Metagenomic sequencing reveals swine lung microbial communities and metagenome-assembled genomes associated with lung lesions-a pilot study.
Lung lesions
Lung microbiome
Metagenome-assembled genomes
Metagenomic sequencing
Pig
Journal
International microbiology : the official journal of the Spanish Society for Microbiology
ISSN: 1618-1905
Titre abrégé: Int Microbiol
Pays: Switzerland
ID NLM: 9816585
Informations de publication
Date de publication:
Nov 2023
Nov 2023
Historique:
received:
11
11
2022
accepted:
11
03
2023
revised:
28
02
2023
medline:
3
11
2023
pubmed:
19
3
2023
entrez:
18
3
2023
Statut:
ppublish
Résumé
Low microbial biomass in the lungs, high host-DNA contamination and sampling difficulty limit the study on lung microbiome. Therefore, little is still known about lung microbial communities and their functions. Here, we perform a preliminary exploratory study to investigate the composition of swine lung microbial community using shotgun metagenomic sequencing and compare the microbial communities between healthy and severe-lesion lungs. We collected ten lavage-fluid samples from swine lungs (five from healthy lungs and five from severe-lesion lungs), and obtained their metagenomes by shotgun metagenomic sequencing. After filtering host genomic DNA contamination (93.5% ± 1.2%) in the lung metagenomic data, we annotated swine lung microbial communities ranging from four domains to 645 species. Compared with previous taxonomic annotation of the same samples by the 16S rRNA gene amplicon sequencing, it annotated the same number of family taxa but more genera and species. We next performed an association analysis between lung microbiome and host lung-lesion phenotype. We found three species (Mycoplasma hyopneumoniae, Ureaplasma diversum, and Mycoplasma hyorhinis) were associated with lung lesions, suggesting they might be the key species causing swine lung lesions. Furthermore, we successfully reconstructed the metagenome-assembled genomes (MAGs) of these three species using metagenomic binning. This pilot study showed us the feasibility and relevant limitations of shotgun metagenomic sequencing for the characterization of swine lung microbiome using lung lavage-fluid samples. The findings provided an enhanced understanding of the swine lung microbiome and its role in maintaining lung health and/or causing lung lesions.
Identifiants
pubmed: 36933182
doi: 10.1007/s10123-023-00345-1
pii: 10.1007/s10123-023-00345-1
doi:
Substances chimiques
RNA, Ribosomal, 16S
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
893-906Subventions
Organisme : Guangdong Sail Plan Introduction of Innovative and Entrepreneurship Research Team Program
ID : 2016YT03H062
Organisme : National Swine Industry and Technology System of China
ID : nycytx-009
Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.
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