Probiotic dosing of ruminococcus flavefaciens affects rumen microbiome structure and function in reindeer

Abstract

Highly cellulolytic bacterial species such as <i>Ruminococcus flavefaciens</i> are regarded essential for the microbial breakdown of cellulose in the rumen. We have investigated the effect of ruminal dosing of <i>R. flavefaciens</i> strain 8/94-32 during realimentation of starved reindeer (males, n = 3). Microbiome function measured as in situ digestion of cellulose and food pellets (percent DMD; dry matter disappearance) decreased after probiotic dosing. Microbial community analyses (>100,000 16S rDNA gene sequences for 27 samples) demonstrated that ruminal dosing influenced the microbiome structure; reflected by increased phylogenetic distances from background samples (unweighted UniFrac analysis) and reduced species diversity and evenness. Despite the inability to detect strain 8/94-32 post-dosing, the relative abundance of its affiliate family <i>Ruminococcaceae</i> remained consistent throughout the trial, whilst a dominant peak in the genus Prevotella and decline in uncharacterized <i>Bacteroidetes</i> (uBacNR) were observed in treatment samples. No clear relationships were observed between the relative abundance of <i>Ruminococcaceae, Prevotella</i> and uBacNR with cellulose DMD; however, <i>Prevotella</i> (negative) and uBacNR (positive) exhibited relationships with pellet DMD. These unexpected effects of ruminal dosing of a cellulolytic bacterium on digestibility are relevant for other studies on rumen manipulation.