The transcriptome construction and microbial succession pattern in the intestinal tract of 3–5 month-old yak calves

Abstract This study investigated age-dependent intestinal development in yak calves by integrating intestinal morphology, 16S rRNA sequencing, and jejunal transcriptome analyses across 3, 4, and 5 months of age. Results demonstrated progressive intestinal maturation characterized by preferential development of the large intestine, dynamic microbial succession, and enhanced metabolic functions. Functional prediction revealed enrichment of pathways associated with nucleotide metabolism, energy metabolism, amino acid metabolism, and microbial biosynthesis in older calves. Transcriptomic analysis identified ROS1 and several immune-related genes (including SAMD9, RIG-I, IFIH1, EIF2AK2, IL12RB2, and RSAD2) as potential regulators of jejunal development and immune maturation. GO and KEGG analyses further indicated significant enrichment of immune activation, immune cell differentiation, and immune regulatory pathways. These findings provide novel insights into host–microbiota interactions underlying early intestinal development in yak calves.