An ambient temperature collection and stabilization strategy for canine microbiota studies

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.

Visualizing the Growth and Division of Rat Gut Bacteria by D-Amino Acid-Based in vivo Labeling and FISH Staining

“…The capability to differentiate bacteria of certain taxa growing at different stages, also offers an opportunity to better understand a complete cell cycle in vivo. Moreover, studies on gut microbiota of other mammalian hosts such as guinea pig (Hildebrand et al, 2012), pigs (Lamendella et al, 2011;Quan et al, 2020;Tang et al, 2020), dogs (Lin C. Y. et al, 2020), cats (Lyu et al, 2020), and primates such as chimpanzees (Moeller et al, 2016) and macaques (Manuzak et al, 2020), might also benefit by this integrative labeling techniques.…”

On the Variability of Microbial Populations and Bacterial Metabolites within the Canine Stool. An in-Depth Analysis

“…and Firmicutes in the inner part of human stool [ 15 ]. In a study conducted with 30 female Beagles, Lin et al found differences in the canine microbiota when comparing faecal aliquots [ 20 ]. However, none of the nine microbial genera who differed in the study by Lin et al [ 20 ] were analysed in the present study, with the exception of Clostridia.…”

“…In a study conducted with 30 female Beagles, Lin et al found differences in the canine microbiota when comparing faecal aliquots [ 20 ]. However, none of the nine microbial genera who differed in the study by Lin et al [ 20 ] were analysed in the present study, with the exception of Clostridia. The authors collected the fresh faecal specimens from both ends and the middle of each faecal sample, but they did not clarify if subsamples were collected from the centre or the surface of the stool.…”

“…Although the microbial groups selected for this study are representative of the main key taxa of the dog’s microbiota, it must be pointed that they do not fully represent the entirety of the microbiota. In contrast, Lin et al observed changes in nine microbial genera using the Illumina MiSeq platform, which allowed a more comprehensive analysis of the complex and diverse faecal microbial communities [ 20 ].…”

“…Several authors reported discrepancies in the abundances of bacterial taxa between studies, attributed mainly to inter-individual differences [ 8 , 9 ], different DNA extraction protocols and sample storage conditions [ 10 , 11 , 12 ], and the application of different Next Generation Sequencing protocols [ 13 , 14 ]. Few papers focused the attention on the impact that different sampling methods have on the variability of the human [ 15 , 16 , 17 , 18 , 19 ] and canine [ 20 ] stool microbial community, while only Gratton et al highlighted that spot sampling of faecal specimens resulted in a high degree of metabolic variation within human stool [ 21 ]. In veterinary medicine, most of the studies that are available perform DNA extraction using small aliquots of faeces with no homogenisation procedure of the sample.…”