The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets

Exploring the popularity of raw meat-based diets for dogs and cats: A cross-sectional opinion survey in Spain

BACKGROUND

Research on the general public's knowledge and usage patterns of pet food, particularly regarding raw meat-based diets (RMBDs), is limited in many countries, including Spain.

METHODS

An anonymous cross-sectional web-based survey was conducted to assess the Spanish population's understanding and perceptions of RMBDs for cats and dogs.

RESULTS

Of the 712 respondents, 46.77% were familiar with RMBDs, and 6% of pet owners reported using them. Dogs (7.61%) were more likely to be fed an RMBDs than cats (3.23%). While 66% of those familiar with RMBDs believed in their benefits, 96.40% recognised potential disadvantages. Concerns about risks to pets (63%) and those handling the food items (44.74%) were noted. Moreover, almost one in four owners (22.58%) who fed their pet an RMBDs lived with immunologically vulnerable people. Interestingly, confidence in veterinary advice was lower among owners using these diets.

LIMITATIONS

Limitations intrinsic to questionnaire studies, such as potential response bias, are acknowledged.

CONCLUSION

The study highlights the importance of improved veterinarian‒client communication regarding pet nutrition, emphasising the need for veterinarians to play a more active educational role.

The Microbiome in Critical Illness

Evidence suggests that the intestinal microbiome may play an important role in the pathogenesis and progression of acute critical illness in humans and other mammals, although evidence in small animal medicine is sparse. Moreover, the intestinal microbiota plays many important metabolic roles (production of short-chain fatty acids, trimethylamine-N-oxide, and normal bile acid metabolism) and is crucial for immunity as well as defense against enteropathogens. The use of probiotics and fecal microbiota transplantation as instruments to modulate the intestinal microbiota seems to be safe and effective in studies on critically ill dogs with acute gastrointestinal diseases.

Presence of Potential Enteropathogenic Bacteria in Cats and Association With Diarrhea in Multicat Households

BACKGROUND

Diarrhea in cats is common in multicat households, and fecal panels are frequently used to diagnose potential enteropathogenic bacteria.

OBJECTIVES

To evaluate the presence of potential fecal enteropathogenic bacteria and their association with diarrhea in multicat households. The null hypothesis was that potential enteropathogenic bacteria were not related to diarrhea in the cohort.

ANIMALS

In total, 234 cats from 41 privately owned catteries were included.

METHODS

In this prospective study, feces were evaluated for consistency according to a visual scoring system (Purina Fecal Score). Scores from 4 to 7 were defined as diarrhea. Quantitative PCR for Escherichia coli, Clostridium perfringens encoding the α toxin gene (cpa), Clostridium perfringens encoding the enterotoxin gene (cpe), Clostridioides difficile, Campylobacter jejuni/coli, and Salmonella enterica was used. Logistic regression was used to evaluate the impact of selected bacteria on diarrheic feces (fecal score ≥ 4). p values were corrected for multiple comparisons (q values in results). A q value < 0.05 was considered to indicate statistical significance.

RESULTS

23/234 cats (9.8%) had diarrhea. None of the selected bacteria were significantly associated with diarrhea (cpa: q = 0.10, cpe: q = 0.20, C. jejuni: q = 0.70). E. coli was detected in all tested fecal samples (100%). The associations of Cl. difficile (detected in 2.3% of cats), C. coli (0%), and S. enterica (0.9%) with diarrhea could not be evaluated due to the small sample sizes.

CONCLUSIONS AND CLINICAL IMPORTANCE

Fecal bacteria detected via PCR were not associated with clinical signs of diarrhea in multicat households. These data do not support the use of PCR for fecal bacteria for baseline routine diagnostic work-up of diarrhea in cats.

A bi-variate framework to model microbiome resilience in healthy dogs

Introduction

Ecological resilience is the capacity of an ecosystem to maintain its state and recover from disturbances. This concept can be applied to the gut microbiome as a marker of health.

Methods

Several metrics have been proposed to quantify microbiome resilience, based on the prior choice of some salient feature of the trajectories of microbiome change. We propose a data-driven approach based on compositional and functional data analysis to quantify microbiome resilience. We demonstrate the validity of our approach through applications to sled dogs undergoing three types of exercise: running on an exercise wheel, pulling an all-terrain vehicle, and pulling a sled.

Results

Microbiota composition was clearly impacted by each exercise type. Log-ratio analysis was utilized for dimensionality reduction and identified 33 variables (taxa) explaining 90% of the variance. Functional principal component analysis identified two scores (FPCA 1 and FPCA2) which explained 76% and 19% of the variability of the trajectories, respectively. More resilient trajectories corresponded to low values of FPCA1 and FPCA2 values close to zero. Levels of chemokines MCP-1 and KC-like, which increased significantly after exercise and returned to pre-exercise levels within 24 h, were significantly associated with FPCA scores as well.

Discussion

To our knowledge, this is the first study proposing a principled approach to quantify microbiome resilience in healthy dogs and associate it with immune response to exercise-related stress.

Effects of a Western Diet on Colonic Dysbiosis, Bile Acid Dysmetabolism and Intestinal Inflammation in Clinically Healthy Dogs

BACKGROUND

Consumption of a high-fat, high-carbohydrate Western-style diet (WD) associated with obesity and inflammation in humans has not been investigated in dogs.

AIMS

To determine the effects of WD on inflammatory indices, microbiome, and fecal bile acids (BAs) in dogs.

ANIMALS

Ten adult clinically healthy dogs.

METHODS

A dietary trial compared the effects of two home-prepared diets: a high-fiber, low-fat control diet (CD) to a diet containing the macronutrient composition of WD (low-fiber, high fat). Dietary treatments were given sequentially for three feeding periods, each lasting 1 month. Outcome measures included molecular/microbiologic testing of colonic biopsies, histopathology, inflammatory biomarkers, and quantification of fecal BA following each feeding period.

RESULTS

Cell markers of apoptosis (TUNEL-positive cells: CD1, 0.36% ± 0.2%; WD, 0.79% ± 0.5%; CD2, 0.42% ± 0.3%; 95% CI) and inflammation (NF-ĸB area: CD1, 8.09% ± 3.3%; WD, 11.58% ± 3.4%; CD2 7.25% ± 3.8%; 95% CI), as well as serum high-sensitivity C-reactive protein (CD1, 2.0 ± 0.4 ng/mL; WD, 2.76 ± 0.23 ng/mL; CD2, 2.29 ± 0.25 ng/mL; 95% CI), were increased (p < 0.05) in dogs fed WD versus CD. Other perturbations seen with WD ingestion included altered (p < 0.05) colonic mucosal bacteria (bacterial counts: CD1, 301.5 ± 188.5; WD, 769.8 ± 431.9; CD2, 542.1 ± 273.9; 95% CI) and increased (p < 0.05) fecal cholic acid (median and interquartile range/IQR: CD1, 9505 [2384-33 788] peak heights; WD, 34 131 [10 113-175 909] peak heights) and serum myeloperoxidase (CD1, 46.98 ± 16.6 ng/mL; WD, 82.93 ± 33.6 ng/mL; CD2, 63.52 ± 29.5 ng/mL; 95% CI).

CONCLUSIONS AND CLINICAL IMPORTANCE

WD fed to clinically healthy dogs promotes colonic dysbiosis, altered fecal BA, and low-grade inflammation independent of obesity.

Gut Metabolome in Companion Animal Nutrition-Linking Diets to Health

Tailoring diet to support a healthy gut microbiome is key for animal well-being. The gut metabolome, including all small molecules in the gut, is central to diet-microbiome-health interactions. While comprehension of the gut metabolome in companion animal nutrition is emerging, a substantial number of studies have been undertaken to elucidate the metabolomic shifts and identify specific marker metabolites influenced by diverse dietary interventions. By employing various metabolomic approaches, researchers have extensively documented the effects of different diet types, nutrient compositions, and dietary supplements on the gut metabolome in dogs and cats. Despite these advancements, there remains several notable limitations, including a lack of integrated microbiome analysis, incomplete understanding of specific marker metabolites, and an over-reliance on extrapolating findings from human studies. Therefore, this review aims to summarize the current understanding of the canine and feline gut metabolome, while exploring future possibilities and challenges for the field.

Response of the gut microbiome and metabolome to dietary fiber in healthy dogs

Dietary fiber confers multiple health benefits originating from the expansion of beneficial gut microbial activity. However, very few studies have established the metabolic consequences of interactions among specific fibers, microbiome composition, and function in either human or representative animal models. In a study design reflective of realistic population dietary variation, fecal metagenomic and metabolomic profiles were analyzed from healthy dogs fed 12 test foods containing different fiber sources and quantities (5-13% as-fed basis). Taxa and functions were identified whose abundances were associated either with overall fiber intake or with specific fiber compositions. Fourteen microbial species were significantly enriched in response to ≥1 specific fiber source; enrichment of fiber-derived metabolites was more pronounced in response to these fiber sources. Positively associated fecal metabolites, including short-chain fatty acids, acylglycerols, fiber bound sugars, and polyphenols, co-occurred with microbes enriched in specific food groups. Critically, the specific metabolite pools responsive to differential fiber intake were dependent on differences both in individual microbial community membership and in overall ecological configuration. This helps to explain, for the first time, differences in microbiome-diet associations observed in companion animal epidemiology. Thus, our study corroborates findings in human cohorts and reinforces the role of personalized microbiomes even in seemingly phenotypically homogeneous subjects.

IMPORTANCE

Consumption of dietary fiber changes the composition of the gut microbiome and, to a larger extent, the associated metabolites. Production of health-relevant metabolites such as short-chain fatty acids from fiber depends both on the consumption of a specific fiber and on the enrichment of beneficial metabolite-producing species in response to it. Even in a seemingly homogeneous population, the benefit received from fiber consumption is personalized and emphasizes specific fiber-microbe-host interactions. These observations are relevant for both population-wide and personalized nutrition applications.

Current Evidence on Raw Meat Diets in Pets: A Natural Symbol, but a Nutritional Controversy

Feeding raw meat to cats and dogs has become a common practice in Western countries. Many pet owners cite their pets' wild carnivore ancestry and believe raw meat diets are healthier, citing higher nutritional value, a lack of processing, low-carbohydrate content, and/or the presence of whole ingredients. However, due to the risks associated with raw meat-based diets (e.g., microbial contamination, nutritional imbalances) and growing concerns about food sustainability, most nutritional specialists and public health stakeholders question the practice of feeding raw meat. In this context, the vast majority of owners' claims regarding the beneficial health effects of raw meat diets lack scientific substantiation, while professional advice primarily focuses on risks, often overlooking potential positive health effects. To better understand the effects of raw meat diets on the health of cats and dogs, this review summarises the latest scientific evidence and discusses both the potential health benefits and the risks associated with these diets.

The fecal metabolomic signature of a plant-based (vegan) diet compared to an animal-based diet in healthy adult client-owned dogs

Despite the rising popularity of plant-based (vegan) diets for dogs, the metabolic effects of plant-based diets in dogs have not been thoroughly investigated. Evaluating the impact of a vegan diet on the fecal metabolome in dogs could offer valuable insight into the effects on gastrointestinal and overall health. This study evaluated the fecal metabolic signature of an experimental extruded vegan diet (PLANT) compared to a commercial extruded animal-based diet (MEAT) in healthy adult dogs. Sixty-one client-owned healthy adult dogs completed a randomized, double-blinded longitudinal study consisting of a 4-wk acclimation period, where all dogs received the MEAT diet, followed by a 12-wk experimental period where they either continued with the MEAT diet or switched to the PLANT diet. Fecal collections occurred at baseline (after 4-wk acclimation) and exit (after the experimental period). Fecal metabolites were quantified using 1H nuclear magnetic resonance spectroscopy. Multiple mixed model gamma linear regression was used to evaluate the association of metabolite concentration against age, sex, and body weight, along with an interaction between diet and time. Sixty-six metabolites were quantified. Only 2/66 metabolites differed between groups at baseline and within the MEAT diet group over time. In contrast, 46/66 metabolites differed in concentrations over time in response to feeding the PLANT diet. At the exit time-point, dogs fed the PLANT diet had increased metabolites related to carbohydrate fermentation, such as acetic (P < 0.01) and propanoic (P < 0.01) acid and increases in sugar metabolites when compared to the MEAT group. These findings indicate that the fecal metabolic signature of dogs fed a plant-based diet is distinct from dogs fed an animal-based diet, even if both diets have a similar nutrient profile and are processed similarly.

Apparent total tract nutrient digestibility of frozen raw, freeze-dried raw, fresh, and extruded dog foods and their effects on serum metabolites and fecal characteristics, metabolites, and microbiota of healthy adult dogs

Various pet food diet formats are available, but many are poorly studied. The objective of this study was to determine the apparent total tract macronutrient digestibility (ATTD) of frozen raw, freeze-dried raw, fresh, and extruded dog foods and assess their effects on serum metabolites, hematology, and fecal characteristics, metabolites, and microbiota of healthy adult dogs. Ten beagle dogs (4.10 ± 0.74 yr) were used in a replicated 5 × 5 Latin square study to test the following diets: Chicken and Barley Recipe (extruded; Hill's Science Diet [EXT]), Chicken and White Rice Recipe (fresh; Just Food for Dogs [FRSH]), Chicken Formula (frozen raw; Primal [FRZN]), Chicken and Sorghum Hybrid Freeze-dried Formula (freeze-dried raw; Primal [HFD]), and Chicken Dinner Patties (freeze-dried raw; Stella & Chewy's [FD]). The experiment was composed of five 35-d periods, with each ending with fecal and blood collections. Data were analyzed using Mixed Models in SAS 9.4, with P < 0.05 being significant. Treatment was a fixed effect and dog a random effect. Protein ATTD was higher for FRZN and FD than other diets and higher for HFD than FRSH and EXT. Fat ATTD was higher for HFD than FRZN and EXT and lower for EXT than other diets. Fecal output was higher for dogs fed EXT than those fed other diets and higher for dogs fed FRSH than those fed FRZN, HFD, or FD. Fecal pH was lower in dogs fed EXT and FRSH than those fed other diets. Fecal scores were higher (looser) in dogs fed EXT and FRSH than those fed FRZN and FD. Fecal dry matter was higher in dogs fed FD than those fed other diets and higher in those fed FRZN and HFD than those fed EXT and FRSH. In general, fecal short-chain fatty acids were highest in dogs fed EXT, intermediate in dogs fed FRSH and HFD, and lowest in dogs fed FRZN and FD. Fecal isobutyrate and isovalerate were highest in dogs fed HFD, lowest in dogs fed FRSH, and intermediate in dogs fed other diets. Fecal primary bile acids were higher, while secondary bile acids were lower in dogs fed FRSH than in dogs fed other diets. Fecal microbiota were greatly impacted by diet, with alpha diversity, beta diversity, and relative abundances of over 40 bacterial genera being different among treatments. This study shows that dietary format may lead to great differences in nutrient digestibility and fecal characteristics, metabolites, and microbiota. More research is needed to distinguish the effects of ingredient source, processing method, and nutrient composition.

Industrial diet intervention modulates the interplay between gut microbiota and host in semi-stray dogs

BACKGROUND

The gut microbiota and derived metabolites play a key role in regulating host physiology. Diet is identified as a key regulatory factor of the microbiota composition and, potentially, of subsequent functionalities. Demonstrating the role of diet may be complex as most human studies are cross-sectional and dietary intervention is often accompanied by hygienic changes. The objective of the present study was to investigate the impact of an industrial diet on the modulation of the microbiota and targeted functionalities using a canine "natural" model.

RESULTS

We carried out a controlled dietary trial in a cohort of Tunisian semi-stray dogs. We made a transition from a natural diet to an industrial kibble diet and monitored the composition of the fecal microbiota, the concentration of short-chain fatty acids (SCFA) and bile acids (BAs), and protease activities. We demonstrated that dietary change significantly decreased fecal primary bile acids levels and protease activities. Interestingly, correlation analyses demonstrated that variation of specific microbial genera were associated with modulated physiological parameters.

CONCLUSIONS

Our study reveals that an industrial diet induces beneficial changes in microbial composition and functions characterised by increased diversity, synthesis of SCFA and secondary bile acids production, stressing the key role of the diet-microbiota-dog crosstalk.

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.

Species-level characterization of the core microbiome in healthy dogs using full-length 16S rRNA gene sequencing

Despite considerable interest and research in the canine fecal microbiome, our understanding of its species-level composition remains incomplete, as the majority of studies have only provided genus-level resolution. Here, we used full-length 16S rRNA gene sequencing to characterize the fecal microbiomes of 286 presumed healthy dogs living in homes in North America who are devoid of clinical signs, physical conditions, medication use, and behavioral problems. We identified the bacterial species comprising the core microbiome and investigated whether a dog's sex & neuter status, age, body weight, diet, and geographic region predicted microbiome variation. Our analysis revealed that 23 bacterial species comprised the core microbiome, among them Collinsella intestinalis, Megamonas funiformis, Peptacetobacter hiranonis, Prevotella copri, and Turicibacter sanguinis. The 23 taxa comprised 75% of the microbiome on average. Sterilized females, dogs of intermediate body sizes, and those exclusively fed kibble tended to harbor the most core taxa. Host diet category, geographic region, and body weight predicted microbiome beta-diversity, but the effect sizes were modest. Specifically, the fecal microbiomes of dogs fed kibble were enriched in several core taxa, including C. intestinalis, P. copri, and Holdemanella biformis, compared to those fed raw or cooked food. Conversely, dogs on a raw food diet exhibited higher abundances of Bacteroides vulgatus, Caballeronia sordicola, and Enterococcus faecium, among others. In summary, our study provides novel insights into the species-level composition and drivers of the fecal microbiome in healthy dogs living in homes; however, extrapolation of our findings to different dog populations will require further study.

The Relationship between Canine Behavioral Disorders and Gut Microbiome and Future Therapeutic Perspectives

Canine behavioral disorders have become one of the most common concerns and challenging issues among dog owners. Thus, there is a great demand for knowledge about various factors affecting dogs' emotions and well-being. Among them, the gut-brain axis seems to be particularly interesting, especially since in many instances the standard treatment or behavioral therapies insufficiently improve animal behavior. Therefore, to face this challenge, the search for novel therapeutic methods is highly required. Existing data show that mammals' gut microbiome, immune system, and nervous system are in continuous communication and influence animal physiology and behavior. This review aimed to summarize and discuss the most important scientific evidence on the relationship between mental disorders and gut microbiota in dogs, simultaneously presenting comparable outcomes in humans and rodent models. A comprehensive overview of crucial mechanisms of the gut-brain axis is included. This refers especially to the neurotransmitters crucial for animal behavior, which are regulated by the gut microbiome, and to the main microbial metabolites-short-chain fatty acids (SCFAs). This review presents summarized data on gut dysbiosis in relation to the inflammation process within the organism, as well as the activation of the hypothalamic-pituitary-adrenal (HPA) axis. All of the above mechanisms are presented in this review in strict correlation with brain and/or behavioral changes in the animal. Additionally, according to human and laboratory animal studies, the gut microbiome appears to be altered in individuals with mental disorders; thus, various strategies to manipulate the gut microbiota are implemented. This refers also to the fecal microbiome transplantation (FMT) method, based on transferring the fecal matter from a donor into the gastrointestinal tract of a recipient in order to modulate the gut microbiota. In this review, the possible effects of the FMT procedure on animal behavioral disorders are discussed.

Comparative analysis of gut microbiota in children with obstructive sleep apnea: assessing the efficacy of 16S rRNA gene sequencing in metabolic function prediction based on weight status

Background

Analyzing bacterial microbiomes consistently using next-generation sequencing (NGS) is challenging due to the diversity of synthetic platforms for 16S rRNA genes and their analytical pipelines. This study compares the efficacy of full-length (V1-V9 hypervariable regions) and partial-length (V3-V4 hypervariable regions) sequencing of synthetic 16S rRNA genes from human gut microbiomes, with a focus on childhood obesity.

Methods

In this observational and comparative study, we explored the differences between these two sequencing methods in taxonomic categorization and weight status prediction among twelve children with obstructive sleep apnea.

Results

The full-length NGS method by Pacbio® identified 118 genera and 248 species in the V1-V9 regions, all with a 0% unclassified rate. In contrast, the partial-length NGS method by Illumina® detected 142 genera (with a 39% unclassified rate) and 6 species (with a 99% unclassified rate) in the V3-V4 regions. These approaches showed marked differences in gut microbiome composition and functional predictions. The full-length method distinguished between obese and non-obese children using the Firmicutes/Bacteroidetes ratio, a known obesity marker (p = 0.046), whereas the partial-length method was less conclusive (p = 0.075). Additionally, out of 73 metabolic pathways identified through full-length sequencing, 35 (48%) were associated with level 1 metabolism, compared to 28 of 61 pathways (46%) identified through the partial-length method. The full-length NGS also highlighted complex associations between body mass index z-score, three bacterial species (Bacteroides ovatus, Bifidobacterium pseudocatenulatum, and Streptococcus parasanguinis ATCC 15912), and 17 metabolic pathways. Both sequencing techniques revealed relationships between gut microbiota composition and OSA-related parameters, with full-length sequencing offering more comprehensive insights into associated metabolic pathways than the V3-V4 technique.

Conclusion

These findings highlight disparities in NGS-based assessments, emphasizing the value of full-length NGS with amplicon sequence variant analysis for clinical gut microbiome research. They underscore the importance of considering methodological differences in future meta-analyses.

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

BACKGROUND

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

HYPOTHESIS/OBJECTIVES

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

ANIMALS

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

METHODS

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

RESULTS

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

CONCLUSIONS AND CLINICAL IMPORTANCE

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

Fecal microbiota composition, serum metabolomics, and markers of inflammation in dogs fed a raw meat-based diet compared to those on a kibble diet

Introduction

Despite the potential health risks associated with feeding raw and non-traditional diets, the use of these diets in dogs is increasing, yet the health outcomes associated with these diets is not well understood. This study investigates the effect of feeding dogs a kibble or raw meat-based diets on fecal microbiota composition, serum metabolomics and inflammatory markers.

Methods

Clinically healthy dogs with a history of consuming either kibble (KD, n = 27) or raw meat-based diets (RMBD, n = 28) for more than 1 year were enrolled. Dogs were fed a standardized diet of either a single brand of KD or RMBD for 28 days. Serum and fecal samples were collected for analysis of microbiota, metabolomics, and inflammatory markers. Multiple regression analysis was performed for each of the metabolites and inflammatory markers, with feed group, age and BCS included as independent variables.

Results

The fecal microbiota composition differed between the KD and RMBD groups. Beta-diversity and some indices of alpha-diversity (i.e., Shannon and Simpson) were different between the two diet groups. Sixty- three serum metabolites differed between KD and RMBD-fed dogs with the majority reflecting the differences in macronutrient composition of the two diets.Fecal IAP, IgG and IgA were significantly higher in RMBD dogs compared to KD dogs, while systemic markers of inflammation, including serum c-reactive protein (CRP), galectin, secretory receptor of advanced glycation end-products (sRAGE), haptoglobin, and serum IgG were similar in dogs fed either diet.

Discussion

Diet composition significantly affected fecal microbiota composition and metabolome. Although it had a potentially beneficial effect on local inflammatory markers, feeding RMBD had no impact on systemic inflammation. The influence of these changes on long term health outcomes provides an area for future study.

Using meta-analysis to understand the impacts of dietary protein and fat content on the composition of fecal microbiota of domestic dogs (Canis lupus familiaris): A pilot study

The interplay between diet and fecal microbiota composition is garnering increased interest across various host species, including domestic dogs. While the influence of dietary macronutrients and their associated microbial communities have been extensively reviewed, these reviews are descriptive and do not account for differences in microbial community analysis, nor do they standardize macronutrient content across studies. To address this, a meta-analysis was performed to assess the impact of dietary crude protein ("protein") and dietary crude fat ("fat") on the fecal microbiota composition in healthy dogs. Sixteen publications met the eligibility criteria for the meta-analysis, yielding a final data set of 314 dogs. Diets were classed as low, moderate, high, or supra in terms of protein or fat content. Sequence data from each publication were retrieved from public databases and reanalyzed using consistent bioinformatic pipelines. Analysis of community diversity indices and unsupervised clustering of the data with principal coordinate analysis revealed a small effect size and complete overlap between protein and fat levels at the overall community level. Supervised clustering through random forest analysis and partial least squares-discriminant analysis indicated alterations in the fecal microbiota composition at a more individual taxonomic level, corresponding to the levels of protein or fat. The Prevotellaceae Ga6A1 group and Enterococcus were associated with increasing levels of protein, while Allobaculum and Clostridium sensu stricto 13 were associated with increasing levels of fat. Interestingly, the random forest analyses revealed that Sharpea, despite its low relative abundance in the dog's fecal microbiome, was primarily responsible for the separation of the microbiome for both protein and fat. Future research should focus on validating and understanding the functional roles of these relatively low-abundant genera.

Determination of Bile Acids in Canine Biological Samples: Diagnostic Significance

The comprehensive examination of bile acids is of paramount importance across various fields of health sciences, influencing physiology, microbiology, internal medicine, and pharmacology. While enzymatic reaction-based photometric methods remain fundamental for total BA measurements, there is a burgeoning demand for more sophisticated techniques such as liquid chromatography-tandem mass spectrometry (LC-MS/MS) for comprehensive BA profiling. This evolution reflects a need for nuanced diagnostic assessments in clinical practice. In canines, a BA assessment involves considering factors, such as food composition, transit times, and breed-specific variations. Multiple matrices, including blood, feces, urine, liver tissue, and gallbladder bile, offer insights into BA profiles, yet interpretations remain complex, particularly in fecal analysis due to sampling challenges and breed-specific differences. Despite ongoing efforts, a consensus regarding optimal matrices and diagnostic thresholds remains elusive, highlighting the need for further research. Emphasizing the scarcity of systematic animal studies and underscoring the importance of ap-propriate sampling methodologies, our review advocates for targeted investigations into BA alterations in canine pathology, promising insights into pathomechanisms, early disease detection, and therapeutic avenues.

Collaborative Metabolism: Gut Microbes Play a Key Role in Canine and Feline Bile Acid Metabolism

Bile acids, produced by the liver and secreted into the gastrointestinal tract, are dynamic molecules capable of impacting the overall health of dogs and cats in many contexts. Importantly, the gut microbiota metabolizes host primary bile acids into chemically distinct secondary bile acids. This review explores the emergence of new literature connecting microbial-derived bile acid metabolism to canine and feline health and disease. Moreover, this review highlights multi-omic methodologies for translational research as an area for continued growth in veterinary medicine aimed at accelerating microbiome science and medicine as it pertains to bile acid metabolism in dogs and cats.

Fecal supernatants from dogs with idiopathic epilepsy activate enteric neurons

Introduction

Alterations in the composition and function of the gut microbiome have been reported in idiopathic epilepsy (IE), however, interactions of gut microbes with the enteric nervous system (ENS) in this context require further study. This pilot study examined how gastrointestinal microbiota (GIM), their metabolites, and nutrients contained in intestinal contents communicate with the ENS.

Methods

Fecal supernatants (FS) from healthy dogs and dogs with IE, including drug-naïve, phenobarbital (PB) responsive, and PB non-responsive dogs, were applied to cultured myenteric neurons to test their activation using voltage-sensitive dye neuroimaging. Additionally, the concentrations of short-chain fatty acids (SCFAs) in the FS were quantified.

Results

Our findings indicate that FS from all examined groups elicited neuronal activation. Notably, FS from PB non-responsive dogs with IE induced action potential discharge in a higher proportion of enteric neurons compared to healthy controls, which exhibited the lowest burst frequency overall. Furthermore, the highest burst frequency in enteric neurons was observed upon exposure to FS from drug-naïve dogs with IE. This frequency was significantly higher compared to that observed in PB non-responsive dogs with IE and showed a tendency to surpass that of healthy controls.

Discussion

Although observed disparities in SCFA concentrations across the various FS samples might be associated with the induced neuronal activity, a direct correlation remains elusive at this point. The obtained results hint at an involvement of the ENS in canine IE and set the basis for future studies.

In Vitro Assessment of Postbiotic and Probiotic Commercial Dietary Supplements Recommended for Counteracting Intestinal Dysbiosis in Dogs

Many environmental aspects influence the preservation of a beneficial microbiome in dogs, and gut dysbiosis occurs when imbalances in the intestinal ecosystem cause functional changes in the microbial populations. The authors evaluated the effects of two specific commercial dietary supplements: a combination of a postbiotic and prebiotics (Microbiotal cane®) and a probiotic product (NBF 1®) recommended for counteracting intestinal dysbiosis in dogs, on the gut canine microbiota composition and its metabolic activities (production of short-chain fatty acids). The investigation was performed using an in vitro fermentation system inoculated with dog fecal samples. Microbiotal cane® promoted a more immediate increase in Lactobacillus spp. after the first 6 h of fermentation, whereas NBF 1® promoted the increase at the end of the process only. The two supplements supported an increase in the Bifidobacterium spp. counts only after 24 h. The in vitro abilities of Microbiotal cane® and NBF 1® to increase selectively beneficial bacterial groups producing acetic, propionic, and butyric acids suggest a possible positive effect on the canine gut microbiota, even if further in vivo studies are needed to confirm the beneficial effects on the intestinal health.

Gut Microbiota Exchange in Domestic Animals and Rural-urban People Axis

In recent years, one of the most critical topics in microbiology that can be addressed is microbiome and microbiota. The term microbiome contains both the microbiota and structural elements, metabolites/signal molecules, and the surrounding environmental conditions, and the microbiota consists of all living members forming the microbiome. Among; the intestinal microbiota is one of the most important microbiota, also called the gut microbiota. After colonization, the gut microbiota can have different functions, including resistance to pathogens, maintaining the intestinal epithelium, metabolizing dietary and pharmaceutical compounds, and controlling immune function. Recently, studies have shown that the gut microbiota can prevent the formation of fat in the body. In this study, we examined the gut microbiota in various animals, including dogs, cats, dairy cows, sheep, chickens, horses, and people who live in urban and rural areas. Based on the review of various studies, it has been determined that the population of microbiota in animals and humans is different, and various factors such as the environment, nutrition, and contact with animals can affect the microbiota of people living in urban and rural areas.

Faecal metabolome responses to an altered dietary protein:carbohydrate ratio in adult dogs

High-protein diets may aid weight loss and weight maintenance programs in both humans and dogs, although the effect of dietary protein levels on gut metabolism and functionality has not been studied in depth. The current study aimed to investigate the effect of an altered dietary protein:carbohydrate ratio on gut function in adult dogs by means of faecal metabolomic fingerprinting. More specifically, functional metabolic differences in dogs fed a high-protein/low-carbohydrate (HPLC) vs. low-protein/high-carbohydrate (LPHC) diet were studied by equally allocating twelve clinically healthy (6 lean and 6 obese) Beagles into two groups in a cross-over design, with each group receiving two isocaloric diets for four weeks. The faecal metabolome revealed that different protein:carbohydrate ratio can influence host and/or gut microbiome metabolism and function, while no effect was observed on the body condition. Targeted analysis demonstrated that the HPLC diet significantly increased the concentration of indole, spermidine, and pipecolinic acid and decreased the concentration of azelaic acid, D-fructose, mannose, and galactose (p < 0.05). Multivariate modelling (OPLS-DA) of the untargeted faecal metabolome revealed distinctly different metabolomic profiles following the HPLC vs. LPHC diet, with 18 altered pathways. The HPLC diet influenced amino acid and lipid metabolism, potentially promoting weight loss and immune function, whereas the LPHC diet affected carbohydrate fermentation and may promote anti-oxidative function.

Effect of Different Feeds on the Fungi Microbiome of Suffolk Crossed with Tibetan Sheep

The gut microbiome plays an important role in the metabolism, nutrient absorption and immunocompetency of animals. The dynamics of the microbiota can be influenced by modulatory factors that involve nutrition, environment, health, diseases, etc. Few reports have been documented regarding the effects of different feeds on the fungi microbiome of Suffolk crossed with Tibetan sheep. A total of 30 Suffolk crossed with Tibetan sheep (ST sheep) were selected for the study and randomly divided into five equal groups (n = 6): AZ, BZ, CZ, DZ and EZ. Group AZ was fed with alfalfa and oat grass, whereas group BZ was fed with mixture of concentrated feed, alfalfa and oat grass. Groups CZ, DZ and EZ were fed with concentrated feed #1, #2 and #3, respectively. All experimental animals were fed twice a day for four months, and rectum samples were collected for microbiota analysis. Results revealed that 2,781,461 raw reads and 2,333,239 clean reads were achieved in the ST sheep. When compared with the sheep of groups AZ and BZ (164), the shared amplicon sequence variants (ASVs) between AZ and CZ (109), AZ (113) and DZ (118) as well as AZ along with EZ were fewer. Conspicuous different phyla (8) and genera (56) were examined and compared with free-range sheep in AZ. Genera including Xeromyces, Kazachstania, Cordyceps, Rhodotorula, Pichia, Spor, etc. were found higher in animals in the CZ, DZ and EZ groups. The results of this study provide new insights regarding the effects of different feeds on the fungi microbiome of sheep farmed on the plateau. We concluded that the differences in feed in Suffolk crossed with Tibetan sheep altered their gut microbiota.

Early life programming by diet can play a role in risk reduction of otitis in dogs

Introduction

Otitis in dogs is often chronic while local treatment primarily consists of flushing, antibiotics, and/or antifungals. We were interested in finding early life variables that associate with otitis later in life, preferably some that could be modified.

Methods

A cross-sectional hypothesis-driven study with longitudinal data was performed to search for associations between pre- and postnatal exposures, and the incidence of owner-reported otitis in dogs at over 1 year of age. The multivariate logistic regression analysis study included data from 3,064 dogs and explored 26 different early life variables at four early life stages: prenatal, neonatal, postnatal, and puppyhood. We compared two feeding patterns, a non-processed meat-based diet (NPMD, raw) and an ultra-processed carbohydrate-based diet (UPCD, dry).

Results

We report that eating a NPMD diet significantly decreased the risk of otitis later in life, while eating a UPCD diet significantly increased the risk. This was seen in different life stages of mother or puppy: The maternal diet during pregnancy (p=0.011) and the puppies' diet from 2 to 6 months of age (p=0.019) were both significantly associated with otitis incidence later in life, whereas the puppies' first solid diet, was associated in the same way, but did not reach significance (p=0.072). Also, analyzing food ratios showed that when puppies were consuming >25% of their food as NPMD it significantly decreased their incidence of otitis later in life, while a ratio of >75% UPCD in their diet significantly increased their risk of otitis. Also, if the dog was born in the current family, was exposed to sunlight for more than 1 hour daily, and was raised on a dirt floor during puppyhood, there was a lower risk of otitis development later in life.

Discussion

The findings only suggest causality, and further studies are required. However, we propose that veterinarians, breeders, and owners can impact otitis risk by modifying factors such as diet and environment.

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

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

Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats

Changes in diet and environment can lead to acute diarrhea in companion animals, but the composition and interactions of the gut microbiome during acute diarrhea remain unclear. In this multicenter case-control study, we investigated the relationship between intestinal flora and acute diarrhea in two breeds of cats. Acutely diarrheic American Shorthair (MD, n = 12) and British Shorthair (BD, n = 12) and healthy American Shorthair (MH, n = 12) and British Shorthair (BH, n = 12) cats were recruited. Gut microbial 16S rRNA sequencing, metagenomic sequencing, and untargeted metabolomic analysis were performed. We observed significant differences in beta-diversity (Adonis, P < 0.05) across breeds and disease state cohorts. Profound differences in gut microbial structure and function were found between the two cat breeds. In comparison to healthy British Shorthair cats, Prevotella, Providencia, and Sutterella were enriched while Blautia, Peptoclostridium, and Tyzzerella were reduced in American Shorthair cats. In the case-control cohort, cats with acute diarrhea exhibited an increased abundance of Bacteroidota, Prevotella, and Prevotella copri and a decreased abundance of Bacilli, Erysipelotrichales, and Erysipelatoclostridiaceae (both MD and BD cats, P < 0.05). Metabolomic analysis identified significant changes in the BD intestine, affecting 45 metabolic pathways. Moreover, using a random forest classifier, we successfully predicted the occurrence of acute diarrhea with an area under the curve of 0.95. Our findings indicate a distinct gut microbiome profile that is associated with the presence of acute diarrhea in cats. However, further investigations using larger cohorts of cats with diverse conditions are required to validate and extend these findings. IMPORTANCE Acute diarrhea is common in cats, and our understanding of the gut microbiome variations across breeds and disease states remains unclear. We investigated the gut microbiome of two cat breeds (British Shorthair and American Shorthair) with acute diarrhea. Our study revealed significant effects of breeds and disease states on the structure and function of the gut microbiota in cats. These findings emphasize the need to consider breed-related factors in animal nutrition and research models. Additionally, we observed an altered gut metabolome in cats with acute diarrhea, closely linked to changes in bacterial genera. We identified a panel of microbial biomarkers with high diagnostic accuracy for feline acute diarrhea. These findings provide novel insights into the diagnosis, classification, and treatment of feline gastrointestinal diseases.

Gut Colonization by ESBL-Producing Escherichia coli in Dogs Is Associated with a Distinct Microbiome and Resistome Composition

The gut microbiome of humans and animals acts as a reservoir of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC). Dogs are known for having a high prevalence of ESBL-EC in their gut microbiota, although their ESBL-EC carrier status often shifts over time. We hypothesized that the gut microbiome composition of dogs is implicated in ESBL-EC colonization status. Therefore, we assessed whether ESBL-EC carriage in dogs is associated with changes in the gut microbiome and resistome. Fecal samples were collected longitudinally from 57 companion dogs in the Netherlands every 2 weeks for a total of 6 weeks (n = 4 samples/dog). Carriage of ESBL-EC was determined through selective culturing and PCR and in line with previous studies, we observed a high prevalence of ESBL-EC carriage in dogs. Using 16s rRNA gene profiling we found significant associations between detected ESBL-EC carriage and an increased abundance of Clostridium sensu stricto 1, Enterococcus, Lactococcus, and the shared genera of Escherichia-Shigella in the dog microbiome. A resistome capture sequencing approach (ResCap) furthermore, revealed associations between detected ESBL-EC carriage and the increased abundance of the antimicrobial resistance genes: cmlA, dfrA, dhfR, floR, and sul3. In summary, our study showed that ESBL-EC carriage is associated with a distinct microbiome and resistome composition. IMPORTANCE The gut microbiome of humans and animals is an important source of multidrug resistant pathogens, including beta-lactamase-producing Escherichia coli (ESBL-EC). In this study, we assessed if the carriage of ESBL-EC in dogs was associated with changes in gut composition of bacteria and antimicrobial resistant genes (ARGs). Therefore, stool samples from 57 dogs were collected every 2 weeks for a total of 6 weeks. Sixty eight percent of the dogs carried ESBL-EC during at least one of the time points analyzed. By investigating the gut microbiome and resistome composition, we observed specific changes at time points when dogs were colonized with ESBL-EC compared to time points whenESBL-EC were not detected. In conclusion, our study highlights the importance to study the microbial diversity in companion animals, as gut colonization of particular antimicrobial resistant bacteria might be an indication of a changed microbial composition that is associated with the selection of particular ARGs.

A multi-strain probiotic promoted recovery of puppies from gastroenteritis in a randomized, double-blind, placebo-controlled study

Objective and animals

Acute diarrhea is among the most common causes of veterinary consultations for dogs. A double-blind, placebocontrolled intervention trial was done with 120 puppies with gastroenteritis. These dogs were 1 to 4 mo old, male and female, of various breeds and sizes.

Procedure

Dogs were randomly allocated into 2 groups: Those in the treated group (TG) received a multi-strain probiotic with Lactobacillus johnsonii CRL1693, Ligilactobacillus murinus CRL1695, Limosilactobacillus mucosae CRL1696, and Ligilactobacillus salivarius CRL1702 (1 × 109 CFU/mL) daily for 7 d, whereas those in the control group (CG) received a placebo. All puppies received intravenous fluids, an antiparasitic, amoxicillin PO, and enrofloxacin SC.

Results

At the start of the trial, the 2 groups were similar. Probiotic administration for 7 d normalized fecal consistency, with 69, 50, and 80% of small, medium, and large puppies in the TG achieving a fecal score of 1 (separate hard lumps) at 7 d, significantly better than puppies in the CG. After 7 d of treatment, most puppies (70%) in the TG had an excellent recovery, whereas in the CG, recoveries were 35.7% "bad" and 30.4% "fair." Therefore, treatment with probiotics hastened recovery (P < 0.0001). At the end of the trial, there was a significant increase of cultivable lactobacilli in the feces of TG puppies, but no significant differences between the 2 groups in numbers of total mesophylls, enterobacteria, or Gram-positive cocci. Total mortality was 5.8%, including 4 puppies from the CG and 3 from the TG.

Conclusion

In a randomized, double-blind, placebo-controlled study, puppies with gastroenteritis symptoms receiving a multi-strain probiotic had rapid improvement, implying beneficial effects on the microbiota and its functionality.

Integrating (Nutri-)Metabolomics into the One Health Tendency-The Key for Personalized Medicine Advancement

Metabolomics is an advanced technology, still under development, with multiple research applications, especially in the field of health. Individual metabolic profiles, the functionality of the body, as well as its interaction with the environment, can be established using this technology. The body's response to various external factors, including the food consumed and the nutrients it contains, has increased researchers' interest in nutrimetabolomics. Establishing correlations between diet and the occurrence of various diseases, or even the development of personalized nutrition plans, could contribute to advances in precision medicine. The interdependence between humans, animals, and the environment is of particular importance today, with the dramatic emergence and spread of zoonotic diseases, food, water and soil contamination, and the degradation of resources and habitats. All these events have led to an increase in risk factors for functional diseases, burdening global health. Thus, this study aimed to highlight the importance of metabolomics, and, in particular, nutrimetabolomics, as a technical solution for a holistic, collaborative, and precise approach for the advancement of the One Health strategy.

Taxonomic, Genomic, and Functional Variation in the Gut Microbiomes of Wild Spotted Hyenas Across 2 Decades of Study

The gut microbiome provides vital functions for mammalian hosts, yet research on its variability and function across adult life spans and multiple generations is limited in large mammalian carnivores. Here, we used 16S rRNA gene and metagenomic high-throughput sequencing to profile the bacterial taxonomic composition, genomic diversity, and metabolic function of fecal samples collected from 12 wild spotted hyenas (Crocuta crocuta) residing in the Masai Mara National Reserve, Kenya, over a 23-year period spanning three generations. The metagenomic data came from four of these hyenas and spanned two 2-year periods. With these data, we determined the extent to which host factors predicted variation in the gut microbiome and identified the core microbes present in the guts of hyenas. We also investigated novel genomic diversity in the mammalian gut by reporting the first metagenome-assembled genomes (MAGs) for hyenas. We found that gut microbiome taxonomic composition varied temporally, but despite this, a core set of 14 bacterial genera were identified. The strongest predictors of the microbiome were host identity and age, suggesting that hyenas possess individualized microbiomes and that these may change with age during adulthood. The gut microbiome functional profiles of the four adult hyenas were also individual specific and were associated with prey abundance, indicating that the functions of the gut microbiome vary with host diet. We recovered 149 high-quality MAGs from the hyenas' guts; some MAGs were classified as taxa previously reported for other carnivores, but many were novel and lacked species-level matches to genomes in existing reference databases. IMPORTANCE There is a gap in knowledge regarding the genomic diversity and variation of the gut microbiome across a host's life span and across multiple generations of hosts in wild mammals. Using two types of sequencing approaches, we found that although gut microbiomes were individualized and temporally variable among hyenas, they correlated similarly to large-scale changes in the ecological conditions experienced by their hosts. We also recovered 149 high-quality MAGs from the hyena gut, greatly expanding the microbial genome repertoire known for hyenas, carnivores, and wild mammals in general. Some MAGs came from genera abundant in the gastrointestinal tracts of canid species and other carnivores, but over 80% of MAGs were novel and from species not previously represented in genome databases. Collectively, our novel body of work illustrates the importance of surveying the gut microbiome of nonmodel wild hosts, using multiple sequencing methods and computational approaches and at distinct scales of analysis.

The effect of puppyhood and adolescent diet on the incidence of chronic enteropathy in dogs later in life

Diet has a key role in the homeostasis of the gut microenvironment, influencing the microbiome, the gut barrier, host immunity and gut physiology. Yet, there is little information on the role of early diet in the onset of inflammatory gastrointestinal disorders later in life, especially in dogs. Therefore, the aim of the present cross-sectional, epidemiological study with longitudinal data, was to explore associations of companion dogs' early life diet style and food items with owner-reported chronic enteropathy (CE) incidence in later life. Food frequency questionnaire data from Finnish companion dogs was analyzed using principal component analysis and logistic regression. We found that feeding a non-processed meat-based diet and giving the dog human meal leftovers and table scraps during puppyhood (2-6 months) and adolescence (6-18 months) were protective against CE later in life. Especially raw bones and cartilage as well as leftovers and table scraps during puppyhood and adolescence, and berries during puppyhood were associated with less CE. In contrast, feeding an ultra-processed carbohydrate-based diet, namely dry dog food or "kibble" during puppyhood and adolescence, and rawhides during puppyhood were significant risk factors for CE later in life.

Fecal Microbiota, Bile Acids, Sterols, and Fatty Acids in Dogs with Chronic Enteropathy Fed a Home-Cooked Diet Supplemented with Coconut Oil

Medium-chain fatty acids (MCFAs) are considered to be interesting energy sources for dogs affected by chronic enteropathies (CE). This study analyzed the clinical scores, fecal microbiota, and metabolomes of 18 CE dogs fed a home-cooked diet (HCD) supplemented with virgin coconut oil (VCO), a source of MCFA, at 10% of metabolizable energy (HCD + VCO). The dogs were clinically evaluated with the Canine Chronic Enteropathy Activity Index (CCECAI) before and at the end of study. Fecal samples were collected at baseline, after 7 days of HCD, and after 30 days of HCD + VCO, for fecal score (FS) assessment, microbial analysis, and determination of bile acids (BA), sterols, and fatty acids (FA). The dogs responded positively to diet change, as shown by the CCECAI improvement (p = 0.001); HCD reduced fecal fat excretion and HCD + VCO improved FS (p < 0.001), even though an increase in fecal moisture occurred due to HCD (p = 0.001). HCD modified fecal FA (C6:0: +79%, C14:0: +74%, C20:0: +43%, C22:0: +58%, C24:0: +47%, C18:3n-3: +106%, C20:4n-6: +56%, and monounsaturated FA (MUFA): -23%, p < 0.05) and sterol profile (coprostanol: -27%, sitostanol: -86%, p < 0.01). VCO increased (p < 0.05) fecal total saturated FA (SFA: +28%, C14:0: +142%, C16:0 +21%, C22:0 +33%) and selected MCFAs (+162%; C10:0 +183%, C12:0 +600%), while reducing (p < 0.05) total MUFA (-29%), polyunsaturated FA (-26%), campesterol (-56%) and phyto-/zoosterols ratio (0.93:1 vs. 0.36:1). The median dysbiosis index was <0 and, together with fecal BA, was not significantly affected by HCD nor by VCO. The HCD diet increased total fecal bacteria (p = 0.005) and the abundance of Fusobacterium spp. (p = 0.028). This study confirmed that clinical signs, and to a lesser extent fecal microbiota and metabolome, are positively influenced by HCD in CE dogs. Moreover, it has been shown that fecal proportions of MCFA increased when MCFAs were supplemented in those dogs. The present results emphasize the need for future studies to better understand the intestinal absorptive mechanism of MCFA in dogs.

Standardized amino acid digestibility and nitrogen-corrected true metabolizable energy of frozen and freeze-dried raw dog foods using precision-fed cecectomized and conventional rooster assays

Commercial raw or minimally-processed diets, often referred to holistically as raw meat-based diets (RMBD) represent a small portion of the pet food market, but the growth of this sector has been significant in recent years. While traditionally, high-moisture, frozen options were the standard format of commercially available raw diets, freeze-dried raw diets have become more prevalent as of late. Despite the increasing popularity of these commercial raw diet formats, there is a dearth of literature describing their nutritional properties, particularly regarding freeze-dried diets. Therefore, the objective of this experiment was to determine and compare the standardized amino acid (AA) digestibilities and nitrogen-corrected true metabolizable energy (TMEn) of raw frozen and freeze-dried dog foods using precision-fed cecectomized and conventional rooster assays. Three formats of frozen or freeze-dried raw diets provided by Primal Pet Foods (Fairfield, CA, USA) were tested: traditional freeze-dried nuggets (T-FDN), hybrid freeze-dried nuggets (H-FDN), and frozen nuggets (FZN). Diets were fed to cecectomized roosters (4 roosters/diet) to determine AA digestibilities, while conventional roosters (4 roosters/diet) were used to determine TMEn. In both cases, after 26 h of feed withdrawal, roosters were tube-fed 12 to 13 g of test diets and 12 to 13 g of corn. Following crop intubation, excreta were collected for 48 h. Endogenous corrections for AA were made using five additional cecectomized roosters. All data were analyzed using the Mixed Models procedure of SAS version 9.4. There were no significant differences in standardized AA digestibilities among diets, with digestibilities being high for all diets tested. For most of the indispensable AA, digestibilities were greater than or equal to 90% for all diets. Histidine and lysine were the exceptions, with digestibilities ranging from 82% to 87% and 87% to 92%, respectively. Moreover, the reactive lysine:total lysine ratio, a measure of heat damage, ranged from 0.91 to 0.95. TMEn values were higher (P = 0.0127) in T-FDN (6.1 kcal/g) and FZN (5.9 kcal/g) than H-FDN (5.3 kcal/g) and were most similar to those estimated by Atwater factors. In general, all diets tested had high AA digestibilities and had TMEn values that were most similar to Atwater factors.

High-protein dried distillers grains in dog diets: diet digestibility and palatability, intestinal fermentation products, and fecal microbiota

This study aimed to evaluate the effects of high-protein dried distillers grains (HPDDG) on palatability and metabolizable energy (ME) of the diet, apparent total tract digestibility (ATTD) of nutrients and energy, intestinal fermentation products, and fecal microbiota in dogs. Four diets containing 0, 70, 140, and 210 g/kg of HPDDG were manufactured. To evaluate the ME and the ATTD of macronutrients of HPDDG itself, an additional test diet was manufactured containing 70% of the control diet formula (0 g/kg) and 300 g/kg of HPDDG. Fifteen adult Beagle dogs were distributed in a randomized block design, with two periods of 15 d each (n = 6). The HPDDG digestibility was obtained using the Matterson substitution method. For the palatability test, 16 adult dogs were used, comparing the diets: 0 vs. 70 g/kg of HPDDG and 0 vs. 210 g/kg of HPDDG. The ATTD of HPDDG were: dry matter = 85.5%, crude protein = 91.2%, and acid-hydrolyzed ether extract = 84.6% and the ME content was 5,041.8 kcal/kg. The ATTD of macronutrients and ME of the diets and the fecal dry matter, score, pH, and ammonia of the dogs did not differ among treatments (P > 0.05). There was a linear increase in the fecal concentrations of valeric acid with the inclusion of HPDDG in the diet (P < 0.05). Streptococcus and Megamonas genera reduced linearly (P < 0.05), and Blautia, Lachnospira, Clostridiales, and Prevotella genera showed a quadratic response to the inclusion of HPDDG in the diet (P < 0.05). Alpha-diversity results showed an increase (P < 0.05) in the number of operational taxonomic units and Shannon index and a trend (P = 0.065) for a linear increase in the Chao-1 index with the dietary inclusion of HPDDG. Dogs preferred the 210 g/kg diet over the 0 g/kg HPDDG diet (P < 0.05). These results demonstrate that the HPDDG evaluated does not affect the utilization of nutrients in the diet, but it may modulate the fecal microbiome of dogs. In addition, HPDDG may contribute to diet palatability for dogs.

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.

Longitudinal fecal microbiome and metabolite data demonstrate rapid shifts and subsequent stabilization after an abrupt dietary change in healthy adult dogs

Background

Diet has a large influence on gut microbiota diversity and function. Although previous studies have investigated the effect of dietary interventions on the gut microbiome, longitudinal changes in the gut microbiome, microbial functions, and metabolite profiles post dietary interventions have been underexplored. How long these outcomes require to reach a steady-state, how they relate to one another, and their impact on host physiological changes are largely unknown. To address these unknowns, we collected longitudinal fecal samples following an abrupt dietary change in healthy adult beagles (n = 12, age: 5.16 ± 0.87 year, BW: 13.37 ± 0.68 kg) using a crossover design. All dogs were fed a kibble diet (control) from d1-14, and then fed that same diet supplemented with fiber (HFD) or a protein-rich canned diet (CD) from d15-27. Fresh fecal samples were collected on d13, 16, 20, 24, and 27 for metabolite and microbiome assessment. Fecal microbial diversity and composition, metabolite profiles, and microbial functions dramatically diverged and stabilized within a few days (2 d for metabolites; 6 d for microbiota) after dietary interventions. Fecal acetate, propionate, and total short-chain fatty acids increased after change to HFD, while fecal isobutyrate, isovalerate, total branched-chain fatty acids, phenol, and indole increased after dogs consumed CD. Relative abundance of ~ 100 bacterial species mainly belonging to the Firmicutes, Proteobacteria, and Actinobacteria phyla increased in HFD. These shifts in gut microbiome diversity and composition were accompanied by functional changes. Transition to HFD led to increases in the relative abundance of KEGG orthology (KO) terms related to starch and sucrose metabolism, fatty acid biosynthesis, and amino sugar and nucleotide sugar metabolism, while transition to CD resulted in increased relative abundance of KO terms pertaining to inositol phosphate metabolism and sulfur metabolism. Significant associations among fecal microbial taxa, KO terms, and metabolites were observed, allowing for high-accuracy prediction of diet group by random forest analysis.

Conclusions

Longitudinal sampling and a multi-modal approach to characterizing the gastrointestinal environment allowed us to demonstrate how drastically and quickly dietary changes impact the fecal microbiome and metabolite profiles of dogs following an abrupt dietary change and identify key microbe-metabolite relationships that allowed for treatment prediction.

The Kitty Microbiome Project: Defining the Healthy Fecal "Core Microbiome" in Pet Domestic Cats

Here, we present a taxonomically defined fecal microbiome dataset for healthy domestic cats (Felis catus) fed a range of commercial diets. We used this healthy reference dataset to explore how age, diet, and living environment correlate with fecal microbiome composition. Thirty core bacterial genera were identified. Prevotella, Bacteroides, Collinsella, Blautia, and Megasphaera were the most abundant, and Bacteroides, Blautia, Lachnoclostridium, Sutterella, and Ruminococcus gnavus were the most prevalent. While community composition remained relatively stable across different age classes, the number of core taxa present decreased significantly with age. Fecal microbiome composition varied with host diet type. Cats fed kibble had a slightly, but significantly greater number of core taxa compared to cats not fed any kibble. The core microbiomes of cats fed some raw food contained taxa not as highly prevalent or abundant as cats fed diets that included kibble. Living environment also had a large effect on fecal microbiome composition. Cats living in homes differed significantly from those in shelters and had a greater portion of their microbiomes represented by core taxa. Collectively our work reinforces the findings that age, diet, and living environment are important factors to consider when defining a core microbiome in a population.

The relationship between pelvic floor functions and vaginal microbiota in 6-8 weeks postpartum women

The impairment of pelvic floor muscle functions and Lactobacillus-deficient vaginal microbiota is common in postpartum women. However, few studies have explored the correlation between pelvic floor muscle functions and vaginal microbiota. Given this research gap, our study aims to investigate any potential association between these two conditions of postpartum women (6-8 weeks after childbirth). A total of 230 women who required postpartum pelvic floor function examination at Peking University International Hospital from December 2021 to April 2022 were enrolled in this study. The collected questionnaire information included progestational weight, body mass index (BMI), weight gain during pregnancy, neonatal weight, delivery type, multiparity, postpartum time, and urinary incontinence (UI). A total of 187 samples of vaginal secretions were collected, and the vaginal microbiota was detected by 16S rRNA sequence analysis. Finally, 183 samples were analyzed in the trial. All individuals were divided into two groups according to the results of pelvic floor muscle assessment to explore the difference between the incidence of postpartum urinary incontinence and vaginal microbiota. We found that the prevalence of UI was higher in the group with weakened pelvic floor muscles. Vaginal delivery, overweight, age, neonatal weight, and weight gain during pregnancy were all risk factors for postpartum urinary incontinence. The vaginal microbiome was no longer Lactobacillus dominant of most postpartum women (91.8%), while the diversity of microbiota increased. The Lactobacillus-deficient community, commonly labeled as community state type (CST) IV, was sub-divided into four communities. The abundance of vaginal Lactobacillus decreased in the group with compromised pelvic muscle functions, while the species richness and diversity increased significantly. In conclusion, the decreased pelvic floor muscle functions of postpartum women 6-8 weeks after delivery may disrupt the balance of vaginal microbiota, and the restoration of pelvic floor functions may contribute to a healthy and balanced vaginal microbiota.

Gut microbiome of captive wolves is more similar to domestic dogs than wild wolves indicated by metagenomics study

Adaptation during the domestication from wolves (Canis lupus) to dogs (Canis lupus familiaris) is a debated ecological topic. Changes in food and environment are major divergences in the domestication of dogs. Gut microbes play an important role in animal adaptation to the food and environmental changes. In this study, shotgun sequencing was performed to compare the species diversity and functional diversity of gut microbes in wild wolves (group CLW, n = 3), captive wolves (group CLC, n = 4), and domestic dogs (group CLF, n = 4). The results found that Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria and Actinobacteria were the most abundant phyla and Bacteroides, Fusobacterium, Prevotella, Megamonas, Paraprevotella, Faecalibacterium, Clostridium were the most abundant genera in the gut of wolves and dogs. Groups CLW, CLC and CLF have shown significant difference in gut microbial species diversity and functional diversity. Bacteroides, Fusobacterium and Faecalibacterium were most abundant genera in groups CLW, CLC and CLF, respectively. Their abundance varied significantly among groups. Compared to the wild wolves, the intestinal microbiol genes of domestic dogs were significantly enriched in the carbohydrate metabolism pathway of KEGG database. One hundred and seventy-seven enzymes were detected with significantly higher abundance in group CLF than that in group CLW, and 49 enzymes showed extremely significant higher abundance in group CLF than that in group CLW (q < 0.01) base on the function abundance annotated in CAZy database. It is noteworthy that there were also significant differences in the abundance of 140 enzymes between groups CLC and CLW (q < 0.05). Clustering analysis based on both the species and the function abundance of intestinal microbiota all found that groups CLC and CLF clustered into one branch, while samples from group CLW clustered into the other branch. This result suggests that captive wolves are more similar to domestic dogs than wild wolves in both species composition and function composition of intestinal microbiota.

Gut microbiota development in the growing dog: A dynamic process influenced by maternal, environmental and host factors

Microorganisms of the gastrointestinal tract play a crucial role in the health, metabolism and development of their host by modulating vital functions such as digestion, production of key metabolites or stimulation of the immune system. This review aims to provide an overview on the current knowledge of factors shaping the gut microbiota of young dogs. The composition of the gut microbiota is modulated by many intrinsic (i.e., age, physiology, pathology) and extrinsic factors (i.e., nutrition, environment, medication) which can cause both beneficial and harmful effects depending on the nature of the changes. The composition of the gut microbiota is quickly evolving during the early development of the dog, and some crucial bacteria, mostly anaerobic, progressively colonize the gut before the puppy reaches adulthood. Those bacterial communities are of paramount importance for the host health, with disturbance in their composition potentially leading to altered metabolic states such as acute diarrhea or inflammatory bowel disease. While many studies focused on the microbiota of young children, there is still a lack of knowledge concerning the development of gut microbiota in puppies. Understanding this early evolution is becoming a key aspect to improve dogs' short and long-term health and wellbeing.

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.

Fresh Food Consumption Increases Microbiome Diversity and Promotes Changes in Bacteria Composition on the Skin of Pet Dogs Compared to Dry Foods

The skin is the first barrier the body has to protect itself from the environment. There are several bacteria that populate the skin, and their composition may change throughout the dog’s life due to several factors, such as environmental changes and diseases. The objective of this research was to determine the skin microbiome changes due to a change in diet on healthy pet dogs. Healthy client-owned dogs (8) were fed a fresh diet for 30 days then dry foods for another 30 days after a 4-day transition period. Skin bacterial population samples were collected after each 30-day feeding period and compared to determine microbiome diversity. Alpha diversity was higher when dogs were fed the fresh diet compared to the dry foods. Additionally, feeding fresh food to dogs increased the proportion of Staphylococcus and decreased Porphyromonas and Corynebacterium. In conclusion, changing from fresh diet to dry foods promoted a relative decrease in skin microbiome in healthy pet dogs.

Molecular ecology and risk factors for third-generation cephalosporin-resistant Escherichia coli carriage by dogs living in urban and nearby rural settings

Objectives

To compare faecal third-generation cephalosporin-resistant (3GC-R) Escherichia coli isolates from dogs living in a city and in a rural area ∼30 km away; to compare isolates from dogs, cattle and humans in these regions; and to determine risk factors associated with 3GC-R E. coli carriage in these two cohorts of dogs.

Methods

Six hundred dogs were included, with faecal samples processed to recover 3GC-R E. coli using 2 mg/L cefotaxime. WGS was by Illumina and risk factor analyses were by multivariable linear regression using the results of an owner-completed survey.

Results

3GC-R E. coli were excreted by 20/303 rural and 31/297 urban dogs. The dominant canine 3GC-R ST was ST963 (bla_CMY-2), which also accounted for 25% of CMY-2-producing E. coli in humans. Phylogenetic overlap between cattle and rural dog CTX-M-14-producing E. coli ST117 was observed as well as acquisition of pMOO-32-positive E. coli ST10 by a rural dog, a plasmid common on cattle farms in the area. Feeding raw meat was associated with carrying 3GC-R E. coli in rural dogs, but not in urban dogs, where swimming in rivers was a weak risk factor.

Conclusions

Given clear zoonotic potential for resistant canine E. coli, our work suggests interventions that may reduce this threat. In rural dogs, carriage of 3GC-R E. coli, particularly CTX-M producers, was phylogenetically associated with interaction with local cattle and epidemiologically associated with feeding raw meat. In urban dogs, sources of 3GC-R E. coli appear to be more varied and include environments such as rivers.

Gut Microbiota and Lymphocyte Subsets in Canine Leishmaniasis

Gut microbiota seems to interact with immune system. Canine leishmaniasis pathogenesis and severity of disease lean on the host immunity, but there is no information in literature about gut microbiota in infected animals. Thus, this study aims to compare the microbiota composition and leukocyte subset of healthy dogs with those of asymptomatic dogs exposed to Leishmania spp. and dogs with clinical leishmaniasis. Thirty-nine dogs were enrolled and grouped into three groups: healthy, exposed asymptomatic and infected symptomatic for Leishmania spp. Flow cytometry on whole blood evaluated the prevalence of CD4, CD5, CD8, CD11b, CD14, and CD21 positive cells. Gut microbiota was investigated using a next generation sequencing (NGS) technique. Firmicutes resulted significantly more abundant in the healthy dogs compared with the other two groups. Conversely, Proteobacteria were more abundant in symptomatic dogs. Even in rarest phyla comparison some significant differences were found, as well as in comparison at classes, order, family and genus levels. The symptomatic group had lower concentration of all the lymphocyte classes (CD5, CD21, CD4, CD8) compared to the other groups. A lower abundance of Firmicutes is reported in literature in diseased animals compared to the healthy ones and this is in agreement with the results of this study. Increased Proteobacteria in sick animals could suggest a dysbiosis status, even without distinct gastrointestinal signs. The leukocyte classes results indicate a decreased Th1 response in symptomatic dogs. Studies also investigating the cytokine response could deepen the knowledge on the pathogenesis of canine leishmaniasis.

Commercial Extruded Plant-Based Diet Lowers Circulating Levels of Trimethylamine N-Oxide (TMAO) Precursors in Healthy Dogs: A Pilot Study

Elevations in circulating trimethylamine N-oxide (TMAO) and its precursors are observed in humans and dogs with heart failure and are associated with adverse outcomes in people. Dietary intervention that reduces or excludes animal ingredients results in rapid reduction of plasma TMAO and TMAO precursors in people, but the impact of diet in dogs has not been studied. The objective of the current study was to determine the effect of diet on plasma TMAO and 2 of its precursors (choline and betaine) in dogs fed a commercial extruded plant-based diet (PBD) or a commercial extruded traditional diet (TD) containing animal and plant ingredients. Sixteen healthy adult mixed breed dogs from a university colony were enrolled in a randomized, 2-treatment, 2-period crossover weight-maintenance study. Mean (SD) age and body weight of the dogs were 2.9 years (± 1.7) and 14.5 kg (± 4.0), respectively. Eight dogs were female (3 intact, 5 spayed) and 8 dogs were male (4 intact, 4 castrated). Plasma choline, betaine and TMAO were quantified by LC-SID-MRM/MS at baseline, and after 4 weeks on each diet. Choline and betaine were also quantified in the diets. Plasma choline levels were significantly lower (P = 0.002) in dogs consuming a PBD (Mean ± SD, 6.8 μM ± 1.2 μM) compared to a TD (Mean ± SD, 7.8 μM ± 1.6 μM). Plasma betaine levels were also significantly lower (P = 0.03) in dogs consuming a PBD (Mean ± SD, 109.1 μM ± 25.3 μM) compared to a TD (Mean ± SD, 132.4 μM ± 32.5 μM). No difference (P = 0.71) in plasma TMAO was detected in dogs consuming a PBD (Median, IQR, 2.4 μM, 2.1 μM) compared to a TD (Median, IQR, 2.3 μM, 1.1 μM). Betaine content was lower in the PBD than in the TD while choline content was similar in the diets. Our findings indicate consumption of a commercial extruded PBD for 4 weeks reduces circulating levels of the TMAO precursors choline and betaine, but not TMAO, in healthy adult dogs.

Evidence that faecal carriage of resistant Escherichia coli by 16-week-old dogs in the United Kingdom is associated with raw feeding

We report a survey (August 2017 to March 2018) and risk factor analysis of faecal carriage of antibacterial-resistant (ABR) Escherichia coli in 223 16-week-old dogs in the United Kingdom. Raw feeding was associated with the presence of fluoroquinolone-resistant (FQ-R) E. coli and those resistant to tetracycline, amoxicillin, and streptomycin, but not to cefalexin. Whole genome sequencing of 36 FQ-R E. coli isolates showed a wide range of sequence types (STs), with almost exclusively mutational FQ-R dominated by ST744 and ST162. Comparisons between E. coli isolates from puppies known to be located within a 50 × 50 km region with those isolated from human urinary tract infections (isolated in parallel in the same region) identified an ST744 FQ-R lineage that was carried by one puppy and caused one urinary tract infection. Accordingly, we conclude that raw feeding is associated with carriage of ABR E. coli in dogs even at 16 weeks of age and that bacteria carried by puppies are shared with humans. We therefore suggest that those who feed their dogs raw meat seriously consider the potential ABR-transmission threat their pet may become as a result and deploy appropriate hygiene practices in mitigation.

Geographically diverse canid sampling provides novel insights into pre-industrial microbiomes

Canine microbiome studies are often limited in the geographic and temporal scope of samples studied. This results in a paucity of data on the canine microbiome around the world, especially in contexts where dogs may not be pets or human associated. Here, we present the shotgun sequences of fecal microbiomes of pet dogs from South Africa, shelter and stray dogs from India, and stray village dogs in Laos. We additionally performed a dietary experiment with dogs housed in a veterinary medical school, attempting to replicate the diet of the sampled dogs from Laos. We analyse the taxonomic diversity in these populations and identify the underlying functional redundancy of these microbiomes. Our results show that diet alone is not sufficient to recapitulate the higher diversity seen in the microbiome of dogs from Laos. Comparisons to previous studies and ancient dog fecal microbiomes highlight the need for greater population diversity in studies of canine microbiomes, as modern analogues can provide better comparisons to ancient microbiomes. We identify trends in microbial diversity and industrialization in dogs that mirror results of human studies, suggesting future research can make use of these companion animals as substitutes for humans in studying the effects of industrialization on the microbiome.

Domestic Environment and Gut Microbiota: Lessons from Pet Dogs

Accumulating data show the involvement of intestinal microbiota in the development and maintenance of numerous diseases. Many environmental factors influence the composition and function of the gut microbiota. An animal model subjected to the same environmental constraints that will allow better characterization of the microbiota–host dialogue is awaited. The domestic dog has physiological, dietary and pathological characteristics similar to those of humans and shares the domestic environment and lifestyle of its owner. This review exposes how the domestication of dogs has brought them closer to humans based on their intrinsic and extrinsic similarities which were discerned through examining and comparing the current knowledge and data on the intestinal microbiota of humans and canines in the context of several spontaneous pathologies, including inflammatory bowel disease, obesity and diabetes mellitus.