BioinformaticsMicrobiomeScientificLabrador vs Beagle: An Exploration of the Canine Gut Microbiome

8 July 2022by Dana Walsh0

By Barış Özdinç

 

Dogs have been man’s best friend for centuries and continue to be popular pets today. According to the American Pet Products Association National Pet Owners Survey, 53.4% of American households own a dog. People love their dogs like family members and may be naturally interested in ways in which to improve their furry companion’s health and longevity. The gut microbiome has known impacts on human health, including body weight, immunity, and metabolism. It has similar impacts on dog health (Pilla 2019) and may even influence the dog’s owner’s microbiome, especially if that owner is an infant (Tun 2017). It is known that human genetics can influence the gut microbiome, and a previous study indicates that different dog breeds, which differ genetically, may have specific gut microbiota signatures (Reddy 2019). In our microbiome dataset comparison this week, we look at gut microbiome differences between 32 beagles and 32 labradors. This data comes from a study by Coelho et al. (2018), who fed the dogs the same baseline diet. We imported the publicly available data using the Sequence Read Archive importer tool on the CosmosID-HUB, filtered the data, and analyzed the microbiome variation.

Figure 1: A heatmap illustrating bacterial species abundance of samples from beagle (blue) and labrador (green) cohorts.

 

Comparing the two breeds bacterial species abundance scores in the heatmap (Figure 1) illustrates an intermixing of the samples, highlighting that dog breed may not be strongly associated with gut bacteriome variation, at least at the species level. There is an interesting cluster on the right end of the heatmap composed of mainly beagle samples with high abundance of Lachnospiraceae. When we instead look at the phylum level in Figure 2 we see some clustering by breed, with labradors having more Bacteroidetes and beagles having more Firmicutes. On either end of the heatmap are clusters with mostly beagle samples, one with similar Bacteroidetes and Firmicutes abundances and another with extreme Firmicutes abundance but lower Bacteroidetes. Although the dogs started the study on the same diet, they differed in sex, age, and body weight. One of these confounding factors may influence the clustering we observe among the beagle microbiomes.

 

Figure 2: A heatmap illustrating bacterial phlya abundance of samples from beagle (blue) and labrador (green) cohorts.

 

We next performed alpha and beta diversity testing on the samples to identify significant differences in diversity between the breeds. None of the tested alpha diversity indexes (CHAO1, Simpson and Shannon) were significantly different, highlighting that beagles and labradors have similar amounts of different species with similar abundance in their guts. Investigating beta diversity differences provides a slightly different story. Here, the Jaccard dissimilarity matrix comparison of the two breeds showed a difference (p = 0.021), implying that some taxa are present or absent only in one breed or the other. The Bray-Curtis dissimilarity matrix was not significant (p = 0.059, Figure 3). This suggests that the significance found by the Jaccard index may be driven by low-abundance species that may not drive an overall difference between the communities.

 

Figure 3: A PCoA plot illustrating the beta diversity analysis of the Bray-Curtis dissimilarity matrix of beagles (blue) and labradors (green).

 

To identify specific taxa that may be significantly different between the breeds, we used the differential abundance tool LEfSe (Linear discriminant analysis effect size). LefSe identified 9 differentially abundant species in beagles and 13 in labradors (Figure 4). These results suggest that beagles may be prone to gastroenteritis due to significant enrichment of Helicobacter winghamensis and Campylobacter upsaliensis. These bacteria are known agents of gastroenteritis in dogs, as well as gastrointestinal disorders in humans (Solnick et al. 2002, Bourke et al. 1998). Species that are differentially abundant in labradors include: Prevotella copri and Prevotella pectiovora, which are associated with plant-rich diets (Kovatcheva-Datchary et al. 2015); Parabacteroides distasonis, which may alleviate obesity and metabolic dysfunction (Wang et al. 2019); Paraprevotella xylaniphila, which is associated with an active lifestyle (Bressa et al. 2017); and Turibacter sanguinis, which plays important roles in serotonin metabolism in humans (Fung et al. 2019). To conclude, LefSe analysis suggests that beagles have more enrichment of dysbiotic species, but labradors have more beneficial bacteria enriched in their guts. These findings show that the gut microbiome may differ by dog breed and influence the health of the animal. In this comparison we have not taken into account any differences by dog age, sex, or body weight. These factors are known to influence the gut microbiome in humans and are likely to do so in dogs as well. In a later update we will explore dog microbiome variation by these factors and determine their influence on the differences we found this week. Stay tuned for more!

Figure 3: A barchart illustrating the significantly differentially abundant species in beagles (blue) and labradors (green). Effect sizes are shown on the x-axis.

 

Dana Walsh

Dana Walsh is a microbiome scientist whose career has consisted of a blend of wet bench and computational research. Currently, she is a Microbiome Scientist for CosmosID where she helps clients with custom microbiome analysis and interpretation as well as exploring new tools and methods for microbiome studies. She applies cutting-edge tools to integrate multi-omics data, including taxonomic, functional, meta-transcriptomics and metabolomics data, in order to help clients derive meaning from their results.

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