A simplified protocol for DNA extraction from FTA cards for faecal microbiome studies
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A simplified protocol for DNA extraction from FTA cards for faecal microbiome studies. / Botnen, Amanda Bolt; Bjørnsen, Mads Bjørn; Alberdi, Antton; Gilbert, M. Thomas P.; Aizpurua, Ostaizka.
In: Heliyon, Vol. 9, No. 1, e12861, 2023.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - A simplified protocol for DNA extraction from FTA cards for faecal microbiome studies
AU - Botnen, Amanda Bolt
AU - Bjørnsen, Mads Bjørn
AU - Alberdi, Antton
AU - Gilbert, M. Thomas P.
AU - Aizpurua, Ostaizka
N1 - Publisher Copyright: © 2023 The Authors
PY - 2023
Y1 - 2023
N2 - As metagenomic studies continue to increase in size and complexity, they are often required to incorporate data from geographically isolated locations or longitudinal time samples. This represents a technical challenge, given that many of the commonly used methods used for sample collection, storage, and DNA extraction are sensitive to differences related to the time, storage and chemistry involved. FTA cards have been previously proposed as a simple, reliable and cost-efficient method for the preservation of animal faecal microbiomes. In this study, we report a simplified extraction methodology for recovering microbiome DNA from faeces stored on FTA cards and compare its performance to a common alternative means of characterising such microbiomes; namely, immediate freezing of the faeces followed by DNA extraction using the Qiagen PowerSoil DNA isolation kit. Our results show that overall the application of our simplified DNA extraction methodology yields microbial community results that have higher diversity and an expanded core microbiome than that found using the PowerSoil methodology. This suggests that the FTA card extraction method presented here is a viable alternative for metagenomic studies using faecal material when traditional freeze-based storage methods are not feasible.
AB - As metagenomic studies continue to increase in size and complexity, they are often required to incorporate data from geographically isolated locations or longitudinal time samples. This represents a technical challenge, given that many of the commonly used methods used for sample collection, storage, and DNA extraction are sensitive to differences related to the time, storage and chemistry involved. FTA cards have been previously proposed as a simple, reliable and cost-efficient method for the preservation of animal faecal microbiomes. In this study, we report a simplified extraction methodology for recovering microbiome DNA from faeces stored on FTA cards and compare its performance to a common alternative means of characterising such microbiomes; namely, immediate freezing of the faeces followed by DNA extraction using the Qiagen PowerSoil DNA isolation kit. Our results show that overall the application of our simplified DNA extraction methodology yields microbial community results that have higher diversity and an expanded core microbiome than that found using the PowerSoil methodology. This suggests that the FTA card extraction method presented here is a viable alternative for metagenomic studies using faecal material when traditional freeze-based storage methods are not feasible.
KW - 16S rRNA
KW - Cats
KW - Dry preservatives
KW - Longitudinal studies
KW - Metabarcoding
KW - Metagenomics
KW - Microbiota
KW - PowerSoil
U2 - 10.1016/j.heliyon.2023.e12861
DO - 10.1016/j.heliyon.2023.e12861
M3 - Journal article
C2 - 36699263
AN - SCOPUS:85146341324
VL - 9
JO - Heliyon
JF - Heliyon
SN - 2405-8440
IS - 1
M1 - e12861
ER -
ID: 340110539