Summary
Under natural farming, environmental pathogenic microorganisms may invade and affect swine lungs, further resulting in lung lesions. However, few studies on swine lung microbiota and their potential relationship with lung lesions were reported. Here, we sampled 20 pigs from a hybrid herd raised under natural conditions; we recorded a lung‐lesion phenotype and investigated lung microbial communities by sequencing the V3‐V4 region of 16S
rRNA
gene for each individual. We found reduced microbial diversity but more biomass in the severe‐lesion lungs.
Methylotenera
,
Prevotella
,
Sphingobium
and
Lactobacillus
were the prominent bacteria in the healthy lungs, while
Mycoplasma
,
Ureaplasma
,
Sphingobium
,
Haemophilus
and
Phyllobacterium
were the most abundant microbes in the severe‐lesion lungs. Notably, we identified 64 lung‐lesion‐associated
OTU
s, of which two classified to
Mycoplasma
were positively associated with lung lesions and 62 showed negative association including thirteen classified to
Prevotella
and six to
Ruminococcus
. Cross‐validation analysis showed that lung microbiota explained 23.7% phenotypic variance of lung lesions, suggesting that lung microbiota had large effects on promoting lung healthy. Furthermore, 22
KEGG
pathways correlated with lung lesions were predicted. Altogether, our findings improve the knowledge about swine lung microbial communities and give insights into the relationship between lung microbiota and lung lesions.