Gut Microbial Diversity Analysis of Different Native Chickens and Screening of Chicken-Derived Probiotics

Simple Summary The gut microbiota plays a vital role in the growth and development of chickens, while environmental and host factors can influence its composition. This study sheds light on the variations in gut microbial diversity and structural composition among native chickens from different geographical environments, as well as different breeds of broiler and laying hens, revealing the presence of distinct microbial communities. Additionally, our investigation into chicken-derived probiotics, specifically Lactobacillus agilis MH1 and Lactobacillus salivarius ZJ1, uncovered their probiotic properties, favorable genomic profiles, and their ability to alleviate enteritis in mice. These findings provide a critical theoretical foundation for the study of native chickens and offer valuable guidance for the subsequent development and formulation of chicken-derived probiotics.Abstract The gut microbiota plays a critical role in the growth, development, nutritional digestion, and overall health of chickens. Furthermore, certain probiotics isolated from poultry intestines have demonstrated the potential to enhance immune function and production performance in chickens. To investigate the differences in gut microbiota among chickens from various geographical environments and different breeds of broiler and laying hens, we conducted 16S rRNA sequencing on the fecal microbiota of 140 Chinese native chickens and ten Roman layers. In addition, we isolated and screened the potential probiotics to examine their biological characteristics, genome profiles, and functionality in animals. Our findings revealed the significant variations in gut microbiota composition and structure between Tibetan chickens (ZJ), which reside in high-altitude regions, and Meihua chickens (MH) and Xuhai chickens (XH), which inhabit low-altitude regions. Specifically, Cupriavidus and Candidatus_Bacilloplasma were identified as unique microbial communities in high and low altitudes, respectively. Notably, among regions with similar altitudes, Luning chickens (LN) exhibited the lowest alpha diversity, accompanied by a remarkably high relative abundance of Firmicutes and Lactobacillus. Conversely, Wugu chickens (WGs) and Yaoshan chickens (YSs) displayed similar gut microbiota profiles. Furthermore, distinctive gut microbiota patterns were observed between the different breeds of broilers and laying hens. Commercial Roman layers (LMs) exhibited significantly lower alpha diversity compared to native chickens, and broilers and laying hens predominantly harbored Firmicutes, Bacteroidota, and Proteobacteria. Of particular interest, the probiotics Lactobacillus agilis MH1 and Lactobacillus salivarius ZJ1, derived from chicken feces, exhibited favorable genomic profiles, and demonstrated anti-colitis effects and immunomodulatory functions. These findings provide a crucial theoretical foundation for native chicken research and offer insights for the future development and formulation of chicken-derived probiotics.