Effects of different feeding methods on the intestinal microbiota and metabolites of Nanjiang yellow goats

【Objective】 This study aimed to investigate the effects of different feeding methods on intestinal microbiota and metabolites of Nanjiang yellow goats， and to provide a theoretical basis for the healthy breeding and precise nutritional regulation of Nanjiang yellow goats.【Method】 Ewes of Nanjiang yellow goats were randomly divided into a barn feeding group （SSMF） and a grazing group （FMMF）. The SSMF group was fed at 8：00 and 17：00 daily， while the FMMF group was allowed to graze naturally from 7：00 to 18：00 daily. Venous blood was collected to measure serum biochemical and immune indexes. Fecal microbial DNA was extracted， and the intestinal microbiota structure was analyzed by 16S rRNA sequencing. Fecal metabolites were measured using metabolomics， and multi-omics correlation analysis was performed.【Result】 The triglyceride content in the FMMF group was significantly lower than that in the SSMF group （P<0.05， the same below）， and the total protein content was higher in the SMMF group， without significant differences （P>0.05， the same below）. No significant difference was found in immune indicators immunoglobulin A， immunoglobulin G， immunoglobulin M， interleukin-2， interleukin-4， interleukin-6， and tumor necrosis factor-α concentration between the SSMF and FMMF groups. The Chao1 index and Shannon index in the SSMF group exhibited extremely significantly higher than those in the FMMF group （P<0.01， the same below）. The structure and metabolite profiles of intestinal microbiota in the SSMF and FMMF groups were clearly separated， and significant differences were found in metabolites. At the phylum level， Firmicutes and Bacteroidetes were the most dominant phyla in both the SSMF and FMMF groups， and the proportions of Firmicutes and Bacteroidetes were higher in the SSMF group than in the FMMF group. Correlation analysis showed that： serum IL-2 concentration was significantly negatively correlated with Probable_genus_10 and Porphyromonadaceae_unclassified； the serum IgA concentration was significantly negatively correlated with Schwarzia spp. and Faecalibacterium spp.， and significantly positively correlated with Clostridium spp.； Prevotellaceae_unclassified was significantly positively correlated with LysoPG 18：3， and extremely significantly positively correlated with 7-hydroxy-3,4',8-trimethoxyflavone； Bacteroidaceae_unclassified showed an extremely significant positive correlation with limaprost； Ruminococcus showed an extremely significant positive correlation with azelaic acid， and a positive correlation with traumatin， dodecanedioic acid.【Conclusion】 Different feeding methods alter the intestinal microbiota structure and metabolite profile of Nanjiang yellow goats， and may affect nutrient utilization efficiency， immune status， and energy metabolism processes through the microbiome-host metabolic axis. Barn feeding not only improves energy utilization efficiency of feed but also fosters a more diverse intestinal micro-ecosystem， thus promoting overall nutrient utilization and health metabolism in the Nanjiang yellow goats.