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

Abstract

22The feeding regime of early supplementary solid diet improved rumen 23 development and ruminant production. However, the signature microbiota linking 24 dietary regimes to rumen function shifts and hosts are still unclear. We analyzed the 25 rumen microbiome and functions affected by supplementation of solid diet using a 26 combination of machine learning algorithms. The volatile fatty acids (i.e., acetate, 27 propionate and butyrate) fermented by microbes increased significantly in the 28 supplementary solid diet groups. The predominant genera altered significantly from 29 unclassified Sphingobacteriaceae (non-supplementary group) to Prevotella 30 (supplementary solid diet groups) RandomForest classification model revealed 31 signature microbiota for solid diet that positively correlated with macronutrient intake, 32 and linearly increased with volatile fatty acids production. The nutrient specific 33 bacteria for carbohydrate and protein were also identified. According to FishTaco 34 analysis, a set of intersecting core species contributed with rumen function shifts by 35 solid diet. The core community structures consisted of specific signature microbiota 36 and their symbiotic partners are manipulated by extra nutrients from concentrate 37 and/or forage, and then produce more volatile fatty acids to promote rumen 38 development and functions eventually host development. Our study provides 39 mechanism of microbiome governing by solid diet and highlights the signatures 40 microbiota for animal health and production. 41 Importance 42Small ruminants are essential protein sources for human, so keeping them health and 43 3 increasing their production are important. The microbial communities resided in 44 rumen play key roles to convert fiber resources to human food. Moreover, rumen 45 physiology experience huge changes after birth, and understanding its microbiome 46 roles could provide insights for other species. Recently, our studies and others have 47 shown that diet changed rumen microbial composition and goat performance. In this 48 study, we identified core community structures that were affected by diet and 49 associated to the rumen development and goat production. This outcome could 50 potentially allow us to select specific microbiome to improve rumen physiology and 51 functions, maintain host health and benefit animal production. Therefore, it gives a 52 significant clue that core microbiome manipulation by feeding strategies can increase 53 animal products. To our knowledge, we firstly used FishTaco for determination of 54 link between signatures abundances and rumen function shifts. 55 Keywords: goats, rumen microbiota, solid diet, rumen development, neutral detergent 56 fibers, volatile fatty acids 57 58 4 Introduction 59 With the development of next generation sequencing, the roles of gut 60 microbiome have been dramatically understood. The early life diet, especially 61 introduction of solid diet, is an important driver in shaping long-term and adult gut 62 microbiome profiles due...