GI17 - To Sample or Not to Sample: Capturing Feline Fecal Microbiome Changes with High-frequency Sample Collection

Abstract: Background: Microbiome-based fecal evaluations are promising diagnostic tools for assessing feline health. However, given inherent daily changes in the gut microbiome, the ideal sampling frequency is unknown.

Hypothesis: High-frequency fecal sampling is more effective than weekly sampling at capturing changes in the feline fecal microbiome in response to a new diet.

Animals: This clinical trial was performed in six healthy and sterilized purpose-bred cats (3 male, 3 female) group-housed in a research facility.

Methods: All cats were fed an adult commercial wet food diet, at maintenance needs, to which they had no previous exposure. Feces was collected daily for 36 days. 16s rRNA microbiome analysis (V4 region) was performed using R-Studio. Pairwise PERMANOVA evaluated changes in composition. A subset of data (once-weekly samples) was compared to the high-frequency (daily) dataset to evaluate daily versus weekly fecal sampling effects.

Results: With high-frequency sampling, the fecal microbiome composition of each cat differed by day (P < 0.01). Despite being co-housed, daily sampling identified distinct microbiome compositions between cats at all time points (P < 0.0001). With once weekly sampling, no compositional differences between cats were detected and there were decreased differences over time (sampling week) (P < 0.05) for all cats.

Conclusions and Clinical Importance: Daily sampling or pooled samples may more accurately capture fecal microbiome dynamics compared to weekly sampling. Ongoing analysis will evaluate taxa contributing to daily versus weekly microbiome changes and compare sampling frequencies (e.g. twice weekly) to daily sampling to establish appropriate sampling frequencies for future microbiome studies.