Abstract
BackgroundPreweaned rumen development is vital for animal health and efficient fermentation. In this study, we integrated ruminal transcriptomic and metagenomic data to explore the dynamics of rumen functions, microbial colonization, and their functional interactions during the first 8 weeks of life in goats.ResultsThe dynamic rumen transcriptomic and microbial profiles both exhibited two distinct phases during early rumen development. The differentially expressed genes of the rumen transcriptome between the two phases showed that the immune-related response was enriched in the first phase and nutrient-related metabolism was enriched in the second phase, whereas the differentially expressed genes of the rumen microbiome were enriched in bacteriocin biosynthesis and glycolysis/gluconeogenesis activities. The developmental shift in the rumen transcriptome (at d 21) was earlier than the feed stimulus (at d 25) and the shift in the rumen microbiome (at d 42). Additionally, 15 temporal dynamic rumen gene modules and 20 microbial modules were revealed by coexpression network analysis. Functional correlations between the rumen and its microbiome were primarily involved in rumen pH homeostasis, nitrogen metabolism and the immune response. Rumen gene modules associated with the microbial alpha diversity index were also enriched in the immune response process.ConclusionsThe present study touched the critical developmental process of rumen functions, microbial colonization and their functional interactions during preweaned development. Taken together, these results demonstrated that rumen development at the first phase is more likely a programmed process rather than stimulation from feed and the microbiome, while the shift of rumen metagenomes was likely regulated by both the diet and host. The intensive functional correlations between rumen genes and the microbiome demonstrated that synergistic processes occurred between them during early rumen development.
Highlights
Preweaned rumen development is vital for animal health and efficient fermentation
This study provides a clearer understanding of rumen functional development, microbial colonization and their functional interactions in young ruminants that occur during the establishment from non-ruminant to ruminant, which may provide a mean to manipulate this process in the future to improve efficiency and productivity of ruminants
Gene ontology (GO) enrichment analysis of Differentially expressed genes (DEGs) between d 1 vs. d 7 was enriched in the immune system process
Summary
We integrated ruminal transcriptomic and metagenomic data to explore the dynamics of rumen functions, microbial colonization, and their functional interactions during the first 8 weeks of life in goats. Ruminant livestock has a complex digestive system that allows them to convert human-indigestible plant biomass into high-quality products such as milk and meat, due to complex microbiomes residing in the rumen. Promoting rumen functional development has always been a crucial target of neonatal livestock management [1]. The establishment of rumen function and its microbiota during postnatal development can be influenced by the changes in feeding management, such as weaning and diets [2]. The process from non-ruminant to ruminant is a key stage in the establishment of the microbiome, and the development of rumen immunity and growth [8, 9]
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