Culture-based assessment of the fecal microbiome using fecal culture profiles frequently is performed in dogs with chronic diarrhea, but the diagnostic value of this approach has not been determined.
To compare the reported results of fecal culture profiles and the polymerase chain reaction-based dysbiosis index (DI) between dogs with chronic diarrhea and healthy dogs; to assess interlaboratory variability in bacterial and fungal cultures among 3 veterinary diagnostic laboratories (diagnostic laboratory 1 [L1], diagnostic laboratory 2 [L2], diagnostic laboratory 3 [L3]); and to compare the reported interpretation of culture profiles (normobiosis versus dysbiosis) with those of the DI.
Eighteen dogs with chronic diarrhea (CDG) and 18 healthy control dogs (HG).
In this prospective, case-control study, fecal samples were submitted to 3 commercial laboratories for fecal culture. The microbiota was assessed using PCR assays. Dogs receiving antimicrobials were excluded.
Dysbiosis index was significantly increased in CDG (mean, 0.9; SD, 3.8; 95% confidence interval [CI], -1.0; 2.8) compared to HG (mean, -3.0; SD, 2.8; CI, -4.3; -1.6; P = .0002), whereas cultures from all laboratories failed to detect significant differences (P = .66, .18, and .66, respectively). Hemolytic Escherichia coli was the only potential enteropathogen on culture, but no significant difference was found between CDG and HG. For diagnosis of dysbiosis, culture showed no agreement with DI (L1, κ = -0.21; CI, -0.44; -0.02; L2, κ = -0.33; CI, -0.58; -0.08; L3, κ = -0.25; CI, -0.39; -0.11). Furthermore, variability among the 3 laboratories was high (L1/L2, κ = 0.15; CI, -0.05; 0.35; L1/L3, κ = -0.08; CI, -0.01; -0.16; L2/L3, κ = -0.06; CI, -0.33; -0.20).
Fecal cultures failed to distinguish between diseased and healthy dogs, and a high level of interlaboratory variation for culture was found.

© 2020 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals LLC. on behalf of the American College of Veterinary Internal Medicine.