Ecological characterization of the colonic microbiota of normal and diarrheic dogs

Antibiotic-induced dysbiosis in the SCIME™ recapitulates microbial community diversity and metabolites modulation of in vivo disease

Establishing the context

Intestinal dysbiosis is a significant concern among dog owners, and the gut health of pets is an emerging research field. In this context, the Simulator of the Canine Intestinal Microbial Ecosystem (SCIME™) was recently developed and validated with in vivo data.

Stating the purpose/introducing the study

The current study presents a further application of this model by using amoxicillin and clavulanic acid to induce dysbiosis, aiming to provoke changes in microbial community and metabolite production, which are well-known markers of the disease in vivo.

Describing methodology

Following the induction of dysbiosis, prebiotic supplementation was tested to investigate the potential for microbiota recovery under different dietary conditions.

Presenting the results

The results showed that antibiotic stimulation in the SCIME™ model can produce significant changes in microbial communities and metabolic activity, including a decrease in microbial richness, a reduction in propionic acid production, and alterations in microbial composition. Additionally, changes in ammonium and butyric acid levels induced by the tested diets were observed.

Discussing the findings

This alteration in microbial community and metabolites production mimicks in vivo canine dysbiosis patterns. A novel dynamic in vitro model simulating canine antibiotic-induced dysbiosis, capable of reproducing microbial and metabolic changes observed in vivo, has been developed and is suitable for testing the effects of nutritional changes.

Canine Mucosal Artificial Colon: development of a new colonic in vitro model adapted to dog sizes

Differences in dog breed sizes are an important determinant of variations in digestive physiology, mainly related to the large intestine. In vitro gut models are increasingly used as alternatives to animal experiments for technical, cost, societal, and regulatory reasons. Up to now, only one in vitro model of the canine colon incorporates the dynamics of different canine gut regions, yet no adaptations exist to reproduce size-related digestive parameters. To address this limitation, we developed a new model of the canine colon, the CANIne Mucosal ARtificial COLon (CANIM-ARCOL), simulating main physiochemical (pH, transit time, anaerobiosis), nutritional (ileal effluent composition), and microbial (lumen and mucus-associated microbiota) parameters of this ecosystem and adapted to three dog sizes (i.e., small under 10 kg, medium 10-30 kg, and large over 30 kg). To validate the new model regarding microbiota composition and activities, in vitro fermentations were performed in bioreactors inoculated with stools from 13 dogs (4 small, 5 medium, and 4 large). After a stabilization period, microbiota profiles clearly clustered depending on dog size. Bacteroidota and Firmicutes abundances were positively correlated with dog size both in vitro and in vivo, while opposite trends were observed for Actinobacteria and Proteobacteria. As observed in vivo, microbial activity also increased with dog size in vitro, as evidenced from gas production, short-chain fatty acids, ammonia, and bile acid dehydroxylation. In line with the 3R regulation, CANIM-ARCOL could be a relevant platform to assess bilateral interactions between food and pharma compounds and gut microbiota, capturing inter-individual or breed variabilities. KEY POINTS: • CANIM-ARCOL integrates main canine physicochemical and microbial colonic parameters • Gut microbiota associated to different dog sizes is accurately maintained in vitro • The model can help to move toward personalized approach considering dog body weight.

Effects of Increasing Levels of Purified Beta-1,3/1,6-Glucans on the Fecal Microbiome, Digestibility, and Immunity Variables of Healthy Adult Dogs

Yeast-purified beta-1,3/1,6-glucans (BG) can modulate dogs' immune systems and microbiome, but the optimal inclusion dose remains unknown. The aim of the study was to evaluate the effects of 0.0, 0.07, 0.14, and 0.28% inclusion of BG in a dry extruded diet on the digestibility, immunity, and fecal microbiota of healthy adult dogs. Eight male and female border collies [n = 4; body condition score (BCS) = 5] and English cocker spaniels (n = 4; BCS = 5), aged 3.5 ± 0.5 years, were randomly distributed into two 4 × 4 balanced Latin squares. Fecal microbiota (using 16S rRNA sequencing, Illumina®), apparent digestibility coefficients (ADC) of nutrients, fecal concentrations of short-chain fatty acids (SCFA) and branched-chain fatty acids (BCFA), ammoniacal nitrogen, lactic acid, IgA and pH, lymphocyte immunophenotyping, intensity and percentage of phagocytosis and oxidative burst were determined. No differences were observed in Faith (p = 0.1414) and Pielou-evenness (p = 0.1151) between treatments, but beta diversity was different between 0.0% and 0.14% BG groups (p = 0.047). Moreover, the Firmicutes phylum was the most abundant in all groups and exhibited the highest relative abundance after the consumption of 0.14% BG, a finding considered beneficial for the canine microbiome. The Erysipelotrichaceae and Ruminococcaceae families, along with the Faecalibacterium and Prevotella genera, considered favorable for their involvement in butyrate production and other metabolites, showed increased abundance after the consumption of 0.14% BG. The potentially pathogenic Proteobacteria phylum displayed lower abundance after the consumption of 0.14% BG. Fecal concentrations of the evaluated compounds and pH did not differ after consumption of the BG at all percentages. Higher crude protein ADC was found after 0.14 and 0.28% BG consumption (p < 0.0001), but no differences were found for other nutrients. Phagocytosis, oxidative burst, and lymphocyte populations were not modulated by any of the treatments; however, 0.14% BG modulated the lymphocyte T CD4+:CD8+ ratio (p = 0.0368), an important marker of immune system efficiency. The inclusion of 0.14% BG resulted in the best responses and was the best dose evaluated.

The use of metronidazole in acute diarrhea in dogs: a narrative review

Acute diarrhea is a common reason for non-wellness veterinary visits in dogs. Treatment for acute diarrhea usually consists of supportive care with nutritional intervention, fluid therapy, anthelmintics, and often an antibiotic - commonly metronidazole in North America. The empirical use of metronidazole for acute diarrhea in dogs has been a common practice in veterinary medicine for many decades; however, recent studies evaluating its use suggest it may be inappropriately utilized in many cases. Herein, we review the evidence evaluating the use of metronidazole and other antibiotics in acute diarrhea in the human and veterinary literature. Recommendations on the use of metronidazole and other antibiotics as well as other therapeutic considerations in the treatment of acute diarrhea are also provided.

The Effects of Bacillus licheniformis—Fermented Products on the Microbiota and Clinical Presentation of Cats with Chronic Diarrhea

Bacillus licheniformis-fermented products (BLFP) are probiotics with antibacterial, antiviral, and anti-inflammatory properties that can improve growth performance. This study aimed to compare the fecal microbiota of diarrheal cats with chronic diarrhea (n = 8) with that of healthy cats (n = 4) from the same household using next-generation sequencing, and evaluate the effectiveness of oral administration of BLFP in relieving clinical signs and altering the intestinal microbiota in diarrheal cats. Six out of eight diarrheal cats showed clinical improvement after BLFP administration for 7 days, and the stool condition of the other two was normal. A higher Firmicutes/Bacteroidetes ratio was noted in the feces of diarrheal cats without clinical improvement as compared with those in the healthy cats and in the diarrheal cats with clinical improvement after receiving BLFP. The phylum Bacteroidetes and class Bacteroidia decreased significantly in diarrheal cats regardless of BLFP administration. Blautia spp., Ruminococcus torques, and Ruminococcus gnavus, which belong to the Clostridium cluster XIVa and have been reported as beneficial to intestinal health, increased significantly in feces after treatment. Furthermore, Clostridium perfringens also significantly decreased in diarrheal cats after BLFP administration. Overall, BLFP could be a potential probiotic to relieve gastrointestinal symptoms and improve fecal microbiota in cats with chronic diarrhea.

From Chihuahua to Saint-Bernard: how did digestion and microbiota evolve with dog sizes

Health and well-being of dogs are of paramount importance to their owners. Digestion plays a key role in dog health, involving physicochemical, mechanical and microbial actors. However, decades of breeding selection led to various dog sizes associated with different digestive physiology and disease sensitivity. Developing new products requires the consideration of all the multi-faceted aspects of canine digestion, the evaluation of food digestibility, drug release and absorption in the gut. This review paper provides an exhaustive literature survey on canine digestive physiology, focusing on size effect on anatomy and digestive parameters, with graphical representation of data classified as "small", "medium" and "large" dogs. Despite the huge variability between protocols and animals, interesting size effects on gastrointestinal physiology were highlighted, mainly related to the colonic compartment. Colonic measurements, transit time permeability, fibre degradation, faecal short-chain fatty acid concentration and faecal water content increase while faecal bile acid concentration decreases with body size. A negative correlation between body weight and Proteobacteria relative abundance was observed suggesting an effect of dog body size on faecal microbiota. This paper gathers helpful in vivo data for academics and industrials and supports the development of new food and pharma products to move towards canine personalized nutrition and health.

Phenotypic correlates of the working dog microbiome

Dogs have a key role in law enforcement and military work, and research with the goal of improving working dog performance is ongoing. While there have been intriguing studies from lab animal models showing a potential connection between the gut microbiome and behavior or mental health there is a dearth of studies investigating the microbiome-behavior relationship in working dogs. The overall objective of this study was to characterize the microbiota of working dogs and to determine if the composition of the microbiota is associated with behavioral and performance outcomes. Freshly passed stools from each working canine (Total n = 134) were collected and subject to shotgun metagenomic sequencing using Illumina technology. Behavior, performance, and demographic metadata were collected. Descriptive statistics and prediction models of behavioral/phenotypic outcomes using gradient boosting classification based on Xgboost were used to study associations between the microbiome and outcomes. Regarding machine learning methodology, only microbiome features were used for training and predictors were estimated in cross-validation. Microbiome markers were statistically associated with motivation, aggression, cowardice/hesitation, sociability, obedience to one trainer vs many, and body condition score (BCS). When prediction models were developed based on machine learning, moderate predictive power was observed for motivation, sociability, and gastrointestinal issues. Findings from this study suggest potential gut microbiome markers of performance and could potentially advance care for working canines.

Developmental intestinal microbiome alterations in canine fading puppy syndrome: a prospective observational study

Fading puppy syndrome (FPS) is a fatal condition in neonatal dogs. Intestinal microbial alterations, although never investigated, may be involved in its pathophysiology. The study examined the occurrence of FPS and its associations with dam, puppy, and husbandry characteristics, compared the intestinal microbial diversity of healthy puppies and those with FPS, and examined whether intestinal microbiomes are predictive of FPS. Day 1 and 8 post-partum (PP) rectal swabs were collected from healthy puppies and puppies which later developed FPS. Microbial compositional structure, including alpha and beta diversities and relative abundance of specific taxa were compared between groups, and microbial data was applied to a machine-learning model to assess the predictive performance of microbial indices of FPS or death. FPS occurred in 22/165 puppies (13%), with a 100% mortality rate. FPS was associated (P < 0.001) with decreased Day 1 PP puppy activity. Day 1 (P = 0.003) and 8 (P = 0.005) PP rectal beta diversities were different in puppies with FPS vs healthy ones. Increased Proteobacteria/Firmicutes ratio, increased relative abundance of Pasteurellaceae, and decreased relative abundance of Clostridia and Enterococcus were associated with FPS. A machine-learning model showed that Day 1 PP rectal microbiome composition accurately predicted FPS-related death. We found that specific rectal microbial phenotypes are associated with FPS, reflecting the significant role of microbiome alterations in this phenomenon. These findings may serve as useful microbial indices for early diagnosis of puppies at risk of FPS and may provide specific therapeutic targets.

Longitudinal Survey of Fecal Microbiota in Healthy Dogs Administered a Commercial Probiotic

The aim of this longitudinal microbiome study was to investigate the effects of a commercially available veterinary synbiotic product (Blackmore's® Paw DigestiCare 60™) on the fecal microbiome of healthy dogs using 16S rRNA gene microbial profiling. Fifteen healthy, privately-owned dogs participated in a 2-week trial administration of the product. Fecal samples were collected at different time points, including baseline (prior to treatment), during administration and after discontinuation of product. Large intra- and inter-individual variation was observed throughout the study, but microbiome composition at higher phylogenetic levels, alpha and beta diversity were not significantly altered after 2 weeks of probiotic administration, suggesting an absence of probiotic impact on microbial diversity. Administration of the synbiotic preparation did, however, result in transient increases in probiotic species from Enterococacceae and Streptococacceae families as well as an increase in Fusobacteria; with the fecal microbiota partially reverting to its baseline state 3-weeks after cessation of probiotic administration.

Prevalence and Predictors of Antimicrobial Resistance Among Enterococcus spp. From Dogs Presented at a Veterinary Teaching Hospital, South Africa

Background: While surveillance of antimicrobial drug resistance is ongoing in human medicine in South Africa, there is no such activity being performed in veterinary medicine. As a result, there is a need to investigate antimicrobial resistance among enterococci isolated from dogs in South Africa to improve understanding of the status of antimicrobial drug resistance given its public and veterinary public health importance. This study investigated antimicrobial resistance and factors associated with resistance profiles of enterococci isolated from dogs presented for veterinary care at a veterinary teaching hospital in South Africa. Methods: In total 102 Enterococcus isolated between 2007 and 2011 by a bacteriology laboratory at a teaching hospital were included in this study. Antimicrobial susceptibility of the isolates was determined against a panel of 18 antimicrobials using the Kirby Bauer disc diffusion technique. Univariate analysis was used to assess simple associations between year, season, breed group, age group, sex, and specimen as covariates and extensive drug resistance (XDR) as the outcome. Variables that were significant in the univariate analysis at a generous p-value ≤ 0.2 were included in the multivariable logistic models to investigate predictors of XDR. Results: All the Enterococcus isolates were resistant to at least one antimicrobial. High proportions of isolates were resistant against lincomycin (93%), kanamycin (87%), orbifloxacin (85%), and aminogycoside-lincosamide (77%). Ninety three percent (93%), 35.3, and 8.8% of the isolates exhibited multi-drug, extensive-drug and pan-drug resistance, respectively. Only year was significantly (p = 0.019) associated with extensive-drug resistance. Conclusion: Given the zoonotic potential of Enterococcus spp., the high antimicrobial resistance and multi-drug resistance observed in this study are a public health concern from one health perspective. The identified resistance to various antimicrobials may be useful in guiding clinicians especially in resource scarce settings where it is not always possible to perform AST when making treatment decisions.

High-Fat Diets Led to OTU-Level Shifts in Fecal Samples of Healthy Adult Dogs

High fat diets have been reported to negatively affect the microbiota in both mice and humans. However, there is a lack of studies in canine models. The variation among the gastrointestinal (GI) tract anatomy/physiology and typical diet compositions of these animal species may lead to vastly different results. Due to the large inclusion rate of dietary fat in pet food, it is critical to understand its effects in a canine model. Therefore, the study objective was to report the effects of high fat, low carbohydrate diets on the fecal microbiota in healthy adult dogs. Eight adult beagles were randomly assigned to one of four dietary treatments within each 15-day period of a replicated 4x4 Latin Square design. Diets contained 32% (T1), 37% (T2), 42% (T3), and 47% (T4) fat. T2, T3, and T4 were created by adding increasing levels of canola oil to T1, a commercially manufactured canned canine diet, which served as the control diet. Fresh fecal samples were collected during the last 5 days of each period for microbial analysis. DNA was extracted from fecal samples and paired-end 16S rRNA gene amplicon sequencing was performed using the Illumina MiSeq platform. When comparing whole microbial communities using PERMANOVA, no significant differences were observed among treatments (P = 0.735). Individual OTUs were analyzed using the GLIMMIX procedure of SAS with fixed effects of diet and room, and the random effects of period and animal. Out of the 100 most abundant individual OTUs, 36 showed significant differences in abundance based on treatment (q < 0.05). Overall, OTUs assigned to genera related to fat digestion increased while OTUs assigned to genera involved in carbohydrate digestion decreased. In conclusion, the microbial community adapted to dietary intervention without jeopardizing the health of the animals, evaluated by body condition score, fecal characteristics, and blood parameters.

Characterization of gut microbiomes of household pets in the United States using a direct-to-consumer approach

The role of gut microbiomes as important regulators of mammalian health is increasingly recognized, although feline and canine gut microbiomes remain poorly characterized. In this proof-of-concept study, we assessed the utility of a direct-to-consumer approach to executing pet microbiome studies. We characterized the gut microbiomes of 238 pets (46 cats and 192 dogs) by generating ~11 million merged reads that were mapped to the V4 region of 16S ribosomal RNA gene at a sequencing depth of 45,806 (±22,325) reads per sample. Analyses of these reads revealed that both feline and canine gut microbiomes are dominated by three major phyla, namely Firmicutes, Proteobacteria, and Bacteroides and that alpha diversity is higher in the feline gut. In addition to interspecies differences between the feline and canine gut, we also detected appreciable intraspecies bacterial variation within the canine population. While the dogs in this dataset could be assigned to three distinct clusters based on their gut microbiome, no clustering was observed within the feline population. Integration of additional data obtained from survey questionnaires revealed that geography and body weight may be associated with canine gut microbiome composition. Furthermore, we found that both the inter and intraspecies differences are more pronounced at finer taxonomic levels, indicating that strain-level investigations may be necessary in the future. This study demonstrates that the direct-to-consumer approach overcomes existing limitations in pet microbiome research, for example, it allows collection of large numbers of pet samples. The direct-to-consumer approach has proven successful in human genomics as well as human microbiomics and this study demonstrates that by building partnerships with an engaged general public this approach can also propel the field of pet microbiomics forward.

Metagenomic analysis revealed beneficial effects of probiotics in improving the composition and function of the gut microbiota in dogs with diarrhoea

The aim of the present study was to evaluate the effects of probiotics on the composition and function of the gut microbiota in dogs with diarrhoea. Forty dogs with diarrhoea were randomly allocated to the treatment group or control group. Probiotics, containing Lactobacillus casei Zhang, Lactobacillus plantarum P-8, and Bifidobacterium animalis subsp. lactis V9, were only fed to 20 treated dogs for 60 days. The faecal samples of all dogs at day 0 and day 60 were analyzed using a metagenomic approach. The results showed a significantly higher microbial diversity and an obvious change in the structure of the gut microbiota in the treatment group. There was also an increase in the abundance of some beneficial bacteria in differently aged dogs, such as Lactobacillus johnsonii (P < 0.05), Lactobacillus reuteri (P < 0.01), Lactobacillus acidophilus (P < 0.05) and Butyricicoccus pullicaecorum (P < 0.05), and a reduction in the abundance of many opportunistic pathogenic bacteria such as Clostridium perfringens (P < 0.05) and Stenotrophomonas maltophilia (P < 0.05) with the supplementation of probiotics. Intriguingly, the correlated networks among some pathogenic bacteria decreased following the administration of probiotics. Additionally, metagenomic analysis revealed the upregulation of pathways involved in the metabolism of amino acids and biosynthesis of secondary metabolites, accompanied by the downregulation of pathways associated with virulence of pathogenic bacteria and cell signaling, suggesting that probiotics could improve the health of dogs with diarrhoea through regulation of the gut microbiota. Our research provides new information relevant to the treatment of diarrhoea in animals and humans.

Role of gut microbiota in dog and cat's health and diseases

Mammalian gastrointestinal tract is colonized by a large number of microorganisms, known as gut microbiota, that play a key role in the physiological and pathological states. In particular, the gastrointestinal tract of dogs and cats harbors a complex and highly biodiverse microbial ecosystem. Recent studies see it involved in a wide range of life processes, including energy needs, metabolism, immunological activity, and neuro-behavioral development. This review focuses on the role of the microbiota on the health of pets and will discuss changes that occur in the disease.

Diets with and without edible cricket support a similar level of diversity in the gut microbiome of dogs

The gut microbiome plays an important role in the health of dogs. Both beneficial microbes and overall diversity can be modulated by diet. Fermentable sources of fiber in particular often increase the abundance of beneficial microbes. Banded crickets (Gryllodes sigillatus) contain the fermentable polysaccharides chitin and chitosan. In addition, crickets are an environmentally sustainable protein source. Considering crickets as a potential source of both novel protein and novel fiber for dogs, four diets ranging from 0% to 24% cricket content were fed to determine their effects on healthy dogs’ (n = 32) gut microbiomes. Fecal samples were collected serially at 0, 14, and 29 days, and processed using high-throughput sequencing of 16S rRNA gene PCR amplicons. Microbiomes were generally very similar across all diets at both the phylum and genus level, and alpha and beta diversities did not differ between the various diets at 29 days. A total of 12 ASVs (amplicon sequence variants) from nine genera significantly changed in abundance following the addition of cricket, often in a dose-response fashion with increasing amounts of cricket. A net increase was observed in Catenibacterium, Lachnospiraceae [Ruminococcus], and Faecalitalea, whereas Bacteroides, Faecalibacterium, Lachnospiracaeae NK4A136 group and others decreased in abundance. Similar changes in Catenibacterium and Bacteroides have been associated with gut health benefits in other studies. However, the total magnitude of all changes was small and only a few specific taxa changed in abundance. Overall, we found that diets containing cricket supported the same level of gut microbiome diversity as a standard healthy balanced diet. These results support crickets as a potential healthy, novel food ingredient for dogs.

Species diversity of fecal microbial flora in Canis lupus familiaris infected with canine parvovirus

Parvovirosis is a highly contagious disease in dogs, often causing acute hemorrhagic enteritis and altering the intestinal microflora. In this study, real-time PCR was used to detect the viral copy numbers in dogs diagnosed with the disease. Hematological and hemobiochemical parameters were also determined. The species and abundances of the fecal microbial flora in both sick and healthy dogs were determined and compared via metagenomic sequencing. The viral copy numbers in the sick dogs were infected with little difference in the positive samples. The blood coagulation time was significantly shorter and the number of white blood cells was significantly greater in the sick dogs. The serum calcium content was slightly increased and the phosphorus content was reduced in the sick dogs. The LDH and CK activities were significantly elevated in the sick dogs. Metagenomic sequencing and analysis revealed relatively more Escherichia, Lachnoclostridium, gnavus group (Ruminococcus), and uncultured_bacterium_f_lachnospiraceae in the infected dogs, whereas the abundance of Collinsella was relatively reduced. Alloprevotella and Sutterella were absent among the fecal microorganisms of the infected dogs. The relative abundances of Romboutsia, Erysipelatoclostridium, Anaerotruncus, and Blautia were significantly increased in the infected dogs. Functional analysis of the metagenomes of the samples indicated a significant enrichment of the 'replication, recombination and repair', 'nucleotide transport and metabolism', 'transcription', and 'defense metabolism' functions in the fecal microbial flora of the infected dogs. In summary, this study provides a scientific theoretical basis for preventing and controlling diarrhea caused by the canine parvovirus.

A Randomized Double Blinded Placebo-Controlled Clinical Trial of a Probiotic or Metronidazole for Acute Canine Diarrhea

Acute diarrhea is a common, often self-limiting, cause of presentation for veterinary care, yet there is a paucity of data on frequently-prescribed treatments. The purpose of this randomized, double blinded placebo-controlled clinical trial was to compare two anecdotally-recommended treatments: a probiotic combination and metronidazole. Sixty dogs without concurrent comorbidities were randomized into three treatment groups. The time to resolution of diarrheal signs was evaluated using owner surveys and fecal scoring charts. Dogs presenting with acute diarrhea achieved acceptable fecal consistency after 3.5 ± 2.2 days when receiving probiotic, 4.6 ± 2.4 days with oral metronidazole, and 4.8 ± 2.9 days with placebo; statistically significant differences were not identified between treatment groups (p = 0.17). These findings failed to provide evidence for the common use of metronidazole in this cohort of dogs with acute canine diarrhea, and a larger study population would be required to identify a statistically significant effect of probiotics.

Efficacy of an orally administered anti-diarrheal probiotic paste (Pro-Kolin Advanced) in dogs with acute diarrhea: A randomized, placebo-controlled, double-blinded clinical study

BACKGROUND

Acute diarrhea is a common clinical presentation of dogs. The effect of specific anti-diarrheal probiotic pastes (ADPPs) in the management of acute, uncomplicated diarrhea in dogs is unknown.

HYPOTHESIS

Administration of an ADPP containing Enterococcus faecium 4b1707 will improve the clinical outcome of acute, uncomplicated diarrhea in dogs compared to placebo.

ANIMALS

One hundred forty-eight client-owned dogs with acute diarrhea as the main clinical sign.

METHODS

Double-blinded, placebo-controlled, randomized, blocked, multicenter clinical field study conducted at 14 primary care veterinary practices in the United Kingdom and Ireland.

RESULTS

The ADPP was associated with better clinical outcome compared to placebo in dogs with acute, uncomplicated diarrhea. Dogs in the ADPP group had a significantly shorter duration of diarrhea (ADPP: median, 32 hours; 95% confidence interval [CI], 2-118; n = 51; Placebo: median, 47 hours; 95% CI, 4-167; n = 58; P = .008) and the rate of resolution of diarrhea was 1.60 times faster in the ADPP group than in the Placebo group (ratio, 1.60; 95% CI, 1.08-2.44; P = .02). Fewer dogs required additional medical intervention (AMI) for non-improvement or worsening in the ADPP group compared to the Placebo group (3.5% of dogs and 14.8% of dogs, respectively), with a relative risk of 0.88 (P = .04; AMI, ADPP, 3.5%, 2/57 dogs; Placebo, 14.8%, 9/61 dogs; relative risk, 0.88; 95% CI, 0.77-0.99).

CONCLUSION AND CLINICAL IMPORTANCE

The ADPP may accelerate resolution of acute diarrhea in dogs and decrease the requirement for AMI.

Comparative molecular analysis of fecal microbiota of bobcats (Lynx rufus) and domestic cats (Felis catus)

The goal of this study was to explore and describe fecal microbiota of captive and wild bobcats (Lynx rufus) and compare the results to those of domestic cats (Felis catus). Fecal samples from 27 bobcats (8 wild, 19 zoo-kept) were used for novel bacterial deoxyribonucleic acid (DNA) identification using next-generation sequencing of the V4 region of the bacterial 16S ribosomal ribonucleic acid (rRNA) gene, analyzed by Illumina sequencing, and then compared to data obtained from a colony of 10 domestic cats. In this study, the microbiota of both species was dominated by Firmicutes, followed by Proteobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia. When compared, fecal samples from bobcats harbored more Proteobacteria and Actinobacteria than fecal samples from domestic cats. There was a remarkable inter-bobcat variation in the relative abundances of the main bacterial genera. There were no significant differences, however, between the main phyla of the microbiota of the wild and domestic bobcats. Proteobacteria in wild bobcats (P = 0.079) and Firmicutes in zoo-kept bobcats (P = 0.079) approached significance. There were no differences in predominant genera between wild and captive bobcats. The results of this study showed that there are notable differences in fecal bacterial communities between domestic cats and both captive and wild bobcats. The lack of significant differences in bacterial communities between wild and zoo-kept bobcats suggests that the varied diet provided for these felids can result in a fecal microbiota resembling that generated by a wild diet.

Effect of an extruded animal protein-free diet on fecal microbiota of dogs with food-responsive enteropathy

Background

Dietary interventions are thought to modify gut microbial communities in healthy individuals. In dogs with chronic enteropathies, resolution of dysbiosis, along with remission of clinical signs, is expected with treatment.

Hypothesis/Objective

To evaluate changes in the fecal microbiota in dogs with food‐responsive chronic enteropathy (FRE) and in healthy control (HC) dogs before and after an elimination dietary trial with an animal protein‐free diet (APFD).

Animals

Dogs with FRE (n = 10) and HC (n = 14).

Methods

Dogs were fed the APFD for 60 days. Fecal microbiota was analyzed by Illumina 16S rRNA sequencing and quantitative polymerase chain reaction (PCR).

Results

A significantly lower bacterial alpha‐diversity was observed in dogs with FRE compared with HC dogs at baseline, and compared with FRE dogs after the trial. Distinct microbial communities were observed in dogs with FRE at baseline compared with HC dogs at baseline and compared with dogs with FRE after the trial. Microbial communities still were different in FRE dogs after the trial compared with HC dogs at baseline. In HC dogs, the fecal microbiota did not show a significant modification after administration of the APFD.

Conclusion and Clinical Importance

Our results suggest that, in FRE dogs, treatment with the APFD led to a partial recovery of the fecal microbiota by significantly increasing microbiota richness, which was significantly closer to a healthy microbiota after the treatment. In contrast, no changes were detected in the fecal microbiota of HC dogs fed the same APFD.

Bacterial diversity in the feces of dogs with CPV infection

Canine parvovirus (CPV) is a contagious disease in dogs that has high morbidity and mortality. In cases of infection, the pups tend to have a higher mortality and more severe clinical symptoms than the adult dogs because the dehydration is difficult for pups to bear. Following the natural infection, there is a rapid antibody response neutralizing the extracellular virus. As a result, virus titers in tissue and feces become markedly reduced. Hence, it is important to have an effective symptomatic therapy of supporting animals to survive in the early stages of CPV infection. Furthermore, the co-infection with bacteria could increase the severity of lesions and clinical signs as well. In this paper, we obtained the bacterial diversity in feces of CPV infected dogs with the enrichment of five bacteria genera (Shigella, Peptoclostridium, Peptostreptococcus, Streptococcus, Fusobacterium). These microorganisms may partly result in the intestinal pathology of the infection. In summary, the discussion of the bacterial biodiversity in feces of CPV infected dogs provides further insights into the pathology of CPV disease and the targets of developing more effective treatment strategies.

A canine-specific probiotic product in treating acute or intermittent diarrhea in dogs: A double-blind placebo-controlled efficacy study

A double-blind placebo-controlled intervention study on 60 dogs recruited from a pool of canine patients visiting a veterinary practice and diagnosed with acute diarrhea was conducted. The dogs received in randomized manner either a sour-milk product containing three canine-derived Lactobacillus sp. probiotics in combination of Lactobacillus fermentum VET 9A, L. rhamnosus VET 16A, and L. plantarum VET 14A (2×10⁹cfu/ml), or placebo. Stool consistency, general well-being, and the numbers of specific pathogens in stool samples were analyzed. Our results demonstrated that the treatment with the study sour-milk product had a normalizing effect on canine stool consistency. The treatment also enhanced the well-being of the pet by maintaining appetite and may reduce vomiting. In addition, the concentrations of Clostridium perfringens and Enterococcus faecium, which typically increase during diarrhea episodes in dogs, were decreased in probiotic group feces when compared with the placebo group. Taken together, the sour-milk with the specific probiotic combination had a normalizing effect on acute diarrhea in dogs which was associated with decreased numbers of potential pathogens in the feces of probiotic-treated dogs.

A critical evaluation of ecological indices for the comparative analysis of microbial communities based on molecular datasets

In times of global change and intensified resource exploitation, advanced knowledge of ecophysiological processes in natural and engineered systems driven by complex microbial communities is crucial for both safeguarding environmental processes and optimising rational control of biotechnological processes. To gain such knowledge, high-throughput molecular techniques are routinely employed to investigate microbial community composition and dynamics within a wide range of natural or engineered environments. However, for molecular dataset analyses no consensus about a generally applicable alpha diversity concept and no appropriate benchmarking of corresponding statistical indices exist yet. To overcome this, we listed criteria for the appropriateness of an index for such analyses and systematically scrutinised commonly employed ecological indices describing diversity, evenness and richness based on artificial and real molecular datasets. We identified appropriate indices warranting interstudy comparability and intuitive interpretability. The unified diversity concept based on 'effective numbers of types' provides the mathematical framework for describing community composition. Additionally, the Bray-Curtis dissimilarity as a beta-diversity index was found to reflect compositional changes. The employed statistical procedure is presented comprising commented R-scripts and example datasets for user-friendly trial application.

Understanding the canine intestinal microbiota and its modification by pro-, pre- and synbiotics - what is the evidence?

Interest in the composition of the intestinal microbiota and possibilities of its therapeutic modifications has soared over the last decade and more detailed knowledge specific to the canine microbiota at different mucosal sites including the gut is available. Probiotics, prebiotics or their combination (synbiotics) are a way of modifying the intestinal microbiota and exert effects on the host immune response. Probiotics are proposed to exert their beneficial effects through various pathways, for example production of antimicrobial peptides, enhancing growth of favourable endogenous microorganisms, competition for epithelial colonisation sites and immune‐modulatory functions. Despite widespread use of pro‐, pre‐ and synbiotics, scientific evidence of their beneficial effects in different conditions of the dog is scarce. Specific effects of different strains, their combination or their potential side‐effects have not been evaluated sufficiently. In some instances, in vitro results have been promising, but could not be transferred consistently into in vivo situations. Specific canine gastrointestinal (GI) diseases or conditions where probiotics would be beneficial, their most appropriate dosage and application have not been assessed extensively. This review summarises the current knowledge of the intestinal microbiome composition in the dog and evaluates the evidence for probiotic use in canine GI diseases to date. It wishes to provide veterinarians with evidence‐based information on when and why these products could be useful in preventing or treating canine GI conditions. It also outlines knowledge about safety and approval of commercial probiotic products, and the potential use of faecal microbial transplantation, as they are related to the topic of probiotic usage.

Characterization of microbial dysbiosis and metabolomic changes in dogs with acute diarrhea

Limited information is available regarding the metabolic consequences of intestinal dysbiosis in dogs with acute onset of diarrhea. The aim of this study was to evaluate the fecal microbiome, fecal concentrations of short-chain fatty acids (SCFAs), as well as serum and urine metabolites in healthy dogs (n=13) and dogs with acute diarrhea (n=13). The fecal microbiome, SCFAs, and serum/urine metabolite profiles were characterized by 454-pyrosequencing of the 16S rRNA genes, GC/MS, and untargeted and targeted metabolomics approach using UPLC/MS and HPLC/MS, respectively. Significantly lower bacterial diversity was observed in dogs with acute diarrhea in regards to species richness, chao1, and Shannon index (p=0.0218, 0.0176, and 0.0033; respectively). Dogs with acute diarrhea had significantly different microbial communities compared to healthy dogs (unweighted Unifrac distances, ANOSIM p=0.0040). While Bacteroidetes, Faecalibacterium, and an unclassified genus within Ruminococcaceae were underrepresented, the genus Clostridium was overrepresented in dogs with acute diarrhea. Concentrations of fecal propionic acid were significantly decreased in acute diarrhea (p=0.0033), and were correlated to a decrease in Faecalibacterium (ρ=0.6725, p=0.0332). The predicted functional gene content of the microbiome (PICRUSt) revealed overrepresentations of genes for transposase enzymes as well as methyl accepting chemotaxis proteins in acute diarrhea. Serum concentrations of kynurenic acid and urine concentrations of 2-methyl-1H-indole and 5-Methoxy-1H-indole-3-carbaldehyde were significantly decreased in acute diarrhea (p=0.0048, 0.0185, and 0.0330, respectively). These results demonstrate that the fecal dysbiosis present in acute diarrhea is associated with altered systemic metabolic states.

The fecal microbiome in cats with diarrhea

Recent studies have revealed that microbes play an important role in the pathogenesis of gastrointestinal (GI) diseases in various animal species, but only limited data is available about the microbiome in cats with GI disease. The aim of this study was to evaluate the fecal microbiome in cats with diarrhea. Fecal samples were obtained from healthy cats (n = 21) and cats with acute (n = 19) or chronic diarrhea (n = 29) and analyzed by sequencing of 16S rRNA genes, and PICRUSt was used to predict the functional gene content of the microbiome. Linear discriminant analysis (LDA) effect size (LEfSe) revealed significant differences in bacterial groups between healthy cats and cats with diarrhea. The order Burkholderiales, the families Enterobacteriaceae, and the genera Streptococcus and Collinsella were significantly increased in diarrheic cats. In contrast the order Campylobacterales, the family Bacteroidaceae, and the genera Megamonas, Helicobacter, and Roseburia were significantly increased in healthy cats. Phylum Bacteroidetes was significantly decreased in cats with chronic diarrhea (>21 days duration), while the class Erysipelotrichi and the genus Lactobacillus were significantly decreased in cats with acute diarrhea. The observed changes in bacterial groups were accompanied by significant differences in functional gene contents: metabolism of fatty acids, biosynthesis of glycosphingolipids, metabolism of biotin, metabolism of tryptophan, and ascorbate and aldarate metabolism, were all significantly (p<0.001) altered in cats with diarrhea. In conclusion, significant differences in the fecal microbiomes between healthy cats and cats with diarrhea were identified. This dysbiosis was accompanied by changes in bacterial functional gene categories. Future studies are warranted to evaluate if these microbial changes correlate with changes in fecal concentrations of microbial metabolites in cats with diarrhea for the identification of potential diagnostic or therapeutic targets.

Gut microbiota of humans, dogs and cats: current knowledge and future opportunities and challenges

High-throughput DNA sequencing techniques allow for the identification and characterisation of microbes and their genes (microbiome). Using these new techniques, microbial populations in several niches of the human body, including the oral and nasal cavities, skin, urogenital tract and gastrointestinal tract, have been described recently. Very little data on the microbiome of companion animals exist, and most of the data have been derived from the analysis of the faeces of healthy laboratory animals. High-throughput assays provide opportunities to study the complex and dense populations of the gut microbiota, including bacteria, archaea, fungi, protozoa and viruses. Our laboratory and others have recently described the predominant microbial taxa and genes of healthy dogs and cats and how these respond to dietary interventions. In general, faecal microbial phylogeny (e.g. predominance of Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria) and functional capacity (e.g. major functional groups related to carbohydrate, protein, DNA and vitamin metabolism; virulence factors; and cell wall and capsule) of the canine and feline gut are similar to those of the human gut. Initial sequencing projects have provided a glimpse of the microbial super-organism that exists within the canine and feline gut, but leaves much to be explored and discovered. As DNA provides information only about potential functions, studies that focus on the microbial transcriptome, metabolite profiles, and how microbiome changes affect host physiology and health are clearly required. Future studies must determine how diet composition, antibiotics and other drug therapies, breed and disease affect or are affected by the gut microbiome and how this information may be used to improve diets, identify disease biomarkers and develop targeted disease therapies.

Fecal microbiota of cats with naturally occurring chronic diarrhea assessed using 16S rRNA gene 454-pyrosequencing before and after dietary treatment

BACKGROUND

The gastrointestinal (GI) microbiota has a strong impact on the health of cats and these populations can be altered in GI disease. Little research has been done to associate improvement in diarrhea with changes in GI microbiota.

OBJECTIVE

To evaluate GI microbiota changes associated with diet change and related improvement in diarrhea in cats with chronic naturally occurring diarrhea.

ANIMALS

Fifteen adult Domestic Shorthair cats with naturally occurring chronic diarrhea.

METHODS

Controlled crossover dietary trial for management of diarrhea. Fecal microbiome was assessed using 454-pyrosequencing. Relationships among fecal score (FS), diet, and microbiome were explored using partial least square method, partial least square method - discriminant analysis, and orthogonal partial least square method with discriminant analysis (OPLS-DA).

RESULTS

Dominant bacterial phyla included the Firmicutes and Bacteroidetes, followed by Fusobacteria, Proteobacteria, Tenericutes, and Actinobacteria. Orthogonal partial least squares (OPLS-DA) clustering showed significant microbial differences within cats when fed Diet X versus Diet Y, and with Diet Y versus baseline. Significant correlations were found between the microbiome and FSs. Those bacteria with the strongest correlation with FS included Coriobacteriaceae Slackia spp., Campylobacter upsaliensis, Enterobacteriaceae Raoultella spp., Coriobacteriaceae Collinsella spp., and bacteria of unidentified genera within the families of Clostridiales Lachnospiracea and Aeromonadales Succinivibrionacease, suggesting that increased numbers of these organisms may be important to gut health.

CONCLUSIONS AND CLINICAL IMPORTANCE

Alterations in intestinal microbiota were associated with improvement in diarrhea, but, from our data we cannot conclude if changes in the microbiome caused the improvement in diarrhea, or vice versa.

Characterization of the fungal microbiome (mycobiome) in fecal samples from dogs

The prevalence and phylogenetic description of fungal organisms and their role as part of the intestinal ecosystem have not yet been studied extensively in dogs. This study evaluated the fungal microbiome of 19 dogs (12 healthy dogs and 7 dogs with acute diarrhea) using fungal tag-encoded FLX-Titanium amplicon pyrosequencing. Five distinct fungal phyla were identified, with Ascomycota (medians: 97.9% of obtained sequences in healthy dogs and 98.2% in diseased dogs) and Basidiomycota (median 1.0% in healthy dogs and median 0.5% in diseased dogs) being the most abundant fungal phyla. A total of 219 fungal genera were identified across all 19 dogs with a median (range) of 28 (4–69) genera per sample. Candida was the most abundant genus found in both the diseased dogs (median: 1.9%, range: 0.2%–38.5% of sequences) and healthy dogs (median: 5.2%, range: 0.0%–63.1% of sequences). Candida natalensis was the most frequently identified species. No significant differences were observed in the relative proportions of fungal communities between healthy and diseased dogs. In conclusion, fecal samples of healthy dogs and dogs with acute diarrhea harbor various fungal genera, and their role in gastrointestinal health and disease warrants further studies.

Synbiotic administration of canine-derived strain Lactobacillus fermentum CCM 7421 and inulin to healthy dogs

The canine-derived strain Lactobacillus fermentum CCM 7421 has been demonstrated to exert certain health benefits as a probiotic in dogs. Synbiotic combinations are widely used but are rarely studied in dogs. In this study the prebiotic inulin in combination with L. fermentum CCM 7421 was tested for its effects on faecal microbial populations, faecal characteristics, and blood biochemistry in canine experiments. Healthy adult dogs (n = 36) were randomly assigned to 1 of 3 treatment groups (12 dogs/treatment): (i) the control group (C), (ii) the probiotic group (LF group: L. fermentum CCM 7421, 10(8) CFU/mL of Ringer buffer, 0.1 mL/kg of body mass), and (iii) the synbiotic group (LF+I group: L. fermentum CCM 7421 + inulin (I; Raftifeed IPS) added as 1% of diet). The experiment lasted for 7 weeks with a 2-week treatment period. We detected a significant increase of lactic acid bacteria (LF versus C, day 7; LF versus C and LF versus LF+I, days 28 and 49), a decrease of clostridia (LF versus C, day 14), a lower pH value (LF versus LF+I, day 28), and a higher ammonia concentration (LF versus LF+I, days 14 and 49) in faecal samples. The synbiotic LF+I combination did not intensify the probiotic L. fermentum CCM 7421 efficacy, but its slight laxative effect can be useful to prevent constipation, e.g., in senior dogs.

2011 and 2012 Early Careers Achievement Awards: use of genomic biology to study companion animal intestinal microbiota

Although dogs and cats are quite different than many livestock species in that they have evolved by eating diets high in fat and protein and low in carbohydrates, the gastrointestinal microbiota still play a key role in the gut and overall host health of these species. Early experiments in this field used culture-based techniques to evaluate the effects of dietary ingredients, such as fibers and prebiotics, on microbiota and indices of gut health (e.g., fecal scores, pH, fermentative end products). Such studies, however, were limited in scope and lacked precision as it pertained to the microbiota. The DNA-based techniques that have become available over the past decade have greatly upgraded research capabilities and have provided a more encompassing view of the canine and feline gastrointestinal microbiomes. High-throughput sequencing techniques that are much cheaper and faster than Sanger sequencing have been a key development in this progress. Sequence data not only allow for the identification of all microbial taxa but also provide information regarding functional capacity when a shotgun sequencing approach is used. The few canine and feline studies that have used 454 pyrosequencing have identified the predominant microbial taxa and metabolic functions present in healthy populations, differences between healthy and diseased dog and cat populations, and the effects of diet (e.g., dietary fibers, prebiotics, protein to carbohydrate ratio) on gastrointestinal microbiota. Although these studies have provided a foundation from which to work, more research is needed to increase our general understanding of the gastro-intestinal microbiome, how it impacts host health, how its composition and activity may be altered by age, genetic, or environmental factors, and test whether specific pathogens or disease signatures can be identified and used in diagnosis and/or treatment of disease.

The fecal microbiome in dogs with acute diarrhea and idiopathic inflammatory bowel disease

BACKGROUND

Recent molecular studies have revealed a highly complex bacterial assembly in the canine intestinal tract. There is mounting evidence that microbes play an important role in the pathogenesis of acute and chronic enteropathies of dogs, including idiopathic inflammatory bowel disease (IBD). The aim of this study was to characterize the bacterial microbiota in dogs with various gastrointestinal disorders.

METHODOLOGY/PRINCIPAL FINDINGS

Fecal samples from healthy dogs (n = 32), dogs with acute non-hemorrhagic diarrhea (NHD; n = 12), dogs with acute hemorrhagic diarrhea (AHD; n = 13), and dogs with active (n = 9) and therapeutically controlled idiopathic IBD (n = 10) were analyzed by 454-pyrosequencing of the 16S rRNA gene and qPCR assays. Dogs with acute diarrhea, especially those with AHD, had the most profound alterations in their microbiome, as significant separations were observed on PCoA plots of unweighted Unifrac distances. Dogs with AHD had significant decreases in Blautia, Ruminococcaceae including Faecalibacterium, and Turicibacter spp., and significant increases in genus Sutterella and Clostridium perfringens when compared to healthy dogs. No significant separation on PCoA plots was observed for the dogs with IBD. Faecalibacterium spp. and Fusobacteria were, however, decreased in the dogs with clinically active IBD, but increased during time periods of clinically insignificant IBD, as defined by a clinical IBD activity index (CIBDAI).

CONCLUSIONS

Results of this study revealed a bacterial dysbiosis in fecal samples of dogs with various GI disorders. The observed changes in the microbiome differed between acute and chronic disease states. The bacterial groups that were commonly decreased during diarrhea are considered to be important short-chain fatty acid producers and may be important for canine intestinal health. Future studies should correlate these observed phylogenetic differences with functional changes in the intestinal microbiome of dogs with defined disease phenotypes.

Current state of knowledge: the canine gastrointestinal microbiome

Gastrointestinal (GI) microbes have important roles in the nutritional, immunological, and physiologic processes of the host. Traditional cultivation techniques have revealed bacterial density ranges from 10(4) to 10(5) colony forming units (CFU)/g in the stomach, from 10(5) to 10(7) CFU/g in the small intestine, and from 10(9) to 10(11) CFU/g in the colon of healthy dogs. As a small number of bacterial species can be grown and studied in culture, however, progress was limited until the recent emergence of DNA-based techniques. In recent years, DNA sequencing technology and bioinformatics have allowed for better phylogenetic and functional/metabolic characterization of the canine gut microbiome. Predominant phyla include Firmicutes, Bacteroidetes, Fusobacteria, Proteobacteria, and Actinobacteria. Studies using 16S ribosomal RNA (rRNA) gene pyrosequencing have demonstrated spatial differences along the GI tract and among microbes adhered to the GI mucosa compared to those in intestinal contents or feces. Similar to humans, GI microbiome dysbiosis is common in canine GI diseases such as chronic diarrhea and inflammatory bowel diseases. DNA-based assays have also identified key pathogens contributing to such conditions, including various Clostridium, Campylobacter, Salmonella, and Escherichia spp. Moreover, nutritionists have applied DNA-based techniques to study the effects of dietary interventions such as dietary fiber, prebiotics, and probiotics on the canine GI microbiome and associated health indices. Despite recent advances in the field, the canine GI microbiome is far from being fully characterized and a deeper characterization of the phylogenetic and functional/metabolic capacity of the GI microbiome in health and disease is needed. This paper provides an overview of recent studies performed to characterize the canine GI microbiome.

A molecular enrichment strategy based on cpn60 for detection of epsilon-proteobacteria in the dog fecal microbiome

Members of the rare microbiome can be important components of complex microbial communities. For example, pet dog ownership is a known risk factor for human campylobacteriosis, and Campylobacter is commonly detected in dog feces by targeted assays. However, these organisms have not been detected by metagenomic methods. The goal of this study was to characterize fecal microbiota from healthy and diarrheic pet dogs using two different levels of molecular detection. PCR amplification and pyrosequencing of the universal cpn60 gene target was used to obtain microbial profiles from each dog. To investigate the relatively rare epsilon-proteobacteria component of the microbiome, a molecular enrichment was carried out using a PCR that first amplified the cpn10-cpn60 region from epsilon-proteobacteria, followed by universal cpn60 target amplification and pyrosequencing. From the non-enriched survey, the major finding was a significantly higher proportion of Bacteroidetes, notably Bacteroides vulgatus, in healthy dogs compared to diarrheic dogs. Epsilon-proteobacteria from the genera Helicobacter and Campylobacter were also detected at a low level in the non-enriched profiles of some dogs. Molecular enrichment increased the proportion of epsilon-proteobacteria sequences detected from each dog, as well as identified novel, presumably rare sequences not seen in the non-enriched profiles. Enriched profiles contained known species of Arcobacter, Campylobacter, Flexispira, and Helicobacter and identified two possibly novel species. These findings add to our understanding of the canine fecal microbiome in general, the epsilon-proteobacteria component specifically, and present a novel modification to traditional metagenomic approaches for study of the rare microbiome.

Dogs leaving the ICU carry a very large multi-drug resistant enterococcal population with capacity for biofilm formation and horizontal gene transfer

The enterococcal community from feces of seven dogs treated with antibiotics for 2–9 days in the veterinary intensive care unit (ICU) was characterized. Both, culture-based approach and culture-independent 16S rDNA amplicon 454 pyrosequencing, revealed an abnormally large enterococcal community: 1.4±0.8×10⁸ CFU gram⁻¹ of feces and 48.9±11.5% of the total 16,228 sequences, respectively. The diversity of the overall microbial community was very low which likely reflects a high selective antibiotic pressure. The enterococcal diversity based on 210 isolates was also low as represented by Enterococcus faecium (54.6%) and Enterococcus faecalis (45.4%). E. faecium was frequently resistant to enrofloxacin (97.3%), ampicillin (96.5%), tetracycline (84.1%), doxycycline (60.2%), erythromycin (53.1%), gentamicin (48.7%), streptomycin (42.5%), and nitrofurantoin (26.5%). In E. faecalis, resistance was common to tetracycline (59.6%), erythromycin (56.4%), doxycycline (53.2%), and enrofloxacin (31.9%). No resistance was detected to vancomycin, tigecycline, linezolid, and quinupristin/dalfopristin in either species. Many isolates carried virulence traits including gelatinase, aggregation substance, cytolysin, and enterococcal surface protein. All E. faecalis strains were biofilm formers in vitro and this phenotype correlated with the presence of gelE and/or esp. In vitro intra-species conjugation assays demonstrated that E. faecium were capable of transferring tetracycline, doxycycline, streptomycin, gentamicin, and erythromycin resistance traits to human clinical strains. Multi-locus variable number tandem repeat analysis (MLVA) and pulsed-field gel electrophoresis (PFGE) of E. faecium strains showed very low genotypic diversity. Interestingly, three E. faecium clones were shared among four dogs suggesting their nosocomial origin. Furthermore, multi-locus sequence typing (MLST) of nine representative MLVA types revealed that six sequence types (STs) originating from five dogs were identical or closely related to STs of human clinical isolates and isolates from hospital outbreaks. It is recommended to restrict close physical contact between pets released from the ICU and their owners to avoid potential health risks.

Companion animals symposium: microbes and gastrointestinal health of dogs and cats

Recent molecular studies have revealed complex bacterial, fungal, archaeal, and viral communities in the gastrointestinal tract of dogs and cats. More than 10 bacterial phyla have been identified, with Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, and Actinobacteria constituting more than 99% of all gut microbiota. Microbes act as a defending barrier against invading pathogens, aid in digestion, provide nutritional support for enterocytes, and play a crucial role in the development of the immune system. Of significance for gastrointestinal health is their ability to ferment dietary substrates into short-chain fatty acids, predominantly to acetate, propionate, and butyrate. However, microbes can have also a detrimental effect on host health. Specific pathogens (e.g., Salmonella, Campylobacter jejuni, and enterotoxigenic Clostridium perfringens) have been implicated in acute and chronic gastrointestinal disease. Compositional changes in the small intestinal microbiota, potentially leading to changes in intestinal permeability and digestive function, have been suggested in canine small intestinal dysbiosis or antibiotic-responsive diarrhea. There is mounting evidence that microbes play an important role in the pathogenesis of canine and feline inflammatory bowel disease (IBD). Current theories for the development of IBD favor a combination of environmental factors, the intestinal microbiota, and a genetic susceptibility of the host. Recent studies have revealed a genetic susceptibility for defective bacterial clearance in Boxer dogs with granulomatous colitis. Differential expression of pathogen recognition receptors (i.e., Toll-like receptors) were identified in dogs with chronic enteropathies. Similarly to humans, a microbial dysbiosis has been identified in feline and canine IBD. Commonly observed microbial changes are increased Proteobacteria (i.e., Escherichia coli) with concurrent decreases in Firmicutes, especially a reduced diversity in Clostridium clusters XIVa and IV (i.e., Lachnospiraceae, Ruminococcaceae, Faecalibacterium spp.). This would indicate that these bacterial groups, important short-chain fatty acid producers, may play an important role in promoting intestinal health.

Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats

This study evaluated the fecal microbiota of 12 healthy pet dogs and 12 pet cats using bacterial and fungal tag-encoded FLX-Titanium amplicon pyrosequencing. A total of 120,406 pyrosequencing reads for bacteria (mean 5017) and 5359 sequences (one pool each for dogs and cats) for fungi were analyzed. Additionally, group-specific 16S rRNA gene clone libraries for Bifidobacterium spp. and lactic acid-producing bacteria (LAB) were constructed. The most abundant bacterial phylum was Firmicutes, followed by Bacteroidetes in dogs and Actinobacteria in cats. The most prevalent bacterial class in dogs and cats was Clostridia, dominated by the genera Clostridium (clusters XIVa and XI) and Ruminococcus. At the genus level, 85 operational taxonomic units (OTUs) were identified in dogs and 113 OTUs in cats. Seventeen LAB and eight Bifidobacterium spp. were detected in canine feces. Ascomycota was the only fungal phylum detected in cats, while Ascomycota, Basidiomycota, Glomeromycota, and Zygomycota were identified in dogs. Nacaseomyces was the most abundant fungal genus in dogs; Saccharomyces and Aspergillus were predominant in cats. At the genus level, 33 different fungal OTUs were observed in dogs and 17 OTUs in cats. In conclusion, this study revealed a highly diverse bacterial and fungal microbiota in canine and feline feces.

Prevalence of diarrhea and enteropathogens in racing sled dogs

BACKGROUND

Diarrhea is highly prevalent in racing sled dogs, although the underlying causes are poorly understood.

HYPOTHESIS

Clostridium perfringens enterotoxin (CPE) and Clostridium difficile Toxin A and B are associated with diarrhea in racing sled dogs.

ANIMALS

One hundred and thirty-five sled dogs.

METHODS

Freshly voided feces were obtained from 55 dogs before racing and from 80 dogs after 400 miles of racing. Samples were visually scored for diarrhea, mucus, blood, and melena. CPE and C. difficile Toxin A and B were detected by ELISA. Samples were cultured for C. perfringens, C. difficile, Campylobacter, Salmonella, and Escherichia coli O157; Giardia and Cryptosporidium spp. were detected via immunofluorescence.

RESULTS

Diarrhea occurred in 36% of dogs during racing, and hematochezia, fecal mucus or melena, or all 3 occurred in 57.5% of dogs. Salmonella was isolated from 78.2% of dogs before racing, and from 71.3% of dogs during racing. C. perfringens and C. difficile were isolated from 100 and 58.2% of dogs before racing, and from 95 and 36.3% of dogs during racing. Dogs were more likely to test positive for CPE during than before racing (18.8 versus 5.5%, P = .021); however, no enteropathogens or their respective toxins were significantly associated with hematochezia or diarrhea.

CONCLUSIONS AND CLINICAL IMPORTANCE

Sled dogs participating in long distance racing have a high prevalence of diarrhea and hematochezia that is not associated with common enteropathogens. It is possible that diarrhea and hematochezia represent the effect of prolonged exercise on the gastrointestinal tract.