Machine Learning and Canine Chronic Enteropathies: A New Approach to Investigate FMT Effects

Safety profile and effects on the peripheral immune response of fecal microbiota transplantation in clinically healthy dogs

BACKGROUND

Fecal microbiota transplantation (FMT) is increasingly used for gastrointestinal and extra-gastrointestinal diseases in veterinary medicine. However, its effects on immune responses and possible adverse events have not been systematically investigated.

HYPOTHESIS/OBJECTIVES

Determine the short-term safety profile and changes in the peripheral immune system after a single FMT administration in healthy dogs.

ANIMALS

Ten client-owned, clinically healthy dogs as FMT recipients, and 2 client-owned clinically healthy dogs as FMT donors.

METHODS

Prospective non-randomized clinical trial. A single rectal enema of 5 g/kg was given to clinically healthy canine recipients. During the 28 days after FMT administration, owners self-reported adverse events and fecal scores. On Days 0 (baseline), 1, 4, 10, and 28 after FMT, fecal and blood samples were collected. The canine fecal dysbiosis index (DI) was calculated using qPCR.

RESULTS

No significant changes were found in the following variables: CBC, serum biochemistry, C-reactive protein, serum cytokines (interleukins [IL]-2, -6, -8, tumor necrosis factor [TNF]-α), peripheral leukocytes (B cells, T cells, cluster of differentiation [CD]4+ T cells, CD8+ T cells, T regulatory cells), and the canine DI. Mild vomiting (n = 3), diarrhea (n = 4), decreased activity (n = 2), and inappetence (n = 1) were reported, and resolved without intervention.

CONCLUSIONS AND CLINICAL IMPORTANCE

Fecal microbiota transplantation did not significantly alter the evaluated variables and recipients experienced minimal adverse events associated with FMT administration. Fecal microbiota transplantation was not associated with serious adverse events, changes in peripheral immunologic variables, or the canine DI in the short-term.

Updating the Classification of Chronic Inflammatory Enteropathies in Dogs

Chronic inflammatory enteropathies (CIEs) in dogs are currently classified based on response to sequential treatment trials into food-responsive (FREs); antibiotic-responsive (AREs); immunosuppressant-responsive (IREs); and non-responsive enteropathies (NREs). Recent studies have reported that a proportion of NRE dogs ultimately respond to further dietary trials and are subsequently misclassified. The FRE subset among CIEs is therefore probably underestimated. Moreover, alterations in the gut microbiota composition and function (dysbiosis) have been shown to be involved in CIE pathogenesis in recent research on dogs. Metronidazole and other antibiotics that have been used for decades for dogs with AREs have been demonstrated to result in increased antimicrobial resistance and deleterious effects on the gut microbiota. As a consequence, the clinical approach to CIEs has evolved in recent years toward the gradual abandonment of the use of antibiotics and their replacement by other treatments with the aim of restoring a diverse and functional gut microbiota. We propose here to refine the classification of canine CIEs by replacing the AREs category with a microbiota-related modulation-responsive enteropathies (MrMREs) category.

Microbiome Responses to Oral Fecal Microbiota Transplantation in a Cohort of Domestic Dogs

Fecal microbiota transplants (FMTs) have been successful at treating digestive and skin conditions in dogs. The degree to which the microbiome is impacted by FMT in a cohort of dogs has not been thoroughly investigated. Using 16S rRNA gene sequencing, we document the changes in the microbiome of fifty-four dogs that took capsules of lyophilized fecal material for their chronic diarrhea, vomiting, or constipation. We found that the relative abundances of five bacterial genera (Butyricicoccus, Faecalibacterium, Fusobacterium, Megamonas, and Sutterella) were higher after FMT than before FMT. Fecal microbiome alpha- and beta-diversity were correlated with kibble and raw food consumption, and prior antibiotic use. On average, 18% of the stool donor's bacterial amplicon sequence variants (ASVs) engrafted in the FMT recipient, with certain bacterial taxa like Bacteroides spp., Fusobacterium spp., and Lachnoclostridium spp. engrafting more frequently than others. Lastly, analyses indicated that the degree of overlap between the donor bacteria and the community of microbes already established in the FMT recipient likely impacts engraftment. Collectively, our work provides further insight into the microbiome and engraftment dynamics of dogs before and after taking oral FMTs.

Microbiome Responses to Fecal Microbiota Transplantation in Cats with Chronic Digestive Issues

There is growing interest in the application of fecal microbiota transplants (FMTs) in small animal medicine, but there are few published studies that have tested their effects in the domestic cat (Felis catus). Here we use 16S rRNA gene sequencing to examine fecal microbiome changes in 46 domestic cats with chronic digestive issues that received FMTs using lyophilized stool that was delivered in oral capsules. Fecal samples were collected from FMT recipients before and two weeks after the end of the full course of 50 capsules, as well as from their stool donors (N = 10), and other healthy cats (N = 113). The fecal microbiomes of FMT recipients varied with host clinical signs and dry kibble consumption, and shifts in the relative abundances of Clostridium, Collinsella, Megamonas, Desulfovibrio and Escherichia were observed after FMT. Overall, donors shared 13% of their bacterial amplicon sequence variants (ASVs) with FMT recipients and the most commonly shared ASVs were classified as Prevotella 9, Peptoclostridium, Bacteroides, and Collinsella. Lastly, the fecal microbiomes of cats with diarrhea became more similar to the microbiomes of age-matched and diet-matched healthy cats compared to cats with constipation. Overall, our results suggest that microbiome responses to FMT may be modulated by the FMT recipient's initial presenting clinical signs, diet, and their donor's microbiome.

Characterization of the Blood Microbiome and Comparison with the Fecal Microbiome in Healthy Dogs and Dogs with Gastrointestinal Disease

Recent studies have found bacterial DNA in the blood of healthy individuals. To date, most studies on the blood microbiome have focused on human health, but this topic is an expanding research area in animal health as well. This study aims to characterize the blood microbiome of both healthy dogs and those with chronic gastro-enteropathies. For this study, blood and fecal samples were collected from 18 healthy and 19 sick subjects, DNA was extracted through commercial kits, and the V3-V4 regions of the 16S rRNA gene were sequenced on the Illumina platform. The sequences were analyzed for taxonomic annotation and statistical analysis. Alpha and beta diversities of fecal microbiome were significantly different between the two groups of dogs. Principal coordinates analysis revealed that healthy and sick subjects were significantly clustered for both blood and fecal microbiome samples. Moreover, bacterial translocation from the gut to the bloodstream has been suggested because of found shared taxa. Further studies are needed to determine the origin of the blood microbiome and the bacteria viability. The characterization of a blood core microbiome in healthy dogs has potential for use as a diagnostic tool to monitor for the development of gastro-intestinal disease.

Clinical Effects of Faecal Microbiota Transplantation as Adjunctive Therapy in Dogs with Chronic Enteropathies—A Retrospective Case Series of 41 Dogs

Chronic enteropathies (CE) are common in dogs, but not all affected dogs respond to standard therapy. Successful responses to faecal microbial transplantation (FMT) in dogs with non-responsive CE have been reported in two case series. The objective of this retrospective study was to describe the clinical effects of FMT as an adjunctive therapy in a larger population of dogs with CE. Forty-one dogs aged 0.6–13.0 years (median 5.8) under treatment for CE at one referral animal hospital were included. Dogs were treated with 1–5 (median 3) FMTs as a rectal enema at a dose of 5–7 g/kg body weight. The canine inflammatory bowel disease activity index (CIBDAI) was compared at baseline versus after the last FMT. Stored faecal samples (n = 16) were analysed with the dysbiosis index. CIBDAI at baseline was 2–17 (median 6), which decreased to 1–9 (median 2; p < 0.0001) after FMT. Subsequently, 31/41 dogs responded to treatment, resulting in improved faecal quality and/or activity level in 24/41 and 24/41 dogs, respectively. The dysbiosis index at baseline was significantly lower for good responders versus poor responders (p = 0.043). Results suggest that FMT can be useful as an adjunctive therapy in dogs with poorly responsive CE.