Canines have been domesticated and have coexisted with humans for thousands of years, with most owners considering them family members or cherished companions. Moreover, the number of companion animals in modern society is increasing, with canines becoming significant human companions [1]. Given this trend, there is growing interest in the health and well-being of companion canines [2].

The canine gut microbiome plays a crucial role in maintaining overall health and well-being by influencing various physiological functions, including digestion, immune regulation, energy metabolism, and even behavior and temperament. The gut microbiome of healthy companion canines typically comprises diverse bacterial phyla, such as Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria, and Proteobacteria [3,4,5,6]. These microbial communities form a complex and dynamic ecosystem that closely interacts with the host to support canine health and homeostasis.

A well-balanced microbiome, known as eubiosis, represents an optimized microbial composition that promotes host health and metabolic functions. Eubiosis is shaped by interactions between host physiology and environmental conditions. Biological factors such as age and stress levels critically influence microbial diversity and composition [7]. For example, a recent study analyzing the canine gut microbiome at 15-day intervals revealed that microbial composition can shift even within short periods [8]. This study highlights the microbiota’s sensitivity to age and growth stages, which can have both direct and indirect effects on canine health and welfare. Furthermore, gut microbiota composition can be significantly altered by other factors, such as antibiotic use. Dysbiosis, an imbalance in the gut microbiome, can lead to health issues such as weight fluctuations, metabolic disorders, and behavioral changes [9,10,11,12,13,14]. In addition, the composition and activity of the gut microbiome are closely linked to disease prevention [15, 16]. A stable and well-developed gut microbiota contributes to host defense by preventing colonization by harmful microorganisms. It works in concert with the host’s defense mechanisms, particularly the gut-associated immune system, to resist pathogen invasion [17]. However, when eubiosis is disrupted, dysbiosis may result in an overgrowth of harmful bacteria and a decline in beneficial microbes. This imbalance can trigger immune dysregulation and negatively affect overall well-being [7, 18].

To objectively assess canine gut microbial imbalance, the canine microbiota dysbiosis index (CMDI) was developed [19, 20]. The CMDI is calculated using quantitative PCR analysis of seven major bacterial taxa, comprising both beneficial and potentially harmful bacteria, associated with dysbiosis in canine feces. This allows for the quantification of alterations in the intestinal microbiota. This index is widely used in both clinical and research settings to diagnose intestinal microbiota imbalance and to objectively monitor changes over time [21, 22]. However, beyond such assessment tools, targeted strategies are required to effectively maintain and restore intestinal balance. These strategies should be tailored through a customized management approach that accounts for both physiological characteristics and environmental influences. Strategies to maintain a balanced gut microbiome include providing a diet optimized for the canine’s growth stage, ensuring appropriate levels of protein, fiber, and carbohydrates [23,24,25]. The incorporation of probiotics and prebiotics into the diet is also essential, as they promote the growth of beneficial bacteria and help sustain eubiosis within the gastrointestinal tract [26, 27]. Additionally, restoring beneficial microbial populations following antibiotic use, minimizing exposure to stressors, and ensuring a stable external environment are effective methods for maintaining microbiome balance [28,29,30].

In conclusion, a comprehensive understanding of the diversity and function of the canine gut microbiome, as well as the intrinsic and extrinsic factors that influence and support its maintenance, is crucial for improving canine health and well-being. In this review, we explored the structure and function of the canine gut microbiome, with particular emphasis on its role in health and the key factors that influence and support its maintenance.

The canine gut microbiome is composed of a diverse array of bacterial strains. In healthy canines, the dominant bacterial phyla including Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria, and Proteobacteria contribute to a complex and dynamic gut ecosystem [3,4,5,6]. However, the composition of the gut microbiome can vary depending on the location within the gastrointestinal tract (GIT), as each section presents unique environmental conditions, such as oxygen tension, nutrient availability, and pH levels. These factors lead to variations in microbial distribution [31, 32].

Microbial composition in different sections of the GIT

In the duodenum, the phyla Firmicutes (46.4%), Proteobacteria (26.6%), and Fusobacteria (3.3%–3.6%) are present in relatively high proportions [5]. At the genus level, Helicobacter (29.27%), Lactococcus (7.12%), and Allobaculum (6.96%) are predominant [33,34,35,36] (Fig. 1A). In the jejunum, the dominant phyla include Proteobacteria (46.7%), Spirochaetes (14.2%), and Fusobacteria (5.4%) [37], with Helicobacter (13.17%), Lactobacillus (10.24%), and Actinomyces (8.05%) identified as the dominant genera [33, 36] (Fig. 1B). In the ileum, Firmicutes (59.32%), Tenericutes (15.96%), and Proteobacteria (13.9%) are the predominant phyla, while Mycoplasma (15.95%), Lactobacillus (12.08%), and Candidatus Arthromitus (10.16%) are the most abundant genera [33] (Fig. 1C).

Composition of the canine gut microbiome. (A) Microbial compositions at phylum and genus levels in the duodenum. (B) Microbial compositions at phylum and genus levels in the jejunum. (C) Microbial compositions at phylum and genus levels in the ileum. (D) Microbial compositions at phylum and genus levels in the colon. (The figure was created using freely available images from Freepik: https://www.freepik.com/)

Fecal 16S rRNA gene analysis has shown that the canine distal gut microbiome is primarily composed of Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria, and Proteobacteria [8, 38] (Fig. 1D). Among these, Firmicutes is the most abundant, typically comprising 15.81%–44.8% of the total gut microbiome [38,39,40], with some studies reporting levels as high as 75% [8]. Bacteroidetes is the second most dominant phylum, accounting for approximately 30%–36.75% of the total gut microbiome. This group includes beneficial genera such as Bacteroides and Prevotella, which play essential roles in carbohydrate metabolism and gut health [8, 38, 39]. Actinobacteria makes up 0.33%–3.4% of the gut microbiome and includes Bifidobacterium, a genus known for supporting digestion and enhancing immune function [8, 38].

Roles of major bacterial phyla and key genera in the canine gut microbiome

Firmicutes, Bacteroidetes, and Actinobacteria include beneficial bacteria that play critical roles in digestion and immune function. These bacteria are involved in the breakdown of dietary fiber and carbohydrates, leading to the production of short-chain fatty acids (SCFAs). SCFAs contribute to host energy metabolism, lower pH to inhibit pathogens, and protect the intestinal mucosa to enhance immune responses [3, 41]. Fusobacteria, though less common in other animal species, is frequently found in the canine gut, with reported abundance levels ranging from 8.64% to 39.17% [8, 39, 42]. Although Fusobacterium species are part of the normal microbiota in dogs, certain species, such as Fusobacterium nucleatum, can exacerbate gut inflammation and contribute to intestinal diseases [43, 44]. Proteobacteria, which comprise 5%–15.26% of the canine gut microbiome, includes pathogenic bacteria such as Escherichia coli (E. coli), which produce toxins that promote inflammation [8, 36, 42, 45]. While Fusobacteria and Proteobacteria are less abundant than other phyla, they play crucial roles in maintaining gut balance. However, their overgrowth is often indicative of dysbiosis and has been linked to gut-related disorders, such as inflammatory bowel disease (IBD).

At the genus level, the canine distal gut microbiome is dominated by Fusobacterium, Prevotella, Blautia, Bacteroides, and Clostridium, each of which plays a distinct functional role in gut health [40, 46,47,48,49,50,51,52] (Fig. 1D and Table 1).

Fusobacterium belongs to the Fusobacteria phylum and plays a role in protein degradation and amino acid fermentation, producing butyrate, which supports protein metabolism and inflammation regulation [60]. It is typically found at levels ranging from 7% to 14.3%, with some studies reporting levels as high as 30.52%–49.20%, particularly in response to protein-rich diets and environmental factors [40, 46, 49, 50, 52]. Prevotella belongs to the Bacteroidetes phylum and is involved in carbohydrate and fiber degradation, contributing to energy metabolism through SCFAs production [61]. Its abundance in the canine gut typically ranges from 4% to 9.6%, though some studies have reported levels as high as 28.10% due to dietary and environmental variations [47, 49, 50, 62]. Blautia belongs to the Firmicutes phylum and is known for producing SCFAs, particularly acetate, which helps regulate gut pH, inhibits pathogen growth, and serves as an energy source for intestinal epithelial cells [55]. It is typically detected in the canine gut at levels ranging from 6.87% to 15% [48,49,50]. Bacteroides, a genus within the Bacteroidetes phylum, plays a key role in fiber and polysaccharide degradation, producing SCFAs that provide energy and contribute to immune regulation [58]. Its abundance in the canine gut ranges from 2% to 14.63% [47, 49, 50, 52, 63]. Clostridium belongs to the Firmicutes phylum and is known to produce butyrate which helps protect the intestinal lining and regulate immune responses [56]. It is typically found in the canine gut at levels between 12.69% and 33.7% [49,50,51,52, 64]. However, certain pathogenic species, such as Clostridium perfringens (C. perfringens), can produce toxins that can lead to acute diarrhea and gut inflammation [51, 56].

Overall, the canine gut microbiome consists of a diverse and dynamic microbial community that varies across different sections of the GIT due to unique environmental conditions. While phyla such as Firmicutes, Bacteroidetes, and Actinobacteria play essential roles in digestion, immune regulation, and metabolic function, the presence of Fusobacteria and Proteobacteria must be carefully regulated to maintain gut health. Understanding the distribution and functional roles of microbial communities in the canine gut is crucial for developing targeted strategies to maintain gut microbiome balance and support overall health and canine well-being.

The balance of the gut microbiota in canines can be influenced by various factors, including diet, antibiotics, stress, and environmental conditions [15, 23, 25, 28, 29, 53, 65,66,67,68,69,70,71] (Fig. 2).

Factors influencing the gut microbiome in canines. (The figure was created using freely available images from Freepik: https://www.freepik.com/)

Physiological factors such as age and body size significantly affect the composition and diversity of the gut microbiota, playing a crucial role in canine health and metabolic functions throughout different life stages [53, 67, 68]. Diet composition is another major determinant, as variations in protein, fiber, and carbohydrate intake can substantially alter the gut microbial communities [23, 25, 65]. Additionally, antibiotics and stress can disrupt gut homeostasis by decreasing the abundance of beneficial bacteria and promoting microbial imbalances, potentially leading to digestive and immune-related disorders [15, 28,29,30, 69]. Environmental factors, including living conditions and hygiene levels, also influence gut microbiota diversity [70, 71]. Canines exposed to more diverse microbial environments tend to develop distinct microbial profiles [70, 71]. Understanding the correlation between these factors and the gut microbiota is essential for maintaining microbial balance. Based on this knowledge, targeted strategies, such as probiotic supplementation, dietary modifications, and stress management, can be implemented to help maintain a balanced gut microbiome and support optimal gut health in canines.

Influence of physiological factors on the canine gut microbiome

The composition and balance of the gut microbiome in canines are significantly influenced by physiological factors such as age and body size, all of which play a crucial role in maintaining overall health and supporting metabolic functions throughout a canine’s life cycle [42, 53, 67, 68, 72, 73].

As canines age, their gut microbiome stabilizes and matures [74,75,76,77]. During the early developmental stage, bacterial diversity gradually increases, reaching an optimal balance in adulthood. However, microbial diversity tends to decline in the senior stage, potentially leading to impaired digestive function and weakened immunity [75, 76]. During the puppy stage, nutrients and lactic acid bacteria from breast milk contribute to higher proportions of Firmicutes, Bacteroidetes, and Actinobacteria, which are essential for enhancing digestive function and immune system development during this period [78]. In contrast, older canines tend to exhibit a reduction in Firmicutes and an increase in Proteobacteria [76, 79]. These microbial shifts are associated with reduced digestive efficiency and immune function, creating conditions that favor the growth of pathogenic bacteria and potentially exacerbating gut microbiome dysbiosis [76, 79, 80].

Body size affects the capacity and retention time of the digestive system, altering the gut environment, such as pH levels, which in turn impacts the composition of the intestinal microbial community [73]. Large canines have longer and more voluminous digestive tracts, allowing food to remain in the gut for a longer duration, thereby enhancing digestion and fermentation [53]. This prolonged retention increases the production of SCFAs, which lower gut pH and inhibit the growth of acid-sensitive pathogenic microbes [73, 81]. According to a study by Deschamps et al. [53], large canines have a higher proportion of Firmicutes and a lower proportion of Proteobacteria compared to small canines. This difference is attributed to the more acidic environment created by intestinal fermentation in large canines, which suppresses the growth of Proteobacteria.

In contrast, small canines have relatively shorter intestines, creating a gut environment where the intestinal pH remains closer to neutral. This condition favors the proliferation of microbiota such as Proteobacteria [53, 81]. A high proportion of Proteobacteria is closely associated with gut microbiota dysbiosis, which may negatively affect gut health [8, 42, 67].

Overall, the composition and relative abundance of the gut microbiome in canines vary significantly based on physiological factors, such as age and body size. To maintain a balanced gut microbiome, it is essential to consider these unique characteristics.

Host genetics

The composition and balance of the canine gut microbiome are influenced by host genetic factors, with breed serving as a key indicator of genetic variation [82,83,84,85].

Reddy et al. [82] reported breed-dependent differences in gut microbial composition among small breeds such as Maltese, Poodle, and Miniature Schnauzer. Notably, Maltese dogs exhibited a significantly lower relative abundance of Firmicutes and a higher proportion of Fusobacteria compared to the other breeds. Similarly, Hu et al. [85] examined large breeds including Chinese Kunming Canine, German Shepherd, and Belgian Malinois, and observed marked differences in microbial composition at both the phylum and genus levels, despite identical environmental and dietary conditions. These findings underscore the significant role of host genetics in shaping gut microbiota across both small and large breeds. In another study by Li et al. [83], compared the gut microbiome of three working breeds including German Shepherd, Labrador Retriever, and Springer Spaniel, and found that German Shepherd exhibited significantly higher alpha diversity than the other breeds as measured by the Chao1 and Shannon indices (P < 0.05). These suggest that both compositional and diversity-related differences in the canine gut microbiome may be attributed to breed-specific genetic backgrounds [82, 83, 85].

Melis et al. [84] further emphasized the influence of genetic diversity on microbial balance. In the highly inbred Norwegian Lundehunds, the gut microbiome was characterized by dysbiosis with an elevated Firmicutes/Bacteroidetes ratio and overgrowth of Streptococcus bovis/equinus. In contrast, F1 and F2 crossbred generations displayed a more balanced microbiome composition, marked by a lower Firmicutes/Bacteroidetes ratio and increased abundance of health-associated genera such as Blautia and Fusobacterium. These findings suggest that increased host genetic diversity, achieved through crossbreeding, may promote a more stable and health-associated gut microbiome.

In summary, breed-specific genetic traits significantly influence the composition and diversity of the canine gut microbiome. However, comprehensive studies across a wider range of breeds are needed to fully elucidate the genetic determinants of microbiome variation in dogs.

Diet

Among the various factors influencing the gut microbiome of canines, diet has the most consistent and significant impact throughout their lifetime. The type, form, and composition of a diet can either promote or suppress the growth of specific gut microbiota. Differences in microbiome composition associated with diet are largely attributable to variations in nutrient content, particularly the proportions of protein and carbohydrates, which play a major role in shaping the gut microbiome [23, 63].

Previous studies have demonstrated how the relative proportions of protein, carbohydrates, and fiber influence gut microbial communities [86, 87]. According to a study by Kim et al. [88], canines fed a raw meat diet exhibited increased gut microbial diversity and notable shifts in Fusobacteria abundance at the phylum level. Similarly, other studies have observed that canines fed raw meat-based diets showed increased proportions of Fusobacteria and Clostridium, along with decreased proportions of Firmicutes and Bacteroidetes [25, 89]. These findings align with a study by Sandri et al. [65], which found that canines consuming a high-protein diet had an increased proportion of bacteria belonging to the Fusobacteriaceae family.

In contrast, a study by Lewis et al. [23] reported that canines fed a low-protein, high-carbohydrate diet exhibited an increased proportion of bacteria associated with SCFAs production, including Prevotella copri, which is involved in carbohydrate fermentation. Similar changes in intestinal microflora were observed in canines that consumed prebiotics such as inulin and fructooligosaccharides. A review by Pilla and Suchodolski [24] further supported that a diet including prebiotics promotes SCFAs production and increases the proportion of beneficial bacteria such as Bifidobacterium and Faecalibacterium.

Additionally, a study by Panasevich et al. [86] found that a diet containing potato fiber may have a prebiotic effect and contribute to improving the intestinal environment of companion canines. As the concentration of potato fiber increased, the proportion of Firmicutes increased, while the proportion of Fusobacteria decreased, suggesting that the inclusion of potato fiber can influence gut microbiota composition.

Collectively, these findings emphasize the crucial role of diet in maintaining and improving gut microbiome balance in canines.

Antibiotics

Unlike physiological factors or diet, which consistently influence the gut microbiota throughout a canine's life, antibiotics have a temporary but significant impact on the gut microbial community [15, 28, 69, 90].

While antibiotics are primarily used to suppress specific pathogenic bacteria, their excessive or prolonged use can disrupt microbial balance by indiscriminately eliminating beneficial bacterial populations, leading to dysbiosis [28, 45, 91,92,93,94]. For instance, antibiotics such as metronidazole may reduce the populations of certain microbial groups while increasing the relative abundance of E. coli, which can exacerbate intestinal inflammation [15].

A study by Whittemore et al. [28] demonstrated significant alterations in the canine gut microbiome following the administration of enrofloxacin and metronidazole, as assessed by 16S rRNA gene sequencing. All dogs received antibiotics for 21 d, followed by either a placebo or a synbiotic supplement. After antibiotic treatment, the abundance of Clostridium hiranonis (C. hiranonis), Faecalibacterium, and Turicibacter markedly decreased, leading to severe microbiome disruption. In the placebo group, microbial composition did not recover even after 56 days, resulting in prolonged gut dysbiosis. In contrast, partial restoration of beneficial bacteria was observed in the synbiotic group. Additionally, a decrease in alpha diversity indicated reduced microbial richness, while beta diversity analysis revealed significant differences in microbiome composition between the groups. Metabolomic analysis also showed distinct alterations in SCFAs, bile acids, and tryptophan metabolites [70]. These findings highlight the negative impact of prolonged antibiotic use on gut microbial diversity while suggesting the potential benefits of synbiotics in promoting microbiome recovery.

Similarly, research by Pilla et al. [15] demonstrated that metronidazole significantly reduced both the diversity and abundance of the canine gut microbiota. Specifically, bacteria associated with SCFAs production, anti-inflammatory activity, and immune regulation, such as Fusobacteria, Faecalibacterium, and C. hiranonis, declined substantially [15, 95].

A study by Marshell-Jones et al. [69] further investigated the impact of metronidazole on the canine gut microbiome, noting that while some beneficial bacteria increased post-treatment, overall microbial diversity decreased. This reduction in diversity was accompanied by an increase in antibiotic-resistant genera such as Lactobacillus, Bifidobacterium, and Enterococcus, while beneficial carbohydrate-fermenting bacteria, such as members of the Erysipelotrichaceae family, declined. Notably, gut dysbiosis persisted for 4–6 weeks after discontinuation of the antibiotic, demonstrating its prolonged effects on digestive and immune functions.

Tylosin, a macrolide antibiotic commonly used to treat chronic intermittent diarrhea and other gastrointestinal disorders in canines, has also been shown to reduce gut microbial diversity and alter the relative abundance of specific microbial taxa. Following tylosin administration, an increase in the proportion of Firmicutes and a corresponding decrease in Bacteroidetes have been observed, leading to microbiome imbalance. Additionally, tylosin has been associated with an increase in Enterococcus and Clostridium species. These alterations in the gut microbiome may also influence metabolic processes by modifying the gut metabolite profile, potentially affecting digestion and immune function [90].

In summary, antibiotic use can have profound and often adverse effects on gut microbiome balance, diversity, and associated metabolic processes. Careful antibiotic use, combined with strategies such as synbiotic supplementation, is crucial for mitigating these adverse effects and supporting the recovery of the gut ecosystem.

Stress

Stress is a significant factor that influences the gut microbiome in companion canines. Unlike more consistent factors such as diet, which have long-term effects, stress can exert both acute and chronic impacts on the gut microbiome, depending on the nature, intensity, and duration of the stressor [29, 30, 96,97,98]. Acute stressors, such as environmental changes or alterations in routine, can temporarily disrupt gut microbiota composition. In contrast, chronic stress has been associated with more sustained alterations, potentially leading to dysbiosis and negatively affecting overall health [29, 97, 98].

Previous studies have shown that stress hormones like cortisol and norepinephrine can increase the virulence of certain pathogenic bacteria, such as Salmonella enterica, by up to tenfold [30, 96]. Excessive cortisol secretion contributes to reduced populations of beneficial bacteria, increased intestinal permeability, and overgrowth of pathogenic microbes, which can have adverse effects on canine health. Additionally, a study by Sacoor et al. [29] demonstrated that stress negatively impacts gut barrier integrity, triggering inflammatory responses and highlighting critical interactions between gut microbiota and immune responses in mental health issues such as anxiety disorders.

Recent studies have further demonstrated that stress significantly influences gut microbiota composition in canines, leading to measurable changes in microbial diversity [29, 30, 97, 98].

According to Mondo et al. [30], stressed canines exhibited a significant increase in Proteobacteria (P < 0.001) and a decrease in Clostridia (P = 0.008) compared to non-stressed controls, patterns that are often associated with dysbiosis and inflammatory responses. Furthermore, the abundance of Bacteroidaceae was significantly higher in stressed canines (P < 0.02) compared to the non-stressed group, suggesting a microbial imbalance caused by stress exposure.

Additionally, microbial diversity analyses revealed that α-diversity was significantly reduced in the stressed group compared to non-stressed canines (P < 0.05), indicating decreased microbial richness and evenness. In contrast, β-diversity analysis confirmed distinct microbial community structures between stressed and non-stressed canines (P < 0.01), further supporting the impact of stress on gut microbiome composition [30]. These findings suggest that stressed canines may struggle to maintain microbial diversity, fostering an environment where specific pathogenic microbes dominate [29, 30, 96,97,98,99].

Collectively, these findings emphasize the importance of stress management in maintaining the balance of the intestinal microbial community in companion canines, highlighting the need for interventions to mitigate stress-related gut dysbiosis and its associated health consequences.

Rearing environment

The environment in which companion canines are raised significantly influences the diversity of their gut microbiome [70, 71, 100]. A study by Vilson et al. [70] compared the gut microbial diversity of puppies raised in metropolitan, small-town, and rural environments. The results revealed that puppies raised in metropolitan areas exhibited higher microbial diversity (Shannon diversity index: 3.36 ± 0.63) compared to those raised in rural (2.91 ± 0.83) or small-town environments (2.95 ± 0.81). This suggests that diverse environmental stimuli in urban settings play a crucial role in gut microbiome development. Notably, the Shannon diversity index of urban puppies was 15%–20% higher than that of puppies raised in other environments, potentially due to greater exposure to a wider range of microbial sources. These findings emphasize the need to consider environmental factors when aiming to maintain gut microbiome balance in companion canines [100, 101].

In a study by Tanprasertsuk et al. [71], significant differences in the canine gut microbiota composition were observed between groups with different housing conditions. In household environments, Proteobacteria were identified as the most abundant phylum, while Firmicutes dominated in private kennel settings, and Actinobacteria were prevalent in controlled research environments. The study also employed α-diversity and β-diversity indices to measure microbial diversity. Canines raised in private kennels exhibited significantly higher microbial diversity compared to those raised in household environments, while canines in controlled research environments showed greater α-diversity than household-raised canines. Furthermore, β-diversity analysis revealed significant structural differences in the gut microbiome among the three groups, underscoring the importance of rearing environments in maintaining gut microbiome balance [71].

However, Tanprasertsuk et al. [71] noted that dietary differences among the groups might have contributed to the observed microbiome changes. Therefore, it cannot be conclusively determined that these differences were solely due to environmental factors [24, 87, 102]. Further studies that control for diet and other confounding variables are necessary to isolate the specific impact of environmental factors on the gut microbiome [71].

In conclusion, the balance of the gut microbiome in companion canines is significantly influenced by rearing environments. A tailored approach that considers rearing environments is essential for maintaining and improving canine health. Continuous monitoring and management of environmental conditions are particularly important for sustaining gut microbiome equilibrium.

The gut microbiome of canines plays a vital role in overall health, influencing key physiological functions such as digestion, immune responses, and behavioral temperament [66, 103] (Fig. 3).

The relationship between physiological functions and the gut microbiome in canines. (The figure was created using freely available images from Freepik: https://www.freepik.com/)

Specifically, maintaining gut eubiosis is essential for inhibiting the growth of pathogenic microorganisms and regulating immune responses, thereby positively impacting overall canine health [3, 75, 86, 104]. For example, a balanced gut microbiome supports emotional stability and stress resilience by modulating the gut-brain axis, while also enhancing nutrient absorption and energy utilization [29, 96]. Therefore, understanding the gut microbiome can contribute to improving physiological functions, behavioral regulation, and the prevention and management of disease in companion canines [45]. This highlights the importance of maintaining gut eubiosis through targeted interventions such as probiotics, prebiotics, and dietary adjustments, all of which play a crucial role in enhancing the overall health and quality of life of canines.

Weight management and gut microbiome

Maintaining a balanced gut microbiome is essential for canine weight management, as microbial composition influences metabolic processes, energy regulation, and nutrient absorption. Imbalances in the gut microbiota can lead to weight fluctuations, whereas a well-maintained microbiome supports healthier weight control [3, 9, 41, 105].

According to a previous study, obese canines showed an increased proportion of Firmicutes and a decreased proportion of Bacteroidetes compared to non-obese individuals [105]. This trend has been consistently observed in subsequent study, with a higher Firmicutes/Bacteroidetes ratio detected in obese canines, suggesting a potential link between gut microbial composition and energy extraction efficiency [106].

This association suggests that weight gain in canines may be linked to changes in microbial-mediated energy efficiency. The Firmicutes phylum is known to produce metabolites such as SCFAs during intestinal metabolism, which plays a crucial role in digestion and overall host health [3, 53, 54]. For instance, species such as Lactobacillus acidophilus, Clostridium butyricum, and Oscillibacter within Firmicutes produce lactic acid, which promotes intestinal health by lowering luminal pH, inhibiting pathogen overgrowth, and encouraging the proliferation of beneficial bacteria [104, 107,108,109]. Furthermore, SCFAs serve as a direct energy source for intestinal cells, enhancing nutrient utilization and overall energy extraction from the diet [107, 110].

However, excessive SCFAs production can lead to an energy surplus, contributing to increased body fat accumulation [9, 111]. This aligns with findings that a higher proportion of Firmicutes is often associated with weight gain due to enhanced energy extraction from the diet [3, 9, 41, 112,113,114,115,116,117]. In contrast, Bacteroidetes are less efficient at extracting energy from food than Firmicutes, which explains why a higher proportion of Bacteroidetes is less correlated with weight gain [9, 112]. Therefore, effective weight management in canines requires maintaining the composition and balance of the gut microbiome. The use of probiotics may aid in this process by promoting gut health and supporting a balanced microbiome [3, 15, 80].

However, the association between the Firmicutes-to-Bacteroidetes ratio and obesity is not always consistent across animal species. For example, while obese companion dogs tend to exhibit an increased Firmicutes/Bacteroidetes ratio, the opposite trend has been reported in companion cats, where obesity is associated with a significantly lower Firmicutes/Bacteroidetes ratio. These contrasting results suggest that the relationship between the Firmicutes/Bacteroidetes ratio and obesity may vary by species and does not necessarily follow a universal pattern [118].

Among probiotic strains, Lacticaseibacillus rhamnosus (L. rhamnosus) GG has demonstrated significant potential for weight management. According to a study by Kim et al. [119], L. rhamnosus GG increased adiponectin secretion, thereby activating the adenosine monophosphate-activated protein kinase (AMPK) pathway. This activation suppressed weight gain and liver fat accumulation in obese animal, suggesting its potential as a therapeutic agent for preventing metabolic syndrome [119]. Similarly, Zhang et al. [120] demonstrated that the culture supernatant of L. rhamnosus GG reduced hepatic fat accumulation by enhancing AMPK activation, suppressing lipid synthesis-related gene expression, and promoting fatty acid β-oxidation. These findings suggest that probiotics with similar properties to L. rhamnosus GG may contribute to weight management and metabolic health in canines by modulating gut microbiome composition and function. Therefore, restoring gut microbiome balance through probiotic interventions holds promises for supporting healthy weight management in canines.

Disease and gut microbiome

Inflammatory bowel disease (IBD)

IBD is a chronic inflammatory condition of the GIT that is closely associated with gut microbiome imbalance [4, 11, 19, 44, 121,122,123].

Previous studies have reported that the small intestinal microbiome of canines with IBD differs significantly from that of healthy canines, as revealed by β-diversity analysis. Canines with IBD exhibit significantly lower species richness, indicating reduced gut microbiome diversity [5, 11]. Dysbiosis in the gut microbiome of canines with IBD can lead to a reduction in metabolic products such as SCFAs resulting in a weakened protective function of the intestinal mucosa and an increase in intestinal pH, which promotes the proliferation of pathogenic bacteria. The microbial imbalance contributes to a self-perpetuating cycle that impairs metabolic homeostasis and immune responses, promoting the chronic progression and exacerbation of IBD [123].

In particular, studies have shown that the gut microbiome of canines with IBD was characterized by a marked decrease in the phyla Firmicutes and Bacteroidetes and an increase in Proteobacteria compared to healthy canines. These shifts were often associated with the overgrowth of pathogenic bacteria such as E. coli [11, 121, 122]. This microbial imbalance caused by pathogenic bacteria damages intestinal epithelial cells, allowing bacterial metabolites and toxins to enter the bloodstream through a weakened intestinal barrier. This process triggers excessive immune responses, further contributing to the chronic progression and persistence of IBD [4, 19].

To address these issues, therapeutic strategies such as fecal microbiota transplantation (FMT) and probiotic administration have been explored [44, 124]. FMT involves the transplantation of gut microbiota from a healthy canine into a canine with IBD [124], and has been reported to restore gut microbiome balance, reduce gut inflammation, and improve clinical symptoms [44]. Therefore, restoring gut microbiome balance through targeted interventions could serve as a fundamental approach to improving symptoms and managing IBD in canines.

Diabetes

Diabetes mellitus in canines is a chronic endocrine disorder characterized by insufficient insulin production and is closely associated with gut microbiome imbalances [12, 125,126,127,128]. Previous studies have indicated that gut dysbiosis exacerbates both local and systemic inflammation, thereby exacerbating the progression of diabetes and its associated complications [12, 126,127,128].

For example, Jaffey et al. [125] found that diabetic canines exhibited a higher relative abundance of fungal species within the Candida genus compared to healthy canines. Similarly, research by Kwong et al. [126] showed an increase in Clostridioides difficile and Butyricicoccus pullicaecorum in diabetic canines, suggesting a link between metabolic dysregulation and microbial imbalance caused by the excessive proliferation of carbohydrate-dependent microbes. These findings align with previous studies investigating the gut microbiome of diabetic canines [127, 128]. On the contrary, Sharma et al. [12] reported that promoting the growth of beneficial bacteria and enhancing intestinal barrier function can help alleviate diabetes-related inflammation and improve overall health. These findings support the notion that restoring gut microbiome balance represents a promising therapeutic strategy for managing diabetes in canines and enhancing overall well-being.

Chronic liver disease

Chronic liver disease in canines is closely linked to disruptions in gut microbiota balance [13, 129, 130]. Habermaass et al. [13] reported that canines with chronic liver disease exhibited a marked reduction in C. hiranonis and Ruminococcus faecis, both of which play a role in bile acid metabolism and SCFAs production. Conversely, the relative abundance of potentially pathogenic genera such as Escherichia, Shigella and Serratia was significantly elevated in these canines. In addition, research by Cerquetella et al. [130] demonstrated that such microbial imbalances can increase intestinal permeability, allowing bacterial metabolites and endotoxins to enter the bloodstream and reach the liver, which may contribute to hepatic inflammation and liver dysfunction.

To mitigate these adverse effects, synbiotic supplementation, combining probiotics and prebiotics, has emerged as a promising intervention for canines with chronic liver disease [129, 131]. According to Habermaass et al. [131], synbiotics promoted the growth of beneficial bacteria while suppressing harmful microbial populations, thereby restoring microbial balance. This microbial modulation was associated with reduction in serum alanine aminotransferase and improvement in liver function. Additionally, Giuffrè et al. [129] suggested that synbiotics helped stabilize bile acid metabolism and enhanced the antimicrobial environment within the gut, offering further protection for hepatic function. Collectively, these findings underscore the importance of maintaining gut microbiota balance in the management of chronic liver disease and highlight the therapeutic potential of microbiome targeted interventions in improving liver health in canines [129, 131].

Skin diseases

Studies in humans have revealed a correlation between gut microbiota and skin health, highlighting the significance of the gut-skin axis in maintaining dermatological homeostasis [132,133,134]. As such, recent research in canines suggested that alterations in gut microbial composition may also influence skin health [132, 135], implying that the gut-skin axis may also play a significant role in canine skin health. Furthermore, recent study has highlighted the critical role of the gut microbiome in skin barrier function, reinforcing the strong connection between the gut and dermatologic health in companion canine [135].

For example, a study involving Finnish Lapphunds and Labrador Retrievers found that healthy canines exhibited a higher abundance of Prevotella, Lachnospiraceae, and Fusobacterium, whereas canines with atopic dermatitis showed reduced microbial diversity and richness, along with increased levels of Escherichia and Shigella [14]. Additionally, Thomsen et al. [136] demonstrated that Fusobacterium (20.6%) and Megamonas (18.4%) were abundant in healthy canines. However, these microbial groups in canines with atopic dermatitis were significantly reduced to 0.06% and 0.0003%, respectively. In contrast, Escherichia, Shigella and Clostridium were notably increased in canines with atopic dermatitis. These findings suggest that atopic dermatitis is associated with the overgrowth of proinflammatory gut bacteria and a significant reduction in beneficial microbial species [137].

L. rhamnosus has been shown to play a key role in modulating immune responses and reducing inflammation by suppressing the production of inflammatory cytokines. In chronic inflammatory diseases such as atopic dermatitis, L. rhamnosus activates immune cells to regulate immunoglobulin E (IgE) levels and modulates T-helper cell type 2 (Th-2) immune responses through interleukin-10 (IL-10), leading to a reduction in inflammation [135]. This process not only alleviates skin inflammation but also strengthens the skin barrier, enhancing resistance to external irritants.

These findings underscore the importance of gut microbiome balance in immune modulation and skin health. Restoring a healthy gut microbial composition may serve as an effective strategy to alleviate chronic inflammatory skin disorders such as atopic dermatitis and to support overall dermatological well-being of companion canines.

Behavior/Temperament and gut microbiome

The gut microbiome can influence canine behavior and temperament through the gut-brain axis [14, 29, 103, 138]. According to Mondo et al. [66], aggressive canines exhibited a higher relative abundance of Catenibacterium and Megamonas compared to non-aggressive counterparts, indicating a potential gut microbiota imbalance. This dysbiosis may disrupt hormonal signaling and neural communication through the gut-brain axis, potentially exacerbating stress responses and impulsive behaviors. Similarly, Beerda et al. [139] found that gut microbiota imbalance was associated with systemic inflammation, leading to elevated cortisol levels and increased production of pro-inflammatory cytokines. These changes impair stress-regulating mechanisms and may heighten stress sensitivity and aggressive tendencies in canines. These findings suggest that gut microbiome balance plays a crucial role in behavioral regulation, stress responses, and overall temperament in canines.

Moreover, a reduction in beneficial bacteria such as Lactobacillus has been shown to disrupt the regulation of neurotransmitters including gamma-aminobutyric acid (GABA) and serotonin, both of which are critical for maintaining emotional stability and nervous system homeostasis [138]. The disruption in GABA expression reduces the brain's ability to mitigate stress responses, further intensifying behaviors linked to anxiety and impulsivity [66, 103].

To address these issues, the use of beneficial bacteria has been suggested as an effective intervention. For instance, L. rhamnosus has been reported to improve the gut microbial environment and alleviate stress responses [29, 137]. Studies have shown that L. rhamnosus lowered circulating cortisol levels, a key stress hormone, thereby reducing anxiety and stress responses [138, 140, 141]. These findings suggest that beneficial bacteria such as L. rhamnosus may contribute to neurological stability in canines.

In support of this, Hsiao et al. [103] emphasized the role of gut microbiome balance in stabilizing the nervous system, reducing anxiety, and promoting positive behavioral changes. Similarly, several studies suggested that stabilizing and maintaining gut microbiome balance can reduce stress and anxiety responses, ultimately leading to improved behavior and more stable temperament in canines [29, 137, 138]. Above all, maintaining a balanced gut microbiome is essential for regulating the gut-brain axis and enhancing nervous system function [29, 137].

The gut microbiome of companion canines plays a crucial role in their overall health, and maintaining its balance can be achieved through various strategies (Fig. 4).

Strategies for maintaining a balanced gut microbiome in canine. (The figure was created using freely available images from Freepik: https://www.freepik.com/)

Approaches to promoting gut microbiome health include dietary adjustments, probiotic and prebiotic supplementation, appropriate medication, antioxidant use, and lifestyle modifications [15, 67, 142]. Among these strategies, probiotics are widely used to correct dysbiosis by promoting the growth of beneficial bacteria, while prebiotics serve as a nutrient source for beneficial microbes, contributing to gut microbiome homeostasis [15, 27, 143].

Probiotics are live microorganisms that, when consumed in sufficient amounts, provide health benefits to the host [144]. They enhance gut microbiota balance by promoting beneficial bacteria, inhibiting pathogenic microorganisms, and improving overall gut health. Commonly used strains such as Lactobacillus spp. and Bifidobacterium spp. have demonstrated beneficial effects on canine health [109, 142]. For example, L. rhamnosus has been shown to regulate immune responses and reduce inflammation by suppressing the production of proinflammatory cytokines. In chronic inflammatory diseases such as atopic dermatitis, L. rhamnosus activates immune cells, regulates IgE levels, and modulates Th-2 immune responses through IL-10, thereby reducing inflammatory reactions. This process alleviates skin inflammation, strengthens the skin barrier, and enhances resistance to external irritants [145].

The benefits of probiotics can be further enhanced when combined with prebiotics. Prebiotics are indigestible dietary components that promote the growth of beneficial bacteria while inhibiting harmful microbes [27, 146, 147]. For instance, chicory-derived oligosaccharides have been shown to increase the Bifidobacterium abundance while reducing C. perfringens, thereby contributing to gut microbial balance [148].

Dietary composition significantly influences gut microbiota. High-protein and high-carbohydrate diets differentially influence microbial profiles, with high-protein diets shown to increase fecal pH and alter fatty acid concentrations [27, 63, 142]. Studies also indicate that natural diets foster greater gut microbiome diversity than commercial diets [7]. Additionally, antioxidant supplementation, such as bromelain, quercetin, and lentinula edodes, has been shown to increase the proportions of Bifidobacterium and Lactobacillaceae, promoting microbial balance and reducing inflammation [7].

Certain medications can positively influence the gut microbiome [136, 149]. For example, oclacitinib, a Janus kinase inhibitor used in canine atopic dermatitis reduces inflammation by inhibiting cytokine signaling. It has also been shown to increase the abundance of Fusobacterium while decreasing the prevalence of inflammatory microbes such as Escherichia, Shigella and Clostridium in canines with atopic dermatitis [136]. However, while antibiotics are effective in eliminating pathogenic microorganisms, they can also disrupt the gut microbiome by depleting beneficial bacteria. Therefore, supplementing with probiotics following antibiotic treatment is crucial to restoring microbial balance and preventing dysbiosis [148].

FMT has emerged as a promising intervention for restoring gut microbiome diversity and suppressing the overgrowth of harmful microorganisms [44, 150]. This technique involves transplanting fecal microbiota from a healthy donor into a canine with gut dysbiosis. Research suggests that FMT is particularly effective for conditions such as IBD, metabolic disorders, and chronic diarrhea, which are difficult to manage with conventional treatments [150]. By reintroducing a diverse microbial community, FMT helps regulate host metabolism and immune functions, restoring gut microbiome balance.

In summary, maintaining gut microbiome balance in companion canines involves a multifaceted approach, including probiotic and prebiotic supplementation to promote the growth of beneficial bacteria, antioxidant supplementation to support microbial stability, dietary adjustments tailored to the canine’s health needs, and stress reduction to support gut health. Implementing these strategies helps preserve microbial homeostasis, thereby improving overall health, immune regulation, and well-being in companion canines.

This review highlights the connection between the canine gut microbiome and various aspects of overall health, including digestion, metabolism, immune regulation, behavior, temperament, and skin health. The canine gut microbiome consists of a diverse array of bacterial strains that form a complex ecosystem interacting closely with the host to maintain health and physiological homeostasis. However, the canine gut microbiome can be influenced by multiple factors, such as age, physiology, living environment, diet, antibiotic use, stress, and host genetics. If these factors are not properly managed, microbial imbalance (dysbiosis) may occur, potentially exacerbating health issues such as IBD, diabetes, dermatological disorders, and behavioral changes. Therefore, effective gut microbiome management is essential for optimizing physiological functions, ultimately enhancing the health and quality of life of companion canines. Strategies to promote gut microbiome health, such as dietary adjustments, administration of probiotics and prebiotics, appropriate medication, and lifestyle modifications are increasingly being implemented.

Overall, this review provides insights into the structure and function of the canine gut microbiome, emphasizing its role in health and the factors that influence its balance and maintenance.