A dysbiosis index to assess microbial changes in fecal samples of dogs with chronic inflammatory enteropathy

Abstract

Recent studies have identified various bacterial groups that are altered in dogs with chronic inflammatory enteropathies (CE) compared to healthy dogs. The study aim was to use quantitative PCR (qPCR) assays to confirm these findings in a larger number of dogs, and to build a mathematical algorithm to report these microbiota changes as a dysbiosis index (DI). Fecal DNA from 95 healthy dogs and 106 dogs with histologically confirmed CE was analyzed. Samples were grouped into a training set and a validation set. Various mathematical models and combination of qPCR assays were evaluated to find a model with highest discriminatory power. The final qPCR panel consisted of eight bacterial groups: total bacteria, Faecalibacterium, Turicibacter, Escherichia coli, Streptococcus, Blautia, Fusobacterium and Clostridium hiranonis. The qPCR-based DI was built based on the nearest centroid classifier, and reports the degree of dysbiosis in a single numerical value that measures the closeness in the l2 - norm of the test sample to the mean prototype of each class. A negative DI indicates normobiosis, whereas a positive DI indicates dysbiosis. For a threshold of 0, the DI based on the combined dataset achieved 74% sensitivity and 95% specificity to separate healthy and CE dogs.

Longitudinal assessment of microbial dysbiosis, fecal unconjugated bile acid concentrations, and disease activity in dogs with steroid‐responsive chronic inflammatory enteropathy

“…To evaluate specific bacteria groups of interest to intestinal health, qPCR was performed as described previously . Select bacterial taxa that have been previously shown to be altered when comparing healthy dogs and dogs with intestinal inflammation were used to evaluate dysbiosis based on an index recently published …”

“…20 Select bacterial taxa that have been previously shown to be altered when comparing healthy dogs and dogs with intestinal inflammation were used to evaluate dysbiosis based on an index recently published. 21 Dogs with abnormalities that were deemed to be clinically significant were excluded.…”

Pre- and Post-Race Intestinal Microbiota in Long-Distance Sled Dogs and Associations with Performance

“…The level of dysbiosis-associated bacteria was determined by utilizing a recently developed dysbiosis index for dogs based on 7 bacterial subgroups, including Faecalibacterium, Turicibacter, Streptococcus, Escherichia coli, Blautia, Fusobacterium, and Clostridium hiranonis [6]. The sequencing-based dysbiosis index was calculated based on summing the log10 number of reads for OTUs classified to genera/species positively associated with dysbiosis, with subsequent subtraction of the log10 number of reads belonging to OTUs classified to genera/species negatively associated with dysbiosis.…”

“…Dysbiosis in both dogs and humans has been associated with gut-related diseases, such as inflammatory bowel disease (IBD) [2,4,6]. However, how the normobiotic microbiota is associated with good health remains less clear.…”

“…The dysbiosis-associated bacteria were measured using a newly developed dysbiosis index for dogs. The index is based on seven key bacterial taxa, with relation to both inflammation and bile acid metabolism [6].…”