Rapid Communication: 16S ribosomal ribonucleic acid characterization of liver abscesses in feedlot cattle from three states in the United States

Invited review: "Probiotic" approaches to improving dairy production: Reassessing "magic foo-foo dust"

The gastrointestinal microbial consortium in dairy cattle is critical to determining the energetic status of the dairy cow from birth through her final lactation. The ruminant's microbial community can degrade a wide variety of feedstuffs, which can affect growth, as well as production rate and efficiency on the farm, but can also affect food safety, animal health, and environmental impacts of dairy production. Gut microbial diversity and density are powerful tools that can be harnessed to benefit both producers and consumers. The incentives in the United States to develop Alternatives to Antibiotics for use in food-animal production have been largely driven by the Veterinary Feed Directive and have led to an increased use of probiotic approaches to alter the gastrointestinal microbial community composition, resulting in improved heifer growth, milk production and efficiency, and animal health. However, the efficacy of direct-fed microbials or probiotics in dairy cattle has been highly variable due to specific microbial ecological factors within the host gut and its native microflora. Interactions (both synergistic and antagonistic) between the microbial ecosystem and the host animal physiology (including epithelial cells, immune system, hormones, enzyme activities, and epigenetics) are critical to understanding why some probiotics work but others do not. Increasing availability of next-generation sequencing approaches provides novel insights into how probiotic approaches change the microbial community composition in the gut that can potentially affect animal health (e.g., diarrhea or scours, gut integrity, foodborne pathogens), as well as animal performance (e.g., growth, reproduction, productivity) and fermentation parameters (e.g., pH, short-chain fatty acids, methane production, and microbial profiles) of cattle. However, it remains clear that all direct-fed microbials are not created equal and their efficacy remains highly variable and dependent on stage of production and farm environment. Collectively, data have demonstrated that probiotic effects are not limited to the simple mechanisms that have been traditionally hypothesized, but instead are part of a complex cascade of microbial ecological and host animal physiological effects that ultimately impact dairy production and profitability.

Evaluating the liver abscess microbiota of beef cattle during a reduction in tylosin supplementation shows differences according to abscess size and fraction

Liver abscesses (LA) resulting from bacterial infection in cattle pose a significant global challenge to the beef and dairy industries. Economic losses from liver discounts at slaughter and reduced animal performance drive the need for effective mitigation strategies. Tylosin phosphate supplementation is widely used to reduce LA occurrence, but concerns over antimicrobial overuse emphasize the urgency to explore alternative approaches. Understanding the microbial ecology of LA is crucial to this, and we hypothesized that a reduced timeframe of tylosin delivery would alter LA microbiomes. We conducted 16S rRNA sequencing to assess severe liver abscess bacteriomes in beef cattle supplemented with in-feed tylosin. Our findings revealed that shortening tylosin supplementation did not notably alter microbial communities. Additionally, our findings highlighted the significance of sample processing methods, showing differing communities in bulk purulent material and the capsule-adhered material. Fusobacterium or Bacteroides ASVs dominated LA, alongside probable opportunistic gut pathogens and other microbes. Moreover, we suggest that liver abscess size correlates with microbial community composition. These insights contribute to our understanding of factors impacting liver abscess microbial ecology and will be valuable in identifying antibiotic alternatives. They underscore the importance of exploring varied approaches to address LA while reducing reliance on in-feed antibiotics.

Whole-body microbiota of newborn calves and their response to prenatal vitamin and mineral supplementation

Early life microbial colonization and factors affecting colonization patterns are gaining interest due to recent developments suggesting that early life microbiome may play a role in Developmental Origins of Health and Disease. In cattle, limited information exists on the early microbial colonization of anatomical sites involved in bovine health beyond the gastrointestinal tract. Here, we investigated 1) the initial microbial colonization of seven different anatomical locations in newborn calves and 2) whether these early life microbial communities and 3) serum cytokine profiles are influenced by prenatal vitamin and mineral (VTM) supplementation. Samples were collected from the hoof, liver, lung, nasal cavity, eye, rumen (tissue and fluid), and vagina of beef calves that were born from dams that either received or did not receive VTM supplementation throughout gestation (n = 7/group). Calves were separated from dams immediately after birth and fed commercial colostrum and milk replacer until euthanasia at 30 h post-initial colostrum feeding. The microbiota of all samples was assessed using 16S rRNA gene sequencing and qPCR. Calf serum was subjected to multiplex quantification of 15 bovine cytokines and chemokines. Our results indicated that the hoof, eye, liver, lung, nasal cavity, and vagina of newborn calves were colonized by site-specific microbiota, whose community structure differed from the ruminal-associated communities (0.64 ≥ R² ≥ 0.12, p ≤ 0.003). The ruminal fluid microbial community was the only one that differed by treatment (p < 0.01). However, differences (p < 0.05) by treatment were detected in microbial richness (vagina); diversity (ruminal tissue, fluid, and eye); composition at the phylum and genus level (ruminal tissue, fluid, and vagina); and in total bacterial abundance (eye and vagina). From serum cytokines evaluated, concentration of chemokine IP-10 was greater (p = 0.02) in VTM calves compared to control calves. Overall, our results suggest that upon birth, the whole-body of newborn calves are colonized by relatively rich, diverse, and site-specific bacterial communities. Noticeable differences were observed in ruminal, vaginal, and ocular microbiota of newborn calves in response to prenatal VTM supplementation. These findings can derive future hypotheses regarding the initial microbial colonization of different body sites, and on maternal micronutrient consumption as a factor that may influence early life microbial colonization.

Liver abscess microbiota of feedlot steers finished in natural and traditional management programs

Liver abscess etiology in feedlot steers involves the escape of bacteria from the digestive tract to form a polymicrobial abscess within or on the external surface of the liver. However, little is known about the effects of feedlot finishing systems on the microbial composition of the liver abscess purulent material. Liver abscesses were collected at the time of harvest from steers originating from a single feedlot managed in either a traditional program (which included tylosin phosphate supplementation) or a natural program (without tylosin phosphate supplementation). The purulent material of liver abscesses from traditionally managed steers (N = 53 abscesses) and that of naturally managed steers (N = 62 abscesses) was characterized using the V4 region of the 16S rRNA gene. Two phyla and three genera were found in greater than 1% relative abundance across all abscesses. The genus Fusobacterium was identified in all liver abscess samples and accounted for 64% of sequencing reads. Bacteroides and Porphyromonas genera accounted for 33% and 1% of reads, respectively. Trueperella was more likely to be found in the liver abscesses of naturally managed steers than traditionally managed steers (P = 0.022). Over 99% of the genus-level bacterial sequences observed across all liver abscesses belonged to Gram-negative genera. Bacteria known to colonize both the rumen and hindgut were identified within liver abscesses. No differences in alpha diversity or beta diversity were detected between liver abscess communities (between the two management programs or individual pens) when tested as richness, Shannon Diversity Index, or weighted UniFrac distances (P > 0.05). These results were consistent with previous identification of Fusobacterium necrophorum as the primary bacteriologic agent within liver abscesses and emphasized the relationship between the gastrointestinal microbiota and liver abscess formation. Though the microbiota of the liver abscess purulent material was similar between steers fed an antibiotic-free diet and those fed an antibiotic-containing diet from the same feedlot, divergence was detected in liver abscess communities with some being dominated by Fusobacterium and others being dominated by Bacteroides.

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

Liver abscesses (LAs) are extremely prevalent in cattle and result in significant economic losses due to liver condemnation, decreased growth and production, and lower carcass quality. LAs are commonly attributed to the transition to diets high in rapidly fermentable starch which results in rumen epithelial inflammation that allows pathogenic bacteria to gain entry to liver through transport via the hepatic portal vein. The most common intervention for LAs is the inclusion of antibiotics in feedlot diets, under the supervision of a veterinarian; this treatment is associated with reduced occurrence of LAs in this and other studies. Here, through the largest LA 16S rRNA gene sequencing study to date, we demonstrate that the inclusion of tylosin and antibiotic alternatives (the essential oil limonene and Saccharomyces cerevisiae fermentation product) had little impact on LA microbial community composition. Importantly, members of Bacteroidetes (Bacteroides spp. and Porphyromonas spp.) were identified as the dominant taxa in conjunction with low proportions of Fusobacteria in nearly a quarter (61/259) of all LA communities analyzed in this study. The relative abundances of the phyla Fusobacteria and Bacteroidetes had a strongly negative correlation, and LA microbial communities rarely contained high abundances of both of these dominant phyla. Further, based on the presence of taxa discriminant of Bacteroidetes-dominated LAs within over 400 bovine gut communities, we provide evidence suggestive of Bacteroidetes-dominated abscess communities originating in more distal portions of the bovine gut. Together, these findings suggest that some LA microbial communities may originate from portions of the gut other than the rumen.

Bacterial Distribution and Community Structure in Beef Cattle Liver and Bile at Slaughter

ABSTRACT

In this study, the distribution of hygienic indicator bacteria in cattle livers and bile was examined at slaughterhouses. One hundred twenty-seven cattle livers with gallbladders were carefully eviscerated from carcasses at 10 slaughterhouses. Microbiological examination revealed that nine bile samples (7.1% prevalence) and 19 liver parenchyma samples (15.0% prevalence) were positive for Enterobacteriaceae (EB) with means ± standard deviations of 3.68 ± 4.63 log CFU/mL and 1.59 ± 2.47 log CFU/g, respectively; thus, bacterial contamination was apparent even at the postevisceration stage. Subsequently, 70 cattle livers were obtained at the postprocessing and storage stage from 7 of the 10 slaughterhouses. Microbiological analysis revealed significantly higher levels of EB in the liver parenchyma (3.00 ± 3.89 log CFU/g, P = 0.011) than those at the postevisceration stage, suggesting that bacterial dissemination and/or replication occurred in the liver parenchyma during processing and storage. According to 16S rRNA ion semiconductor sequencing analysis of representative samples from 12 cattle, Proteobacteria, Firmicutes, and Actinobacteria were dominant in both the parenchyma and bile in which EB and Escherichia coli were predominant among livers with higher EB levels. These results suggest that bile plays a role as a vehicle for bacterial transmission to the liver parenchyma. This study is the first to evaluate bacterial distribution and community structure in the liver and biliary microecosystem of cattle at slaughter. Our data support the use of EB testing of bile to screen cattle livers contaminated with high levels of fecal indicator bacteria.

HIGHLIGHTS

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

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.

Bacterial community analysis of purulent material from liver abscesses of crossbred cattle and Holstein steers fed finishing diets with or without tylosin

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 5 phyla, 14 families, 98 genera, and 102 amplicon sequence variants (ASV) in the 4 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 3 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 4 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.

Rumen epithelial transcriptome and microbiome profiles of rumen epithelium and contents of beef cattle with and without liver abscesses

Abscess is the highest cause of liver condemnation and is estimated to cost the beef industry US$64 million annually. Fusobacterium necrophorum, commonly found in the bovine rumen, is the primary bacteria associated with liver abscess in cattle. Theoretically, damage to the rumen wall allows F. necrophorum to invade the bloodstream and colonize the liver. The objective of this study was to determine the changes in gene expression in the rumen epithelium and microbial populations adherent to the rumen epithelium and in the rumen contents of beef cattle with liver abscesses compared with those with no liver abscesses. Rumen epithelial tissue and rumen content were collected from 31 steers and heifers with liver abscesses and 30 animals with no liver abscesses. Ribonucleic acid (RNA) sequencing was performed on the rumen epithelium, and a total of 221 genes were identified as differentially expressed in the animals with liver abscesses compared with animals with no abscesses, after removal of genes that were identified as a result of interaction with sex. The nuclear factor kappa-light-chain enhancer of activated B cells signaling and interferon signaling pathways were significantly enriched in the differentially expressed gene (DEG) set. The majority of the genes in these pathways were downregulated in animals with liver abscesses. In addition, RNA translation and protein processing genes were also downregulated, suggesting that protein synthesis may be compromised in animals with liver abscesses. The rumen content bacterial communities were significantly different from the rumen wall epimural bacterial communities. Permutational multivariate analysis of variance (PERMANOVA) analysis did not identify global differences in the microbiome of the rumen contents but did identify differences in the epimural bacterial communities on the rumen wall of animals without and with liver abscesses. In addition, associations between DEG and specific bacterial amplicon sequence variants of epimural bacteria were observed. The DEG and bacterial profile on the rumen papillae identified in this study may serve as a method to monitor animals with existing liver abscesses or to predict those that are more likely to develop liver abscesses.

Investigation of tylosin in feed of feedlot cattle and effects on liver abscess prevalence, and fecal and soil microbiomes and resistomes1

Liver abscesses in feedlot cattle are detrimental to animal performance and economic return. Tylosin, a macrolide antibiotic, is used to reduce prevalence of liver abscesses, though there is variable efficacy among different groups of cattle. There is an increased importance in better understanding the etiology and pathogenesis of this condition because of growing concern over antibiotic resistance and increased scrutiny regarding use of antibiotics in food animal production. The objective of this study was to compare the microbiomes and antimicrobial resistance genes (resistomes) of feces of feedlot cattle administered or not administered tylosin and in their pen soil in 3 geographical regions with differing liver abscess prevalences. Cattle (total of 2,256) from 3 geographical regions were selected for inclusion based on dietary supplementation with tylosin (yes/no). Feces and pen soil samples were collected before harvest, and liver abscesses were identified at harvest. Shotgun and 16S rRNA amplicon sequencing were used to evaluate the soil and feces. Microbiome and resistome composition of feces (as compared by UniFrac distances and Euclidian distances, respectively) did not differ (P > 0.05) among tylosin or no tylosin-administered cattle. However, feedlot location was associated with differences (P ≤ 0.05) of resistomes and microbiomes. Using LASSO, a statistical model identified both fecal and soil microbial communities as predictive of liver abscess prevalence in pens. This model explained 75% of the variation in liver abscess prevalence, though a larger sample size would be needed to increase robustness of the model. These data suggest that tylosin exposure does not have a large impact on cattle resistomes or microbiomes, but instead, location of cattle production may be a stronger driver of both the resistome and microbiome composition of feces.

Lower Respiratory Tract Microbiome and Resistome of Bovine Respiratory Disease Mortalities

Bovine respiratory disease (BRD) continues to be a serious health problem in beef cattle production. A multifactorial condition, BRD encompasses several types of pneumonia that are associated with multiple viral and bacterial agents. Comprehensive identification of microbes associated with BRD fatalities could enhance our understanding of the range of pathogens that contribute to the disease and identify new therapeutic targets. This study used metagenomic analysis to describe the lower respiratory tract microbiome and resistome of 15 feedlot cattle BRD and 3 non-BRD mortalities along with any affiliated integrative and conjugative elements (ICEs). Known bacterial pathogens associated with BRD, including Histophilus somni, Mannheimia haemolytica, and Mycoplasma bovis, were relatively abundant (> 5%) in most, but not all samples. Other relatively abundant genera (> 1%) included Acinetobacter, Bacillus, Bacteroides, Clostridium, Enterococcus, and Pseudomonas. Antimicrobial resistance genes (ARGs) comprised up to 0.5% of sequences and many of these genes were associated with ICEs previously described within the Pasteurellaceae family. A total of 20 putative ICEs were detected among 16 samples. These results document the wide diversity of microorganisms in the lower respiratory tract of cattle that have succumbed to BRD. The data also strongly suggest that antimicrobial-resistant Pasteurellaceae strains are prevalent in BRD cases in Alberta and that the resistance observed is associated with ICEs. The presence of ICEs harboring a wide array of ARGs holds significant consequence for the effectiveness of drug therapies for the control of BRD in beef cattle.

An Advanced Understanding of Uterine Microbial Ecology Associated with Metritis in Dairy Cows

Metritis, the inflammation of the uterus caused by polymicrobial infections, is a prevalent and costly disease to the dairy industry as it decreases milk yield, survival, and the welfare of dairy cows. Although affected cows are treated with broad-spectrum antibiotics such as ceftiofur, endometrial and ovarian function are not fully recovered, which results in subfertility and infertility. According to culture-dependent studies, uterine pathogens include Escherichia coli, Trueperella pyogenes, Fusobacterium necrophorum, and Prevotella melaninogenica. Recent studies using high-throughput sequencing observed very low relative abundance of Escherichia coli, Trueperella pyogenes, and Prevotella melaninogenica in cows with metritis. Herein, we propose that metritis is associated with a dysbiosis of the uterine microbiota, which is characterized by high abundance of Bacteroides, Porphyromonas, and Fusobacterium.

An assessment of the effectiveness of virginiamycin on liver abscess incidence and growth performance in feedlot cattle: a comprehensive statistical analysis

The judicious use of commercial products in livestock operations can be part of a sustainable and environmentally friendly production scenario. This study was designed to gather published data of virginiamycin (VM) used in feedlot conditions of the United States and analyze its effectiveness and optimum dosage in reducing the liver abscess incidence (LAI). The dataset contained 26 studies that evaluated more than 7,156 animals of diverse breeds fed in several regions in the United States under different management. Statistical analyses included contingency tables to assess the nonparametric independence of the LAI, meta regression analysis to remove study effects and to evaluate LAI and animal performance, broken-line analysis to determine thresholds of VM dosage on LAI, and residual-based shading mosaic plots to illustrate the contingency analysis. There were 1,391 of 5,430 animals with LAI scores 1, 2, or 3 (LAI1-3) and 651 of 4,690 animals with LAI A+ (score 3). Our analyses suggested that there was a significant dependency (χ2P-value < 0.001) and significant asymmetry (McNemar's test P-value < 0.001) between LAI and VM treatment for both LAI1-3 and LAI A+. For the LAI1-3 group, only 22.5% of the treated animals had liver abscesses compared with 31.7% of the control animals. The metaregression analysis indicated that LAI1-3 was linearly reduced (P < 0.001) by about 0.42% per mg/kg of DM of VM. The lower 95% confidence interval of the intercept for LAI1-3 and LAI A+ obtained with a generalized nonlinear mixed regression was 18.7 and 20.3 mg/kg of DM, respectively. The broken-line regression analysis identified 2 thresholds for LAI (23.9 and 12.3 mg/kg of DM) at which the reduction in total LAI1-3 and LAI A+, respectively, would decrease faster as VM dosage increases (from 2.14% to 6% and from 1.91% to 4.33% per mg of VM per kg of DM, respectively). Additionally, our analyses indicated that after accounting for the study effects, VM significantly increased ADG at 2.08 g BW/d per mg/kg DM compared with 0.92 g BW/d per mg/kg DM for monensin (P < 0.001), suggesting that VM was about 2.3 times more effective in increasing ADG for the same dosage and feeding period length. All analyses yielded consistent results that led us to conclude that VM is effective in reducing LAI when fed between approximately 12 and 24 mg/kg of DM, and the maximum reduction might occur at approximately 24 mg/kg of DM or higher.