The Intestinal Microbiome in Dogs with Chronic Enteropathies and Cobalamin Deficiency or Normocobalaminemia—A Comparative Study

SIMPLE SUMMARY: Cobalamin is a vitamin that all cells of humans and animals, as well as bacteria, need to survive. If the intestine of dogs is diseased, serum cobalamin levels can decrease in some of these dogs. There are no studies in dogs using modern techniques to compare the gut bacteria in dogs with chronic gut inflammation with or without low serum cobalamin levels. Therefore, we compared the gut bacteria in 47 dogs with chronic gut inflammation. Twenty-nine of them had a low serum cobalamin level, while 18 did not. We found that those dogs with a decreased serum cobalamin level had severe alterations in the composition of their intestinal bacteria, while those with a normal serum cobalamin level did not. Oral or injectable supplements did not correct the changes in intestinal bacteria, suggesting that low serum cobalamin levels are an indicator of changes in intestinal bacteria rather than their cause. ABSTRACT: Cobalamin deficiency is a common sequela of chronic enteropathies (CE) in dogs. Studies comparing the intestinal microbiome of CE dogs with cobalamin deficiency to those that are normocobalaminemic are lacking. Therefore, our aim was to describe the fecal microbiome in a prospective, comparative study evaluating 29 dogs with CE and cobalamin deficiency, 18 dogs with CE and normocobalaminemia, and 10 healthy control dogs. Dogs with cobalamin deficiency were also analyzed after oral or parenteral cobalamin supplementation. Overall microbiome composition (beta diversity) at baseline was significantly different in CE dogs with cobalamin deficiency when compared to those with normocobalaminemia (p = 0.001, R = 0.257) and to healthy controls (p = 0.001, R = 0.363). Abundances of Firmicutes and Actinobacteria were significantly increased (q = 0.010 and 0.049), while those of Bacteroidetes and Fusobacteria were significantly decreased (q = 0.002 and 0.014) in CE dogs with cobalamin deficiency when compared to healthy controls. Overall microbiome composition in follow-up samples remained significantly different after 3 months in both dogs receiving parenteral (R = 0.420, p = 0.013) or oral cobalamin supplementation (R = 0.251, p = 0.007). Because cobalamin supplementation, in combination with appropriate therapy, failed to restore the microbiome composition in the dogs in our study, cobalamin is unlikely to be the cause of those microbiome changes but rather an indicator of differences in underlying pathophysiology that do not influence clinical severity but result in a significant aggravation of dysbiosis.