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

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.

A meta-analysis of liver microbiome in beef and dairy cattle using metatranscriptome sequencing reads

“…By triggering the release of a vast number of inflammatory cytokines in various cell types, LPS can cause significant inflammation (Ngkelo, Meja et al 2012). Quite interestingly, Proteobacteria was identified as one of the predominant phylum in non-abscessed livers (Stotz, Henry et al 2021), consistent with the report that this phylum is dominant in the rumen (Mann, Wetzels et al 2018).…”

“…Though T. pyogenes is a commensal bacterium, it is a common opportunistic pathogen, which causes purulent or necrotic lesions in several different tissues, including uterus (Amos, Healey et al 2014, Bicalho, Lima et al 2016, mammary gland (Madsen, Aalbaek et al 1992, Rezanejad, Karimi et al 2019, liver (Tadepalli, Narayanan et al 2009), and hoof (Kontturi, Junni et al 2019). Stotz and coauthors (Stotz, Henry et al 2021) reported Tenericutes was identified as a dominant phylum second to Fusobacteria and Bacteroidetes in severely abscessed liver samples. In the same study, Cyanobacteria was identified as the dominant phyla in non-abscessed and scarred liver samples.…”

Not All Liver Abscesses Are Created Equal: The Impact of Tylosin and Antibiotic Alternatives on Bovine Liver Abscess Microbial Communities and a First Look at Bacteroidetes-Dominated Communities

“…While Fusobacteria-dominated communities were still by far the most common, Bacteroidetes-dominated communities represented almost a quarter (23%) of the abscesses sampled in this study. When compared across treatment groups in previous 16S sequencing studies, members of Bacteroidetes were the second or third most abundant phyla after Fusobacteria within abscesses ( Weinroth et al, 2017 ; Amachawadi et al, 2021 ; Stotz et al, 2021 ) but have not previously been demonstrated as the dominant members of individual abscesses. Within these Bacteroidetes-dominated communities, the genera Bacteroides and Porphyromonas were the most abundant, species of which have previously been isolated from LAs.…”

“…Members of Acinetobacter , Campylobacter , Helocococcus , Parvimonas , Pseudomonas , and Psychrobacter have all been associated with wound infections in the gut ( Collins et al, 2004 ; Eliopoulos et al, 2008 ; Price et al, 2009 ; Okuda et al, 2010 ; Kaakoush et al, 2014 ), and despite their differential abundance between abscesses community type, their presence in LAs further emphasizes the importance of keeping a polymicrobial perspective when considering causes and potential prevention strategies for LA syndrome in cattle. Trueperella is commonly identified as a predominant microbial community member and considered a potential secondary etiological agent of bovine LAs ( Reinhardt and Hubbert, 2015 ; Weinroth et al, 2017 ; Stotz et al, 2021 ), and its increased abundance in Bacteroidetes-dominated LAs is an important finding that emphasizes the importance of discriminating between community types in future research.…”

“…Culture-independent studies employing 16S rRNA gene sequencing or shotgun metagenomics to investigate LA pathogens within the context of their entire microbial communities are rare. To date, three studies using 16S rRNA sequencing have identified Fusobacteria, Bacteroidetes, and Proteobacteria as the most abundant microbial phyla in LAs ( Weinroth et al, 2017 ; Amachawadi et al, 2021 ; Stotz et al, 2021 ). Compared to its prevalence in culture-based studies, the increased abundances of Bacteroidetes and Proteobacteria may suggest they play larger roles within LA microbial communities than previously thought.…”