Chen Xi, Guo Qing, Li Ying-Ying, Song Tie-Ying, Ge Jun-Qing
Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China.
Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China.
Front Vet Sci. 2023 Oct 17;10:1257573. doi: 10.3389/fvets.2023.1257573. eCollection 2023.
Porcine enteric diseases including swine dysentery involves a wide range of possible aetiologies and seriously damages the intestine of pigs of all ages. Metagenomic next-generation sequencing is commonly used in research for detecting and analyzing pathogens. In this study, the feces of pigs from a commercial swine farm with dysentery-like diarrhea was collected and used for microbiota analysis by next-generation sequencing. While spp. was not detected in diarrheal pig fecal samples, indicating that the disease was not swine dysentery. The quantity of microbial population was extremely lowered, and the bacterial composition was altered with a reduction in the relative abundance of the probiotics organisms, Firmicutes and Bacteroidetes, with an increase in pathogens like Fusobacterium and Proteobacteria, in which the specific bacteria were identified at species-level. Viral pathogens, porcine circovirus type 2, porcine lymphotropic herpesviruses 1, and porcine mastadenovirus A were also detected at pretty low levels. Carbohydrate-active enzymes (CAZy) analysis indicated that the constitute of Firmicutes and Bacteroidete were also changed. Further, the Kyoto Encyclopedia of Genes and Genomes (KEGG) alignment analysis indicated that the microbiota of diarrheal pigs had a lower ability in utilizing energy sources but were enriched in multi-drug resistance pathways. Comprehensive Antibiotic Resistance Database (CARD) and Virulence Factors of Pathogenic Bacteria (VFDB) analysis indicated that genes for elfamycin and sulfonamide resistance and the iron uptake system were enriched in diarrheal pigs. This revealed potential bacterial infection and can guide antibiotic selection for treating dysentery. Overall, our data suggested that alterations in both the population and functional attributes of microbiota in diarrheal pigs with decreased probiotic and increased pathogenic microorganisms. These results will help elucidate the mechanism of dysentery-like diarrhea and the development of approaches to control the disease.
包括猪痢疾在内的猪肠道疾病涉及多种可能的病因，会严重损害各年龄段猪的肠道。宏基因组下一代测序常用于病原体检测和分析研究。在本研究中，收集了一家商业养猪场患有痢疾样腹泻的猪的粪便，并通过下一代测序用于微生物群分析。虽然在腹泻猪粪便样本中未检测到 spp.，表明该疾病不是猪痢疾。微生物种群数量极低，细菌组成发生改变，益生菌厚壁菌门和拟杆菌门的相对丰度降低，而诸如梭杆菌属和变形菌门等病原体增加，其中特定细菌在种水平上得以鉴定。还检测到极低水平的病毒病原体，猪圆环病毒2型、猪嗜淋巴细胞性疱疹病毒1型和猪腺病毒A。碳水化合物活性酶（CAZy）分析表明，厚壁菌门和拟杆菌门的组成也发生了变化。此外，京都基因与基因组百科全书（KEGG）比对分析表明，腹泻猪的微生物群利用能源的能力较低，但在多药耐药途径中富集。综合抗生素抗性数据库（CARD）和病原菌毒力因子数据库（VFDB）分析表明，腹泻猪中埃弗霉素和磺胺类抗性基因以及铁摄取系统富集。这揭示了潜在的细菌感染，并可为治疗痢疾的抗生素选择提供指导。总体而言，我们的数据表明，腹泻猪中微生物群的数量和功能属性均发生改变，益生菌减少，致病微生物增加。这些结果将有助于阐明痢疾样腹泻的发病机制以及制定控制该疾病的方法。
