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. Importance Small 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.

9 groups (Table S6)  (area under the curve) of 1.00 (specificity 1.00, sensitivity 1.00) were selected from 188 AUCRF model (Table S7; Figure S2). High AUC (0.931) was still observed at 50 th 189 feature suggesting those signatures being able to accurately predict whether goats was relative abundance and prevalence (11.13%; 6/6) as compared with MRC (0.03%, 2/6) 195 and MCA (0.04%, 2/6). OTU24 as qualitative signatures had more abundance 2.16% 196 in MRO. Other species associated with Prevotella that was enriched genus in solid 197 diet groups were also found more abundant in MRO,including OTU119,OTU42 and 198 OTU60. For MCA microbiome, OTU6 and OTU104 affiliated with predominant 199 Prevotella increased. We observed the relative abundances of OTU6 was 0.01% 1.35% 200 and 5.89% in MRO, MRC and MCA (prevalence 2/6, 6/6 and 6/6). OTU87  Then, we performed pair wise AUCRF comparisons to validate these predictors. 208 The results confirmed that most of the classified biomarkers could also be listed  The rumen microbiota had high prediction accuracy (>73%) to explain nutrients 224 intake (Table S8) sub-communities to response solid diet feeding and drive function shifts.

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The VFAs that are products of the fermentation of diets are essential to the 355 rumen papillae development and nutrient source for host requirements (15). In stimulation from solid diet, the chemical effects of nutrient intake may be another 367 reason leading to increase of VFA. Therefore, early supplementation of solid diet 368 leading to high nutrient intake increases rumen VFA production and nitrogen 369 utilization efficiency, which reflects that microbiome experienced solid diets had a 370 strong ability to utilize nutrient.

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In pace with the change of rumen environment, this study also observed that the 372 membership and structure of microbiota also altered by supplied with concentrate or 373 forage compared with only fluid diet groups. Significant lower alpha diversity in 374 starter feed-lambs and distinct beta diversity between starter feed-and breast milk-fed 375 lambs were also reported (11). High bacterial richness in fluid diet groups might be 376 temporary phenomenon at d60. Others confirmed that rumen microbiota at d70 had a 377 lower richness compared with it at d42 (8  replicates and four kids per pen were as a replicate.

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Goat kids remained with their mother and received breast milk from 0 to 20 days.

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During 20 to 60 days of age, they were separated with their dams and the above 3 545 kinds of diets were provided to corresponding groups. Other feeding management 546 including vaccination, cleaning and disinfection of pens followed farm normal policy.