Objective Avian Leukosis Virus (ALV) and Salmonella pullorum (SP) are two major pathogens that seriously threaten the healthy development of the poultry industry and cause huge economic losses. Therefore, this study focused on Huxiu chickens in Huaiyang area, aiming to explore the changes in intestinal flora after single infection and co-infection, in order to provide scientific basis for a deeper understanding of the pathogenic mechanism of the pathogens and disease prevention and control.

Method This study employed 16S rRNA gene sequencing technology to conduct a comprehensive assessment of the differences in intestinal microbial diversity, community structure, and functional pathways among the control group (Ctrl), the group with single infection of Pullorum disease (PD), the group with single infection of Avian leukemia (AL), and the co-infection group (DBL).

Result Compared with the Ctrl group, the PD, AL, and DBL groups exhibited a marked reduction in the number of OTUs and a significant decrease in alpha diversity (P < 0.05). Partial Least Squares-Discriminant Analysis (PLS-DA) revealed distinct clustering and separation of the microbial communities among the groups. At the phylum level, the ratio of Bacillota to Bacteroidota (the F/B ratio) was significantly reduced in the infected groups. At the genus level, the abundance of opportunistic pathogens, such as Acinetobacter, Chryseobacterium, and Saccharibacteria, were increased in the infection groups. Based on LEfSe results, the Bacilli characterized the microbiota of the PD group, whereas the Mediterraneibacter was enriched in the AL group. The DBL group was primarily distinguished by a significant enrichment of Enterobacteriaceae. KEGG functional prediction indicated that pathways related to the metabolism of cofactors and vitamins, and transport and catabolism were significantly enriched in the PD, AL, and DBL groups. Furthermore, the microbial community structure of the DBL group was highly similar to that of the AL group, with no significant differences observed in taxonomic composition or functional pathways. These results highlight the consistent patterns of gut microbiota dysbiosis and functional evolution between the AL and PD infection models.

Conclusion SP, ALV, and co-infection (DBL) all severely disrupted the homeostasis of the cecal microbiota in chickens. In response to the nutritional environment alterations induced by infection, the gut microbiota appears to employ compensatory regulatory mechanisms to enhance nutrient acquisition and metabolic capacity. Furthermore, SP and ALV may share common underlying pathogenic mechanisms, with ALV playing a dominant role during co-infection.