Effects of in-Feed Administration of a Saccharomyces Cerevisiae Fermentation Product on the Liver Abscess Microbiome and Liver Abscess Rate in Cattle Reared to Produce Natural-Branded Beef

Liver abscesses are the leading cause for liver condemnation in cattle. Liver abscess bacteriology has traditionally been evaluated using culture-based methods, with most commonly isolated organisms including Trueperella pyogenes and Fusobacterium necrophorum. Investigation into feed additive antibiotic alternatives, such as Saccharomyces cerevisiae fermentation products (SCFP), show potential to reduce abscess prevalence and fecal pathogen shedding. However, the effects of SCFP on the microbiome of abscesses are not well characterized. The primary objective of this study was to evaluate the effects of feeding SCFP on liver abscess rate and microbiome in natural-branded beef. The secondary objective was to characterize the liver abscess flora and diversity using 16S ribosomal RNA marker genes to determine operational taxonomic units (OTUs), and to compare these results to traditional cultural findings. In a controlled, randomized, triple-blinded trial, cattle were assigned to two dietary treatment groups and blocked by weight when placed in a Colorado feedlot in March 2016. Cattle were sorted into 14 pen blocks (28 pens total; 4325 head), and were reared similarly. Treated pens received SCFP (18 g/day) in their diet, and control pens were fed a base ration. At harvest, liver abscess rates were scored for individual animals. Five liver abscesses per pen were collected, and purulent material was saved. The content was cultured anaerobically, and isolates were saved for characterization and antimicrobial susceptibility testing. Additionally, DNA was isolated, and the bacterial community (microbiome) was characterized by 16S rRNA sequencing, where universal PCR primers amplify specific hyper-variable V4 regions within the 16S region. Paired-end reads were trimmed and filtered for quality. They were then assigned OTUs using open reference OTU picking in QIIME, rare OTUs were filtered, sequences were rarefied to 93243 reads, and beta diversity was estimated using unweighted Unifrac distances. The mean total abscess prevalence at harvest across 28 pens was 38.5% (95% CI 37.0 to 39.9%). Cattle with severe abscesses represented 15.7% of all abscesses (95% CI 14.6 to 16.8%). From blinded analysis of data from 13 pens, taxa belonging to the phyla Fusobacterium, Bacteroides, and unassigned taxa were most abundantly represented. Actinobacteria (including Trueperella) had lower relative abundance across samples. There was a correlation between pen and differences in the microbiota accounting for 55% of variation in the PCoA plot. OTU differences in the genus, Fusobacterium, are driving some of the differences in clustering by abscess rate and pen block.