Abstract
Similar to humans, the fecal microbiome of dogs may be useful in diagnosing diseases or assessing dietary interventions. The accuracy and reproducibility of microbiome data depend on sample integrity, which can be affected by storage methods. Here, we evaluated the ability of a stabilization device to preserve canine fecal samples under various storage conditions simulating shipping in hot or cold climates. Microbiota data from unstabilized samples stored at room temperature (RT) and samples placed in PERFORMAbiome·GUT collection devices (PB-200) (DNA Genotek, Inc. Ottawa, Canada) and stored at RT, 37 °C, 50 °C, or undergoing repeated freeze–thaw cycles, were compared with freshly extracted samples. Alpha- and beta diversity indices were not affected in stabilized samples, regardless of storage temperature. Unstabilized samples stored at RT, however, had higher alpha diversity. Moreover, the relative abundance of dominant bacterial phyla (Firmicutes, Fusobacteria, Bacteriodetes, and Actinobacteria) and 24 genera were altered in unstabilized samples stored at RT, while microbiota abundance was not significantly changed in stabilized samples stored at RT. Our results suggest that storage method is important in microbiota studies and that the stabilization device may be useful in maintaining microbial profile integrity, especially for samples collected off-site and/or those undergoing temperature changes during shipment or storage.
Highlights
Similar to humans, the fecal microbiome of dogs may be useful in diagnosing diseases or assessing dietary interventions
The microbiome field has much to offer, but appropriate sample collection and storage methods are needed for sample integrity and accurate and reproducible data
All baseline samples were extracted on the collection day within 2 hours, including three stabilized samples (D0-37/50, D0-FT, D0-room temperature (RT)) and one unstabilized sample (D0-UNST) were compared
Summary
The fecal microbiome of dogs may be useful in diagnosing diseases or assessing dietary interventions. The accuracy and reproducibility of microbiome data depend on sample integrity, which can be affected by storage methods. Our results suggest that storage method is important in microbiota studies and that the stabilization device may be useful in maintaining microbial profile integrity, especially for samples collected off-site and/or those undergoing temperature changes during shipment or storage. The microbiome field has much to offer, but appropriate sample collection and storage methods are needed for sample integrity and accurate and reproducible data. Previous studies used a commercially available ambient temperature stabilization device OMNIgeneGUT (DNA Genotek, Inc. Ottawa, Canada) to collect and store human fecal samples. Canada) to collect and store human fecal samples Results suggested that this device maintained the integrity of microbiome data and allowed for a higher recovery of nucleic acids at room temperature when compared with freezing at − 20 °C23–25. There is, limited information about canine fecal sample collection and storage methods
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