Dataset Information

Topography of the respiratory, oral, and guttural pouch bacterial and fungal microbiotas in horses.

ABSTRACT:

Background

The lower respiratory tract microbiota of the horse is different in states of health and disease, but the bacterial and fungal composition of the healthy respiratory tract of the horse has not been studied in detail.

Hypothesis

The respiratory tract environment contains distinct niche microbiotas, which decrease in species richness at more distal sampling locations.

Objective

Characterize the bacterial and fungal microbiotas along the upper and lower respiratory tract of the horse.

Animals

Healthy Argentinian Thoroughbred horses (n = 11) from the same client-owned herd.

Methods

Prospective cross-sectional study. Eleven upper and lower respiratory tract anatomical locations (bilateral nasal, bilateral deep nasal, nasopharynx, floor of mouth, oropharynx, arytenoids, proximal and distal trachea, guttural pouch) were sampled using a combination of swabs, protected specimen brushes, and saline washes. Total DNA was extracted from each sample and negative control, and the 16S rRNA gene (V4) and ITS2 region were sequenced. Community composition, alpha-diversity, and beta-diversity were compared among sampling locations.

Results

Fungal species richness and diversity were highest in the nostrils. More spatial heterogeneity was found in bacterial composition than in fungal communities. The pharyngeal microbiota was most similar to the distal tracheal bacterial and fungal microbiota in healthy horses and therefore may serve as the primary source of bacteria and fungi to the lower respiratory tract.

Conclusions and clinical importance

The pharynx is an important location that should be targeted in respiratory microbiota research in horses. Future studies that investigate whether biomarkers of respiratory disease can be reliably detected in nasopharyngeal swab samples are warranted.

SUBMITTER: Bond S

PROVIDER: S-EPMC9889660 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Topography of the respiratory, oral, and guttural pouch bacterial and fungal microbiotas in horses.

Bond Stephanie S McMullen Christopher C Timsit Edouard E Léguillette Renaud R

Journal of veterinary internal medicine 20230106 1

<h4>Background</h4>The lower respiratory tract microbiota of the horse is different in states of health and disease, but the bacterial and fungal composition of the healthy respiratory tract of the horse has not been studied in detail.<h4>Hypothesis</h4>The respiratory tract environment contains distinct niche microbiotas, which decrease in species richness at more distal sampling locations.<h4>Objective</h4>Characterize the bacterial and fungal microbiotas along the upper and lower respiratory ...[more]

PMID: 36607177

Similar Datasets

Project description:Background: The management of bleeding originating from the guttural pouch (GP) has a high success rate, but the resolution of the macroscopic inflammatory lesions in the case of mycosis (GPM) is highly variable; the resolution of neurological disorders is inconstant and challenging. Objectives: Our aim was to test the feasibility and safety of topical oxygen therapy (TOT) in horses after induction of GPM and in cases with naturally occurring disease. Study design: This study was an in vivo experimental and retrospective two-phase study. Methods: During phase 1, the pilot study, both GPs were inoculated with Aspergillus fumigatus. One GP was randomly assigned to receive one to four TOT 30 min sessions with 100% medical oxygen at 9 L/min. Follow-up endoscopic images were assessed for scoring macroscopic inflammatory lesions of the pharynx and both GPs. In phase 2, the clinical study, TOT was administered for 45 to 60 min at 15 L/min in six horses presenting with GPM. Results: In phase 1, TOT administration was easy to perform in the standing horse with no adverse effects. After more than two administrations, macroscopic inflammatory lesions decreased more quickly in size in the treated GP. In phase 2, horses were treated with TOT only (n = 1) or combined with a transarterial coil embolization (TACE) procedure (n = 5). After TOT and discharge from the hospital, nasal discharge resolved in three horses, and improvement was noted in the fourth one. Between days 2 and 10 after admission, upper respiratory tract endoscopy (URTE) indicated size reduction and alteration in the appearance of all the macroscopic inflammatory lesions. The partial or total recovery of neurological disorders (2/4 laryngeal hemiparesis, 3/5 dysphagia, 1/2 dorsal displacement of the soft palate (DDSP), and 1/1 Horner's syndrome) was recorded. Main limitations: In phase 1, the small number of horses did not allow for statistically significant conclusions; in phase 2, clinical signs at admission varied between horses, which made comparison difficult. Conclusions: In adult horses, TOT alone or in combination with TACE is feasible and safe with a propensity to reverse the course and the progression of inflammatory lesions without additional local or systemic treatment.

Project description:UNLABELLED:The ability to cultivate food is an innovation that has produced some of the most successful ecological strategies on the planet. Although most well recognized in humans, where agriculture represents a defining feature of civilization, species of ants, beetles, and termites have also independently evolved symbioses with fungi that they cultivate for food. Despite occurring across divergent insect and fungal lineages, the fungivorous niches of these insects are remarkably similar, indicating convergent evolution toward this successful ecological strategy. Here, we characterize the microbiota of ants, beetles, and termites engaged in nutritional symbioses with fungi to define the bacterial groups associated with these prominent herbivores and forest pests. Using culture-independent techniques and the in silico reconstruction of 37 composite genomes of dominant community members, we demonstrate that different insect-fungal symbioses that collectively shape ecosystems worldwide have highly similar bacterial microbiotas comprised primarily of the genera Enterobacter, Rahnella, and Pseudomonas. Although these symbioses span three orders of insects and two phyla of fungi, we show that they are associated with bacteria sharing high whole-genome nucleotide identity. Due to the fine-scale correspondence of the bacterial microbiotas of insects engaged in fungal symbioses, our findings indicate that this represents an example of convergence of entire host-microbe complexes. IMPORTANCE:The cultivation of fungi for food is a behavior that has evolved independently in ants, beetles, and termites and has enabled many species of these insects to become ecologically important and widely distributed herbivores and forest pests. Although the primary fungal cultivars of these insects have been studied for decades, comparatively little is known of their bacterial microbiota. In this study, we show that diverse fungus-growing insects are associated with a common bacterial community composed of the same dominant members. Furthermore, by demonstrating that many of these bacteria have high whole-genome similarity across distantly related insect hosts that reside thousands of miles apart, we show that these bacteria are an important and underappreciated feature of diverse fungus-growing insects. Because of the similarities in the agricultural lifestyles of these insects, this is an example of convergence between both the life histories of the host insects and their symbiotic microbiota.

Project description:Although culture-independent techniques have refuted lung sterility in health, controversy about contamination during bronchoscope passage through the upper respiratory tract (URT) has impeded research progress. We sought to establish whether bronchoscopic sampling accurately reflects the lung microbiome in health and to distinguish between two proposed routes of authentic microbial immigration, (i) dispersion along contiguous respiratory mucosa and (ii) subclinical microaspiration. During bronchoscopy of eight adult volunteers without lung disease, we performed seven protected specimen brushings (PSB) and bilateral bronchoalveolar lavages (BALs) per subject. We amplified, sequenced, and analyzed the bacterial 16S rRNA gene V4 regions by using the Illumina MiSeq platform. Rigorous attention was paid to eliminate potential sources of error or contamination, including a randomized processing order and the inclusion and analysis of exhaustive procedural and sequencing control specimens. Indices of mouth-lung immigration (mouth-lung community similarity, bacterial burden, and community richness) were all significantly greater in airway and alveolar specimens than in bronchoscope contamination control specimens, indicating minimal evidence of pharyngeal contamination. Ecological indices of mouth-lung immigration peaked at or near the carina, as predicted for a primary immigration route of microaspiration. Bacterial burden, diversity, and mouth-lung similarity were greater in BAL than PSB samples, reflecting differences in the sampled surface areas. (This study has been registered at ClinicalTrials.gov under registration no. NCT02392182.)IMPORTANCE This study defines the bacterial topography of the healthy human respiratory tract and provides ecological evidence that bacteria enter the lungs in health primarily by microaspiration, with potential contribution in some subjects by direct dispersal along contiguous mucosa. By demonstrating that contamination contributes negligibly to microbial communities in bronchoscopically acquired specimens, we validate the use of bronchoscopy to investigate the lung microbiome.

Project description:BackgroundBacterial bronchopneumonia (BP) is the leading cause of morbidity and mortality in cattle. The nasopharynx is generally accepted as the primary source of pathogenic bacteria that cause BP. However, it has recently been shown in humans that the oropharynx may act as the primary reservoir for pathogens that reach the lung. The objective was therefore to describe the bacterial microbiota present along the entire cattle respiratory tract to determine which upper respiratory tract (URT) niches may contribute the most to the composition of the lung microbiota.MethodsSeventeen upper and lower respiratory tract locations were sampled from 15 healthy feedlot steer calves. Samples were collected using a combination of swabs, protected specimen brushes, and saline washes. DNA was extracted from each sample and the 16S rRNA gene (V3-V4) was sequenced. Community composition, alpha-diversity, and beta-diversity were compared among sampling locations.ResultsMicrobiota composition differed across sampling locations, with physiologically and anatomically distinct locations showing different relative abundances of 1137 observed sequence variants (SVs). An analysis of similarities showed that the lung was more similar to the nasopharynx (R-statistic = 0.091) than it was to the oropharynx (R-statistic = 0.709) or any other URT sampling location. Five distinct metacommunities were identified across all samples after clustering at the genus level using Dirichlet multinomial mixtures. This included a metacommunity found primarily in the lung and nasopharynx that was dominated by Mycoplasma. Further clustering at the SV level showed a shared metacommunity between the lung and nasopharynx that was dominated by Mycoplasma dispar. Other metacommunities found in the nostrils, tonsils, and oral microbiotas were dominated by Moraxella, Fusobacterium, and Streptococcus, respectively.ConclusionsThe nasopharyngeal bacterial microbiota is most similar to the lung bacterial microbiota in healthy cattle and therefore may serve as the primary source of bacteria to the lung. This finding indicates that the nasopharynx is likely the most important location that should be targeted when doing bovine respiratory microbiota research. Video abstract.

Project description:BackgroundUnderstanding the complex structures and interactions of the bacterial communities inhabiting the upper (URT) and lower (LRT) respiratory tract of pigs is at an early stage. The objective of this study was to characterize the bacterial topography of three URT (nostrils, choana, and tonsils) and LRT (proximal trachea, left caudal lobe and secondary bronchi) sites in pigs. Thirty-six post-mortem samples from six pigs were analysed by 16S rRNA gene quantification and sequencing, and the microbiota in nostrils and trachea was additionally profiled by shotgun sequencing.ResultsThe bacterial composition obtained by the two methods was congruent, although metagenomics recovered only a fraction of the diversity (32 metagenome-assembled genomes) due to the high proportion (85-98%) of host DNA. The highest abundance of 16S rRNA copies was observed in nostrils, followed by tonsils, trachea, bronchi, choana and lung. Bacterial richness and diversity were lower in the LRT compared to the URT. Overall, Firmicutes and Proteobacteria were identified as predominant taxa in all sample types. Glasserella (15.7%), Streptococcus (14.6%) and Clostridium (10.1%) were the most abundant genera but differences in microbiota composition were observed between the two tracts as well as between sampling sites within the same tract. Clear-cut differences were observed between nasal and tonsillar microbiomes (R-values 0.85-0.93), whereas bacterial communities inhabiting trachea and lung were similar (R-values 0.10-0.17). Moraxella and Streptococcus were more common in bronchial mucosal scraping than in lavage, probably because of mucosal adherence. The bacterial microbiota of the choana was less diverse than that of the nostrils and similar to the tracheal microbiota (R-value 0.24), suggesting that the posterior nasal cavity serves as the primary source of bacteria for the LRT.ConclusionWe provide new knowledge on microbiota composition and species abundance in distinct ecological niches of the pig respiratory tract. Our results shed light on the distribution of opportunistic bacterial pathogens across the respiratory tract and support the hypothesis that bacteria present in the lungs originate from the posterior nasal cavity. Due to the high abundance of host DNA, high-resolution profiling of the pig respiratory microbiota by shotgun sequencing requires methods for host DNA depletion.

Dataset Information

Topography of the respiratory, oral, and guttural pouch bacterial and fungal microbiotas in horses.

Background

Hypothesis

Objective

Animals

Methods

Results

Conclusions and clinical importance

Publications

Topography of the respiratory, oral, and guttural pouch bacterial and fungal microbiotas in horses.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets