| Summary: | This study aimed to investigate the changes in abomasum transcriptome and the associated microbial community structure in young calves with artificially dosed, adult rumen contents. Eight young bull calves were randomly dosed with freshly extracted rumen contents from an adult cow (high efficiency (HE), <i>n</i> = 4), or sterilized rumen content (Con, <i>n</i> = 4). The dosing was administered within 3 days of birth, then at 2, 4, and 6 weeks following the initial dosing. Abomasum tissues were collected immediately after sacrifice at 8 weeks of age. Five genera (<i>Tannerella, Desulfovibrio, Deinococcus, Leptotrichia, and Eubacterium</i>; <i>P</i> < 0.05) showed significant difference in abundance between the treatments. A total of 975 differentially expressed genes were identified (<i>P</i> < 0.05, fold-change > 1.5, mean read-counts > 5). Pathway analysis indicated that up-regulated genes were involved in immune system process and defense response to virus, while the down-regulated genes involved in ion transport, ATP biosynthetic process, and mitochondrial electron transport. Positive correlation (r > 0.7, <i>P</i> < 0.05) was observed between <i>TRPM4</i> gene and <i>Desulfovibrio</i>, which was significantly higher in the HE group. <i>TRPM4</i> had a reported role in the immune system process. In conclusion, the dosing of adult rumen contents to calves can alter not only the composition of active microorganisms in the abomasum but also the molecular mechanisms in the abomasum tissue, including reduced protease secretion and decreased hydrochloric acid secretion.
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