Comparative analysis of the pulmonary microbiome in healthy and diseased pigs

Li, Zongjie; Wang, Xin; Di, Di; Pan, Ruyi; Gao, Yun; Xiao, Changguang; Li, Beibei; Wei, Jianchao; Liu, Ke; Qiu, Yafeng; Ma, Zhiyong

doi:10.1007/s00438-020-01722-5

Cited by 15 publications

(18 citation statements)

References 36 publications

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“…We only identified four studies investigating the LRT microbiota composition in healthy pigs by 16S rRNA gene sequencing (Table 1), and their results often diverged. Two studies reported Proteobacteria and Firmicutes as the main phyla, but the third most dominant [43][44][45]. The discrepancies between the three studies could be due to age disparities in the studied animals, and to methodological differences in sampling and data analysis ( Table 1).…”

Section: Bacterial Topography Of the Healthy Respiratory Tractmentioning

confidence: 98%

“…Genera that include common bacterial PRDC pathogens, namely Streptococcus, Haemophilus, Pasteurella, and Bordetella, were found to be more relatively abundant in BAL samples from diseased animals, often in combination with a reduction of beneficial genera (e.g. Lactococcus and Lactobacillus) [44]. PRDC is also associated with changes in the composition of the URT microbiota, as evidenced by the higher abundance of Moraxella, Veillonella, and Porphyromonas in the oropharynx of PRDC-affected pigs [41].…”

Section: Relationship Of the Respiratory Microbiome With Diseasementioning

confidence: 99%

“…The discrepancies between the three studies could be due to age disparities in the studied animals, and to methodological differences in sampling and data analysis ( Table 1). The breeding environment could also have contributed to such discrepancies, given that in one study animals were housed in separate units in a biosafety level 2 (BSL2) facility [45], whereas animals were raised under natural conditions in the other two studies [43,44]. In addition, two studies failed to include negative and positive control samples [44,45], and some of the genera identified (e.g.…”

Section: Bacterial Topography Of the Healthy Respiratory Tractmentioning

confidence: 99%

“…The breeding environment could also have contributed to such discrepancies, given that in one study animals were housed in separate units in a biosafety level 2 (BSL2) facility [45], whereas animals were raised under natural conditions in the other two studies [43,44]. In addition, two studies failed to include negative and positive control samples [44,45], and some of the genera identified (e.g. Sphingobium and Escherichia) could be potential contaminants, especially in low biomass samples (see Section Methodological study limitations).…”

Section: Bacterial Topography Of the Healthy Respiratory Tractmentioning

confidence: 99%

“…The relationship between the respiratory microbiota and PRDC was evaluated by two recent studies comparing healthy and diseased pigs [41,44]. Genera that include common bacterial PRDC pathogens, namely Streptococcus, Haemophilus, Pasteurella, and Bordetella, were found to be more relatively abundant in BAL samples from diseased animals, often in combination with a reduction of beneficial genera (e.g.…”

Section: Relationship Of the Respiratory Microbiome With Diseasementioning

confidence: 99%

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The porcine respiratory microbiome: recent insights and future challenges

et al. 2021

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Understanding the structure of the respiratory microbiome and its complex interactions with opportunistic pathogenic bacteria has become a topic of great scientific and economic interest in livestock production, given the severe consequences of respiratory disease on animal health and welfare. The present review focuses on the microbial structures of the porcine upper and lower airways, and the factors that influence microbiome development and onset of respiratory disease. Following a literature search on PubMed and Scopus, 21 articles were selected based on defined exclusion criteria (20 studies performed by 16S rRNA gene sequencing and one by shotgun metagenomics). Analysis of the selected literature indicated that the microbial structure of the upper respiratory tract undergoes a remarkable evolution after birth and tends to stabilise around weaning. Antimicrobial treatment, gaseous ammonia concentration, diet and floor type are amongst the recognized environmental factors influencing microbiome structure. The predominant phyla of the upper respiratory tract are Proteobacteria and Firmicutes with significant differences at the genus level between the nasal and the oropharyngeal cavity. Only five studies investigated the lower respiratory tract and their results diverged in relation to the relative abundance of these two phyla and even more in the composition of the lung microbiome at the genus level, likely because of methodological differences. Reduced diversity and imbalanced microbial composition are associated with an increased risk of respiratory disease. However, most studies presented methodological pitfalls concerning specimen collection, sequencing target and depth, and lack of quality control. Standardization of sampling and sequencing procedures would contribute to a better understanding of the structure of the microbiota inhabiting the lower respiratory tract and its relationship with pig health and disease.

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Section: Bacterial Topography Of the Healthy Respiratory Tractmentioning

confidence: 98%

Section: Relationship Of the Respiratory Microbiome With Diseasementioning

confidence: 99%

Section: Bacterial Topography Of the Healthy Respiratory Tractmentioning

confidence: 99%

Section: Bacterial Topography Of the Healthy Respiratory Tractmentioning

confidence: 99%

Section: Relationship Of the Respiratory Microbiome With Diseasementioning

confidence: 99%

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The porcine respiratory microbiome: recent insights and future challenges

et al. 2021

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Comprehensive lung microbial gene and genome catalogs assist the mechanism survey of Mesomycoplasma hyopneumoniae strains causing pig lung lesions

Li,

Huang,

Zhou

et al. 2024

iMeta

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Understanding the community structure of the lower respiratory tract microbiome is crucial for elucidating its roles in respiratory tract diseases. However, there are few studies about this topic due to the difficulty in obtaining microbial samples from both healthy and disease individuals. Here, using 744 high‐depth metagenomic sequencing data of lower respiratory tract microbial samples from 675 well‐phenotyped pigs, we constructed a lung microbial gene catalog containing the largest scale of 10,031,593 nonredundant genes to date, 44.8% of which are novel. We obtained 356 metagenome‐assembled genomes (MAGs) which were further clustered into 256 species‐level genome bins with 41.8% being first reported in the current databases. Based on these data sets and through integrated analysis of the isolation of the related bacterial strains, in vitro infection, and RNA sequencing, we identified and confirmed that Mesomycoplasma hyopneumoniae (M. hyopneumoniae) MAG_47 and its adhesion‐related virulence factors (VFs) were associated with lung lesions in pigs. Differential expression levels of adhesion‐ and immunomodulation‐related VFs likely determined the heterogenicity of adhesion and pathogenicity among M. hyopneumoniae strains. M. hyopneumoniae adhesion activated several pathways, including nuclear factor kappa‐light‐chain‐enhancer of activated B, mitogen‐activated protein kinase, cell apoptosis, T helper 1 and T helper 2 cell differentiation, tumor necrosis factor signaling, interleukin‐6/janus kinase 2/signal transducer and activator of transcription signaling, and response to reactive oxygen species, leading to cilium loss, epithelial cell‒cell barrier disruption, and lung tissue lesions. Finally, we observed the similar phylogenetic compositions of the lung microbiome between humans with Mycoplasma pneumoniae and pigs infected with M. hyopneumoniae. The results provided important insights into pig lower respiratory tract microbiome and its relationship with lung health.

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

Huang

Zhang

et al. 2023

Int Microbiol

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Comparative analysis of the pulmonary microbiome in healthy and diseased pigs

Cited by 15 publications

References 36 publications

The porcine respiratory microbiome: recent insights and future challenges

The porcine respiratory microbiome: recent insights and future challenges

Comprehensive lung microbial gene and genome catalogs assist the mechanism survey of Mesomycoplasma hyopneumoniae strains causing pig lung lesions

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

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