Background: To date, no studies have evaluated the stability of the fecal microbiome of healthy dogs over six months. Knowledge of microbiome dynamics and stability could enhance its use as a diagnostic and therapeutic tool. Hypothesis/
Objectives: Determine the degree of temporal variability observed in canine fecal microbiomes and identify the bacterial species that are the most dynamic over time. Animals: Thirty-five healthy pet dogs with no history of clinical signs, physical conditions, or medication use were sampled longitudinally over a median of 1.07 years (0.3–2.64 years), with samples collected every 30 days.
Methods: Full-length PacBio 16S rRNA gene sequence data from fecal samples were analyzed in R. Microbiome variability was assessed using sample distance to centroid, which captures how much a dog's microbiome deviates from its compositional center. Temporal variability of 28 core bacterial species was quantified using Coefficients of Variation.
Results: Fecal microbiome composition was highly variable over time in the surveyed dogs and also showed individual-specific signatures. All 28 bacterial species exhibited substantial temporal fluctuations (median CV: 80%–323%). Megamonas funiformis, Prevotella copri, Peptacetobacter hiranonis, Blautia marasmi, and Collinsella intestinalis were the most stable, while Escherichia coli, Streptococcus gallolyticus, Enterococcus faecium, and Enterococcus hirae were the most dynamic.
Conclusions: The fecal microbiomes of healthy dogs vary considerably over time, indicating that temporal variability is an inherent characteristic of canine microbial communities. These findings highlight the need for longitudinal sampling in microbiome studies, particularly for therapeutic interventions.
