Breed and ruminal fraction effects on bacterial and archaeal community composition in sheep

• Published in: Scientific reports Vol. 13; no. 1; p. 3336
• Main Authors: McLoughlin, Steven, Spillane, Charles, Campion, Francis P., Claffey, Noel, Sosa, Chrystian C., McNicholas, Yvonne, Smith, Paul E., Diskin, Michael G., Waters, Sinéad M.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 27-02-2023; Nature Publishing Group; Nature Portfolio
• Subjects: 704/158/855; 704/172/4081; Animals; Archaea - genetics; Bacteria; Campylobacter; Cattle; Clostridiales; Community composition; Efficiency; Emissions; Feed conversion; Feed efficiency; Geographical distribution; Grass silage; Humanities and Social Sciences; Microbial activity; multidisciplinary; Plant Breeding; RNA, Ribosomal, 16S - genetics; rRNA 16S; Rumen; Science; Science (multidisciplinary); Sheep; Veillonellaceae
• DOI: 10.1038/s41598-023-28909-1
• EISSN: 2045-2322

While the breed of cattle can impact on the composition and structure of microbial communities in the rumen, breed-specific effects on rumen microbial communities have rarely been examined in sheep. In addition, rumen microbial composition can differ between ruminal fractions, and be associated with ruminant feed efficiency and methane emissions. In this study, 16S rRNA amplicon sequencing was used to investigate the effects of breed and ruminal fraction on bacterial and archaeal communities in sheep. Solid, liquid and epithelial rumen samples were obtained from a total of 36 lambs, across 4 different sheep breeds (Cheviot (n = 10), Connemara (n = 6), Lanark (n = 10) and Perth (n = 10)), undergoing detailed measurements of feed efficiency, who were offered a nut based cereal diet 
ad-libitum
supplemented with grass silage. Our results demonstrate that the feed conversion ratio (FCR) was lowest for the Cheviot (most efficient), and highest for the Connemara breed (least efficient). In the solid fraction, bacterial community richness was lowest in the Cheviot breed, while
Sharpea azabuensis
was most abundant in the Perth breed. Lanark, Cheviot and Perth breeds exhibited a significantly higher abundance of epithelial associated
Succiniclasticum
compared to the Connemara breed. When comparing ruminal fractions,
Campylobacter
, Family XIII,
Mogibacterium
, and Lachnospiraceae
UCG-008
were most abundant in the epithelial fraction. Our findings indicate that breed can impact the abundance of specific bacterial taxa in sheep while having little effect on the overall composition of the microbial community. This finding has implications for genetic selection breeding programs aimed at improving feed conversion efficiency of sheep. Furthermore, the variations in the distribution of bacterial species identified between ruminal fractions, notably between solid and epithelial fractions, reveals a rumen fraction bias, which has implications for sheep rumen sampling techniques.