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Bacterial topography of the upper and lower respiratory tract in pigs

BACKGROUND: Understanding 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 tonsi...

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Autores principales: Pirolo, Mattia, Espinosa-Gongora, Carmen, Alberdi, Antton, Eisenhofer, Raphael, Soverini, Matteo, Eriksen, Esben Østergaard, Pedersen, Ken Steen, Guardabassi, Luca
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9843957/
https://www.ncbi.nlm.nih.gov/pubmed/36647171
http://dx.doi.org/10.1186/s42523-023-00226-y
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author Pirolo, Mattia
Espinosa-Gongora, Carmen
Alberdi, Antton
Eisenhofer, Raphael
Soverini, Matteo
Eriksen, Esben Østergaard
Pedersen, Ken Steen
Guardabassi, Luca
author_facet Pirolo, Mattia
Espinosa-Gongora, Carmen
Alberdi, Antton
Eisenhofer, Raphael
Soverini, Matteo
Eriksen, Esben Østergaard
Pedersen, Ken Steen
Guardabassi, Luca
author_sort Pirolo, Mattia
collection PubMed
description BACKGROUND: Understanding 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. RESULTS: The 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. CONCLUSION: We 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-023-00226-y.
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spelling pubmed-98439572023-01-18 Bacterial topography of the upper and lower respiratory tract in pigs Pirolo, Mattia Espinosa-Gongora, Carmen Alberdi, Antton Eisenhofer, Raphael Soverini, Matteo Eriksen, Esben Østergaard Pedersen, Ken Steen Guardabassi, Luca Anim Microbiome Research BACKGROUND: Understanding 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. RESULTS: The 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. CONCLUSION: We 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-023-00226-y. BioMed Central 2023-01-16 /pmc/articles/PMC9843957/ /pubmed/36647171 http://dx.doi.org/10.1186/s42523-023-00226-y Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Research
Pirolo, Mattia
Espinosa-Gongora, Carmen
Alberdi, Antton
Eisenhofer, Raphael
Soverini, Matteo
Eriksen, Esben Østergaard
Pedersen, Ken Steen
Guardabassi, Luca
Bacterial topography of the upper and lower respiratory tract in pigs
title Bacterial topography of the upper and lower respiratory tract in pigs
title_full Bacterial topography of the upper and lower respiratory tract in pigs
title_fullStr Bacterial topography of the upper and lower respiratory tract in pigs
title_full_unstemmed Bacterial topography of the upper and lower respiratory tract in pigs
title_short Bacterial topography of the upper and lower respiratory tract in pigs
title_sort bacterial topography of the upper and lower respiratory tract in pigs
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9843957/
https://www.ncbi.nlm.nih.gov/pubmed/36647171
http://dx.doi.org/10.1186/s42523-023-00226-y
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