Amplicon-based metagenomic association analysis of gut microbiota in relation to egg-laying period and breeds of hens

Abstract Background Gut microbiota plays a vital role in the maintenance of gut homeostasis and the improvement of performance. The gut microbiota of laying hens is visibly different in different laying stages, which correlates significantly with egg production. To better understand the association between characteristics of microbial community and different laying periods in Hyland brown and Isa laying hens, we conducted a 16S rRNA amplicon sequencing survey. Results Our result revealed the diversity of bacteria in the early laying period was commonly higher than peak, and in Hyland brown laying hens were generally higher than Isa. Principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) revealed that the structure and composition of the gut microbiota of laying hens exhibited significant differences among different groups. Phylum Firmicutes, Bacteroidota, Proteobacteria, and Fusobacteriota were found that dominated in the host’s feces. Therein, the abundance of Fusobacteriota was higher in the peak period than in the early period, while the abundance of Cyanobacteria in the early period was higher in two breeds of hens. Furthermore, random forest based on machine learning showed that there were several distinctly abundant genera, which can be used as potential biomarkers to differentiate the different groups of laying periods and breeds. In addition, the prediction of biological function indicated the existing discrepancy in microbial function among the microbiota of four groups. Conclusions Our findings provide new insights for understanding the bacterial diversity and intestinal flora composition of different strains of laying hens during different laying periods, and contributed beneficially to improving the production performance of laying hens and preventing chicken diseases.