The effect of the macrolide antibiotic tylosin on microbial diversity in the canine small intestine as demonstrated by massive parallel 16S rRNA gene sequencing

The influence of 'biotics' on the gut microbiome of dogs and cats

A global rise in pet ownership and an increasing tendency towards the humanisation of pets have resulted in a greater focus on improving animal health and longevity. These developments coincide with the increased recognition of the role of the gut microbiome in animal health. The gut microbiome has been shown to play a prominent role in gastrointestinal health, and it is becoming increasingly clear that these health benefits extend beyond the gut and into different physiological systems, such as the immune system. Dietary supplementation with products known as 'biotics', which include probiotics, prebiotics, synbiotics and postbiotics, is a strategy used to modify the gut microbiome and promote host health. Although biotics have been successfully used in companion animals, questions remain regarding appropriate biotic selection, mechanisms of action, optimum inclusion levels and safety. This review aims to summarise the effects of biotics on the gut microbiome of dogs and cats and assess their potential role in supporting gastrointestinal health.

Harnessing the microbiome: probiotics, antibiotics and their role in canine and feline gastrointestinal disease

Unfavourable alterations of the host microbial environment, known as dysbiosis, have been identified in many canine and feline gastrointestinal (GI) diseases. As a result, normalisation of microbial composition and function has become an important therapeutic target. Given the complex and individualistic interplay between the resident microbiota, host and environment, a multimodal approach is often necessary when addressing dysbiosis in dogs and cats with GI disease. Systemic antibiotics are often empirically used to treat acute and chronic GI diseases. However, with modern genomic techniques demonstrating the profound negative effect antibiotics can have on the GI microbiota and the rapid emergence of resistant bacteria globally, there has been an increased focus on identifying antibiotic alternatives for use in small animal practice. Biotics, such as prebiotics, probiotics and synbiotics, are of growing interest due to their potential supportive effect on the microbiota. This article reviews the evidence for the use of biotics in canine and feline GI disease, highlighting how judicious use of antibiotics and targeted probiotic supplementation can enhance patient outcomes by promoting a balanced gut microbial environment.

Dysbiosis index and fecal concentrations of sterols, long-chain fatty acids and unconjugated bile acids in dogs with inflammatory protein-losing enteropathy

Introduction

Canine protein-losing enteropathy (PLE) is a syndrome characterized by gastrointestinal loss of proteins. While fecal microbiome and metabolome perturbations have been reported in dogs with chronic enteropathy, they have not been widely studied in dogs with PLE. Therefore, the study aims were to investigate gut microbiome and targeted fecal metabolites in dogs with inflammatory PLE (iPLE) and evaluate whether treatment affects these changes at short-term follow-up.

Methods

Thirty-eight dogs with PLE and histopathological evidence of gastrointestinal inflammation and 47 healthy dogs were enrolled. Fecal samples were collected before endoscopy (T0) and after one month of therapy (T1). Microbiome and metabolome alterations were investigated using qPCR assays (dysbiosis index, DI) and gas chromatography/mass spectrometry (long-chain fatty acids, sterols, unconjugated bile acids), respectively.

Results

Median (min-max) DI of iPLE dogs was 0.4 (-5.9 to 7.7) and was significantly higher (p < 0.0001) than median DI in healthy dogs [-2.0 (-6.0 to 5.3)]. No significant associations were found between DI and selected clinicopathological variables. DI did not significantly differ between T0 and T1. In iPLE dogs, at T0, myristic, palmitic, linoleic, oleic, cis-vaccenic, stearic, arachidonic, gondoic, docosanoic, erucic, and nervonic acids were significantly higher (p < 0.0001) than healthy dogs. In iPLE dogs, oleic acid (p = 0.044), stearic acid (p = 0.013), erucic acid (p = 0.018) and nervonic acid (p = 0.002) were significantly decreased at T1. At T0, cholesterol and lathosterol (p < 0.0001) were significantly higher in iPLE dogs compared to healthy dogs, while total measured phytosterols were significantly lower (p = 0.001). No significant differences in total sterols, total phytosterols and total zoosterols content were found at T1, compared to T0. At T0, total primary bile acids and total secondary bile acids did not significantly differ between healthy control dogs and iPLE dogs. No significant differences in fecal bile acid content were found at T1.

Discussion

Dysbiosis and lipid metabolism perturbations were observed in dogs with iPLE. Different therapeutic protocols lead to an improvement of some but not all metabolome perturbations at short-term follow-up.

Oral Fecal Microbiota Transplantation in Dogs with Tylosin-Responsive Enteropathy-A Proof-of-Concept Study

A clinical trial was conducted to evaluate the effect of fecal microbiota transplantation (FMT) on the canine chronic enteropathy clinical activity index (CCECAI), fecal consistency, and microbiome of dogs with tylosin-responsive enteropathy (TRE). The trial consisted of four phases: (1) screening with discontinuation of tylosin for 4 weeks, (2) inclusion with re-introduction of tylosin for 3-7 days, (3) treatment with FMT/placebo for 4 weeks, and (4) post-treatment with follow-up for 4 weeks after treatment cessation. The study found that the treatment efficacy of FMT (71.4%) was slightly higher than that of placebo (50%), but this difference was not statistically significant due to underpowering. The most abundant bacterial species detected in the fecal microbiomes of dogs with TRE before FMT or placebo treatment were Blautia hansenii, Ruminococcus gnavus, Escherichia coli, Clostridium dakarense, Clostridium perfringens, Bacteroides vulgatus, and Faecalimonas umbilicata. After FMT, the microbiomes exhibited increases in Clostridium dakarense, Clostridium paraputrificum, and Butyricicoccus pullicaecorum. The microbiome alpha diversity of TRE dogs was lower when on tylosin treatment compared to healthy dogs, but it increased after treatment in both the FMT and placebo groups. Comparisons with the stool donor showed that, on average, 30.4% of donor strains were engrafted in FMT recipients, with the most common strains being several Blautia sp., Ruminococcus gnavus, unclassified Lachnoclostridium, Collinsella intestinalis, and Fournierella massiliensis.

Decoding the Gut Microbiome in Companion Animals: Impacts and Innovations

The changing notion of "companion animals" and their increasing global status as family members underscores the dynamic interaction between gut microbiota and host health. This review provides a comprehensive understanding of the intricate microbial ecology within companion animals required to maintain overall health and prevent disease. Exploration of specific diseases and syndromes linked to gut microbiome alterations (dysbiosis), such as inflammatory bowel disease, obesity, and neurological conditions like epilepsy, are highlighted. In addition, this review provides an analysis of the various factors that impact the abundance of the gut microbiome like age, breed, habitual diet, and microbe-targeted interventions, such as probiotics. Detection methods including PCR-based algorithms, fluorescence in situ hybridisation, and 16S rRNA gene sequencing are reviewed, along with their limitations and the need for future advancements. Prospects for longitudinal investigations, functional dynamics exploration, and accurate identification of microbial signatures associated with specific health problems offer promising directions for future research. In summary, it is an attempt to provide a deeper insight into the orchestration of multiple microbial species shaping the health of companion animals and possible species-specific differences.

Gut microbiome perturbation and its correlation with tylosin pharmacokinetics in healthy and infected pigs

Tylosin, an antibiotic with a long history in treating respiratory bacterial infections, has unknown effects on the gut microbiota of healthy and infected pigs. The study aimed to investigate the effect of a therapeutic dose of tylosin on swine gut microbiota and explored the relationship between this effect and tylosin pharmacokinetics (PK). We also assessed whether changes in gut microbiota after tylosin administration differ between healthy animals (n = 7) and animals intranasally co-infected (n = 7) with Actinobacillus pleuropneumoniae and Pasteurella multocida. Both groups were intramuscularly administered with tylosin (20 mg/kg). The 16S rRNA gene analyses revealed a significantly lower species richness and diversity, after tylosin treatment, in the infected than the healthy pigs, with infected pigs having lower levels of Bacteroidetes and Firmicutes and higher levels of Proteobacteria. Greater tylosin exposure (greater area under curve (AUC) and maximum plasma concentration (Cmax), and slower elimination (longer terminal half-life, T1/2) were observed in healthy than infected pigs. Relative abundance of Lactobacillus, Oscillibacter, Prevotella, and Sporobacter was positively and significantly correlated with AUC and Cmax, whereas the abundance of Acinetobacter, Alishewanella, and Pseudomonas was positively and significantly correlated with T1/2 and mean residence time (MRT) of tylosin. Our findings, for the first time, demonstrated significant changes in swine gut microbiota after a single therapeutic dose of tylosin was administered, whereas the effect of these changes on tylosin PK was not evident.

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.

Impact of fecal sample preservation and handling techniques on the canine fecal microbiota profile

Canine fecal microbiota profiling provides insight into host health and disease. Standardization of methods for fecal sample storage for microbiomics is currently inconclusive, however. This study investigated the effects of homogenization, the preservative RNAlater, room temperature exposure duration, and short-term storage in the fridge prior to freezing on the canine fecal microbiota profile. Within 15 minutes after voiding, samples were left non-homogenized or homogenized and aliquoted, then kept at room temperature (20-22°C) for 0.5, 4, 8, or 24 hours. Homogenized aliquots then had RNAlater added or not. Following room temperature exposure, all aliquots were stored in the fridge (4°C) for 24 hours prior to storing in the freezer (-20°C), or stored directly in the freezer. DNA extraction, PCR amplification, then sequencing were completed on all samples. Alpha diversity (diversity, evenness, and richness), and beta diversity (community membership and structure), and relative abundances of bacterial genera were compared between treatments. Homogenization and RNAlater minimized changes in the microbial communities over time, although minor changes in relative abundances occurred. Non-homogenized samples had more inter-sample variability and greater changes in beta diversity than homogenized samples. Storage of canine fecal samples in the fridge for 24 h prior to storage in the freezer had little effect on the fecal microbiota profile. Our findings suggest that if immediate analysis of fecal samples is not possible, samples should at least be homogenized to preserve the existing microbiota profile.

Pseudogenomic insights into the evolution of Mycobacterium ulcerans

BACKGROUND

Buruli ulcer (BU) disease, caused by Mycobacterium ulcerans (MU), and characterized by necrotic ulcers is still a health problem in Africa and Australia. The genome of the bacterium has several pseudogenes due to recent evolutionary events and environmental pressures. Pseudogenes are genetic elements regarded as nonessential in bacteria, however, they are less studied due to limited available tools to provide understanding of their evolution and roles in MU pathogenicity.

RESULTS

This study developed a bioinformatic pipeline to profile the pseudogenomes of sequenced MU clinical isolates from different countries. One hundred and seventy-two MU genomes analyzed revealed that pseudogenomes of African strains corresponded to the two African lineages 1 and 2. Pseudogenomes were lineage and location specific and African lineage 1 was further divided into A and B. Lineage 2 had less relaxation in positive selection than lineage 1 which may signify different evolutionary points. Based on the Gil-Latorre model, African MU strains may be in the latter stages of evolutionary adaption and are adapting to an environment rich in metabolic resources with a lower temperature and decreased UV radiation. The environment fosters oxidative metabolism and MU may be less reliant on some secondary metabolites. In-house pseudogenomes from Ghana and Cote d'Ivoire were different from other African strains, however, they were identified as African strains.

CONCLUSION

Our bioinformatic pipeline provides pseudogenomic insights to complement other whole genome analyses, providing a better view of the evolution of the genome of MU and suggest an adaptation model which is important in understanding transmission. MU pseudogene profiles vary based on lineage and country, and an apparent reduction in insertion sequences used for the detection of MU which may adversely affect the sensitivity of diagnosis.

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.

Characteristics of the Digestive Tract of Dogs and Cats

As for other mammals, the digestive system of dogs (facultative carnivores) and cats (obligate carnivores) includes the mouth, teeth, tongue, pharynx, esophagus, stomach, small intestine, large intestine, and accessory digestive organs (salivary glands, pancreas, liver, and gallbladder). These carnivores have a relatively shorter digestive tract but longer canine teeth, a tighter digitation of molars, and a greater stomach volume than omnivorous mammals such as humans and pigs. Both dogs and cats have no detectable or a very low activity of salivary α-amylase but dogs, unlike cats, possess a relatively high activity of pancreatic α-amylase. Thus, cats select low-starch foods but dogs can consume high-starch diets. In contrast to many mammals, the vitamin B12 (cobalamin)-binding intrinsic factor for the digestion and absorption of vitamin B12 is produced in: (a) dogs primarily by pancreatic ductal cells and to a lesser extent the gastric mucosa; and (b) cats exclusively by the pancreatic tissue. Amino acids (glutamate, glutamine, and aspartate) are the main metabolic fuels in enterocytes of the foregut. The primary function of the small intestine is to digest and absorb dietary nutrients, and its secondary function is to regulate the entry of dietary nutrients into the blood circulation, separate the external from the internal milieu, and perform immune surveillance. The major function of the large intestine is to ferment undigested food (particularly fiber and protein) and to absorb water, short-chain fatty acids (serving as major metabolic fuels for epithelial cells of the large intestine), as well as vitamins. The fermentation products, water, sloughed cells, digestive secretions, and microbes form feces and then pass into the rectum for excretion via the anal canal. The microflora influences colonic absorption and cell metabolism, as well as feces quality. The digestive tract is essential for the health, survival, growth, and development of dogs and cats.

Noninvasive sampling of the small intestinal chyme for microbiome, metabolome and antimicrobial resistance genes in dogs, a proof of concept

BACKGROUND

The gastrointestinal microbiome and metabolome vary greatly throughout the different segments of the gastrointestinal tract, however current knowledge of gastrointestinal microbiome and metabolome in health and disease is limited to fecal samples due to ease of sampling. The engineered Small Intestinal MicroBiome Aspiration (SIMBA™) capsule allows specific sampling of the small intestine in humans. We aimed to determine whether administration of SIMBA™ capsules to healthy beagle dogs could reliably and safely sample the small intestinal microbiome and metabolome when compared to their fecal microbiome and metabolome.

RESULTS

Eleven beagle dogs were used for the study. Median transit time of capsules was 29.93 h (range: 23.83-77.88). Alpha diversity, as measured by the Simpson diversity, was significantly different (P = 0.048). Shannon diversity was not different (P = 0.114). Beta diversity results showed a significant difference between capsule and fecal samples regarding Bray-Curtis, weighted and unweighted unifrac (P = 0.002) and ANOSIM distance metric s (R = 0.59, P = 0.002). In addition to observing a statistically significant difference in the microbial composition of capsules and feces, distinct variation in the metabolite profiles was seen between the sample types. Heat map analysis showed 16 compounds that were significantly different between the 2 sampling modes (adj-P value ranged between 0.004 and 0.036) with 10 metabolites more abundant in the capsule than in the feces and 6 metabolites more abundant in the feces compared to the capsules.

CONCLUSIONS

The engineered Small Intestinal MicroBiome Aspiration (SIMBA™) capsule was easy and safe to administer to dogs. Microbiome and metabolome analysis from the capsule samples were significantly different than that of the fecal samples and were like previously published small intestinal microbiome and metabolome composition.

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.

Effects of antimicrobials on the gastrointestinal microbiota of dogs and cats

Among several environmental factors, exposure to antimicrobials has been in the spotlight as a cause of profound and long-term disturbance of the intestinal microbiota. Antimicrobial-induced dysbiosis is a general term and includes decreases in microbial richness and diversity, loss of beneficial bacterial groups, blooms of intestinal pathogens and alterations in the metabolic functions and end-products of the microbiota. Mounting evidence from human and experimental animal studies suggest an association between antimicrobial-induced dysbiosis and susceptibility to gastrointestinal, metabolic, endocrine, immune and neuropsychiatric diseases. These associations are commonly stronger after early life exposure to antimicrobials, a period during which maturation of the microbiota and immune system take place in parallel. In addition, these associations commonly become stronger as the number of antimicrobial courses increases. The repeatability of these findings among different studies as well as the presence of a dose-dependent relationship between antimicrobial exposure and disease development collectively require careful consideration of the need for antimicrobial use. There are limited studies are available in dogs and cats regarding the long-term effects of antimicrobials on the microbiota and subsequent susceptibility to diseases. This review discusses the effects of antimicrobials on the gastrointestinal microbiota and the most important associations between antimicrobial-induced dysbiosis and diseases in humans, dogs, and cats.

Current in Vitro and Animal Models for Understanding Foods: Human Gut-Microbiota Interactions

The food-gut microbiota interaction is an important regulator of human health. Numerous in vitro and animal models have thus been developed in order to simulate the specific food-gut microbiota and/or host-gut microbiota interactions in the human colon. This review summarizes the design principles of each model and discusses their advantages and weaknesses in terms of studying food-gut microbiota interactions. In vitro fermentation models appear to be reliable methods to investigate various aspects involved in the food-gut microbiota interactions in humans. However, many physiological perspectives lack appreciation of these models, such as peristaltic movement, biochemical conditions, and gastrointestinal anatomy. Animal models provide more physiological relevance to human trials compared to in vitro models. However, they may have gastrointestinal tract aspects that are distinct from human subjects. This review contains important information that can help the development of more advanced models to study food-gut microbiota interactions in humans.

Canine chronic enteropathy—Current state-of-the-art and emerging concepts

Over the last decade, chronic inflammatory enteropathies (CIE) in dogs have received great attention in the basic and clinical research arena. The 2010 ACVIM Consensus Statement, including guidelines for the diagnostic criteria for canine and feline CIE, was an important milestone to a more standardized approach to patients suspected of a CIE diagnosis. Great strides have been made since understanding the pathogenesis and classification of CIE in dogs, and novel diagnostic and treatment options have evolved. New concepts in the microbiome-host-interaction, metabolic pathways, crosstalk within the mucosal immune system, and extension to the gut-brain axis have emerged. Novel diagnostics have been developed, the clinical utility of which remains to be critically evaluated in the next coming years. New directions are also expected to lead to a larger spectrum of treatment options tailored to the individual patient. This review offers insights into emerging concepts and future directions proposed for further CIE research in dogs for the next decade to come.

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.

Recovery of Fecal Microbiome and Bile Acids in Healthy Dogs after Tylosin Administration with and without Fecal Microbiota Transplantation

Antibiotics cause gut dysbiosis and bile acid dysmetabolism in dogs. The effect of fecal microbiota transplantation (FMT) on microbiome and metabolome recovery is unknown. This prospective, randomized, placebo-controlled study included sixteen healthy purpose-bred dogs. All dogs received tylosin 20 mg/kg PO once daily (days 1–7) and were randomly assigned to either receive one FMT via enema (day 8), daily oral FMT capsules (days 8–21), or daily placebo capsules (days 8–21). Fecal samples were frozen at regular intervals until day 42. Quantitative PCR for 8 bacterial taxa was performed to calculate the fecal dysbiosis index (FDI) and fecal concentrations of unconjugated bile acids (UBA) were measured using gas chromatography-mass spectrometry. Tylosin altered the abundance of most evaluated bacteria and induced a significant decrease in secondary bile acid concentrations at day 7 in all dogs. However, most parameters returned to their baseline by day 14 in all dogs. In conclusion, tylosin markedly impacted fecal microbiota and bile acid concentrations, although return to baseline values was quick after the antibiotic was discontinued. Overall, FMT did not accelerate recovery of measured parameters. Further studies are warranted to confirm the value of FMT in accelerating microbiota recovery in antibiotic-associated dysbiosis in dogs.

A prospective multicenter study of the efficacy of a fiber-supplemented dietary intervention in dogs with chronic large bowel diarrhea

Background

Chronic large bowel diarrhea is common in dogs and can have a significant impact on their overall health and well being. We evaluated the safety and efficacy of a therapeutic food with select dietary plant fibers known to contain antioxidant and polyphenol compounds on clinical signs in dogs with chronic diarrhea.

Methods

A prospective clinical study was conducted in 31 adult dogs currently experiencing chronic diarrhea from private veterinary practices in the United States. Enrolled dogs were switched to a complete and balanced dry therapeutic food containing whole grains and polyphenol-containing fiber sources for 56 days. Veterinarians evaluated changes from baseline in overall clinical signs, recurrence of clinical signs, and stool parameters at Days 2, 3, 4, 28, and 56. Dog owners evaluated stool consistency daily and nausea/vomiting, quality of life (QoL), and stooling behaviors at Days 1, 14, 28, and 56. Statistical analysis was performed using a mixed-effects model with Day as a fixed-effect.

Results

Assessments of overall clinical response and stool parameters indicated that diarrhea improved significantly within 1 day of initiating the therapeutic food. Veterinarians reported that 68% of dogs had complete resolution of their clinical signs by Day 56 and the remaining 32% experienced improvement (P < 0.05), with no cases of recurrence. Veterinarians also reported improvement in stool consistency (P < 0.001) and reductions of blood and mucus in stool (P < 0.001). Significant improvements in nausea/vomiting, stooling behaviors, and quality of life (QoL) were reported by dog owners after 28 days and were sustained through day 56 (P < 0.05). The therapeutic food was safe and well tolerated.

Conclusions

In dogs with chronic large bowel diarrhea, the therapeutic food rapidly improved stool consistency, resolved clinical signs, and improved stooling behaviors and QoL. Therapeutic foods supplemented with fiber sources rich in antioxidant and anti-inflammatory compounds contribute to rapid resolution of chronic diarrhea without recurrence and may contribute to long term health.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03302-8.

Effect of antimicrobial administration on fecal microbiota of critically ill dogs: dynamics of antimicrobial resistance over time

Background

Multidrug resistance in companion animals poses significant risks to animal and human health. Prolonged antimicrobial drug (AMD) treatment in animals is a potential source of selection pressure for antimicrobial resistance (AMR) including in the gastrointestinal microbiota. We performed a prospective study of dogs treated for septic peritonitis, pyometra, or bacterial pneumonia and collected repeated fecal samples over 60 days. Bacterial cultures and direct molecular analyses of fecal samples were performed including targeted resistance gene profiling.

Results

Resistant Escherichia coli increased after 1 week of treatment (D1:21.4% vs. D7:67.9% P < 0.001) and returned to baseline proportions by D60 (D7:67.9% vs D60:42.9%, P = 0.04). Dogs with septic peritonitis were hospitalized significantly longer than those with pneumonia or pyometra. Based on genetic analysis, Simpson’s diversity index significantly decreased after 1 week of treatment (D1 to D7, P = 0.008), followed by a gradual increase to day 60 (D1 and D60, P = 0.4). Detection of CTX-M was associated with phenotypic resistance to third-generation cephalosporins in E. coli (OR 12.1, 3.3–68.0, P < 0.001). Lincosamide and macrolide-resistance genes were more frequently recovered on days 14 and 28 compared to day 1 (P = 0.002 and P = 0.004 respectively).

Conclusion

AMR was associated with prescribed drugs but also developed against AMDs not administered during the study. Companion animals may be reservoirs of zoonotic multidrug resistant pathogens, suggesting that veterinary AMD stewardship and surveillance efforts should be prioritized.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00178-9.

Clinical evaluation and microbiota analysis in 9 dogs with antibiotic-responsive enteropathy: A prospective comparison study

Background

Antibiotic‐responsive enteropathy (ARE) is diagnosed by excluding other causes of diarrhea and when there is a short‐term response to administration of antibiotics.

Objectives

To characterize the gut microbiota and clinical trend of dogs with suspected ARE and to evaluate the variation in microbiota before (T0), after 30 days (T30) of tylosin treatment, and 30 days after discontinuation of treatment (T60). A further objective was to evaluate whether changes in gut microbiota are related to relapses of diarrhea when the therapy is tapered.

Animals

Study sample (group A) was composed of 15 dogs with chronic diarrhea, group B was composed of 15 healthy dogs. Group A was given tylosin for 30 days.

Methods

A multicentric prospective study. Clinical Indexes, fecal score, and samples for microbiota analysis were collected at T0, T30, and T60 in group A and T0 and T30 in group B. The gut microbiota was analyzed via 16S ribosomal RNA gene. Qiime2 version 2020.2 was used to perform bioinformatic analyses, and Alpha‐ and Beta‐diversity were computed.

Results

Diarrhea recurred after T30 in 9 of 14 dogs, which were classified as affected by ARE. At T0, a difference was noted in the beta‐diversity between groups (Bray Curtis metric P = .006). A T0‐T30 difference in alpha‐diversity was noted in group A (Shannon index P = .001, Faith PD P = .007).

Conclusions and Clinical Importance

Although tylosin influences the microbiota of dogs with ARE, we failed to find any specific characteristic in the microbiota of dogs with ARE.

Analysis and Comparison of Gut Microbiome in Young Detection Dogs

The detection dogs are well-known for their excellent capabilities to sense different kinds of smells, which can play an important role in completing various searching and rescuing missions. The recent studies have demonstrated that the excellent olfactory function of detection dogs might be related with the gut microbes via the bidirectional communications between the gastrointestinal tract and the brain. In this study, the gut microbial communities of three types of breeds of detection dogs (Springer Spaniel, Labrador Retriever, and German Shepherd) were studied and compared. The results revealed that the richness and the diversity of gut microbiome German Shepherd dogs were significantly higher than the Labrador Retriever dogs and the Springer Spaniel dogs. At the phylum level, the most predominant gut microbial communities of the detection dogs were comprised of Fusobacteriota, Bacteroidetes, Firmicutes, Proteobacteria, Campilobacterota, and Actinobacteriota. At the genus level the most predominant gut microbial communities were comprised of Fusobacterium, Megamonas, Prevotella, Alloprevotella, Bacteroides, Haemophilus, Anaerobiospirillum, Helicobacter, Megasphaera, Peptoclostridium, Phascolarctobacterium, and Streptococcus. However, the gut microbial communities of the three dogs group were also obviously different. The mean relative abundance of Fusobacterium, Prevotella, Alloprevotella, Megamonas, Bacteroides, and Phascolarctobacterium presented significant differences in the three groups. According to the portraits and characteristics of the gut microbiome in young detection dogs, multiple kinds of nutritional interventions could be applied to manipulate the gut microbiota, with the aim of improving the health states and the olfactory performances.

Comparative study on fecal flora and blood biochemical indexes in normal and diarrhea British Shorthair cats

In recent years, 16S ribosomal DNA (16S rDNA) sequencing has been widely developed. In the present study, we investigated the changes of fecal flora analyzed by sequencing of 16S rDNA and the alteration of blood biochemical indexes in cats during diarrhea. Seven normal fecal samples and seven fecal samples of British Shorthair cats with bacterial diarrhea about 6 months old were collected. The 16S rDNA V3 region of the bacteria was amplified for high-throughput sequencing. Finally, species analysis at various levels was performed. At the same time, samples of blood were taken to examine the changes of biochemical indexes in cats with diarrhea. The abundance and diversity of microflora in the healthy group were greater than those in the diarrhea group. The normal floras in the feces of healthy cats were Firmicutes, Actinobacteria, Bacteroidetes and Proteobacteria. The content of Proteobacteria and Firmicutes varied greatly in diarrheal cats. In addition, the number of white blood cells, lymphocytes, neutrophils, and globulin were increased in cats with diarrhea, whereas albumin level was decreased in diarrheal cats. In conclusion, the present study suggests 16SrDNA technology showed that the intestinal Proteus was abundant, and the content of Firmicutes was scarce in cats with diarrhea. Escherichia-Shigella was the main pathogens in this sample. Rapid blood biochemical tests may help clinicians to assess the severity and prognosis of cats with diarrhea.

Parvovirus enteritis and other risk factors associated with persistent gastrointestinal signs in dogs later in life: a retrospective cohort study

Background

Parvoviral enteritis (PE) is a viral gastrointestinal (GI) infection of dogs. Recovery from PE has been associated with persistent GI signs later in life. The objectives of this study were: (i) To determine whether dogs that have recovered from PE (post-parvo dogs) had an increased risk of persistent GI signs compared to uninfected control dogs. (ii) To investigate the lifestyle and clinicopathologic factors that are associated with persistent GI signs in post-parvo dogs.

Methods

A total of 86 post-parvo dogs and 52 age-matched control dogs were enrolled in this retrospective cohort study. Many years after hospitalization for PE, the owners were interviewed about the health and habits of their dogs using a questionnaire. We used generalized linear mixed effects models to test whether parvovirus enteritis and other risk factors are associated with owner-recognized general health problems in all dogs and with owner-recognized persistent GI signs in post-parvo dogs.

Results

The prevalence of persistent GI signs was significantly higher in post-parvo dogs compared to control dogs (57% vs 25%, P < 0.001). Markers of disease severity at the time of hospital admission such as neutropenia, low body temperature (BT), and treatment with an antiemetic medication (metoclopramide) were significant risk factors for persistent GI signs in post-parvo dogs. For example, PE-affected dogs that were hypothermic at hospital admission (BT of 37.2 °C) were 16.6 × more likely to have GI signs later in life compared to hyperthermic dogs (BT of 40.4 °C). The presence of persistent GI signs in post-parvo dogs was a risk factor for health problems in other organ systems.

Conclusions

Parvovirus enteritis is a significant risk factor for persistent GI signs in dogs highlighting the importance of prevention. The risk factors identified in the present study may guide future investigations on the mechanisms that link parvovirus enteritis to chronic health problems in dogs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03187-7.

Perspectives and Advances in Probiotics and the Gut Microbiome in Companion Animals

As the number of households that raise dogs and cats is increasing, there is growing interest in animal health. The gut plays an important role in animal health. In particular, the microbiome in the gut is known to affect both the absorption and metabolism of nutrients and the protective functions of the host. Using probiotics on pets has beneficial effects, such as modulating the immune system, helping to reduce stress, protecting against pathogenic bacteria and developing growth performance. The goals of this review are to summarize the relationship between probiotics/the gut microbiome and animal health, to feature technology used for identifying the diversity of microbiota composition of canine and feline microbiota, and to discuss recent reports on probiotics in canines and felines and the safety issues associated with probiotics and the gut microbiome in companion animals.

Short- and long-term effects of amoxicillin/clavulanic acid or doxycycline on the gastrointestinal microbiome of growing cats

Antibiotic treatment in early life influences gastrointestinal (GI) microbial composition and function. In humans, the resultant intestinal dysbiosis is associated with an increased risk for certain diseases later in life. The objective of this study was to determine the temporal effects of antibiotic treatment on the GI microbiome of young cats. Fecal samples were collected from cats randomly allocated to receive either amoxicillin/clavulanic acid (20 mg/kg q12h) for 20 days (AMC group; 15 cats) or doxycycline (10 mg/kg q24h) for 28 days (DOX group;15 cats) as part of the standard treatment of upper respiratory tract infection. In addition, feces were collected from healthy control cats (CON group;15 cats). All cats were approximately two months of age at enrolment. Samples were collected on days 0 (baseline), 20 or 28 (AMC and DOX, respectively; last day of treatment), 60, 120, and 300. DNA was extracted and sequencing of the 16S rRNA gene and qPCR assays were performed. Fecal microbial composition was different on the last day of treatment for AMC cats, and 1 month after the end of antibiotic treatment for DOX cats, compared to CON cats. Species richness was significantly greater in DOX cats compared to CON cats on the last day of treatment. Abundance of Enterobacteriales was increased, and that of Erysipelotrichi was decreased in cats of the AMC group on the last day of treatment compared to CON cats. The abundance of the phylum Proteobacteria was increased in cats of the DOX group on days 60 and 120 compared to cats of the CON group. Only minor differences in abundances between the treatment groups and the control group were present on day 300. Both antibiotics appear to delay the developmental progression of the microbiome, and this effect is more profound during treatment with amoxicillin/clavulanic acid and one month after treatment with doxycycline. Future studies are required to determine if these changes influence microbiome function and whether they have possible effects on disease susceptibility in cats.

Impact of Antibiotic Therapies on Resistance Genes Dynamic and Composition of the Animal Gut Microbiota

Antibiotics are major disruptors of the gastrointestinal microbiota, depleting bacterial species beneficial for the host health and favoring the emergence of potential pathogens. Furthermore, the intestine is a reactor of antibiotic resistance emergence, and the presence of antibiotics exacerbates the selection of resistant bacteria that can disseminate in the environment and propagate to further hosts. We reviewed studies analyzing the effect of antibiotics on the intestinal microbiota and antibiotic resistance conducted on animals, focusing on the main food-producing and companion animals. Irrespective of antibiotic classes and animal hosts, therapeutic dosage decreased species diversity and richness favoring the bloom of potential enteropathogens and the selection of antibiotic resistance. These negative effects of antibiotic therapies seem ineluctable but often were mitigated when an antibiotic was administered by parenteral route. Sub-therapeutic dosages caused the augmentation of taxa involved in sugar metabolism, suggesting a link with weight gain. This result should not be interpreted positively, considering that parallel information on antibiotic resistance selection was rarely reported and selection of antibiotic resistance is known to occur also at low antibiotic concentration. However, studies on the effect of antibiotics as growth promoters put the basis for understanding the gut microbiota composition and function in this situation. This knowledge could inspire alternative strategies to antibiotics, such as probiotics, for improving animal performance. This review encompasses the analysis of the main animal hosts and all antibiotic classes, and highlights the future challenges and gaps of knowledge that should be filled. Further studies are necessary for elucidating pharmacodynamics in animals in order to improve therapy duration, antibiotic dosages, and administration routes for mitigating negative effects of antibiotic therapies. Furthermore, this review highlights that studies on aminoglycosides are almost inexistent, and they should be increased, considering that aminoglycosides are the first most commonly used antibiotic family in companion animals. Harmonization of experimental procedures is necessary in this research field. In fact, current studies are based on different experimental set-up varying for antibiotic dosage, regimen, administration, and downstream microbiota analysis. In the future, shotgun metagenomics coupled with long-reads sequencing should become a standard experimental approach enabling to gather comprehensive knowledge on GIM in terms of composition and taxonomic functions, and of ARGs. Decorticating GIM in animals will unveil revolutionary strategies for medication and improvement of animals' health status, with positive consequences on global health.

Dogs' Microbiome From Tip to Toe

Microbiota and microbiome, which refers, respectively, to the microorganisms and conjoint of microorganisms and genes are known to live in symbiosis with hosts, being implicated in health and disease. The advancements and cost reduction associated with high-throughput sequencing techniques have allowed expanding the knowledge of microbial communities in several species, including dogs. Throughout their body, dogs harbor distinct microbial communities according to the location (e.g., skin, ear canal, conjunctiva, respiratory tract, genitourinary tract, gut), which have been a target of study mostly in the last couple of years. Although there might be a core microbiota for different body sites, shared by dogs, it is likely influenced by intrinsic factors such as age, breed, and sex, but also by extrinsic factors such as the environment (e.g., lifestyle, urban vs rural), and diet. It starts to become clear that some medical conditions are mediated by alterations in microbiota namely dysbiosis. Moreover, understanding microbial colonization and function can be used to prevent medical conditions, for instance, modulation of gut microbiota of puppies is more effective to ensure a healthy gut than interventions in adults. This paper gathers current knowledge of dogs' microbial communities, exploring their function, implications in the development of diseases, and potential interactions among communities while providing hints for further research.

Microbiota and epigenetics: promising therapeutic approaches?

The direct/indirect responsibility of the gut microbiome in disease induction in and outside the digestive tract is well studied. These results are usually from the overpopulation of certain species on the cost of others, interaction with beneficial microflora, interference with normal epigenetic control mechanisms, or suppression of the immune system. Consequently, it is theoretically possible to cure such disorders by rebalancing the microbiome inside our bodies. This can be achieved by changing the lifestyle pattern and diet or by supplementation with beneficial bacteria or their metabolites. Various approaches have been explored to manipulate the normal microbial inhabitants, including nutraceutical, supplementations with prebiotics, probiotics, postbiotics, synbiotics, and antibiotics, or through microbiome transplantation (fecal, skin, or vaginal microbiome transplantation). In the present review, the interaction between the microbiome and epigenetics and their role in disease induction is discussed. Possible future therapeutic approaches via the reestablishment of equilibrium in our internal micro-ecosystem are also highlighted.

Long-Term Recovery of the Fecal Microbiome and Metabolome of Dogs with Steroid-Responsive Enteropathy

The long-term impact of treatment of dogs with steroid-responsive enteropathy (SRE) on the fecal microbiome and metabolome has not been investigated. Therefore, this study aimed to evaluate the fecal microbiome and metabolome of dogs with SRE before, during, and following treatment with standard immunosuppressive therapy and an elimination diet. We retrospectively selected samples from 9 dogs with SRE enrolled in a previous clinical trial, which received treatment for 8 weeks, and had achieved remission as indicated by the post-treatment clinical scores. Long-term (1 year) samples were obtained from a subset (5/9) of dogs. Samples from 13 healthy dogs were included as controls (HC). We evaluated the microbiome using 16S rRNA sequencing and qPCR. To evaluate the recovery of gut function, we measured fecal metabolites using an untargeted approach. While improvement was observed for some bacterial taxa after 8 weeks of treatment, several bacterial taxa remained significantly different from HC. Seventy-five metabolites were altered in dogs with SRE, including increased fecal amino acids and vitamins, suggesting malabsorption as a component of SRE. One year after treatment, however, all bacterial species were evaluated by qPCR and 16S rRNA gene sequencing, and all but thirteen metabolites were no longer different from healthy controls.

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.

Ancient grains as novel dietary carbohydrate sources in canine diets

Ancient grains are becoming an increasingly abundant carbohydrate source in the pet food market as a result of their popularity and novelty in the human market. Thus, it is imperative to evaluate the characteristics of these ingredients in vivo. Ten adult intact female beagles were used in a replicated 5 × 5 Latin square design. Five dietary treatments were evaluated containing either: rice (CON), amaranth (AM), white proso millet (WPM), quinoa (QU), or oat groats (OG). All diets were formulated to include 40% of the test grain and to be isonitrogenous, isocaloric, and nutritionally complete and balanced for adult dogs at maintenance. The objectives were 1) to evaluate the effects of the novel carbohydrate sources on total apparent total tract digestibility (ATTD), fecal microbiota, and fermentative end-product concentrations and 2) to evaluate the effects of novel carbohydrate sources on the postprandial glycemic and insulinemic responses in healthy adult dogs. All diets were well accepted by the dogs and fecal scores remained within the ideal range for all treatments. In terms of ATTD, all diets were well digested by the dogs; WPM had the highest digestibility of dry and organic matter in contrast with dogs fed the other treatments (P < 0.05). Additionally, ATTD of total dietary fiber was highest for WPM (72.6%) in contrast with QU (63.5%) and CON (50.8%) but did not differ from AM (65.7%) and OG (66.6%). Dogs fed AM or OG had greater (P < 0.05) fecal concentrations of total short-chain fatty acids, as well as propionate and butyrate concentrations, than CON. Ancient grain inclusion appears to beneficially shift fecal microbial populations, with increases in relative abundances of butyrogenic bacteria (i.e., members of the Lachnospiraceae family) observed for OG and reductions in Fusobacteriaceae for both AM and OG when compared with CON. Postprandial glycemic and insulinemic responses did not differ among treatments. Together, these data suggest that ancient grains can be included up to 40% of the diet while eliciting beneficial effects on the overall host health without detrimentally affecting nutrient digestibility.

Comparison of Protein Carbonyl (PCO), Paraoxonase-1 (PON1) and C-Reactive Protein (CRP) as Diagnostic and Prognostic Markers of Septic Inflammation in Dogs

Reliable diagnostic and prognostic markers of sepsis are lacking, but essential in veterinary medicine. We aimed to assess the accuracy of C-Reactive Protein (CRP), protein carbonyls (PCO) and paraoxonase-1 (PON1) in differentiating dogs with sepsis from those with sterile inflammation and healthy ones, and predict the outcome in septic dogs. These analytes were retrospectively evaluated at admission in 92 dogs classified into healthy, septic and polytraumatized. Groups were compared using the Kruskal–Wallis test, followed by a Mann–Whitney U test to assess differences between survivors and non-survivors. Correlation between analytes was assessed using the Spearman’s test, and their discriminating power was assessed through a Receiver Operating Characteristic (ROC) curve. PON1 and CRP were, respectively, significantly lower and higher in dogs with sepsis compared with polytraumatized and clinically healthy dogs (p < 0.001 for both the analytes), and also in dogs with trauma compared with healthy dogs (p = 0.011 and p = 0.017, respectively). PCO were significantly increased in septic (p < 0.001) and polytraumatized (p < 0.005) as compared with healthy dogs. PON1 and CRP were, respectively, significantly lower and higher in dogs that died compared with survivors (p < 0.001 for both analytes). Ultimately, evaluation of CRP and PON1 at admission seems a reliable support to diagnose sepsis and predict outcomes.

Effects of Synbiotics on the Fecal Microbiome and Metabolomic Profiles of Healthy Research Dogs Administered Antibiotics: A Randomized, Controlled Trial

Background: Antibiotic-associated gastrointestinal signs occurred in 100% of dogs administered enrofloxacin with metronidazole in a previous study, and signs partially were mitigated by synbiotics. The objective of this randomized, double-blinded, placebo-controlled trial was to compare the fecal microbiome and metabolome of dogs administered enrofloxacin and metronidazole, followed by either a placebo or a bacterial/yeast synbiotic combination.

Methods: Twenty-two healthy research dogs were randomized to two treatment groups. There were three study periods: baseline, treatment, and washout. Dogs were administered enrofloxacin (10 mg/kg qd) and metronidazole (12.5 mg/kg BID), followed 1 h later by placebo or a commercially-available synbiotic combination (BID), per os for 21 days with reevaluation 56 days thereafter. Fecal samples were collected on days 5–7 (baseline), 26–28, and 82–84. The fecal microbiome was analyzed by qPCR and sequencing of 16S rRNA genes; time-of-flight mass spectrometry was used to determine metabolomic profiles. Split plot repeated measures mixed model ANOVA was used to compare results between treatment groups. P < 0.05 was considered significant, with Benjamini and Hochberg's False Discovery Rate used to adjust for multiple comparisons.

Results: Alpha diversity metrics differed significantly over time in both treatment groups, with incomplete recovery by days 82–84. Beta diversity and the dysbiosis index differed significantly over time and between treatment groups, with incomplete recovery at days 82–84 for dogs in the placebo group. Significant group-by-time interactions were noted for 15 genera, including Adlercreutzia, Bifidobacterium, Slackia, Turicibacter, Clostridium (including C. hiranonis) [Ruminococcus], Erysipelotrichaceae_g_, [Eubacterium], and Succinivibrionaceae_g_. Concurrent group and time effects were present for six genera, including Collinsella, Ruminococcaceae_g_, and Prevotella. Metabolite profiles differed significantly by group-by-time, group, and time for 28, 20, and 192 metabolites, respectively. These included short-chain fatty acid, bile acid, tryptophan, sphingolipid, benzoic acid, and cinnaminic acid metabolites, as well as fucose and ethanolamine. Changes in many taxa and metabolites persisted through days 82–84.

Conclusion: Antibiotic administration causes sustained dysbiosis and dysmetabolism in dogs. Significant group-by-time interactions were noted for a number of taxa and metabolites, potentially contributing to decreased antibiotic-induced gastrointestinal effects in dogs administered synbiotics.

Comparison of the Therapeutic Effect of Treatment with Antibiotics or Nutraceuticals on Clinical Activity and the Fecal Microbiome of Dogs with Acute Diarrhea

Simple Summary

Acute diarrhea in dogs is one of the most common reasons for veterinary visits. Although this disorder is generally self-limiting, antibiotics are still frequently used as treatment for acute diarrhea in clinical practice. Antimicrobial resistance represents a major challenge for public health and requires immediate and drastic solutions. To date, the emergence and spread of antimicrobial resistance has been attributed to the misuse or indiscriminate use of antibiotics. The aim of this study is to compare the effects on clinical activity and fecal microbiota of the administration of an antibiotic combination in comparison to a nutraceutical product in dogs with acute non-hemorrhagic diarrhea. The results of the present study suggest that this nutraceutical treatment had a similar clinical effect compared to the antibiotic formulation and may represent an alternative to commonly used antimicrobial therapy.

Abstract

Dogs with acute diarrhea are often presented to clinical practice and, although this generally represents a self-limiting condition, antibiotics are still frequently used as treatment. The aim of this study was to evaluate the effects in dogs with acute non-hemorrhagic diarrhea of the administration of an antibiotic combination in comparison to a nutraceutical product. Thirty dogs were enrolled and randomly assigned to two groups: 15 dogs (group A) received a nutraceutical commercial product while 15 dogs (group B) received an antimicrobial combination of metronidazole and spiramycin. For each dog, the Canine Acute Diarrhea Severity Index, the fecal microbiota and the Dysbiosis Index were assessed. Both stool consistency and frequency decreased on day 2 in the dogs of group A compared to baseline, while in group B, these parameters significantly decreased at days 3 and 4. The global concern for rising antibiotic resistance associated with indiscriminate use of antimicrobials, in both humans and animals, suggests the necessity of avoiding empirical and injudicious use of these molecules in diarrheic dogs. These results suggest that the nutraceutical treatment had a similar clinical effect compared to the antibiotic formulation, representing a valid antibiotic-sparing therapeutic approach in canine acute diarrhea.

[Use of antimicrobials in acute canine diarrhea - overview of potential risks, indications and alternatives]

In Germany, antibiotics are frequently used in dogs with gastrointestinal disorders such as acute diarrhea. In line with global efforts to limit antibiotic use, this literature review aims to provide a guideline for the rational and judicious use of antibiotics in acute canine diarrhea. Antibiotics can lead to gastrointestinal side effects and may exert a negative influence on the intestinal microbiota in addition to increasing the occurrence of resistant bacteria. There is also evidence that chronic immunological diseases may be triggered by the administration of antibiotics. Therefore, these should not be administered in uncomplicated acute diarrhea without signs of sepsis or systemic inflammatory reaction. In addition, enteropathogenic bacteria usually do not play a role in the etiology of acute diarrhea. For select clinical entities such as acute hemorrhagic diarrhea syndrome, antibiotic therapy should only be recommended in cases displaying signs of bacterial translocation with subsequent sepsis. In the case of parvovirosis, on the other hand, the administration of antibiotics is unavoidable due to the immunological incompetence of the dog caused by the accompanying severe neutropenia.

Effect of prophylactic use of tulathromycin on gut bacterial populations, inflammatory profile and diarrhea in newborn Holstein calves

This objective of this study was to evaluate the use of tulathromycin on the timing of appearance and number of four indicator organisms representing the gastrointestinal microbial community, the incidence of diarrhea and a measure of the systemic inflammatory profile in Holstein heifers. Twenty-six Holstein heifer calves were distributed between receiving (ATB+) or not receiving (ATB-) tulathromycin at a dose of 2.5 mg/kg by 12 h of age. Samples from the calves were collected at six times during the neonatal period. Stool samples were used to determine the dry matter content and quantitative analysis of specific indicator bacterial populations. Samples of whole blood and serum were collected to determine the total number of neutrophils, the number of CD62L+ neutrophils, quantity of haptoglobin, and to allow for ex vivo measurement of reactive oxygen species. A higher frequency of diarrhea was detected in the ATB+ calves (84.6%) than ATB- (53.8%) on days 13-15 (P = 0.084). ATB- calves had a greater number of Bifidobacterium in stool on day 3-5 (P = 0.002), and on days 7-9 (P = 0.018). The ATB+ calves tended to have a higher number of Escherichia coli in stool on days 20-23 and days 27-30 (P = 0.052 and P = 0.072). Both the total number of neutrophils (P = 0.013) and the capacity for ROS production was higher in ATB- (P = 0.038) than ATB+ calves at all points tested. ATB+ calves had higher levels of haptoglobin (P = 0.032) on days 13-15. Administration of tulathromycin appeared to negatively impact the establishment of a normal microbiome and to modulate the development of innate immune function.

Graded dietary resistant starch concentrations on apparent total tract macronutrient digestibility and fecal fermentative end products and microbial populations of healthy adult dogs

Resistant starch (RS) is fermentable by gut microbiota and effectively modulates fecal short-chain fatty acid concentrations in pigs, mice, and humans. RS may have similar beneficial effects on the canine gut but has not been well studied. The objective of this study was to evaluate the effects of 0%, 1%, 2%, 3%, and 4% dietary RS (Hi-maize 260) on apparent total tract macronutrient digestibility, fecal characteristics, fermentative end-product concentrations, and microbiota of healthy adult dogs. An incomplete 5 × 5 Latin square design with seven dogs and five experimental periods was used, with each treatment period lasting 21 d (days 0 to 17 adaptation; days 18 to 21 fresh and total fecal collection) and each dog serving as its own control. Seven dogs (mean age = 5.3 yr; mean body weight = 20 kg) were randomly allotted to one of five treatments formulated to be iso-energetic and consisting of graded amounts of 100% amylopectin cornstarch, RS, and cellulose and fed as a top dressing on the food each day. All dogs were fed the same amount of a basal diet throughout the study, and fresh water was offered ad libitum. The basal diet contained 6.25% RS (dry matter [DM] basis), contributing approximately 18.3 g of RS/d based on their daily food intake (292.5 g DM/d). Data were evaluated for linear and quadratic effects using SAS. The treatments included 0%, 1%, 2%, 3%, and 4% of an additional RS source. Because Hi-maize 260 is approximately 40% digestible and 60% indigestible starch, the dogs received the following amounts of RS daily: 0% = 18.3 g (18.3 + 0 g), 1% = 20.1 g (18.3 + 1.8 g), 2% = 21.9 g (18.3 + 3.6 g), 3% = 23.7 g (18.3 + 5.4 g), and 4% = 25.5 g (18.3 + 7.2 g). Apparent total tract DM, organic matter, crude protein, fat, and gross energy digestibilities and fecal pH were linearly decreased (P < 0.05) with increased RS consumption. Fecal output was linearly increased (P < 0.05) with increased RS consumption. Fecal scores and fecal fermentative end-product concentrations were not affected by RS consumption. Although most of the fecal microbial taxa were not altered, Faecalibacterium were increased (P < 0.05) with increased RS consumption. The decrease in fecal pH and increase in fecal Faecalibacterium would be viewed as being beneficial to gastrointestinal health. Although our results seem to indicate that RS is poorly and/or slowly fermentable in dogs, the lack of observed change may have been due to the rather high level of RS contained in the basal diet.

State-of-the-Art of the Nutritional Alternatives to the Use of Antibiotics in Humans and Monogastric Animals

Simple Summary

Antibiotic resistance represents a worldwide recognized issue affecting both human and veterinary medicine, with a particular focus being directed towards monogastric animals destined for human consumption. This scenario is the result of frequent utilization of the antibiotics either for therapeutic purposes (humans and animals) or as growth promoters (farmed animals). Therefore, the search for nutritional alternatives has progressively been the object of significant efforts by the scientific community. So far, probiotics, prebiotics and postbiotics are considered the most promising products, as they are capable of preventing or treating gastrointestinal diseases as well as restoring a eubiosis condition after antibiotic-induced dysbiosis development. This review provides an updated state-of-the-art of these nutritional alternatives in both humans and monogastric animals.

Abstract

In recent years, the indiscriminate use of antibiotics has been perpetrated across human medicine, animals destined for zootechnical productions and companion animals. Apart from increasing the resistance rate of numerous microorganisms and generating multi-drug resistance (MDR), the nonrational administration of antibiotics causes sudden changes in the structure of the intestinal microbiota such as dysbiotic phenomena that can have a great clinical significance for both humans and animals. The aim of this review is to describe the state-of-the-art of alternative therapies to the use of antibiotics and their effectiveness in humans and monogastric animals (poultry, pigs, fish, rabbits, dogs and cats). In particular, those molecules (probiotics, prebiotics and postbiotics) which have a direct function on the gastrointestinal health are herein critically analysed in the prevention or treatment of gastrointestinal diseases or dysbiosis induced by the consumption of antibiotics.

Energy depletion and opportunistic microbial colonisation in white syndrome lesions from corals across the Indo-Pacific

Corals are dependent upon lipids as energy reserves to mount a metabolic response to biotic and abiotic challenges. This study profiled lipids, fatty acids, and microbial communities of healthy and white syndrome (WS) diseased colonies of Acropora hyacinthus sampled from reefs in Western Australia, the Great Barrier Reef, and Palmyra Atoll. Total lipid levels varied significantly among locations, though a consistent stepwise decrease from healthy tissues from healthy colonies (HH) to healthy tissue on WS-diseased colonies (HD; i.e. preceding the lesion boundary) to diseased tissue on diseased colonies (DD; i.e. lesion front) was observed, demonstrating a reduction in energy reserves. Lipids in HH tissues were comprised of high energy lipid classes, while HD and DD tissues contained greater proportions of structural lipids. Bacterial profiling through 16S rRNA gene sequencing and histology showed no bacterial taxa linked to WS causation. However, the relative abundance of Rhodobacteraceae-affiliated sequences increased in DD tissues, suggesting opportunistic proliferation of these taxa. While the cause of WS remains inconclusive, this study demonstrates that the lipid profiles of HD tissues was more similar to DD tissues than to HH tissues, reflecting a colony-wide systemic effect and provides insight into the metabolic immune response of WS-infected Indo-Pacific corals.

Synthesis and biological evaluation of semi-synthetic albocycline analogs

Albocycline (ALB) is a unique macrolactone natural product with potent, narrow-spectrum activity against methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-intermediate (VISA), and vancomycin-resistant S. aureus (VRSA) strains (MIC = 0.5-1.0 μg/mL). Described herein is the synthesis and evaluation of a novel series analogs derived from albocycline by functionalization at three specific sites: the C2-C3 enone, the tertiary carbinol at C4, and the allylic C16 methyl group. Exploration of the structure-activity relationships (SAR) by means of minimum inhibitory concentration assays (MICs) revealed that C4 ester analog 6 was twice as potent as ALB, which represents a class of lead compound that can be further studied to address multi-drug resistant pathogens.

Catching a glimpse of the bacterial gut community of companion animals: a canine and feline perspective

Dogs and cats have gained a special position in human society by becoming our principal companion animals. In this context, efforts to ensure their health and welfare have increased exponentially, with in recent times a growing interest in assessing the impact of the gut microbiota on canine and feline health. Recent technological advances have generated new tools to not only examine the intestinal microbial composition of dogs and cats, but also to scrutinize the genetic repertoire and associated metabolic functions of this microbial community. The application of high-throughput sequencing techniques to canine and feline faecal samples revealed similarities in their bacterial composition, with Fusobacteria, Firmicutes and Bacteroidetes as the most prevalent and abundant phyla, followed by Proteobacteria and Actinobacteria. Although key bacterial members were consistently present in their gut microbiota, the taxonomic composition and the metabolic repertoire of the intestinal microbial population may be influenced by several factors, including diet, age and anthropogenic aspects, as well as intestinal dysbiosis. The current review aims to provide a comprehensive overview of the multitude of factors which play a role in the modulation of the canine and feline gut microbiota and that of their human owners with whom they share the same environment.

Physiological influence of tylosin tartrate overdose in vivo in rats

The aim of this study was to evaluate the physiological effects of tylosin in rats. Tylosin was administered orally to pubertal male and female rats at concentrations of 0.005, 0.2, 10 and 200 mg/kg b.w. for 6 weeks. The overall body and organ weights were recorded. Serum levels of immunoglobulins, haematological values, histopathological lesions in different organs, and gene expression profiles in pituitary glands were investigated. The mean platelet volume was increased, and the monocyte count was decreased significantly in both male and female rats treated with tylosin. Compared to the untreated control, alanine transaminase in both types of rats and total serum bilirubin in female rats were increased significantly with the administration of tylosin (200 mg/kg), however, lactate dehydrogenase in female rats was decreased. The levels of immunoglobulin M were reduced in both male and female rats but immunoglobulin G levels were significantly reduced only in female rats which were treated with tylosin. Cell proliferation- and adhesion-associated genes were expressed more but apoptosis gene expressions were decreased in the pituitary gland of tylosin-treated rats. In conclusion, this study revealed that the use of tylosin at therapeutic dosage is possibly not completely safe.

Effects of metronidazole on the fecal microbiome and metabolome in healthy dogs

Background

Metronidazole has a substantial impact on the gut microbiome. However, the recovery of the microbiome after discontinuation of administration, and the metabolic consequences of such alterations have not been investigated to date.

Objectives

To describe the impact of 14‐day metronidazole administration, alone or in combination with a hydrolyzed protein diet, on fecal microbiome, metabolome, bile acids (BAs), and lactate production, and on serum metabolome in healthy dogs.

Animals

Twenty‐four healthy pet dogs.

Methods

Prospective, nonrandomized controlled study. Dogs fed various commercial diets were divided in 3 groups: control group (no intervention, G1); group receiving hydrolyzed protein diet, followed by metronidazole administration (G2); and group receiving metronidazole only (G3). Microbiome composition was evaluated with sequencing of 16S rRNA genes and quantitative polymerase chain reaction (qPCR)‐based dysbiosis index. Untargeted metabolomics analysis of fecal and serum samples was performed, followed by targeted assays for fecal BAs and lactate.

Results

No changes were observed in G1, or G2 during diet change. Metronidazole significantly changed microbiome composition in G2 and G3, including decreases in richness (P < .001) and in key bacteria such as Fusobacteria (q < 0.001) that did not fully resolve 4 weeks after metronidazole discontinuation. Fecal dysbiosis index was significantly increased (P < .001). Those changes were accompanied by increased fecal total lactate (P < .001), and decreased secondary BAs deoxycholic acid and lithocholic acid (P < .001).

Conclusion and Clinical Importance

Our results indicate a minimum 4‐week effect of metronidazole on fecal microbiome and metabolome, supporting a cautious approach to prescription of metronidazole in dogs.

Past, Present, and Future of Gastrointestinal Microbiota Research in Cats

The relationship between microbial community and host has profound effects on the health of animals. A balanced gastrointestinal (GI) microbial population provides nutritional and metabolic benefits to its host, regulates the immune system and various signaling molecules, protects the intestine from pathogen invasion, and promotes a healthy intestinal structure and an optimal intestinal function. With the fast development of next-generation sequencing, molecular techniques have become standard tools for microbiota research, having been used to demonstrate the complex intestinal ecosystem. Similarly to other mammals, the vast majority of GI microbiota in cats (over 99%) is composed of the predominant bacterial phyla Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Many nutritional and clinical studies have shown that cats' microbiota can be affected by several different factors including body condition, age, diet, and inflammatory diseases. All these factors have different size effects, and some of these may be very minor, and it is currently unknown how important these are. Further research is needed to determine the functional variations in the microbiome in disease states and in response to environmental and/or dietary modulations. Additionally, further studies are also needed to explain the intricate relationship between GI microbiota and the genetics and immunity of its host. This review summarizes past and present knowledge of the feline GI microbiota and looks into the future possibilities and challenges of the field.

Phosphorous recovery from a novel recirculating aquaculture system followed by its sustainable reuse as a fertilizer

Phosphorus (P) is an essential element for life that is introduced through feed in modern aquaculture-the fastest growing food production sector. P can also be a source of environmental contamination and eutrophication if mistreated. Fish assimilate only 20-40% of the applied P; the rest is released into the water. The goals of this research were to study the fate of P in a novel intensive near-zero discharge (<1%) recirculating aquaculture system (RAS). We also tested means to recover and reuse the removed P. Water, sludge and the microbial communities in the different treatment units of the system were analyzed. The treated sludge was tested as a potential substitute for P fertilization in a planter experiment. Of the applied P, 29.5% was recovered by fish, 69.8% was found in the fish sludge and 3.8% was released into the water as soluble reactive P. The P concentration in the fish tank remained stable, likely due to its uptake by denitrifying polyphosphate-accumulating organisms and its precipitation in the RAS's anaerobic reactor. Thus, only 1.5% of the applied P was discharged as effluent, and 69% recovered. The dominant minerals were from the apatite group, followed by the struvite family. Differences in mineral abundance between thermodynamic prediction and actual findings were most probably due to biomineralization by bacteria. Similar plant biomass was recorded for the commercial and digested-sludge fertilization treatments. Biological P removal and recovery from RAS was successfully studied and demonstrated.

Evaluation of the bacterial ocular surface microbiome in ophthalmologically normal dogs prior to and following treatment with topical neomycin-polymyxin-bacitracin

The ocular surface microbiome of veterinary species has not been thoroughly characterized using molecular-based techniques, such as next generation sequencing (NGS), as the vast majority of studies have utilized traditional culture-based techniques. To date, there is one pilot study evaluating the ocular surface of healthy dogs using NGS. Furthermore, alterations in the ocular surface microbiome over time and after topical antibiotic treatment are unknown. The objectives of this study were to describe the bacterial composition of the ocular surface microbiome in clinically normal dogs, and to determine if microbial community changes occur over time or following topical antibiotic therapy. Topical neomycin-polymyxin-bacitracin ophthalmic ointment was applied to one eye each of 13 adult dogs three times daily for seven days, while contralateral eyes served as untreated controls. The inferior conjunctival fornix of both eyes was sampled via swabbing at baseline prior to antibiotic therapy (day 0), after 1 week of treatment (day 7), and 4 weeks after discontinuing treatment (day 35). Genomic DNA was extracted from the conjunctival swabs and primers targeting the V4 region of bacterial 16S rRNA genes were used to generate amplicon libraries, which were then sequenced on an Illumina platform. Data were analyzed using Quantitative Insights Into Molecular Ecology (QIIME 2.0). At baseline, the most relatively abundant phyla sequenced were Proteobacteria (49.7%), Actinobacteria (25.5%), Firmicutes (12%), Bacteroidetes (7.5%), and Fusobacteria (1.4%). The most common families detected were Pseudomonadaceae (13.2%), Micrococcaceae (12%), Pasteurellaceae (6.9%), Microbacteriaceae (5.2%), Enterobacteriaceae (3.9%), Neisseriaceae (3.5%), and Corynebacteriaceae (3.3%). Alpha and beta diversity measurements did not differ in both control and treatment eyes over time. This report examines the temporal stability of the canine ocular surface microbiome. The major bacterial taxa on the canine ocular surface remained consistent over time and following topical antibiotic therapy.

Effect of amoxicillin-clavulanic acid on clinical scores, intestinal microbiome, and amoxicillin-resistant Escherichia coli in dogs with uncomplicated acute diarrhea

Background

Despite limited evidence of efficacy, antibiotic treatment is still frequently prescribed in dogs with uncomplicated acute diarrhea (AD).

Objective

To assess whether amoxicillin‐clavulanic acid has a clinical benefit, an effect on the fecal microbiome, and the proportion of amoxicillin‐resistant Escherichia coli in dogs with AD.

Animals

Sixteen dogs with AD of <3 days duration.

Methods

Prospective, placebo‐controlled, double‐blinded study. Clinical scores were compared between client‐owned dogs randomly assigned to an antibiotic (AG) or a placebo (PG) group. The intestinal microbiome was analyzed using quantitative PCR assays. Amoxicillin‐resistant fecal E. coli were assessed semiquantitatively with microbiological methods.

Results

There was no difference in clinical recovery between treated dogs or controls (CADS index day 10: AG group median: 2 (range: 1‐3; CI [1.4; 2.6]); PG group median: 1.6 (range: 1‐3; CI [1.1; 2.4]); P > .99). All dogs gained normal clinical scores (CADS index ≤3) after 1 to 6 days (median 2 days) after presentation. There was no significant difference in the fecal dysbiosis index (during treatment: AG mean −2.6 (SD 3.0; CI [−5.1; 0.0]); PG mean −0.8 (SD 4.0; CI [−4.2; 2.5]; P > .99) or its bacterial taxa. The proportion of resistant fecal E. coli increased (to median: 100%; range: 35%‐100%) during treatment with amoxicillin‐clavulanic acid and was still increased (median: 10%; range 2%‐67%) 3 weeks after treatment, both of which were significantly higher proportions than in the placebo group for both time points (during treatment AG median 100% versus PG median 0.2% (P < .001); after treatment AG median 10% versus PG median 0.0% (P = .002)).

Conclusions and Clinical Importance

Our study suggests that treatment with amoxicillin‐clavulanic acid confers no clinical benefit to dogs with AD, but predisposes the development of amoxicillin‐resistant E. coli, which persist for as long as 3 weeks after treatment. These findings support international guideline recommendations that dogs with diarrhea should not be treated with antimicrobials unless there are signs of sepsis.