Topography of the respiratory tract bacterial microbiota in cattle
Abstract Background Bacterial 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 re...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-06-01
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| Series: | Microbiome |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s40168-020-00869-y |
| _version_ | 1819020501490597888 |
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| author | Christopher McMullen Trevor W. Alexander Renaud Léguillette Matthew Workentine Edouard Timsit |
| author_facet | Christopher McMullen Trevor W. Alexander Renaud Léguillette Matthew Workentine Edouard Timsit |
| author_sort | Christopher McMullen |
| collection | DOAJ |
| description | Abstract Background Bacterial 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. Methods Seventeen 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. Results Microbiota 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. Conclusions The 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. |
| first_indexed | 2024-12-21T03:52:13Z |
| format | Article |
| id | doaj.art-cdef583512c941ee9d92f76dc42b94f7 |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-12-21T03:52:13Z |
| publishDate | 2020-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj.art-cdef583512c941ee9d92f76dc42b94f72022-12-21T19:16:57ZengBMCMicrobiome2049-26182020-06-018111510.1186/s40168-020-00869-yTopography of the respiratory tract bacterial microbiota in cattleChristopher McMullen0Trevor W. Alexander1Renaud Léguillette2Matthew Workentine3Edouard Timsit4Faculty of Veterinary Medicine, University of CalgaryLethbridge Research and Development Center, Agriculture and Agri-Food CanadaFaculty of Veterinary Medicine, University of CalgaryFaculty of Veterinary Medicine, University of CalgaryFaculty of Veterinary Medicine, University of CalgaryAbstract Background Bacterial 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. Methods Seventeen 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. Results Microbiota 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. Conclusions The 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.http://link.springer.com/article/10.1186/s40168-020-00869-yMicrobiomeBovine respiratory diseaseNatural cattleAntibiotic free |
| spellingShingle | Christopher McMullen Trevor W. Alexander Renaud Léguillette Matthew Workentine Edouard Timsit Topography of the respiratory tract bacterial microbiota in cattle Microbiome Microbiome Bovine respiratory disease Natural cattle Antibiotic free |
| title | Topography of the respiratory tract bacterial microbiota in cattle |
| title_full | Topography of the respiratory tract bacterial microbiota in cattle |
| title_fullStr | Topography of the respiratory tract bacterial microbiota in cattle |
| title_full_unstemmed | Topography of the respiratory tract bacterial microbiota in cattle |
| title_short | Topography of the respiratory tract bacterial microbiota in cattle |
| title_sort | topography of the respiratory tract bacterial microbiota in cattle |
| topic | Microbiome Bovine respiratory disease Natural cattle Antibiotic free |
| url | http://link.springer.com/article/10.1186/s40168-020-00869-y |
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