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

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 (<i>p</i> < 0.05). Linear discriminant analysis effect size (LEfSe) identified enrichment of opportunistic-associated taxa in diabetic dogs, including Enterobacterales/Enterobacteriaceae (e.g., <i>Escherichia coli</i>, <i>Klebsiella pneumoniae</i>, <i>Salmonella enterica</i>) and <i>Enterococcus faecalis</i>. In contrast, healthy dogs were enriched for putatively beneficial taxa linked to bile acid and short-chain fatty acid (SCFA) metabolism, including <i>Turicibacter</i> spp. and <i>Romboutsia</i> 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.