Characterization of bacterial DNA identified in abscessed and non-abscessed bovine hepatic tissue at the time of harvest

Abstract

Abstract Bacteriological characterization of bovine liver abscesses has been accomplished by cultural methods but DNA methods are still needed, as many bacteria are not conducive to laboratory culture. In addition to this gap in research, there have been no studies which identify the bacterial presence within healthy, non-abscessed liver tissue. The objective of this study was to compare the bacteriome of both abscessed and non-abscessed bovine livers in an observational case–control study design. Fifty-six livers, obtained from Holstein steers, were scored according to a modified Elanco liver abscess score description where A− was partitioned into active abscesses or scarred where only scars were present. Parenchyma tissue was collected from non-abscessed livers (n = 22) and scarred livers (n = 7), and purulent material was collected from abscessed livers (n = 24), and DNA was extracted for 16s rRNA gene sequence-based bacterial analysis. Across liver samples, 21 total phyla were identified with a mean of 14. Predominant phyla, accounting for >98% of reads, were Fusobacteria (51.7%), Bacteroidetes (26.9%), Proteobacteria (8.03%), Firmicutes (5.39%), Cyanobacteria (3.85%), and Actinobacteria (2.21%). Proteobacteria, Cyanobacteria, and Firmicutes were greater in non-abscessed and scarred livers, whereas Fusobacteria and Bacteroidetes prevailed in abscessed livers. Non-abscessed livers shared 3,059 operational taxonomic units (OTU) with abscessed livers (total OTU of all livers = 4,167), but non-abscessed livers had greater richness and evenness, whereas abscessed livers had greater dominance (P ≤ 0.0014). Liver score affected the relative abundance of OTU (R = 0.463; P = 0.001) but abscessed livers shared ≥ 40% similarity and were not different from each other (P ≥ 0.370). Of the predominant OTU (top 10 as a % of reads), three OTU (Fusobacteria necrophorum, Bacteroides spp., and Trueperella pyogenes) were shared across both abscessed and non-abscessed livers. Fusobacterium necrophorum was the dominant OTU regardless of liver score, and the single most abundant OTU, even among non-abscessed livers. We describe bacterial DNA detected in non-abscessed bovine liver tissue for the first time, which indicates possible presence of viable bacteria with pathogenic potential in apparently healthy liver tissue.