Maturation of the Goat Rumen Microbiota Involves Three Stages of Microbial Colonization

Simple Summary Considerable attention has recently been focused on the rumen microbiome, which has been implicated in regulating a ruminant's nutrient metabolism. From birth onwards, the colonization of the rumen microbial community is thus of crucial importance for growth and fiber digestion of goats. In this study, we have provided details of the progression of changes and colonization of ruminal bacteria and fungi before weaning. We have also predicted the molecular functions of the bacterial microbiota using CowPi. Our finding confirmed that maturation of the goat rumen microbiota involves three stages of core microbial colonization. The study of rumen microbial of young ruminants will benefit the optimization of feeding strategies to promote the development and digestion of a healthy rumen microbiota in later life. Abstract With increasing age, the rumen microbiota of new-born ruminants become central in the translation of fibrous feed substances into essential nutrients. However, the colonization process of the microbial community (especially fungal community) remains poorly understood in ruminants at pre-weaning stages. In this study, the rumen bacterial and fungal colonization processes were investigated in goats at eight stages using amplicon sequencing. For bacteria, we found 36 common core genera at D0, D3, D14, D28, and D56, including mainly Bacillus, Alloprevotella, Bacteroides, Prevotella_1, Lactococcus, and Ruminococcaceae_NK4A214. Firmicutes was the dominant phylum among the total microbiota in newborn goat kids (prior to nursing), while Bacillus, Lactococcus, and Pseudomonas were predominant genera. Interestingly, the proportion of Bacillus was as high as 55% in newborn animals. After milk nursing, the predominant phylum changed to Bacteroidetes, while the proportion of Bacillus and Lactobacillus was very low. CowPi was used to predict the functional gene pathways and we found increases in the abundance of genes associated with amino acid related enzymes, DNA repair and recombination proteins, aminoacyl tRNA biosynthesis, and peptidases after D3. With regard to fungi, we found that there were 51 common genera at day 0 (D0), D3, D14, D28, and D56, including mainly Cryptococcus, Aspergillus, and Caecomyces. Aspergillus occupied approximately 47% at day 0, but then it decreased from day 3 to day 14. This study indicates that the core microbes of rumen emerged shortly after birth, but the abundance was very different from the core genus of the adult rumen. In addition, we also report a detailed scheme of the bacterial and fungal colonization process in rumens and propose three distinct stages during the rumen colonization process in pre-weaning goats, which will offer a reference for the development of milk substitutes for small ruminants.