# Shotgun Metagenomics Reveals Gut Microbiome Remodeling with Altered Taxonomic Composition and Functional Potential in Diabetic Dogs

## TL;DR

This study shows that diabetic dogs have a different gut microbiome compared to healthy dogs, with more harmful bacteria and changes in bacterial functions.

## Contribution

The study identifies specific bacterial taxa and functional pathways altered in diabetic dogs through shotgun metagenomics.

## Key findings

- Diabetic dogs showed higher levels of opportunistic pathogens like Escherichia coli and Klebsiella pneumoniae.
- Functional analysis revealed increased potential for energy metabolism and bacterial colonization in diabetic dogs.
- Healthy dogs had more bacteria linked to beneficial metabolite production, such as Turicibacter and Romboutsia species.

## Abstract

Diabetes is a common metabolic disease in dogs, but how it is related to changes in gut bacteria is still not well understood. In this study, we analyzed stool samples from diabetic and healthy dogs that were kept under similar conditions, including stable diets and no recent use of antibiotics or probiotics. We found that overall bacterial richness was similar between the two groups, but the types of bacteria present were clearly different. Dogs with diabetes had higher levels of bacteria that are often associated with infections, while healthy dogs had more bacteria linked to normal digestion and production of beneficial metabolites. In addition, the gut bacteria of diabetic dogs showed increased genetic potential for energy use, transport of substances, and traits related to bacterial survival and colonization. These results indicate that diabetes in dogs is associated with clear changes in both the composition and potential functions of gut bacteria. Understanding these changes may help develop new strategies to support diabetes management through improving gut health.

Gut microbiota dysbiosis is implicated in metabolic disorders, yet taxonomic and functional alterations in canine diabetes remain incompletely defined. Here, we performed shotgun metagenomic sequencing of fecal samples from 38 diabetic dogs and 37 healthy controls under controlled conditions (no recent antibiotic/probiotic exposure and stable commercial diets). Alpha-diversity indices did not differ between groups, whereas beta-diversity revealed significant separation of community structure at both genus and species levels (p < 0.05). Linear discriminant analysis effect size (LEfSe) identified enrichment of opportunistic-associated taxa in diabetic dogs, including Enterobacterales/Enterobacteriaceae (e.g., Escherichia coli, Klebsiella pneumoniae, Salmonella enterica) and Enterococcus faecalis. In contrast, healthy dogs were enriched for putatively beneficial taxa linked to bile acid and short-chain fatty acid (SCFA) metabolism, including Turicibacter spp. and Romboutsia spp. Functional profiling showed higher abundances of pathways related to carbohydrate/energy metabolism, membrane transport, and virulence/colonization in diabetic dogs; 17 KEGG level-3 pathways and 320 KOs differed at FDR < 0.05, with enriched modules including bacterial secretion systems, lipopolysaccharide biosynthesis, chemotaxis/flagellar assembly, and biofilm formation. Collectively, canine diabetes is associated with a remodeled gut microbiome characterized by expansion of opportunistic pathogens and elevated virulence and metabolic potential, supporting exploration of microbiota-targeted strategies as a complement to conventional management.