PSX-15 Diet-, breed-, and sex-dependent effects in taxonomic and functional signatures of the rumen microbiome in meat goats.

Abstract Goat meat production is influenced by factors such as diet, breed, sex, and age, which also shape the ruminal microbiome. The aim of this study was to determine the effects of dietary concentrate level, breed, and sex on taxonomic and functional profiles of rumen microbial community in growing Boer and Kiko goats. Forty-eight kids (24 Boer and 24 Kiko, one-half wethers and one-half doelings, 5 months of age and 20.3±0.51 kg body weight) were fed with diets containing 30% (30C) and 70% (70C) concentrate, with lespedeza hay as the only forage source. In the first 64 days, all kids were fed the 30C diet and in the last 76 days, they were offered two types of diet. On the final day, the animals were slaughtered, and rumen contents were collected for genomic DNA extraction and sequencing using the Illumina platform with 300 bp paired-end reads. The average count per sample was 28,714, ranging from 27,914 to 29,751. Various alpha diversity indices, including Chao1, Simpson, and Shannon, were higher (P< 0.01) for 30C compared to 70C, while breed and sex had no effect. Principal coordinate analysis also revealed a clear separation (P< 0.01) between 30C and 70C, but no significant separation for breed and sex. Significant (P< 0.05) differences were observed between the two dietary groups, affecting 8 phyla, 11 classes, 14 orders, 18 families, 38 genera, and 52 bacterial species. Breed-related differences were also evident, with significant variation in 2 classes, 1 order, 3 families, 6 genera, and 8 species. In contrast, sex-related differences were relatively minor, with significance observed in only 1 order, 1 family, 2 genera (Parapedobacter; male >female and Dysgonomonas; female >male), and 2 bacterial species. Breed- and sex-related effects were not observed in the archaeal community. However, the abundances of Methanomassiliicoccaceae and Methanomicrobiaceae (family level), Candidatus Methanogranum, Methanobacterium, Methanomicrobium, and Methanosphaera (genus level), as well as four archaeal species, were higher (P< 0.05) in the 30C group compared to the 70C group. A total of 141 predicted functional pathways were affected (P< 0.05) by diet, with 67 pathways showing greater abundance in the 30C group. Twenty-four predicted functional pathways differed (P< 0.05) between the Boer and Kiko breeds, with 11 pathways showing greater abundance in Boer goats. Although sex-related differences in bacterial abundances were minor, 15 pathways were more abundant in males and 3 in females (P< 0.05). In conclusion, diet had the most pronounced effect on the abundance and functional profiles of the rumen microbiota, while breed also contributed to microbial variation, with minor effects observed for sex.