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Vangrinsven E, Duprez JN, Meex C, Taminiau B, Daube G, Billen F, Mainil J, Clercx C. Comparison of culture-dependent and -independent bacterial detection results on nasal swabs in dogs with nasal discharge. J Small Anim Pract 2024; 65:376-386. [PMID: 38594828 DOI: 10.1111/jsap.13734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 01/30/2024] [Accepted: 03/20/2024] [Indexed: 04/11/2024]
Abstract
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.
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Affiliation(s)
- E Vangrinsven
- Department of Clinical Sciences, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - J N Duprez
- Department of Infectious Diseases, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - C Meex
- Laboratory of Clinical Microbiology, Center for Interdisciplinary Research on Medicines (CIRM), University Hospital of Liège, Liège, Belgium
| | - B Taminiau
- Department of Food Sciences - Microbiology, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - G Daube
- Department of Food Sciences - Microbiology, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - F Billen
- Department of Clinical Sciences, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - J Mainil
- Department of Infectious Diseases, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - C Clercx
- Department of Clinical Sciences, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
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Zeineldin M, Barakat R. Host-specific signatures of the respiratory microbiota in domestic animals. Res Vet Sci 2023; 164:105037. [PMID: 37801741 DOI: 10.1016/j.rvsc.2023.105037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/14/2023] [Accepted: 09/23/2023] [Indexed: 10/08/2023]
Abstract
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.
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Affiliation(s)
- Mohamed Zeineldin
- Department of Animal Medicine, College of Veterinary Medicine, Benha University, Benha 13511, Egypt.
| | - Radwa Barakat
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA.
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Vientós‐Plotts AI, Ericsson AC, Reinero CR. The respiratory microbiota and its impact on health and disease in dogs and cats: A One Health perspective. J Vet Intern Med 2023; 37:1641-1655. [PMID: 37551852 PMCID: PMC10473014 DOI: 10.1111/jvim.16824] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 07/10/2023] [Indexed: 08/09/2023] Open
Abstract
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.
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Affiliation(s)
- Aida I. Vientós‐Plotts
- College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
- Department of Veterinary Medicine and Surgery, College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
- Comparative Internal Medicine LaboratoryUniversity of MissouriColumbiaMissouriUSA
| | - Aaron C. Ericsson
- College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
- University of Missouri Metagenomics CenterUniversity of MissouriColumbiaMissouriUSA
- Department of Veterinary Pathobiology, College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
| | - Carol R. Reinero
- College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
- Department of Veterinary Medicine and Surgery, College of Veterinary MedicineUniversity of MissouriColumbiaMissouriUSA
- Comparative Internal Medicine LaboratoryUniversity of MissouriColumbiaMissouriUSA
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Vangrinsven E, Fastrès A, Taminiau B, Billen F, Daube G, Clercx C. Assessment of the nasal microbiota in dogs with fungal rhinitis before and after cure and in dogs with chronic idiopathic rhinitis. BMC Microbiol 2023; 23:104. [PMID: 37061685 PMCID: PMC10105444 DOI: 10.1186/s12866-023-02828-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 03/17/2023] [Indexed: 04/17/2023] Open
Abstract
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.
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Affiliation(s)
- Emilie Vangrinsven
- Department of Clinical Sciences, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
| | - Aline Fastrès
- Department of Clinical Sciences, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Bernard Taminiau
- Department of Food Sciences - Microbiology, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Frédéric Billen
- Department of Clinical Sciences, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Georges Daube
- Department of Food Sciences - Microbiology, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Cécile Clercx
- Department of Clinical Sciences, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
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Li Z, Sun Q, Li Y, Guan Z, Wei J, Li B, Liu K, Shao D, Mi R, Liu H, Qiu Y, Ma Z. Analysis and Comparison of Gut Microbiome in Young Detection Dogs. Front Microbiol 2022; 13:872230. [PMID: 35516435 PMCID: PMC9063727 DOI: 10.3389/fmicb.2022.872230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/14/2022] [Indexed: 01/07/2023] Open
Abstract
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.
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Affiliation(s)
- Zongjie Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Qing Sun
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Yuhao Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Zhixin Guan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Beibei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Ke Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Donghua Shao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Rongsheng Mi
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Haixia Liu
- Beijing Huayuan Biotechnology Research Institute, Beijing, China
| | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
- *Correspondence: Zhiyong Ma
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Vangrinsven E, Fastrès A, Taminiau B, Billen F, Daube G, Clercx C. Correction to: Variations in facial conformation are associated with differences in nasal microbiota in healthy dogs. BMC Vet Res 2022; 18:100. [PMID: 35296323 PMCID: PMC8925189 DOI: 10.1186/s12917-022-03209-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Emilie Vangrinsven
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Liege, Quartier Vallee 2, Avenue de Cureghem 3, 4000, Liege, Belgium.
| | - Aline Fastrès
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Liege, Quartier Vallee 2, Avenue de Cureghem 3, 4000, Liege, Belgium
| | - Bernard Taminiau
- Department of Food Sciences - Microbiology, Faculty of Veterinary Medicine, University of Liege, Quartier Vallee 2, Avenue de Cureghem 3, 4000, Liege, Belgium
| | - Frédéric Billen
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Liege, Quartier Vallee 2, Avenue de Cureghem 3, 4000, Liege, Belgium
| | - Georges Daube
- Department of Food Sciences - Microbiology, Faculty of Veterinary Medicine, University of Liege, Quartier Vallee 2, Avenue de Cureghem 3, 4000, Liege, Belgium
| | - Cécile Clercx
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Liege, Quartier Vallee 2, Avenue de Cureghem 3, 4000, Liege, Belgium
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