Liver abscesses in feedlot cattle are polymicrobial infections. Culture-based studies have identified Fusobacterium necrophorum as the primary causative agent, but a number of other bacterial species are frequently isolated. The incidence of liver abscesses is highly variable and is affected by a number of factors, including cattle type. Holstein steers raised for beef production have a higher incidence than crossbred feedlot cattle. Tylosin is the commonly used antimicrobial feed additive to reduce the incidence of liver abscesses. The objective of this study was to utilize 16S ribosomal RNA amplicon sequence analyses to analyze the bacterial community composition of purulent material of liver abscesses of crossbred cattle (n=24) and Holstein steers (n=24), each fed finishing diet with or without tylosin. DNA was extracted and the V3 and V4 regions of the 16S rRNA gene were amplified, sequenced and analyzed. The minimum, mean, and maximum sequence reads per sample were 996, 177,070, and 877,770, respectively, across all the liver abscess samples. Sequence analyses identified five phyla, 14 families, 98 genera and 102 amplicon sequence variants (ASV) in the four treatment groups. The dominant phyla identified were Fusobacteria (52% of total reads) and Proteobacteria (33%). Of the top 25 genera identified, 17 genera were Gram negative and 8 were Gram positive. The top three genera, which accounted for 75% of the total reads, in the order of abundance, were Fusobacterium, Pseudomonas, and Bacteroides. The relative abundance, expressed as percent of total reads, of phyla, family and genera did not differ (P > 0.05) between the four treatment groups. Generic richness and evenness, determined by Shannon-Weiner and Simpson’s diversity indices, respectively, did not differ between the groups. The UniFrac distance matrices data revealed no clustering of the ASV indicating variance between the samples within each treatment group. Co-occurrence network analysis at the genus level indicated a strong association of Fusobacterium with 15 other genera, and not all of them have been previously isolated from liver abscesses. In conclusion, the culture-independent method identified the bacterial composition of liver abscesses as predominantly Gram negative and Fusobacterium as the dominant genus, followed by Pseudomonas. The bacterial community composition did not differ between crossbred and Holstein steers fed finishing diets with or without tylosin.

The majority of microbiome studies focused on understanding mechanistic relationships between the host and the microbiota have used mice and other rodents as the model of choice. However, the domestic pig is a relevant model that is currently underutilized for human microbiome investigations. In this study, we performed a direct comparison of the engraftment of fecal bacterial communities from human donors between human microbiota-associated (HMA) piglet and mouse models under identical dietary conditions. Analysis of 16S rRNA genes using amplicon sequence variants (ASVs) revealed that with the exception of early microbiota from infants, the more mature microbiotas tested established better in the HMA piglets compared to HMA mice. Of interest was the greater transplantation success of members belonging to phylum Firmicutes in the HMA piglets compared to the HMA mice. Together, these results provide evidence for the HMA piglet model potentially being more broadly applicable for donors with more mature microbiotas while the HMA mouse model might be more relevant for developing microbiotas such as those of infants. This study also emphasizes the necessity to exercise caution in extrapolating findings from HMA animals to humans, since up to 28% of taxa from some donors failed to colonize either model.

Aims: The effect of feeding dried distillers grains with solubles (DDGS) or reduced-fat DDGS (RFDG) on ruminal methanogenesis and the rumen bacterial community of dairy cattle was evaluated. Methods and Results: Treatments were CONT, a diet with no distillers grains; DG, inclusion of 20% DDGS; rfDG, inclusion of 20% RFDG; and MIX, inclusion of 10% DDGS and 10% RFDG. Methane emission was measured; rumen bacterial community was evaluated by sequencing the V4 region of the 16S rRNA gene. Total methane production remained unaffected. However, feeding distillers grains tended to reduce methanogenesis per unit of feed intake, decreased the abundance of the phylum Bacteroidetes and tended to increase Firmicutes. The abundance of Prevotellaceae positively correlated with feed intake; methane emission was positively correlated with the abundance of Prevotellaceae and was negatively correlated with the abundance of Succinivibrionaceae. Conclusions: DDGS or RFDG may reduce methanogenesis per unit of feed intake; shifts in the abundance of predominant ruminal bacterial families may influence methane formation, likely because of their role on hydrogen liberation and utilization pathways. Significance and Impact of the Study: Replacing corn and soybean meal with DDGS or RFDG in dairy rations may reduce the proportion of dietary energy wasted as methane, without detrimental effects on the overall bacterial population.

The objective of this study was to investigate the influence of the rumen bacterial community composition and abundance on marbling grade and breed in Wagyu cattle. Wagyu cattle are known for highly marbled and tender meat with unique flavor. This taste comes from the mono-unsaturated fatty acids, mainly oleic acid (18:1 n-9) which makes Wagyu fat more soft and palatable. It is believed that stearic acid (18:0) is responsible for fat hardness and its desaturation by a Delta-9 desaturase in Wagyu to oleic acid results in the tenderness. In the rumen, the microbial community plays important role in saturation and desaturation of fatty acids by biohydrogenation and in providing energy to the host animal through volatile fatty acids. In this study, we have analyzed the rumen bacterial community structure in 85 Wagyu animals from rumen samples collected at harvesting. Phenotypes of carcass traits were also collected from all animals at harvest. The animals in this study were either crossbred (F1) or full blood (FB) animals and came from 14 different producers which utilized different dietary and management conditions. The V4 region of the 16S rRNA gene was sequenced using the Illumina MiSeq platform to evaluate the microbial community composition in Wagyu cattle. The sequencing data were processed by using custom pipelines. All statistical analysis performed was adjusted to account for producer variation before analyzing for carcass traits. Alpha diversity metrics, Chao1 and observed OTUs, displayed higher (P= 0.001) bacterial richness in F1 than FB and displayed no difference (P >0.4) in bacterial community richness due to marbling grade. The principal coordinate analysis displayed distinct clustering of bacterial communities for FB and F1 which suggested that breed has an effect on the bacterial community composition. Further, these observations were confirmed by PERMANOVA which displayed different (P<0.001) bacterial communities between breeds (FB and F1) and producers while no difference (P>0.05) for marbling grade. Furthermore, we performed analysis to identify differential OTUs between marbling grades and to identify OTUs that were correlated with increased marbling scores. The differential OTUs (P<0.001) identified in the highest marbling grade predominately belonged to families Mogibacteriaceae, Lachnospiraceae and Clostridiaceae. Additionally, several differential OTUs (P<0.001) were also associated with FB, predominantly from bacterial families Spirochaetaceae, Mogibacteriaceae, Lachnospiraceae, Fibrobacteraceae, Ruminococcaceae and Prevotellaceae. The results from this preliminary study demonstrate that the rumen microbial community composition may influence marbling and manipulating the rumen microbial community may lead to increased marbling.

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