Integrated Transcriptomics and Metagenomics Analyze the Dynamic Correlations Between Cecal Mucosal Tissue and Cecal Microbiota in Liangshan Yanying Chickens During Early Postnatal Development

Liangshan Yanying chicken, a precious indigenous Chinese breed listed in the Catalog of Livestock and Poultry Genetic Resources in China, is an economic pillar in Liangshan Yi ethnic area and critical for poverty alleviation-to-rural revitalization transition. It has excellent phenotypic traits, high nutritional value, unique flavor, and strong adaptability to 380–4500 m altitudes. However, the co-evolutionary mechanism between its cecal mucosal tissue and gut microbiota (key to intestinal homeostasis and productivity) remains unclear. We systematically investigated their dynamic crosstalk in 1-, 14-, and 28-day-old chickens (n=10/group) using transcriptomics, metagenomics, bioinformatics, and qPCR. Cecal length increased from 3.77 cm (1 d) to 8.98 cm (28 d), with higher growth rate at 14–28 d. We identified 67 DEGs (34 upregulated immune-related, 33 downregulated development-related) and 16 dynamically changed microbial taxa. Host-microbiota crosstalk was mediated by 52 shared KEGG pathways, with 10 core genes and 13 functional taxa maintaining homeostasis via PI3K-Akt pathway. This study first reveals a "gut microbial homeostasis" model for cecal dynamic homeostasis, providing insights for local poultry intestinal health and breeding.