Characterization of Lung Microbiomes in Pneumonic Hu Sheep Using Culture Technique and 16S rRNA Gene Sequencing

SIMPLE SUMMARY: Pneumonia, which represents a leading cause of mortality among sheep, presents a formidable peril to the sheep industry. In this study, we combine high-throughput 16SrRNA gene sequencing and bacterial culturing to meticulously examine the bacterial community present in lung samples obtained from healthy sheep, those with moderate pneumonia, and those suffering from severe pneumonia. The results demonstrate a significant decrease in pulmonary microbial diversity and alterations in taxonomic composition following the onset of pneumonia. Our results suggest that M. haemolytica and Fusobacterium are the crucial pathogens in the sheep pneumonia. In addition, the occurrence of sepsis in severe pneumonia sheep could contribute to the eventual mortality outcome. Taken together, the results of this study contribute to guiding preventive and therapeutic measures for pneumonia of different severities. ABSTRACT: Hu sheep, a locally bred species in China known for its high productivity, is currently suffering from pneumonia. Here, we combine high-throughput 16SrRNA gene sequencing and bacterial culturing to examine the bacterial community in pneumonic Hu Sheep lungs (p < 0.05). The results showed that the abundance and diversity of lung bacteria in healthy sheep were significantly higher than those in pneumonia sheep (p = 0.139), while there was no significant difference between moderate and severe pneumonia. Furthermore, the composition of the lung microbiota community underwent significant alterations between different levels of pneumonia severity. The application of LEfSe analysis revealed a notable enrichment of Mannheimiae within the lungs of sheep afflicted with moderate pneumonia (p < 0.01), surpassing the levels observed in their healthy counterparts. Additionally, Fusobacterium emerged as the prevailing bacterial group within the lungs of sheep suffering from severe pneumonia. Integrating the results of bacterial isolation and identification, we conclusively determined that Mannheimia haemolytica was the primary pathogenic bacterium within the lungs of sheep afflicted with moderate pneumonia. Furthermore, the exacerbation of pneumonia may be attributed to the synergistic interplay between Fusobacterium spp. and other bacterial species. Our results provide new insights for guiding preventive and therapeutic measures for pneumonia of different severities in sheep.