Host-specific variations in the gut microbiome of cats and dogs identified through culturomics and high-throughput sequencing analysis

Abstract

The gut microbiome plays a critical role in host health, digestion and immunity amongst others. Currently, cats and dogs are widely assumed to have similar gut microbiome compositions and therefore often receive similar veterinary care. This study, therefore, aimed at characterising the canine and feline gut microbiome. This was achieved by implementing a combined approach of culturomics and high-throughput sequencing (HTS) analysis. Culturomics revealed considerable variations between the cultivable populations depending on host species, including targeted bacterial populations and many previously uncultured bacteria. Significant host-specific differences in the gut microbiome were also uncovered using HTS. There was more variation in within-sample (alpha) diversity when assessing the feline faecal samples compared to canine samples. There was no overlap between host species when assessing between-sample (beta) diversity, highlighting the significant difference in composition. Analysis of HTS data also revealed key bacterial genera that shaped the variation between host species. This study also uncovered the influence of 16S rRNA hypervariable region selection on the resulting analyses. Comparing hypervariable regions V4 and V1-V2 resulted in considerable differences in the number of genus-level assignments made and alpha diversity measures, with the V1-V2 reads identifying more taxa and elucidating more variation in diversity estimates. Applying culturomics and HTS to the same sample population also enabled further downstream analysis into the biochemical capabilities of bacterial genera found to influence the diversity between the canine and feline gut microbiome. These findings revealed differences in the biochemical capabilities of canine and feline faecal isolates, particularly in amino acid utilisation and pH tolerance. This study revealed substantial host-specific differences in the canine and feline gut microbiome. Through the amalgamation of findings resulting from culturomics and HTS, this study provides a comprehensive insight into the complexity of the companion animal gut microbiome and provides a better understanding of the requirements for host-specific veterinary care.