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Dot plots showing Chao1 indices (A), Shannon indices (B), and operational taxonomic unit (OTU) richness (C) of microbiota detected in the urine samples, genital swabs, and rectal swabs, collected from 20 healthy female (F, n = 10) and male (M, n = 10) dogs; bar chart showing the number of OTUs detected in X out of 20 urine samples, overlaid with dots indicating the mean relative abundance of those OTUs, demonstrating the high sparsity of the urinary microbiota. *p<0.05, **p<0.01, ***p<0.001.
Source publication
The urinary bladder in healthy dogs has dogmatically been considered free of bacteria. This study used culture independent techniques to characterize the healthy canine urinary microbiota. Urine samples collected by antepubic cystocentesis from dogs without urinary infection were used for DNA extraction. Genital tract and rectal samples were collec...
Contexts in source publication
Context 1
... commonly used metrics of α-diversity were compared between groups, yielding slightly different results. Comparison of Chao1 indices, which preferentially weights the richness of a sample based on the numbers of singletons and double- tons (i.e., sequences detected only once or twice in a given sample, respectively), detected a sig- nificant main effect of sample site (p < 0.0001; F = 16.59), with rectal and genital swab samples harboring the greatest and lowest numbers of distinct sequences respectively (Fig 1A). No sig- nificant effect of sex on the Chao1 index was detected. ...
Context 2
... sig- nificant effect of sex on the Chao1 index was detected. Similarly, testing of the Shannon diver- sity index, a more traditional measure of α-diversity which places more weight on the evenness of taxa, revealed a main effect of sample site (p < 0.0001; F = 94.91), as well as a sig- nificant interaction (p = 0.0036; F = 6.27) between sample site and sex (Fig 1B). Similar to the Chao1 index, there was no main effect of sex on the Shannon diversity index. ...
Context 3
... to the Chao1 index, there was no main effect of sex on the Shannon diversity index. Despite the appreciably lower coverage of urine and genital swab samples reflecting the low biomass of those samples, the overall OTU richness (i.e., number of distinct OTUs detected) of urine sam- ples demonstrated a significant main effect of sample site (Fig 1C, p < 0.0001; F = 23.07), with urine samples harboring, on average, over 20 more OTUs than either of the other sample sites. Again, there was no main effect of sex on richness (p = 0.480; F = 0.51). ...
Context 4
... there was no main effect of sex on richness (p = 0.480; F = 0.51). Lastly, the microbial profile generated from urine samples represented extremely sparse datasets; that is, a high pro- portion of taxa were detected at very low relative abundance and in a limited number of indi- vidual urine samples (Fig 1D). ...
Citations
... Previously, microbiomes were considered as pathogens that lead to diseases [1]; however, it is now evident that they are an important part of the human and animal body, and play a crucial role in host physiology [2][3][4]. Recent advances in culture-independent DNAsequencing technology (i.e., 16S rRNA sequencing) and data analysis methods revealed that every part of a dog's body, such as the oral and nasal cavity [5,6], skin [7,8], and the gastrointestinal [9,10], respiratory [11][12][13], urinary [14], and reproductive [15][16][17] tracts, harbor certain types of microbiota. ...
Fecal microbiota transplantation (FMT) is an emerging therapeutic option for a variety of diseases, and is characterized as the transfer of fecal microorganisms from a healthy donor into the intestinal tract of a diseased recipient. In human clinics, FMT has been used for treating diseases for decades, with promising results. In recent years, veterinary specialists adapted FMT in canine patients; however, compared to humans, canine FMT is more inclined towards research purposes than practical applications in most cases, due to safety concerns. Therefore, in order to facilitate the application of fecal transplant therapy in dogs, in this paper, we review recent applications of FMT in canine clinical treatments, as well as possible mechanisms that are involved in the process of the therapeutic effect of FMT. More research is needed to explore more effective and safer approaches for conducting FMT in dogs.
... 9,10,18 In fact, a comprehensive analysis of the gut and urogenital microbiomes determined that the urogenital microbiome exhibited more pronounced alterations by urolith status than did the gut microbiome. 9 Microbial communities also recently have been identified in the urine of healthy dogs, [19][20][21] but the role of these microbes in CaOx formation in dogs is unknown. Discovery of urogenital microbiome features that discriminate dogs with CaOx urolithiasis from healthy dogs could provide insight into disease pathogenesis. ...
... Increased frequency and abundance of the genera Delftia and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium was observed in subtype 1, whereas subtype Taxonomic profiles in the study urine samples were dominated by members of the Proteobacteria phylum, which is consistent with previous findings in both dogs and cats. 19,20,60 In contrast, the genera ...
... Thus, whether true pathogenic species or strains were present remains unclear. However, this finding is consistent with previous reports in dogs [19][20][21] and highlights the complexity of defining infectious pathogens given emerging awareness of commensal urinary microbes. ...
Background:
Calcium oxalate (CaOx) uroliths are common in dogs. Humans with CaOx urolithiasis exhibit alterations of the urinary and urogenital microbiomes that might mediate urolith formation. Detection of urogenital microbes associated with CaOx in dogs could inform disease pathophysiology.
Objective:
To identify compositional differences in the urogenital microbiome of Miniature Schnauzers with and without CaOx uroliths.
Animals:
Nineteen midstream, voided urine samples from Miniature Schnauzers with (n = 9) and without (n = 10) a history of CaOx urolithiasis.
Methods:
Analytical cross-sectional study. Microbial DNA was extracted from previously frozen urine samples and sequenced for the bacterial 16S rRNA V3-V4 hypervariable regions. Diversity and composition of microbial populations were compared between urolith formers and controls.
Results:
Alpha and beta diversity measures were similar between groups. Five individual bacterial taxa differed in abundance (indicator values >0.5 and P < .05): Acinetobacter, 2 Geobacillus variants, and Hydrogenophaga were overrepresented in the urine of urolith formers, and Sphingopyxis was overrepresented in controls. Two distinct subtypes of urine microbial composition were observed based on beta diversity measures, independent of urolith status, and other clinical variables.
Conclusions and clinical importance:
Although we did not detect a difference in the overall urogenital microbial composition between groups, observed differences in individual bacterial taxa might be clinically relevant. For example, Acinetobacter was overrepresented in urolith formers and is associated with CaOx urolithiasis in humans. Two unique clusters of the microbiome were identified, independent of urolith status, which may represent distinct urotypes present in Miniature Schnauzers.
... Understanding the urinary microbiota of healthy individuals has been instrumental in contributing to our understanding of UT symptoms and disease in humans [see reviews (Whiteside et al., 2015;Neugent et al., 2020)]. More recently, microbiome studies have found bacteria within the UT of other healthy mammals, including canines (Burton et al., 2017) and swine (Torres Luque et al., 2020). Furthermore, through our prior efforts, we have isolated several different bacterial taxa from the UT of healthy cattle (Giannattasio-Ferraz et al., 2020a,b,c,d,e, 2021a. ...
The study of livestock microbiota has immediate benefits for animal health as well as mitigating food contamination and emerging pathogens. While prior research has indicated the gastrointestinal tract of cattle as the source for many zoonoses, including Shiga-toxin producing Escherichia coli and antibiotic resistant bacteria, the bovine urinary tract microbiota has yet to be thoroughly investigated. Here, we describe 5 E. coli and 4 Pseudomonas aeruginosa strains isolated from urine of dairy Gyr cattle. While both species are typically associated with urinary tract infections and mastitis, all of the animals sampled were healthy. The bovine urinary strains were compared to E. coli and P. aeruginosa isolates from other bovine samples as well as human urinary samples. While the bovine urinary E. coli isolates had genomic similarity to isolates from the gastrointestinal tract of cattle and other agricultural animals, the bovine urinary P. aeruginosa strains were most similar to human isolates suggesting niche adaptation rather than host adaptation. Examination of prophages harbored by these bovine isolates revealed similarity with prophages within distantly related E. coli and P. aeruginosa isolates from the human urinary tract. This suggests that related urinary phages may persist and/or be shared between mammals. Future studies of the bovine urinary microbiota are needed to ascertain if E. coli and P. aeruginosa are resident members of this niche and/or possible sources for emerging pathogens in humans.
... 55 Contrary to previously acknowledged, the urinary tract of healthy dogs harbors microorganisms, as reported in a study in which urine was collected by cystocentesis. 56 In that study, Proteobacteria was the dominant phyla, having genera Pseudomonas spp., Acinetobacter spp., and Sphingobium spp. relative abundances up to 80%, 5%, and 4.5% respectively. ...
... relative abundances up to 80%, 5%, and 4.5% respectively. 56 Genital swabs of both males and females had some similarity with urinary microbiota, and dominance of Pseudomonas spp. and Acinetobacter spp. was reported, as in urine. ...
... and Acinetobacter spp. was reported, as in urine. 56 The microbiota of the reproductive tract of male dogs is scarcely documented. In turn, the microbiota of females has been characterized in vaginal swabs and endometrial biopsy samples. ...
Microbiota and microbiome, which refers, respectively, to the microorganisms and conjoint of microorganisms and genes are known to live in symbiosis with hosts, being implicated in health and disease. The advancements and cost reduction associated with high-throughput sequencing techniques have allowed expanding the knowledge of microbial communities in several species, including dogs. Throughout their body, dogs harbor distinct microbial communities according to the location (e.g., skin, ear canal, conjunctiva, respiratory tract, genitourinary tract, gut), which have been a target of study mostly in the last couple of years. Although there might be a core microbiota for different body sites, shared by dogs, it is likely influenced by intrinsic factors such as age, breed, and sex, but also by extrinsic factors such as the environment (e.g., lifestyle, urban vs rural), and diet. It starts to become clear that some medical conditions are mediated by alterations in microbiota namely dysbiosis. Moreover, understanding microbial colonization and function can be used to prevent medical conditions, for instance, modulation of gut microbiota of puppies is more effective to ensure a healthy gut than interventions in adults. This paper gathers current knowledge of dogs’ microbial communities, exploring their function, implications in the development of diseases, and potential interactions among communities while providing hints for further research.
... Given the proven existence of the urinary microbiome in humans and dogs (15,16), it seems reasonable to hypothesize that a feline urinary microbiome also exists and may interact differently with the host depending on the health of the urinary system. Certainly, subclinical bacteriuria is not uncommon in cats (17), and urinary tract diseases, notably CKD and feline idiopathic cystitis (FIC), are common causes of morbidity and mortality in cats. ...
... Our findings also suggest that the feline bladder microbiome is different from the canine bladder microbiome. Notably, while Pseudomonas was detected at relatively low abundances in around half of the control cats, Pseudomonas predominated the urine of both healthy female and male dogs (15). Considering that Pseudomonas also predominated the genital microbiome in most of these dogs (15), this genus was likely a true member of the bladder microbiome with close connections to the genital microbiome, like Lactobacillus in women. ...
... Notably, while Pseudomonas was detected at relatively low abundances in around half of the control cats, Pseudomonas predominated the urine of both healthy female and male dogs (15). Considering that Pseudomonas also predominated the genital microbiome in most of these dogs (15), this genus was likely a true member of the bladder microbiome with close connections to the genital microbiome, like Lactobacillus in women. However, in a culture-dependent study of cats, Pseudomonas was not isolated from samples collected from the genital tract (39), consistent with its less frequent and abundant detection in our study. ...
ABSTRACT Although feline urinary tract diseases cause high morbidity and mortality rates, and subclinical bacteriuria is not uncommon, the feline urinary microbiome has not been characterized. We conducted a case-control study to identify the feline urinary bladder microbiome and assess its association with chronic kidney disease (CKD), feline idiopathic cystitis (FIC), and positive urine cultures (PUCs). Of 108 feline urine samples subjected to 16S rRNA gene sequencing, 48 (44.4%) samples reached the 500-sequence rarefaction threshold and were selected for further analysis, suggesting that the feline bladder microbiome is typically sparse. Selected samples included 17 CKD, 9 FIC, 8 PUC cases and 14 controls. Among these, 19 phyla, 145 families, and 218 genera were identified. Proteobacteria were the most abundant, followed by Firmicutes. Notably, four major urotypes were identified, including two urotypes predominated by Escherichia-Shigella or Enterococcus and two others characterized by relatively high alpha diversity, Diverse 1 and Diverse 2. Urotype was associated with disease status (P value of 0.040), with the Escherichia-Shigella-predominant urotype being present in 53% of CKD cases and in all of the Escherichia coli PUC cases. Reflecting these patterns, the overall microbial composition of CKD cases was more similar to that of E. coli PUC cases than to that of controls (P value of
... Given the proven existence of the urinary microbiome in humans and dogs (15,16), it seems reasonable to hypothesize that a feline urinary microbiome also exists and may interact differently with the host depending on the health of the urinary system. Certainly, subclinical bacteriuria is not uncommon in cats (17), and urinary tract diseases, notably CKD and feline idiopathic cystitis (FIC), are common causes of morbidity and mortality in cats. ...
... Our findings also suggest that the feline bladder microbiome is different from the canine bladder microbiome. Notably, while Pseudomonas was detected at relatively low abundances in around half of the control cats, Pseudomonas predominated the urine of both healthy female and male dogs (15). Considering that Pseudomonas also predominated the genital microbiome in most of these dogs (15), this genus was likely a true member of the bladder microbiome with close connections to the genital microbiome, like Lactobacillus in women. ...
... Notably, while Pseudomonas was detected at relatively low abundances in around half of the control cats, Pseudomonas predominated the urine of both healthy female and male dogs (15). Considering that Pseudomonas also predominated the genital microbiome in most of these dogs (15), this genus was likely a true member of the bladder microbiome with close connections to the genital microbiome, like Lactobacillus in women. However, in a culture-dependent study of cats, Pseudomonas was not isolated from samples collected from the genital tract (39), consistent with its less frequent and abundant detection in our study. ...
Although feline urinary tract diseases cause high morbidity and mortality rates, and subclinical bacteriuria is not uncommon, the feline urinary microbiome has not been characterized. We conducted a case-control study to identify the feline urinary bladder microbiome and assess its association with chronic kidney disease (CKD), feline idiopathic cystitis (FIC), and positive urine cultures (PUCs). Of 108 feline urine samples subjected to 16S rRNA gene sequencing, 48 (44.4%) samples reached the 500-sequence rarefaction threshold and were selected for further analysis, suggesting that the feline bladder microbiome is typically sparse. Selected samples included 17 CKD, 9 FIC, 8 PUC cases and 14 controls. Among these, 19 phyla, 145 families, and 218 genera were identified. Proteobacteria were the most abundant, followed by Firmicutes. Notably, four major urotypes were identified, including two urotypes predominated by Escherichia-Shigella or Enterococcus and two others characterized by relatively high alpha diversity, Diverse 1 and Diverse 2. Urotype was associated with disease status (P value of 0.040), with the Escherichia-Shigella-predominant urotype being present in 53% of CKD cases and in all of the Escherichia coli PUC cases. Reflecting these patterns, the overall microbial composition of CKD cases was more similar to that of E. coli PUC cases than to that of controls (P value of ,0.001). Finally, PUC cases had microbial compositions distinct from those of controls as well as CKD and FIC cases, with significantly lower Shannon diversity and Faith's phylogenetic diversity values.
... In addition, dogs are a valuable translational model for many human diseases, including urogenital diseases like bladder cancer [55]. However, there have only been two studies, to our knowledge, characterizing canine urine microbiota [56,57] and none evaluating canine urine DNA extraction methods. Multiple methods of urine microbial DNA isolation have been reported in human studies [12,51,[58][59][60][61], and there are a few studies that have compared microbial DNA extraction methods. ...
... There are only two studies, to our knowledge, on the healthy canine urine microbiota. Both employed cystocentesis for sampling, and microbial diversity did not differ by sex [56,57]. Hormones have also been linked to changes in the fecal microbiome of women and could feasibly be altering the urine microbiota [84]. ...
... As such, this taxon could represent a skin contaminant or could be a true inhabitant of canine urine. Similarly, Sphingomonas has been reported in the canine vaginal microbiota [56] and could represent a genital contaminant or true inhabitant of urine. In humans, Lactobacillus species are common vaginal microbes, but studies on urine microbiota collected via catheter demonstrate that similar or identical Lactobacillus species are also present and culturable from the bladder and are not just contaminants [6,95,96]. ...
The urinary microbiota is the collection of microbes present in urine that may play a role in host health. Studies of urine microbiota have traditionally relied upon culturing methods aimed at identifying pathogens. However, recent culture-free sequencing studies of the urine microbiota have determined that a diverse array of microbes is present in health and disease. To study these microbes and their potential role in diseases like bladder cancer or interstitial cystitis, consistent extraction and detection of bacterial DNA from urine is critical. However, urine is a low biomass substrate, requiring sensitive methods to capture DNA and making the risk of contamination high. To address this challenge, we collected urine samples from ten healthy dogs and extracted DNA from each sample using five different commercially available extraction methods. Extraction methods were compared based on total and bacterial DNA concentrations and bacterial community composition and diversity assessed through 16S rRNA gene sequencing. Significant differences in the urinary microbiota were observed by dog and sex but not extraction method. The Bacteremia Kit yielded the highest total DNA concentrations (Kruskal-Wallis, p = 0.165, not significant) and the highest bacterial DNA concentrations (Kruskal-Wallis, p = 0.044). Bacteremia also extracted bacterial DNA from the greatest number of samples. Taken together, these results suggest that the Bacteremia kit is an effective option for studying the urine microbiota. This work lays the foundation to study the urine microbiome in a wide range of urogenital diseases in dogs and other species.
... infections (UTIs) in companion dogs emphasize the importance of rapid and reliable microbiome monitoring over time. 2 Urine is an important health barometer with point-of-care screening focused on colorimetric dipstick, specific gravity, and microscopic testing. 3 Urine culture and sensitivity testing by a clinical laboratory typically involves a turn-around time of 2 to 3 days, yet antibiotics are often prescribed empirically in cases with bacteriuria and clinical signs of UTI. ...
... shepherd (3), Australian shepherd (2), American Staffordshire terrier (2), beagle (2), golden retriever (2), pug (2), Siberian husky (2) Anaerococcus, 38 and Actinomyces. 16 In addition, MiDOG LLC has detected Porphyromonas and Peptostreptococcus in a high number of urine samples from dogs with UTI (unpublished data), which is consistent with our findings ( Figure 1D). ...
... Furthermore, we show that conventional urine culture might be inadequate for in-depth clinical assessments of the urine microbiome. All dogs enrolled in this study had negative urine mented several bacterial species in urine collected via cystocentesis from clinically healthy dogs.2 Data presented here demonstrate that urine from asymptomatic dogs can host a relatively rich and diverse microbial community including multiple taxa from at least 2 classes of microorganisms: fungi and bacteria. ...
Background
Urine from clinically healthy dogs is not sterile. Characterizing microbial diversity and abundance within this population of dogs is important to define normal reference ranges for healthy urine.
Objectives
To establish composition and relative representation of bacterial and fungal microbiomes in urine of clinically healthy dogs.
Animals
Fifty clinically healthy dogs.
Methods
Analytic study. Urine sampling via cystocentesis. Comprehensive evaluation of urine including standard urinalysis, culture and sensitivity, next‐generation sequencing (NGS), and bioinformatics to define bacterial and fungal microbiome.
Results
Culture did not yield positive results in any samples. Next‐generation sequencing of urine established low presence of bacteria, fungi, or both in all samples. Diversity and abundance of bacterial and fungal communities varied between urine samples from different dogs. Struvite crystals were associated with bacterial community structure (P = .07) and there was a positive correlation between struvite crystals and pH.
Conclusions and Clinical Importance
The microbiome in urine of clinically healthy dogs has diverse bacterial and fungal species These findings highlight limitations of conventional culture testing and the need for culture‐independent molecular diagnostics to detect microorganisms in urine.
... In humans, as well as in small animals, these complex communities of microbes inhabit predominantly the gastrointestinal tract and oral cavity, but other exposed tissues, such as skin, breast, respiratory and urinary tract, can also harbor unique bacterial communities [4][5][6][7][8][9]. The host microbiota and immune system must communicate to maintain a balance between tolerance and activation, otherwise a dysbiotic state can be established and may incite or sustain diseases, such as cancer [10]. ...
This chapter aims to discuss recent developments in understanding the small animal gut microbiome’s relationship with cancer, focusing on animals as well as a model for studying humans. Based on multidirectional interactions between the microbiome, the environment and the epigenetically/genetically vulnerable host, it intends to address the mechanisms by which microorganisms can contribute to carcinogenesis describing the roles of the microbiome directly in the pathogenesis of the disease through complex interactions between the microbiome and the host’s metabolic and immune systems. The feasibility for developing new cancer diagnostic and prognostic methodologies plus treatments based on small animals’ microbiome profiles are reviewed.
... This is interesting because avian feces contain both feces and urine, and the cloaca contains a mixed population of microbes from the digestive, reproductive and urinary systems [20], therefore it would be expected that feces in birds contain microbes not only from the gut but also from other organs. This thought is based on the presence of a measurable microbiota in urine from humans and other mammals [21,22]. ...
Gut microbial communities play a fundamental role in health and disease, but little is known about the gut microbiota of pet bird species. This is important to better understand the impact of microbes on birds’ health but may also be relevant in a context of zoonoses. Total genomic DNA samples from pooled fecal samples from 30 flocks (4–7 pet birds per flock) representing over 150 birds of six different species (two Passeriformes: Mimus polyglottos (northern mockingbird) and Taeniopygia guttata (zebra finch), and four Psittaciformes: Agapornis spp. (lovebirds), Nymphicus hollandicus (cockatiels), Psephotus haematonotus (red-rumped parrot), and Psittacula krameri (rose-ringed parakeet) were used for 16S rRNA gene analysis. Several taxa were found to be different among the bird species (e.g., lowest median of Lactobacillus: 2.2% in cockatiels; highest median of Lactobacillus: 79.4% in lovebirds). Despite marked differences among individual pooled samples, each bird species harbored a unique fecal bacterial composition, based on the analysis of UniFrac distances. A predictive approach of metagenomic function and organism-level microbiome phenotypes revealed several differences among the bird species (e.g., a higher proportion of proteobacteria with the potential to form biofilms in samples from northern mockingbirds). The results provide a useful catalog of fecal microbes from pet birds and encourage more research on this unexplored topic.
