Transcriptome sequencing reveals non-coding RNAs respond to porcine reproductive and respiratory syndrome virus and Haemophilus parasuis co-infection in Kele piglets.

Co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and Haemophilus parasuis (HPS) has severely restricted the healthy development of pig breeding. Exploring disease resistance of non-coding RNAs in pigs co-infected with PRRSV and HPS is therefore critical to complement and elucidate the molecular mechanisms of disease resistance in Kele piglets and to innovate the use of local pig germplasm resources in China. RNA-seq of lungs from Kele piglets with single-infection of PRRSV or HPS and co-infection of both pathogens was performed. Two hundred and twenty-five differentially expressed long non-coding RNAs (DElncRNAs) and 30 DEmicroRNAs (DEmiRNAs) were identified and characterized in the PRRSV and HPS co-infection (PRRSV-HPS) group. Compared with the single-infection groups, 146 unique DElncRNAs, 17 unique DEmiRNAs, and 206 target differentially expressed genes (DEGs) were identified in the PRRSV-HPS group. The expression patterns of 20 DEmiRNAs and DElncRNAs confirmed by real-time quantitative polymerase chain reaction (RT-qPCR) were consistent with those determined by high-throughput sequencing. In the PRRSV-HPS group, the target DEGs were enriched in eight immune Gene Ontology terms relating to two unique DEmiRNAs and 16 DElncRNAs, and the unique target DEGs participated the host immune response to pathogens infection by affecting 15 immune-related Kyoto Encyclopedia of Genes and Genomes enrichment pathways. Notably, competitive endogenous RNA (ceRNA) networks of different groups were constructed, and the ssc-miR-671-5p miRNA was validated as a potential regulatory factor to regulate DTX4 and AEBP1 genes to achieve innate antiviral effects and inhibit pulmonary fibrosis by dual-luciferase reporter assays. These results provided insight into further study on the molecular mechanisms of resistance to PRRSV and HPS co-infection in Kele piglets.

Exploring the microbial ecosystem of Berchemia polyphylla var. leioclada: a comprehensive analysis of endophytes and rhizospheric soil microorganisms.

Endophytic and rhizospheric microorganisms associated with plants play a crucial role in plant health, pest and disease defense, and fruit yield by actively participating in the plant's adaptation to its environment. In this study, high-throughput sequencing technology was employed to analyze the community structure and diversity of endophytic and rhizospheric soil microorganisms in Berchemia polyphylla var. leioclada. The results revealed significant differences in microbial diversity and community structure between the soil and plant compartments within the same geographic region. Microbial diversity and species composition varied among different geographic locations. The dominant bacteria in plants were Cyanobacteria and Proteobacteria, with dominant genera including Methylobacterium-Methylorubrum, Escherichia-Shigella and Sphingomonas. In contrast, the dominant bacteria in soil were Proteobacteria, Acidobacteriota, and Actinobacteriota, with dominant genera such as Sphingomonas, Conexibacter and Vicinamibacteraceae, with Sphingomonas was considered core groups present in all plant and soil samples. As for fungi, the dominant phyla in both plants and soil were Ascomycota, Basidiomycota, and Mortierellomycota, with different dominant genera between the two compartments, including Fusarium, Septoria, and Mortierella, totaling 59 genera. Linear discriminant analysis at the genus level identified 102 bacterial and 54 fungal indicator taxa associated with plants and soil. Co-occurrence network analysis indicated close interactions among soil bacterial microorganisms. Functional prediction of the top 10 microbial genes revealed three bacterial metabolic pathways shared between soil and plants, while the predominant fungal metabolic types were similar between the two compartments but with varying abundances. This study elucidates the diversity and interplay of endophytic and rhizospheric microorganisms in Berchemia polyphylla var. leioclada across diverse geographical regions, providing insights crucial for the plant's conservation and development.

Transcriptome profiling identifies immune response genes against porcine reproductive and respiratory syndrome virus and Haemophilus parasuis co-infection in the lungs of piglets.

BACKGROUND: Co-infections of the porcine reproductive and respiratory syndrome virus (PRRSV) and the Haemophilus parasuis (HPS) are severe in Chinese pigs, but the immune response genes against co-infected with 2 pathogens in the lungs have not been reported. OBJECTIVES: To understand the effect of PRRSV and/or HPS infection on the genes expression associated with lung immune function. METHODS: The expression of the immune-related genes was analyzed using RNA-sequencing and bioinformatics. Differentially expressed genes (DEGs) were detected and identified by quantitative real-time polymerase chain reaction (qRT-PCR), immunohistochemistry (IHC) and western blotting assays. RESULTS: All experimental pigs showed clinical symptoms and lung lesions. RNA-seq analysis showed that 922 DEGs in co-challenged pigs were more than in the HPS group (709 DEGs) and the PRRSV group (676 DEGs). Eleven DEGs validated by qRT-PCR were consistent with the RNA sequencing results. Eleven common Kyoto Encyclopedia of Genes and Genomes pathways related to infection and immune were found in single-infected and co-challenged pigs, including autophagy, cytokine-cytokine receptor interaction, and antigen processing and presentation, involving different DEGs. A model of immune response to infection with PRRSV and HPS was predicted among the DEGs in the co-challenged pigs. Dual oxidase 1 (DUOX1) and interleukin-21 (IL21) were detected by IHC and western blot and showed significant differences between the co-challenged pigs and the controls. CONCLUSIONS: These findings elucidated the transcriptome changes in the lungs after PRRSV and/or HPS infections, providing ideas for further study to inhibit ROS production and promote pulmonary fibrosis caused by co-challenging with PRRSV and HPS.

Effects of respiratory disease on Kele piglets lung microbiome, assessed through 16S rRNA sequencing.

BACKGROUND AND AIM: Due to the incomplete development of the immune system in immature piglets, the respiratory tract is susceptible to invasion by numerous pathogens that cause a range of potential respiratory diseases. However, few studies have reported the changes in pig lung microorganisms during respiratory infection. Therefore, we aimed to explore the differences in lung environmental microorganisms between healthy piglets and piglets with respiratory diseases. MATERIALS AND METHODS: Histopathological changes in lung sections were observed in both diseased and healthy pigs. Changes in the composition and abundance of microbiomes in alveolar lavage fluid from eleven 4-week-old Chinese Kele piglets (three clinically healthy and eight diseased) were studied by IonS5™ XL sequencing of the bacterial16S rRNA genes. RESULTS: Histopathological sections showed that diseased pigs displayed more lung lesions than healthy pigs. Diseased piglets harbored lower bacterial operational taxonomic units, α-diversity, and bacterial community complexity in comparison to healthy piglets. Taxonomic composition analysis showed that in the diseased piglets, the majority of flora was composed of Ureaplasma, Mycoplasma, and Actinobacillus; while Actinobacillus, Sphingomonas, and Stenotrophomonas were dominant in the control group. The abundance of Ureaplasma was significantly higher in ill piglets (p<0.05), and the phylogenetic tree indicated that Ureaplasma was clustered in Ureaplasma diversum, a conditional pathogen that has the potential to affect the swine respiratory system. CONCLUSION: The results of this study show that the microbial species and structure of piglets' lungs were changed during respiratory tract infection. The finding of Ureaplasma suggested that besides known pathogens such as Mycoplasma and Actinobacillus, unknown pathogens can exist in the respiratory system of diseased pigs and provide a potential basis for clinical treatment.