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Metagenomic sequencing reveals swine lung microbial communities and metagenome-assembled genomes associated with lung lesions—a pilot study

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Abstract

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.

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Data availability

All shotgun metagenomic sequencing data are available through National Center for Biotechnology Information (NCBI) repositories under BioProject ID: PRJNA732170. (www.ncbi.nlm.nih.gov/bioproject/PRJNA732170).

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Funding

This work was supported by grants from National Swine Industry and Technology System of China (nycytx-009), Guangdong Sail Plan Introduction of Innovative and Entrepreneurship Research Team Program (2016YT03H062).

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Authors and Affiliations

  1. State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China

    Jingquan Li, Tao Huang, Mingpeng Zhang, Xinkai Tong, Jiaqi Chen, Zhou Zhang, Fei Huang, Huashui Ai & Lusheng Huang

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  1. Jingquan Li
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  2. Tao Huang
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  3. Mingpeng Zhang
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  4. Xinkai Tong
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  5. Jiaqi Chen
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  6. Zhou Zhang
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  7. Fei Huang
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  8. Huashui Ai
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  9. Lusheng Huang
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Contributions

H.A. conceived and designed the experiments, and revised the manuscript. L.H. conceived and designed the experiments, and revised the manuscript. J. L. analyzed the data, and wrote the manuscript. T. H., M.Z., X. T., J. C., Z. Z., and F.H. collected the samples and performed experiments. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Huashui Ai.

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All experimental animal works were conducted according to the guidelines for the care and use of experimental animals established by the Ministry of Agriculture of China. Animal Care and Use Committee in Jiangxi Agricultural University specially approved this project.

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Li, J., Huang, T., Zhang, M. et al. Metagenomic sequencing reveals swine lung microbial communities and metagenome-assembled genomes associated with lung lesions—a pilot study. Int Microbiol 26, 893–906 (2023). https://doi.org/10.1007/s10123-023-00345-1

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