The Effects of Breeding Methods on Cecal Microflora and Production Traits of Yimeng Black Goats

This study investigated the effects of different breeding methods on the cecal microbiota and production traits of Yimeng Black Goats (YBGs). Twenty-seven 3-month-old male YBGs were assigned to three groups (n = 9 each): total mixed ration once daily (A), concentrate in the morning and roughage in the afternoon (B), or grazing with supplementary feeding (C). Cecal bacterial communities were analyzed via 16S rRNA sequencing, and functional potential was predicted using FAPROTAX. Breeding method significantly altered microbial composition (p < 0.05). Beta diversity was highest in Group C, while alpha diversity remained similar across groups. Bacteroidetes, Firmicutes, and Proteobacteria were dominant; Proteobacteria were most abundant in Group A. At the genus level, relative abundances of nine taxa, including Lactobacillus and Fusobacterium, differed significantly (p < 0.05). At the species level, including Lactobacillus mucosae, Bacteroides massiliensis and Alistipes finegoldii, differed significantly (p < 0.05). Chemoheterotrophy and fermentation functions were most enriched, particularly in Group C. Total weight gain was highest in Group A and lowest in Group C (p < 0.05), while carcass rate showed no significant differences (p > 0.05). Correlation analysis revealed that Proteobacteria, Fusobacteria, and Euryarchaeota as the key phylum, and Bacteroides, Tyzzerella, Fusobacterium, unidentified_Prevotellaceae, Methanovrevibacter and Faecalibacterium as the key genera were influencing the production traits of YBGs. These findings highlight the adaptive responses of the cecal microbiota to breeding methods and their potential links to host performance.