The Signature Microbiota Driving Rumen Function Shifts in Goat Kids Introduced Solid Diet Regimes

The feeding regime of early supplementary solid diet improved rumen development and ruminant production. However, the signature microbiota linking dietary regimes to rumen function shifts and hosts are still unclear. We analyzed the rumen microbiome and functions affected by supplementation of solid diet using a combination of machine learning algorithms. The volatile fatty acids (i.e., acetate, propionate and butyrate) fermented by microbes increased significantly in the supplementary solid diet groups. The predominant genera altered significantly from unclassified Sphingobacteriaceae (non-supplementary group) to Prevotella (supplementary solid diet groups) RandomForest classification model revealed signature microbiota for solid diet that positively correlated with macronutrient intake, and linearly increased with volatile fatty acids production. The nutrient specific bacteria for carbohydrate and protein were also identified. According to FishTaco analysis, a set of intersecting core species contributed with rumen function shifts by solid diet. The core community structures consisted of specific signature microbiota and their symbiotic partners are manipulated by extra nutrients from concentrate and/or forage, and then produce more volatile fatty acids to promote rumen development and functions eventually host development. Our study provides mechanism of microbiome governing by solid diet and highlights the signatures microbiota for animal health and production.ImportanceSmall ruminants are essential protein sources for human, so keeping them health and increasing their production are important. The microbial communities resided in rumen play key roles to convert fiber resources to human food. Moreover, rumen physiology experience huge changes after birth, and understanding its microbiome roles could provide insights for other species. Recently, our studies and others have shown that diet changed rumen microbial composition and goat performance. In this study, we identified core community structures that were affected by diet and associated to the rumen development and goat production. This outcome could potentially allow us to select specific microbiome to improve rumen physiology and functions, maintain host health and benefit animal production. Therefore, it gives a significant clue that core microbiome manipulation by feeding strategies can increase animal products. To our knowledge, we firstly used FishTaco for determination of link between signatures abundances and rumen function shifts.