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Characterization of the upper and lower respiratory tract microbiota in Piedmontese calves

BACKGROUND: The microbiota of the bovine upper respiratory tract has been recently characterized, but no data for the lower respiratory tract are available. A major health problem in bovine medicine is infectious bronchopneumonia, the most common respiratory syndrome affecting cattle. With this stud...

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Autores principales: Nicola, Isabella, Cerutti, Francesco, Grego, Elena, Bertone, Iride, Gianella, Paola, D’Angelo, Antonio, Peletto, Simone, Bellino, Claudio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5697440/
https://www.ncbi.nlm.nih.gov/pubmed/29157308
http://dx.doi.org/10.1186/s40168-017-0372-5
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author Nicola, Isabella
Cerutti, Francesco
Grego, Elena
Bertone, Iride
Gianella, Paola
D’Angelo, Antonio
Peletto, Simone
Bellino, Claudio
author_facet Nicola, Isabella
Cerutti, Francesco
Grego, Elena
Bertone, Iride
Gianella, Paola
D’Angelo, Antonio
Peletto, Simone
Bellino, Claudio
author_sort Nicola, Isabella
collection PubMed
description BACKGROUND: The microbiota of the bovine upper respiratory tract has been recently characterized, but no data for the lower respiratory tract are available. A major health problem in bovine medicine is infectious bronchopneumonia, the most common respiratory syndrome affecting cattle. With this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community composition of the upper and lower respiratory tracts in calves. RESULTS: The microbiota of the upper (nasal swab [NS]) and the lower (trans-tracheal aspiration [TTA]) respiratory tracts of 19 post-weaned Piedmontese calves with (8/19) and without (11/19) clinical signs of respiratory disease, coming from six different farms, was characterized by 16S rRNA gene metabarcoding. A total of 29 phyla (29 in NS, 21 in TTA) and 305 genera (289 in NS, 182 in TTA) were identified. Mycoplasma (60.8%) was the most abundant genus identified in both the NS (27.3%) and TTA (76.7%) samples, followed by Moraxella (16.6%) in the NS and Pasteurella (7.3%) in the TTA samples. Pasteurella multocida (7.3% of total operational taxonomic units [OTUs]) was the most abundant species in the TTA and Psychrobacter sanguinis (1.1% of total OTUs) in the NS samples. Statistically significant differences between the NS and the TTA samples were found for both alpha (Shannon index, observed species, Chao1 index, and Simpson index; P = 0.001) and beta (Adonis; P = 0.001) diversity. Comparison of the NS and TTA samples by farm origin and clinical signs revealed no statistical difference (P > 0.05), except for farm origin for the NS samples when compared by the unweighted UniFrac metric (P = 0.05). CONCLUSIONS: Using 16S rRNA gene sequencing, we characterized the microbiota of the upper and lower respiratory tracts of calves, both healthy individuals and those with clinical signs of respiratory disease. Our results suggest that environmental factors may influence the composition of the upper airway microbiota in cattle. While the two microbial communities (upper and lower airways) differed in microbial composition, they shared several OTUs, suggesting that the lung microbiota may be a self-sustaining, more homogeneous ecosystem, influenced by the upper respiratory tract microbiota. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s40168-017-0372-5) contains supplementary material, which is available to authorized users.
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spelling pubmed-56974402017-12-01 Characterization of the upper and lower respiratory tract microbiota in Piedmontese calves Nicola, Isabella Cerutti, Francesco Grego, Elena Bertone, Iride Gianella, Paola D’Angelo, Antonio Peletto, Simone Bellino, Claudio Microbiome Research BACKGROUND: The microbiota of the bovine upper respiratory tract has been recently characterized, but no data for the lower respiratory tract are available. A major health problem in bovine medicine is infectious bronchopneumonia, the most common respiratory syndrome affecting cattle. With this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community composition of the upper and lower respiratory tracts in calves. RESULTS: The microbiota of the upper (nasal swab [NS]) and the lower (trans-tracheal aspiration [TTA]) respiratory tracts of 19 post-weaned Piedmontese calves with (8/19) and without (11/19) clinical signs of respiratory disease, coming from six different farms, was characterized by 16S rRNA gene metabarcoding. A total of 29 phyla (29 in NS, 21 in TTA) and 305 genera (289 in NS, 182 in TTA) were identified. Mycoplasma (60.8%) was the most abundant genus identified in both the NS (27.3%) and TTA (76.7%) samples, followed by Moraxella (16.6%) in the NS and Pasteurella (7.3%) in the TTA samples. Pasteurella multocida (7.3% of total operational taxonomic units [OTUs]) was the most abundant species in the TTA and Psychrobacter sanguinis (1.1% of total OTUs) in the NS samples. Statistically significant differences between the NS and the TTA samples were found for both alpha (Shannon index, observed species, Chao1 index, and Simpson index; P = 0.001) and beta (Adonis; P = 0.001) diversity. Comparison of the NS and TTA samples by farm origin and clinical signs revealed no statistical difference (P > 0.05), except for farm origin for the NS samples when compared by the unweighted UniFrac metric (P = 0.05). CONCLUSIONS: Using 16S rRNA gene sequencing, we characterized the microbiota of the upper and lower respiratory tracts of calves, both healthy individuals and those with clinical signs of respiratory disease. Our results suggest that environmental factors may influence the composition of the upper airway microbiota in cattle. While the two microbial communities (upper and lower airways) differed in microbial composition, they shared several OTUs, suggesting that the lung microbiota may be a self-sustaining, more homogeneous ecosystem, influenced by the upper respiratory tract microbiota. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s40168-017-0372-5) contains supplementary material, which is available to authorized users. BioMed Central 2017-11-21 /pmc/articles/PMC5697440/ /pubmed/29157308 http://dx.doi.org/10.1186/s40168-017-0372-5 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Nicola, Isabella
Cerutti, Francesco
Grego, Elena
Bertone, Iride
Gianella, Paola
D’Angelo, Antonio
Peletto, Simone
Bellino, Claudio
Characterization of the upper and lower respiratory tract microbiota in Piedmontese calves
title Characterization of the upper and lower respiratory tract microbiota in Piedmontese calves
title_full Characterization of the upper and lower respiratory tract microbiota in Piedmontese calves
title_fullStr Characterization of the upper and lower respiratory tract microbiota in Piedmontese calves
title_full_unstemmed Characterization of the upper and lower respiratory tract microbiota in Piedmontese calves
title_short Characterization of the upper and lower respiratory tract microbiota in Piedmontese calves
title_sort characterization of the upper and lower respiratory tract microbiota in piedmontese calves
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5697440/
https://www.ncbi.nlm.nih.gov/pubmed/29157308
http://dx.doi.org/10.1186/s40168-017-0372-5
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