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Use of Fecal Cultures for Characterizing Intestinal Dysbiosis

Cynthia R. L. Webster, DVM, DACVIM, Cummings School of Veterinary Medicine at Tufts University

Internal Medicine

|March 2021

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In the literature

Werner M, Suchodolski JS, Lidbury JA, Steiner JM, Hartmann K, Unterer S. Diagnostic value of fecal cultures in dogs with chronic diarrhea. J Vet Intern Med. 2021;35(1):199-208.


In dogs, chronic inflammatory enteropathies are a common cause of chronic diarrhea and can be classified as food-responsive (50%-60%), antibiotic-responsive (10%-15%), infectious (10%), or corticosteroid-responsive (10%-20%).1-4 Primary bacterial infection is a rare cause of chronic diarrhea; however, many chronic enteropathies are accompanied by alterations in the composition of the resident bacterial flora. These alterations (ie, intestinal dysbiosis) can contribute to ongoing inflammation, and treatment to reestablish normal bacterial flora can be therapeutic.5-7 Thus, there is clinical interest in the ability to detect the presence of dysbiosis.

It may seem that traditional fecal bacterial culture would be helpful in establishing the presence of dysbiosis; however, plating techniques are inadequate because it is difficult to grow the many anaerobic bacteria that reside in the gut. Culture-independent molecular methods based on characterization of the 16S rRNA genes or shotgun whole genome sequencing give a more accurate depiction but are expensive and not practical for routine clinical testing. One commercial laboratory has validated a PCR-based method that quantifies the abundances of 7 bacterial groups and summarizes them in a single number called the dysbiosis index (DI). In healthy dogs, the DI is <0, and in dogs with chronic diarrhea the DI is typically >2.5-7 

The goal of this prospective case control study was to compare results of traditional fecal culture tests from 3 different commercial laboratories with each other and with the results of DI testing.8 Fecal samples from 18 healthy dogs and 18 dogs with chronic diarrhea were submitted to 3 different commercial laboratories for fecal culture; samples were also sent to a separate laboratory for determination of DI. Each laboratory used specific criteria to define the flora as normal or abnormal.

In the study, control dogs had a mean DI of -3, and dogs with chronic diarrhea had a mean DI of 0.9. Increased DI was found in 8 (44%) dogs with chronic diarrhea and in 1 (6%) control dog. In all 3 laboratories, there was no difference in the proportion of samples that had an abnormal culture between healthy dogs and dogs with chronic diarrhea, and there was no correlation with the DI of study dogs. These results raise the question as to whether these culture-based tests used to characterize the microbiome as normal or abnormal are of clinical use in dogs with chronic diarrhea.


Key pearls to put into practice:


Traditional fecal-culture–based techniques that label the microbiome as normal or abnormal fail to differentiate dogs with and without chronic diarrhea. Selective fecal culture aimed at enriching the growth of potential enteropathogenic bacteria may still be useful to document the presence of individual or population outbreaks with enteropathogenic bacteria.


A PCR-based DI is increased in almost 50% of dogs with chronic diarrhea but in only 6% of dogs without diarrhea.



Antimicrobial drug resistance is a worldwide issue, as the overuse of antibiotics drives development of resistant strains. Reducing overall antimicrobial drug use is thus an important tool in reducing resistance.8 Antibiotic use in dogs with chronic enteropathies should be based on evaluation of validated tests documenting a pathologic role for the bacteria. The current study suggests that standard bacterial culture of fecal samples and accompanying antimicrobial susceptibility patterns should not be used to determine the need for antibiotic therapy in these dogs. In cases in which dysbiosis is documented, alternatives to antimicrobial therapy (eg, pre- and probiotics, fecal microbiota transplant, dietary manipulation) should be considered as first-line therapy.


For global readers, a calculator to convert laboratory values, dosages, and other measurements to SI units can be found here.

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