Characterization of the nasal and oral microbiota of detection dogs

Comparison of culture-dependent and -independent bacterial detection results on nasal swabs in dogs with nasal discharge

OBJECTIVES

The role of bacterial communities in the pathophysiology of canine nasal disease is still unclear. How and when to treat dogs with suspected secondary bacterial rhinitis and on which test to rely before making a decision to treat with antimicrobials has not been established. The objective is to compare the results of bacterial identification using agar-plate cultures and 16S rRNA gene amplicon sequencing in dogs with nasal discharge suspected to be of bacterial origin.

MATERIALS AND METHODS

Twenty-nine client-owned dogs presented for investigation of nasal disease were included in the study. Paired swabs were collected from the same affected nasal cavity. One swab was streaked on 4 agar media (Columbia Blood Agar, MacConkey, Chapman and Edward's). The other swab was stored in a sterile cryotube at -80°. Extracted DNA underwent a polymerase chain reaction targeting the V1-V3 region of the 16S rRNA gene.

RESULTS

At least one of the species detected by amplicon sequencing with a relative abundance of >10% was also identified by culture in 14 cases (48.3%), in association with marked predominance of one taxon (>80% relative abundance) in six of 14 cases. In 12 dogs (41.4%), the cultured isolates were rare or undetected components of the corresponding sequence libraries. A negative culture in the face of bacterial predominance (>50% relative abundance) of a potentially pathogenic bacteria detected by sequencing occurred in 17% (n=5) of cases; however, the use of other agar media may have decreased this percentage.

CLINICAL SIGNIFICANCE

Standard culture does not reliably predict the bacterial profile detected by 16S rRNA gene amplicon sequencing.

Longitudinal Analysis of Canine Oral Microbiome Using Whole Genome Sequencing in Aging Companion Dogs

Aged companion dogs have a high prevalence of periodontal disease and canine cognitive dysfunction syndrome (CCDS) and the two disorders are correlated. Similarly, periodontal disease and Alzheimer's Disease are correlated in people. However, little is known about the oral microbiota of aging dogs. The goal of this project was to characterize the longitudinal changes in oral microbiota in aged dogs. Oral swabs were taken from ten senior client-owned dogs on 2-3 occasions spanning 24 months and they underwent whole genome shotgun (WGS) sequencing. Cognitive status was established at each sampling time. A statistically significant increase in alpha diversity for bacterial and fungal species was observed between the first and last study visits. Bacteroidetes and proteobacteria were the most abundant bacterial phyla. Porphyromonas gulae was the most abundant bacterial species (11.6% of total reads). The species Lactobacillus gasseri had a statistically significant increase in relative abundance with age whereas Leptotrichia sp. oral taxon 212 had a statistically significant positive longitudinal association with cognition score. There is an increased fungal and bacterial alpha diversity in aging dogs over time and nearly universal oral dysbiosis. The role of the oral microbiota, particularly Leptotrichia and P. gulae and P. gingivalis, in aging and CCDS warrants further investigation.

Aerococcus viridans and Public Health: Oral Carriage and Antimicrobial Resistance in Stray Dogs and Cats in Algeria

The current study aimed to determine the occurrence and antimicrobial resistance of oral Aerococcus viridans in stray dogs and cats in Algeria. Oral swabs from 200 stray animals (100 dogs and 100 cats) were collected and cultured on Columbia agar medium supplemented with 5% defibrinated sheep blood. Isolates were identified using analytical profile index Rapid 20 Strep commercial kits, and antibiotic susceptibility was determined using the disk diffusion method. Of the 200 animals sampled, 34 carried A. viridans in their oral cavities, with 26 isolates (76.47%) resistant to at least 2 drugs. Multidrug resistance profiles (to more than three different antimicrobials) were observed only in cats (26.08% of isolates). More isolates were resistant to erythromycin and tetracycline (71% and 65%, respectively) than to other antimicrobials. This is the first research study in Algeria detecting antimicrobial resistance in oral A. viridans isolated from dogs and cats and highlights potential public health concerns. Clinical trials registration number: 01/2018.

Host-specific signatures of the respiratory microbiota in domestic animals

While the importance of respiratory microbiota in maintaining respiratory health is increasingly recognized, we still lack a comprehensive understanding of the unique characteristics of respiratory microbiota specific to individual hosts. This study aimed to address this gap by analyzing publicly available 16S rRNA gene datasets from various domestic animals (cats, dogs, pigs, donkeys, chickens, sheep, and cattle) to identify host-specific signatures of respiratory microbiota. The findings revealed that cattle and pigs exhibited the highest Shannon diversity index and observed features, indicating a greater microbial variety compared to other animals. Discriminant analysis demonstrated distinct composition of respiratory microbiota across different animals, with no overlapping abundant taxa. The linear discriminant analysis effect size highlighted prevalent host-specific microbiota signatures in different animal species. Moreover, the composition and diversity of respiratory microbiota were significantly influenced by various factors such as individual study, health status, and sampling sites within the respiratory tract. While associations between host and respiratory microbiota have been uncovered, the relative contributions of host and environment in the selection of respiratory microbiota and their impact on host fitness remain unclear. Further investigations involving diverse hosts are necessary to fully comprehend the significance of host-microbial coevolution in maintaining respiratory health.

The respiratory microbiota and its impact on health and disease in dogs and cats: A One Health perspective

Healthy lungs were long thought of as sterile, with presence of bacteria identified by culture representing contamination. Recent advances in metagenomics have refuted this belief by detecting rich, diverse, and complex microbial communities in the healthy lower airways of many species, albeit at low concentrations. Although research has only begun to investigate causality and potential mechanisms, alterations in these microbial communities (known as dysbiosis) have been described in association with inflammatory, infectious, and neoplastic respiratory diseases in humans. Similar studies in dogs and cats are scarce. The microbial communities in the respiratory tract are linked to distant microbial communities such as in the gut (ie, the gut-lung axis), allowing interplay of microbes and microbial products in health and disease. This review summarizes considerations for studying local microbial communities, key features of the respiratory microbiota and its role in the gut-lung axis, current understanding of the healthy respiratory microbiota, and examples of dysbiosis in selected respiratory diseases of dogs and cats.

Microbial Complexity of Oral Cavity of Healthy Dogs Identified by Mass Spectrometry and Next-Generation Sequencing

The high complexity of the oral microbiota of healthy dogs and the close exposure of humans to companion animals represent a risk of the transmission of potential zoonotic microorganisms to humans, especially through dog bites, including multidrug-resistant ones. Nonetheless, a limited number of comprehensive studies have focused on the diversity of the microorganisms that inhabit the oral cavities of healthy dogs, particularly based on modern molecular techniques. We investigated bacterial and fungal organisms in the oral cavities of 100 healthy dogs based on a combination of conventional and selective microbiological culture, mass spectrometry (MALDI-TOF MS), and next-generation sequencing. In addition, in vitro antimicrobial susceptibility patterns of isolates and mecA resistance gene were assessed. A total of 213 bacteria and 20 fungi were isolated. Staphylococcus pseudintermedius (40/100 = 40%), α-hemolytic Streptococcus (37/100 = 37%), and Pasteurella stomatis (22/100 = 22%) were the most prevalent bacteria diagnosed by microbiological culture and MALDI-TOF MS, whereas Aspergillus (10/100 = 10%) was the most common fungi identified. Based on next-generation sequencing of selected 20 sampled dogs, Porphyromonas (32.5%), Moraxella (16.3%), Fusobacterium (12.8%), Conchiformibius (9.5%), Bergeyella (5%), Campylobacter (3.8%), and Capnocytophaga (3.4%) genera were prevalent. A high multidrug resistance rate was observed in Staphylococcus pseudintermedius isolates, particularly to azithromycin (19/19 = 100%), penicillin (15/19 = 78.9%), and sulfamethoxazole/trimethoprim (15/19 = 78.9%). In addition, the mecA resistance gene was detected in 6.1% (3/49) of coagulase-positive staphylococci. Here, we highlight the microbial complexity of the oral mucosa of healthy dogs, including potential zoonotic microorganisms and multidrug-resistant bacteria, contributing with the investigation of the microbiota and antimicrobial resistance patterns of the microorganisms that inhabit the oral cavity of healthy dogs.

Assessment of the nasal microbiota in dogs with fungal rhinitis before and after cure and in dogs with chronic idiopathic rhinitis

BACKGROUND

Pathogenesis of canine fungal rhinitis is still not fully understood. Treatment remains challenging, after cure turbinate destruction may be associated with persistent clinical signs and recurrence of fungal rhinitis can occur. Alterations of the nasal microbiota have been demonstrated in dogs with chronic idiopathic rhinitis and nasal neoplasia, although whether they play a role in the pathogenesis or are a consequence of the disease is still unknown. The objectives of the present study were (1) to describe nasal microbiota alterations associated with fungal rhinitis in dogs, compared with chronic idiopathic rhinitis and controls, (2) to characterize the nasal microbiota modifications associated with successful treatment of fungal rhinitis. Forty dogs diagnosed with fungal rhinitis, 14 dogs with chronic idiopathic rhinitis and 29 healthy control dogs were included. Nine of the fungal rhinitis dogs were resampled after successful treatment with enilconazole infusion.

RESULTS

Only disease status contributed significantly to the variability of the microbiota. The relative abundance of the genus Moraxella was decreased in the fungal rhinitis (5.4 ± 18%) and chronic idiopathic rhinitis (4.6 ± 8.7%) groups compared to controls (51.8 ± 39.7%). Fungal rhinitis and chronic idiopathic rhinitis groups also showed an increased richness and α-diversity at species level compared with controls. Increase in unique families were associated with fungal rhinitis (Staphyloccaceae, Porphyromonadaceae, Enterobacteriaceae and Neisseriaceae) and chronic idiopathic rhinitis (Pasteurellaceae and Lactobacillaceae). In dogs with fungal rhinitis at cure, only 1 dog recovered a high relative abundance of Moraxellaceae.

CONCLUSIONS

Results confirm major alterations of the nasal microbiota in dogs affected with fungal rhinitis and chronic idiopathic rhinitis, consisting mainly in a decrease of Moraxella. Besides, a specific dysbiotic profile further differentiated fungal rhinitis from chronic idiopathic rhinitis. In dogs with fungal rhinitis, whether the NM returns to its pre-infection state or progresses toward chronic idiopathic rhinitis or fungal rhinitis recurrence warrants further investigation.

The human and animals' malignant melanoma: comparative tumor models and the role of microbiome in dogs and humans

Currently, the most progressively occurring incident cancer is melanoma. The mouse is the most popular model in human melanoma research given its various benefits as a laboratory animal. Nevertheless, unlike humans, mice do not develop melanoma spontaneously, so they need to be genetically manipulated. In opposition, there are several reports of other animals, ranging from wild to domesticated animals, that spontaneously develop melanoma and that have cancer pathways that are similar to those of humans. The influence of the gut microbiome on health and disease is being the aim of many recent studies. It has been proven that the microbiome is a determinant of the host's immune status and disease prevention. In human medicine, there is increasing evidence that changes in the microbiome influences malignant melanoma progression and response to therapy. There are several similarities between some animals and human melanoma, especially between canine and human oral malignant melanoma as well as between the gut microbiome of both species. However, microbiome studies are scarce in veterinary medicine, especially in the oncology field. Future studies need to address the relevance of gut and tissue microbiome for canine malignant melanoma development, which results will certainly benefit both species in the context of translational medicine.

Nasal microbiota profiles in shelter dogs with dermatological conditions carrying methicillin-resistant and methicillin-sensitive Staphylococcus species

Dermatological conditions may be complicated by Staphylococcus spp. infections influencing skin and nasal microbiota. We investigated the associations between the resident nasal microbiota of shelter dogs with and without dermatological conditions carrying methicillin-resistant and -sensitive Staphylococcus spp. Nasal sampling of 16 dogs with and 52 without dermatological conditions were performed upon shelter admission (baseline), and then bi-weekly until discharge (follow-up). All samples were cultured for Staphylococcus spp., while 52 samples underwent microbiota analysis. Two elastic net logistic regression (ENR) models (Model 1-baseline samples; Model 2-follow-up samples) were developed to identify predictive associations between dermatological conditions and the variables: signalment, antimicrobial treatment, and nasal microbial genera. Follow-up nasal samples of dogs with dermatological conditions had decreased microbiota diversity and abundance compared to dogs without dermatological conditions. Our ENR models identified predictive differences in signalment and nasal microbial genera between baseline and follow-up samples. Co-occurrence networks showed nasal microbial genera were more dissimilar when comparing dogs with and without dermatological conditions at follow-up. Overall, this study is the first to investigate Staphylococcus spp. carriage effects on nasal microbial genera in a canine animal shelter population, and ultimately reveals the importance of investigating decolonisation and probiotic therapies for restoring nasal microbiota.

Characterization of the oral and fecal microbiota associated with atopic dermatitis in dogs selected from a purebred Shiba Inu colony

Atopic dermatitis (AD) is a chronic and relapsing multifactorial inflammatory skin disease that also affects dogs. The oral and gut microbiota are associated with many disorders, including allergy. Few studies have addressed the oral and gut microbiota in dogs, although the skin microbiota has been studied relatively well in these animals. Here, we studied the AD-associated oral and gut microbiota in 16 healthy and nine AD dogs from a purebred Shiba Inu colony. We found that the diversity of the oral microbiota was significantly different among the dogs, whereas no significant difference was observed in the gut microbiota. Moreover, a differential abundance analysis detected the Family_XIII_AD3011_group (Anaerovoracaceae) in the gut microbiota of AD dogs; however, no bacterial taxa were detected in the oral microbiota. Third, the comparison of the microbial co-occurrence patterns between AD and healthy dogs identified differential networks in which the bacteria in the oral microbiota that were most strongly associated with AD were related with human periodontitis, whereas those in the gut microbiota were related with dysbiosis and gut inflammation. These results suggest that AD can alter the oral and gut microbiota in dogs.

Phenotypic correlates of the working dog microbiome

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

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.

Analysis and Comparison of Gut Microbiome in Young Detection Dogs

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

The bacteriome of the oral cavity in healthy dogs and dogs with periodontal disease

OBJECTIVE

To compare the bacteriome of the oral cavity in healthy dogs and dogs with various stages of periodontal disease.

ANIMALS

Dogs without periodontal disease (n = 12) or with mild (10), moderate (19), or severe (10) periodontal disease.

PROCEDURES

The maxillary arcade of each dog was sampled with a sterile swab, and swabs were submitted for next-generation DNA sequencing targeting the V1-V3 region of the 16S rRNA gene.

RESULTS

714 bacterial species from 177 families were identified. The 3 most frequently found bacterial species were Actinomyces sp (48/51 samples), Porphyromonas cangingivalis (47/51 samples), and a Campylobacter sp (48/51 samples). The most abundant species were P cangingivalis, Porphyromonas gulae, and an undefined Porphyromonas sp. Porphyromonas cangingivalis and Campylobacter sp were part of the core microbiome shared among the 4 groups, and P gulae, which was significantly enriched in dogs with severe periodontal disease, was part of the core microbiome shared between all groups except dogs without periodontal disease. Christensenellaceae sp, Bacteroidales sp, Family XIII sp, Methanobrevibacter oralis, Peptostreptococcus canis, and Tannerella sp formed a unique core microbiome in dogs with severe periodontal disease.

CONCLUSIONS AND CLINICAL RELEVANCE

Results highlighted that in dogs, potential pathogens can be common members of the oral cavity bacteriome in the absence of disease, and changes in the relative abundance of certain members of the bacteriome can be associated with severity of periodontal disease. Future studies may aim to determine whether these changes are the cause or result of periodontal disease or the host immune response.

Pet dogs as reservoir of oxacillin and vancomycin-resistant Staphylococcus spp

The aim of this study was to verify the bacterial resistance profile and detect the presence of mecA gene in Staphylococcus spp. isolated from the nasal microbiota of domiciled dogs. For this purpose 100 nasal swabs from 100 domiciled dogs were collected from the central area of the city of Umuarama (PR), along with a questionnaire answered by their owners. After the isolation all Staphylococcus spp. isolates were submitted to the diffusion disc test by the Kirby-Bauer method, and only oxacillin-resistant samples were submitted to the PCR technique to search for the mecA gene and the results were then submitted to statistical analysis to verify possible risk variables. The 100 Staphylococcus spp. and coagulase negative, among which 41 isolates were resistant to oxacillin, no samples were positive for the mecA gene presence, however, 12 resistant to vancomycin were found. It can be concluded that the domiciled dogs are carriers of Staphylococcus spp. multiresistant, being these a possible source of human contamination.

Variations in facial conformation are associated with differences in nasal microbiota in healthy dogs

Background

Extrinsic and intrinsic factors have been shown to influence nasal microbiota (NM) in humans. Very few studies investigated the association between nasal microbiota and factors such as facial/body conformation, age, and environment in dogs. The objectives are to investigate variations in NM in healthy dogs with different facial and body conformations. A total of 46 dogs of different age, living environment and from 3 different breed groups were recruited: 22 meso−/dolichocephalic medium to large breed dogs, 12 brachycephalic dogs and 12 terrier breeds. The nasal bacterial microbiota was assessed through sequencing of 16S rRNA gene (V1-V3 regions) amplicons.

Results

We showed major differences in the NM composition together with increased richness and α-diversity in brachycephalic dogs, compared to meso−/dolichocephalic medium to large dogs and dogs from terrier breeds.

Conclusion

Healthy brachycephalic breeds and their unique facial conformation is associated with a distinct NM profile. Description of the NM in healthy dogs serves as a foundation for future researches assessing the changes associated with disease and the modulation of NM communities as a potential treatment.

Cultivable Oral Microbiota in Puppies

The oral microbiota has been shown to be different in children born by caesarean section and delivered vaginally. The aim of this study was to investigate the oral microbial diversity in healthy puppies and to determine whether the birth mode affects the composition of the oral microbiota. A total of 19 puppies from 4 dams were included in the study. The puppies were divided into two groups depending on the birth mode, vaginal delivery (vaginal born VB) or caesarean delivery (caesar-ean section CS). On the seventh day after birth, swabs of the oral cavity were taken. All samples were analysed by bacteriological cultivation under aerobic and anaerobic conditions. Bacterial colonies were identified by Sanger sequencing of 16S rRNA. A total of 64 bacterial strains belonging to 10 genera were obtained from the oral swabs. The genera Staphylococcus (30.23 % VB and 47.62 % CS) and Enterococcus (25.58 % VB and 33.33 % CS) were the most abundant in both groups. The genera Escherichia (18.60 %) and Enterobacter (16.28 %) were largely present in puppies delivered vaginally, they were not found in puppies born by caesarean section. The other detected genera were present at lower proportions (< 5 %) and varied between the groups. The oral micro-biota of the puppies in the litter was similar, but differed between litters and between groups. Based on these results, we can assume that the birth mode affects the oral microbiota of puppies.

Anti-infection mechanism of a novel dental implant made of titanium-copper (TiCu) alloy and its mechanism associated with oral microbiology

This work was focused on study of anti-infection ability and its underlying mechanism of a novel dental implant made of titanium-copper (TiCu) alloy. In general, most studies on antibacterial implants have used a single pathogen to test their anti-infection ability using infectious animal models. However, dental implant-associated infections are polymicrobial diseases. We innovatively combine the classic ligature model in dogs with sucrose-rich diets to induce oral infections via the canine native oral bacteria. The anti-infection ability, biocompatibility and underlying mechanism of TiCu implant were systematically investigated in comparison with pure Ti implant via general inspection, hematology, imageology (micro-CT), microbiology (16S rDNA and metagenome), histology, and Cu ion detections. Compared with Ti implant, TiCu implant demonstrated remarkable anti-infection potentials with excellent biocompatibility. Additionally, the underlying anti-infection mechanism of TiCu implant was considered to involve maintaining the oral microbiota homeostasis. It was found that the carbohydrates in the plaques formed on the surface of TiCu implant were metabolized through the tricarboxylic acid cycle (TCA) cycles, which prevented the formation of an acidic microenvironment and inhibited the accumulation of acidogens and pathogens, thereby maintaining the microflora balance between aerobic and anaerobic bacteria.

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Anti-infective ability of TiCu implant was proved in the peri-implant infection condition induced by natural oral bacteria.

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TiCu implant maintained the oral microbiota homeostasis and effectively inhibited the peri-implant infections.

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TiCu implant owned good biosafety and anti-infective actions with the potential for clinical applications.

Dogs' Microbiome From Tip to Toe

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

Canibacter oris - a fairly unknown pathogenic agent of bite wound infections

Here, we report on the second case of bite wound infection by Canibacter oris. This bacterium belongs to the family of Microbacteriaceae in the order of Microbacterales in the class of Actinobacteria, which are prevalent in the oral flora. Possibly this bacterium has been overlooked until now, because it cannot be recognized by conventional differentiation methods. MALDI-TOF as well as PCR are able to identify this pathogen.

Associations between dog keeping and indoor dust microbiota

Living with dogs appears to protect against allergic diseases and airway infections, an effect possibly linked with immunomodulation by microbial exposures associated with dogs. The aim of this study was to characterize the influence of dog ownership on house dust microbiota composition. The bacterial and fungal microbiota was characterized with Illumina MiSeq sequencing from floor dust samples collected from homes in a Finnish rural-suburban (LUKAS2, N = 182) birth cohort, and the results were replicated in a German urban (LISA, N = 284) birth cohort. Human associated bacteria variable was created by summing up the relative abundances of five bacterial taxa. Bacterial richness, Shannon index and the relative abundances of seven bacterial genera, mostly within the phyla Proteobacteria and Firmicutes, were significantly higher in the dog than in the non-dog homes, whereas the relative abundance of human associated bacteria was lower. The results were largely replicated in LISA. Fungal microbiota richness and abundance of Leucosporidiella genus were higher in dog homes in LUKAS2 and the latter association replicated in LISA. Our study confirms that dog ownership is reproducibly associated with increased bacterial richness and diversity in house dust and identifies specific dog ownership-associated genera. Dogs appeared to have more limited influence on the fungal than bacterial indoor microbiota.

An unusual case of multiple hepatic and pulmonary abscesses caused by Aggregatibacter aphrophilus in a young man: a case report

Background

Aggregatibacter aphrophilus, formerly known as Haemophilus aphrophilus, belongs to the HACEK organisms, a group of pathogens classically associated with infectious endocarditis. A. aphrophilus is a rarely found pathogen, though abscess formation in various organs has been described, typically due to spread from an infected heart valve. Here we describe the unusual case of multiple hepatic abscesses caused by A. aphrophilus.

Case presentation

A 33-year-old Caucasian man presented at our hospital with fever and malaise, elevated inflammatory markers, and liver enzymes. Imaging was compatible with multiple liver and pulmonary abscesses, without evidence of endocarditis. Cultures of blood and liver abscess material remained without growth. Polymerase chain reaction finally revealed Aggregatibacter aphrophilus in the liver tissue. The patient recovered fully within 6 weeks of doxycycline treatment.

Conclusions

There are only a few case descriptions of liver abscesses caused by A. aphrophilus. As a ubiquitous organism in the gastrointestinal tract, A. aphrophilus may reach the liver via the portal venous system, as well as through hematogenous spread from the oropharynx. HACEK organisms are notoriously difficult to grow on culture, which highlights the diagnostic importance of eubacterial PCR.

Nasal bacterial microbiota during an outbreak of equine herpesvirus 1 at a farm in southern Ontario

The objective of this study was to investigate the nasal bacterial microbiota of healthy horses and horses infected with equine herpesvirus 1 (EHV-1). The nasal bacterial microbiota of 10 horses infected with EHV-1 and 11 control horses from a farm experiencing an outbreak was characterized using the Illumina MiSeq platform targeting the V4 region of the 16S ribosomal RNA gene. The nasal bacterial microbiota of healthy horses and EHV-1 horses was significantly different in community membership and structure. Horses shedding EHV-1 had lower bacterial richness (P = 0.002), evenness (P = 0.008), and diversity (P = 0.026) than healthy horses. Healthy horses had a higher relative abundance of Firmicutes and Bacteroidetes, but lower Proteobacteria than horses with EHV-1 (P < 0.05). This study provides the basis for generating hypotheses and investigations on the role of bacterial-viral interactions in the health and diseases of adult horses.

Oral flora of stray dogs and cats in Algeria: Pasteurella and other zoonotic bacteria

Background and Aim:

Knowledge of potentially pathogenic bacteria presents in the oral cavity of dogs and cats may be helpful in determining appropriate treatment for infected bite wounds. About 120.000 people are exposed to dog and cat bites every year in Algeria, but little is known about the dog and cat oral flora causing bite wound complications. The purpose of this study was to identify potential zoonotic bacteria from oral cavity of dogs and cats and to determine their susceptibility to antibiotics to contribute to the treatment of bite wound infection.

Materials and Methods:

Oral swabs from 100 stray dogs and 100 stray cats were collected and cultured in several media: Chocolate agar, MacConkey agar, and Mannitol Salt Agar. Bacterial isolates were identified using several commercial kits of the analytical profile index and tested for antibiotic susceptibility by disk diffusion method.

Results:

Overall, 185/200 (92.5%) dogs and cats carried zoonotic bacteria in their mouths, of which 55.13% (102/185) had at least two bacterial pathogens. 374 pathogenic strains belonging to 15 genera were isolated: Eleven were Gram-negative (Proteus, Pasteurella, Escherichia, Moraxella, Klebsiella, Acinetobacter, Enterobacter, Pseudomonas, Aeromonas, and NeisseriaHaemophilus) and four were Gram-positive (Staphylococcus, Streptococcus, and Corynebacterium, Bacillus). Fifty-one strains of Pasteurella were isolated from 44 carriers of Pasteurella (21 Pasteurella multocida, 21 Pasteurella pneumotropica, and 9 Pasteurella spp.). Pasteurella strains were tested for antibiotic resistance. Resistance to at least one drug was observed in 8 (15.68%) of Pasteurella isolates and two strains (3.92%) were found to be multidrug-resistant (to two or more drugs). Erythromycin, penicillin, and ampicillin were the antimicrobials to which the isolates showed greater resistance (7.84%, 5.88%, and 3.92%, respectively).

Conclusion:

To the best of our knowledge, this study is the first in Algeria to detect potential human pathogenic bacteria in the oral cavity of dogs and cats. It reveals that these animals have multiple zoonotic bacteria in their mouths including Pasteurella species, which may be multidrug-resistant.

An Assessment of the Stability of the Canine Oral Microbiota After Probiotic Administration in Healthy Dogs Over Time

The administration of an oral probiotic has been demonstrated to impact oral microbial diversity in humans but has not been examined in canines. The objective of this study was to test the hypothesis that oral probiotic administration would impact the oral microbiota of canines compared to control. Working canines in training (n = 13) were assigned to Test or Control groups and acclimated to one of three commercially available study diets utilizing common protein sources (Purina Pro Plan Savor lamb, Purina Pro Plan Sport chicken, Purina Pro Plan Focus salmon) for a minimum of 30 days prior to initiation of the study. Following acclimation, dogs in the Test group began a daily regimen of oral probiotic (Fortiflora® Purina, St. Louis, MO) top-dressed on their midday feeding. Control dogs received their midday feeding with no probiotic. All dogs were sampled once weekly via oral pediatric swabs across the 7-week study. Next generation sequencing (Illumina, MiSeq) was utilized to develop microbial profiles specific to treatment, diet, and time. Bacterial composition was dominated by eight phyla (Proteobacteria 43.8%, Bacteroidetes 22.5%, Firmicutes 18.9%, Actinobacteria 6.1%, Fusobacteria 3.6%, Gracilibacteria 2.1%, SR1 Absconditabacteria 1.5%, and Saccharibacteria 1.3%) representing more than 99% of the relative abundance of the microbial composition. Probiotic administration failed to impact relative abundance at any taxonomic level (P > 0.05). Similarly, no effect on the oral microbiota was measured for diet (P > 0.05). Comparison using a Jaccard Index demonstrate a consistent microbial profile over the 7-week study with no impact evidenced by study week (P = 0.19). The data also revealed a profile of ubiquitous taxa that were present across all dogs and all samples regardless of breed, sex, diet, treatment or other factors. These genera include Actinomyces, Corynebacterium, Capnocytophaga, Flavobacterium, Gemella, Abiotrophia, Streptococcus, and Frederiksenia. These data demonstrate the stability of canine oral microbiota over time.

Evaluation of Healthy Canine Conjunctival, Periocular Haired Skin, and Nasal Microbiota Compared to Conjunctival Culture

Next-generation sequencing (NGS) methods have been used to identify a diverse ocular surface (OS) microbiota in humans. These results have highlighted limitations in microbial detection via traditional culture-based techniques. The OS has mechanisms such as tear film and mechanical blinking, which may aid in preventing adherence and colonization of microbes, suggesting that only low populations of microbes may reside on the OS. Additionally, closely related tissues to the OS are exposed to a similar array of microbes, but demonstrate different defense mechanisms. Information regarding concordance of microbial communities of the OS and nearby tissues is lacking. Our study purposes were to (1) characterize the conjunctival microbiota of healthy dogs, (2) compare the conjunctival microbiota to the periocular haired skin and distal nose, and (3) compare the bacteria identified by culture to NGS of the healthy canine conjunctiva. Here, NGS was used to evaluate samples from 25 healthy adult dogs of the conjunctiva, periocular haired skin, and distal nose. Additional samples were collected from each dog for traditional conjunctival culture. The 16S rRNA gene amplicon libraries were evaluated for coverage, relative abundance, richness, and diversity. Site-dependent similarities evaluated using principal coordinate analysis (PCoA) and PERMANOVA demonstrated relatedness in community compositions between sites. The conjunctiva of healthy dogs yielded a rich and diverse microbiota based on NGS. While some regional continuity was noted, microbial communities of the conjunctiva, periocular haired skin, and nose were significantly different from each other. Comparatively, traditional culture markedly underestimated the number of bacterial taxa present on the healthy canine OS. Findings suggest similarities in nasal and conjunctival microbial communities, which may be a result of similarities in mucosal immunity and anatomic connection via the nasolacrimal system. Further investigation using NGS into changes of the composition of bacterial communities in disease is warranted.

The Effects of Nutrition on the Gastrointestinal Microbiome of Cats and Dogs: Impact on Health and Disease

The gastrointestinal (GI) microbiome of cats and dogs is increasingly recognized as a metabolically active organ inextricably linked to pet health. Food serves as a substrate for the GI microbiome of cats and dogs and plays a significant role in defining the composition and metabolism of the GI microbiome. The microbiome, in turn, facilitates the host's nutrient digestion and the production of postbiotics, which are bacterially derived compounds that can influence pet health. Consequently, pet owners have a role in shaping the microbiome of cats and dogs through the food they choose to provide. Yet, a clear understanding of the impact these food choices have on the microbiome, and thus on the overall health of the pet, is lacking. Pet foods are formulated to contain the typical nutritional building blocks of carbohydrates, proteins, and fats, but increasingly include microbiome-targeted ingredients, such as prebiotics and probiotics. Each of these categories, as well as their relative proportions in food, can affect the composition and/or function of the microbiome. Accumulating evidence suggests that dietary components may impact not only GI disease, but also allergies, oral health, weight management, diabetes, and kidney disease through changes in the GI microbiome. Until recently, the focus of microbiome research was to characterize alterations in microbiome composition in disease states, while less research effort has been devoted to understanding how changes in nutrition can influence pet health by modifying the microbiome function. This review summarizes the impact of pet food nutritional components on the composition and function of the microbiome and examines evidence for the role of nutrition in impacting host health through the microbiome in a variety of disease states. Understanding how nutrition can modulate GI microbiome composition and function may reveal new avenues for enhancing the health and resilience of cats and dogs.

The canine skin and ear microbiome: A comprehensive survey of pathogens implicated in canine skin and ear infections using a novel next-generation-sequencing-based assay

This study analyzed the complex bacterial and fungal microbiota of healthy and clinically affected canine ear and skin samples. A total of 589 canine samples were included: 257 ear swab samples (128 healthy vs. 129 clinically affected) and 332 skin swab samples (172 healthy vs. 160 clinically affected) were analyzed using next-generation sequencing (NGS) to determine both relative and absolute abundances of bacteria and fungi present in the samples. This study highlighted the canine microbiota of clinically affected cases was characterized by an overall loss of microbial diversity, high microbial biomass, with overgrowth of certain members of the microbiota. The observed phenotype of these samples was best described by the combination of both relative and absolute microbial abundances. Compared to healthy samples, 78.3% of the clinically affected ear samples had microbial overgrowth; 69.8% bacterial overgrowth, 16.3% fungal overgrowth, and 7.0% had both bacterial and fungal overgrowth. The most important microbial taxa enriched in clinically affected ears were Malassezia pachydermatis, Staphylococcus pseudintermedius, Staphylococcus schleiferi, and a few anaerobic bacteria such as Finegoldia magna, Peptostreptococcus canis, and Porphyromonas cangingivalis. The anaerobic microbes identified here were previously not commonly recognized as pathogens in canine ear infections. Similar observations were found for skin samples, but yeasts and anaerobes were less abundant when compared to clinically affected cases. Results highlighted herein, signify the potential of NGS-based methods for the accurate quantification and identification of bacterial and fungal populations in diagnosing canine skin and ear infections, and highlight the limitations of traditional culture-based testing.

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

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

The feline cutaneous and oral microbiota are influenced by breed and environment

Previous research revealed the feline skin bacterial microbiota to be site-specific and the fungal microbiota to be individual-specific. The effect of other factors, such as genotype and environment, have not yet been studied in cats, but have been shown to be potentially important in shaping the cutaneous microbiota of other animals. Therefore, the objectives of this study were to evaluate the effect of these factors on the bacterial and fungal microbiota of feline skin and oral cavity. The influence of genotype was assessed through the analysis of different cat breeds, and the influence of environment through comparison of indoor and outdoor cats. DNA was extracted from skin and oral swabs, and bacterial and fungal next-generation sequencing were performed. Analysis of the skin microbiota of different cat breeds revealed significant differences in alpha diversity, with Sphynx and Bengal cats having the most diverse communities. Many taxa were found to be differentially abundant between cat breeds, including Veillonellaceae and Malassezia spp. Outdoor environment exposure had considerable influence on beta diversity, especially in the oral cavity, and resulted in numerous differentially abundant taxa. Our findings indicate that the oral bacterial microbiota and both fungal and bacterial microbiota of feline skin are influenced by breed, and to a lesser degree, environment.

Gut microbiota adaptation to high altitude in indigenous animals

Limited is known about role of gut microbiota in the metabolism of high-altitude-living herbivores, and potential co-evolution between gut microbiome and host genome during high altitude adaptation were not fully understood. Here, DNA from faecal samples was used to investigate the gut microbial compositions and diversity in three host species endemic to the high-altitude Tibetan plateau, the Tibetan antelope (Pantholops hodgsonii, T-antelope, 4300 m) and the Tibetan wild ass (Equus kiang, T-ass, 4300 m), and in the Tibetan sheep (Ovis aries, T-sheep) collected from two different altitudes (T-sheep [k], 4300 m and T-sheep [l] 3000 m). Ordinary sheep (O. aries, sheep) from low altitudes (1800 m) were used for comparison. 16S rRNA gene sequencing revealed that the genera Ruminococcus (22.78%), Oscillospira (20.00%), and Clostridium (10.00%) were common taxa in all high-altitude species (T-antelope, T-ass and T-sheep [k]). Ruminococcaceae, Clostridiales, Clostridia, and Firmicutes showed greater enrichment in the T-antelopes' gut microbiota than in the microbiota of lower-altitude sheep (T-sheep [l] and sheep). The T-antelopes' gut microbiota displayed a higher ratio of Firmicutes to Bacteroidetes than lower-altitude sheep (T-sheep [l] and sheep). A functional capacity analysis of the paired-end metagenomics sequences of the gut metagenomes of high-altitude T-antelopes and T-sheep annotated over 80% of the unique genes to metabolism (especially carbohydrate metabolism pathways) and genetic information processing in the Kyoto Encyclopedia of Genes and Genomes database. The gut metagenome of the T-antelope may have co-evolved with the host genomes (e.g. glycolysis and DNA repair). The higher-altitude herbivores tended to have similar gut microbial compositions, with similar functional capacities, suggesting that their gut microbiota could involved in their high-altitude adaptation.

Characterization of oral microbiota in marmosets: Feasibility of using the marmoset as a human oral disease model

With rapid aging of the world’s population, the demand for research, for a better understanding of aging and aging-related disorders, is increasing. Ideally, such research should be conducted on human subjects. However, due to ethical considerations, animals such as rodents and monkeys are used as alternatives. Among these alternative models, non-human primates are preferred because of their similarities with humans. The small South American common marmoset (Callithrix jacchus) may offer several advantages over other non-human primates in terms of its smaller size, shorter life-span, and dental anatomy identical to humans. The purpose of this study was to determine the viability of using the marmoset as a human oral disease model. We collected saliva samples from eight marmosets and eight human subjects. Prokaryotic DNA was extracted from the saliva samples, and 16S bacterial rRNA gene sequencing was performed on each of the samples. Our results indicated that the types of oral microbiomes detected among human and marmoset samples were nearly indistinguishable. In contrast, the oral microbiomes of our human and marmoset subjects were distinctly different from those reported for rats and dogs, which are currently popular research animals. The oral microbiomes of marmosets showed greater diversity than those of humans. However, the oral microbiota of marmosets exhibited less variation than those of humans, which may be attributed to the fact that the marmoset subjects were kept in a controlled environment with identical lifestyles. The characteristics of its oral microbiota, combined with other technical advantages, suggest that the marmoset may provide the best animal model thus far for the study of oral health. This study characterized the oral microbes of the marmoset, thereby providing information to support future application of the marmoset as a model for age-related oral disease.

Evaluation of the bacterial ocular surface microbiome in clinically normal cats before and after treatment with topical erythromycin

The ocular surface microbiome of veterinary species has not been thoroughly characterized using next generation sequencing. Furthermore, alterations in the feline ocular surface microbiome over time or following topical antibiotic treatment are unknown. Aims of this study were to further characterize the ocular surface microbiome of healthy cats and to identify whether there are microbial community changes over time and following topical antibiotic use. Twenty-four eyes from twelve adult, research-bred, female spayed domestic shorthaired cats were evaluated. Erythromycin ophthalmic ointment (0.5%) was applied to the ocular surface of one randomly assigned eye per cat three times daily for 7 days, while the fellow eye served as an untreated control. The ocular surface was sampled by swabbing the inferior conjunctival fornix of both eyes prior to initiating treatment (day 0), after 1 week of treatment (day 7), and 4 weeks after concluding treatment (day 35). Genomic DNA was extracted from the swabs and sequenced using primers that target the V4 region of bacterial 16S rRNA genes. At baseline, the most common bacterial phyla identified were Proteobacteria (42.4%), Firmicutes (30.0%), Actinobacteria (15.6%), and Bacteroidetes (8.1%). The most abundant bacterial families sequenced were Corynebacteriaceae (7.8%), Helicobacteraceae (7.5%), Moraxellaceae (6.1%), and Comamonadaceae (5.6%). Alpha and beta diversity measurements were largely unchanged in both treatment and control eyes over time. However, univariate and linear discriminant analyses revealed significant and similar changes in the abundance of some bacterial taxa over time in both treatment and control eyes. Overall, the feline ocular surface microbiome remained stable over time and following topical antibiotic therapy.

Novel association of Psychrobacter and Pseudomonas with malodour in bloodhound dogs, and the effects of a topical product composed of essential oils and plant-derived essential fatty acids in a randomized, blinded, placebo-controlled study

BACKGROUND

The pathogenesis and treatment of cutaneous malodour in dogs have not been investigated previously. Staphylococcus and Corynebacterium spp. are associated with human axillary malodour.

HYPOTHESIS

Staphylococcus and Corynebacterium spp. are associated with cutaneous malodour in dogs, and treatment with a topical essential oil-based product will improve malodour and reduce the abundance of odour-causing bacteria.

ANIMALS

Twenty seven bloodhound dogs from a south Texas boarding facility were enrolled in this study.

METHODS AND MATERIALS

Skin swabs were taken from the axilla and dorsum of 27 dogs at initiation of the study. Mean malodour scores were used to assign dogs to control or malodour groups. The malodourous dogs were randomly assigned to a treatment or placebo group, received four weekly topical applications of the spot-on or placebo, and samples were recollected. Next-generation sequencing (NGS) and real-time quantitative PCR (qPCR) were performed on all swabs.

RESULTS

Psychrobacter and Pseudomonas spp. were significantly more abundant (P < 0.001, P = 0.006; respectively), and overall bacterial diversity was reduced (P = 0.0384) on the skin of malodourous dogs. Staphylococcus and Corynebacterium spp. were not associated with malodour. The topical essential oil-based product significantly (P = 0.0078) improved malodour in the treatment group and shifted their bacterial community structure.

CONCLUSIONS AND CLINICAL IMPORTANCE

A novel association of bacterial genera with malodour in bloodhound dogs, identified by NGS, highlights future targets for odour control. The topical treatment significantly reduced malodour. The interaction between the topical treatment and cutaneous microbiota should be further investigated and may be useful in other dermatological conditions involving microbiota.

When the Nose Doesn't Know: Canine Olfactory Function Associated With Health, Management, and Potential Links to Microbiota

The impact of health, management, and microbiota on olfactory function in canines has not been examined in review. The most important characteristic of the detection canine is its sense of smell. Olfactory receptors are primarily located on the ethmoturbinates of the nasal cavity. The vomeronasal organ is an additional site of odor detection that detects chemical signals that stimulate behavioral and/or physiological changes. Recent advances in the genetics of olfaction suggest that genetic changes, along with the unique anatomy and airflow of the canine nose, are responsible for the macrosmia of the species. Inflammation, alterations in blood flow and hydration, and systemic diseases alter olfaction and may impact working efficiency of detection canines. The scientific literature contains abundant information on the potential impact of pharmaceuticals on olfaction in humans, but only steroids, antibiotics, and anesthetic agents have been studied in the canine. Physical stressors including exercise, lack of conditioning, and high ambient temperature impact olfaction directly or indirectly in the canine. Dietary fat content, amount of food per meal, and timing of meals have been demonstrated to impact olfaction in mice and dogs. Gastrointestinal (GI) microbiota likely impacts olfaction via bidirectional communication between the GI tract and brain, and the microbiota is impacted by exercise, diet, and stress. The objective of this literature review is to discuss the specific effects of health, management, and microbiota shifts on olfactory performance in working canines.