study information

Reviewed Marked as Reviewed by Svetlana up on 2025-1-16

study design

laboratory experiment

Citation

PMID PubMed identifier for scientific articles.

35310158

DOI Digital object identifier for electronic documents.

10.7717/peerj.13095

URI

Authors

Bensch HM, Tolf C, Waldenström J, Lundin D, Zöttl M

Journal

PeerJ

Year

2022

Keywords:

16S, Amplicon, DNA metabarcoding, Damaraland mole-rat, Fecal samples, Freeze-drying, Fukomys damarensis, Microbiome

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.

Experiment 1

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Reviewed Marked as Reviewed by Svetlana up on 2025-1-16

Curated date: 2024/11/21

Curator: Tosin

Revision editor(s): Tosin

Subjects

Location of subjects: South Africa

Host species Species from which microbiome was sampled. Contact us to have more species added.: Fukomys damarensis

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Freeze dried specimen Freeze dried specimen,freeze dried specimen

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Frozen samples

Group 1 name Corresponds to the case (exposed) group for case-control studies: Freeze dried samples.

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Freeze dried samples are samples preservation treatment stored and transported at ambient temperature until DNA extraction.

Group 0 sample size Number of subjects in the control (unexposed) group: 20

Group 1 sample size Number of subjects in the case (exposed) group: 20

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: Mann-Whitney (Wilcoxon)

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Richness Number of species: unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: unchanged

Signature 2

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Curated date: 2024/11/21

Curator: Tosin

Revision editor(s): Tosin

Source: Figure 4, Table S1

Description: Log-transformed relative abundances of families with > 1% mean relative abundance between Frozen and Freeze-dried sample preservation treatments.

Abundance in Group 1: decreased abundance in Freeze dried samples.

NCBI	Quality Control	Links
Christensenellaceae
Lachnospiraceae
Oscillospiraceae

Revision editor(s): Tosin