Microbiome-host co-oscillation patterns in shaping ruminal ecosystem from birth to puberty in a goat model

The maturation of the gastrointestinal tract and its interconnected microbial consortia in various ruminant species is essential for their survival and productivity, as this symbiotic group plays a key role in metabolizing phyto-derived feeds into bioavailable nutrients. The rumen mucosa serves as a crucial conduit for complex host-microbiota interplay, while scarce knowledge is available regarding their co-oscillation patterns from birth to puberty. Here, we characterized th overall interaction of five age groups, from 1-day-old to 90-day-old goats. The findings indicated that the composition of the mucosa-attached microbiota underwent significant changes, with Mannheimia, Porphyromonas and Streptococcus taking the lead as the dominant genera at day 1, Akkermansia muciniphila and Lactobacillus amylovorus dominated at day 10, and a mature microbiota characterized by Succiniclasticum ruminis, Ruminococcus albus, Succinivibrio dextrinosolvens, and Fibrobacter succinogenes until day 90. Additionally, the rumen mucosa underwent a three-phase temporal shift during early life, from digestive system to immune development, and finally to nutrient metabolism. Furthermore, the integration of mucosal microbiome and host gene expression profiles uncovered a phase-specific interaction between the microbial community and host epithelium, with the early phase emphasizing digestive and immune development and the later phase focusing on enhanced nutrient metabolism. Collectively, microbiome-host co-oscillation in the rumen mucosa shaped the ruminal ecosystem during early life.