Short communication: Metagenomic evaluation of skin biopsies of udder sores in dairy cows

Quantifying and mapping digital dermatitis-associated bacteria in lesion and nonlesion body sites and dairy farm environment

The source of infection of digital dermatitis (DD), an infectious lameness condition, is still uncertain. In this cross-sectional study, we aimed to identify potential reservoirs of DD bacteria in dairy cattle body sites with different stages of the disease and farm environments. We collected skin swabs from 85 dairy cows from 5 herds, 3 with and 2 without DD, from foot, hock, and udder cleft skin (with lesions or not), saliva, urine, and feces. We also obtained environmental samples. Real-time quantitative PCR targeted Treponema phagedenis, Treponema medium, Treponema pedis, Porphyromonas levii, Bacteroides pyogenes, Fusobacterium necrophorum, and Fusobacterium mortiferum. Digital dermatitis-associated Treponema spp. were exclusively detected in DD-affected herds in DD-foot and other skin lesions, healthy skin, saliva, and environmental samples. In contrast, the non-Treponema spp. were found in samples from both DD-negative and affected herds. As expected, DD lesions had higher bacterial loads than healthy skin. Interestingly, similar counts were observed in udder cleft lesions, indicating a potential opportunistic behavior on compromised skin. None of the targeted species were detected in fecal samples, but P. levii, B. pyogenes, and F. necrophorum were detected in urine. All 7 species were detected in saliva, although in low quantities. No associations were observed between the presence of each bacterial species in DD lesions and urine; however, there was an association between the presence of DD-Treponema spp. in lesions and saliva, hock, and udder skin. Feces and urine do not seem to be a DD bacteria primary source, but saliva and other skin lesions may play a role. Longitudinal studies would improve our understanding of DD-associated bacteria's transient or persistent presence in these sites. Investigating the sources of DD-associated bacteria will guide future interventions to minimize bacterial shedding and transmission, ultimately more effectively reducing bacterial load, transmission, and sources of infection in dairy herds.

An in-depth investigation of the microbiota and its virulence factors associated with severe udder cleft dermatitis lesions

Udder cleft dermatitis (UCD) is a skin condition affecting the anterior parts of the udder in dairy cattle. In the present study, we aimed to shed light on the microbiota in severe UCD lesions versus healthy udder skin by putting forward a taxonomic and functional profile based on a virulence factor analysis. Through shotgun metagenomic sequencing, we found a high proportion of bacteria in addition to a low abundance of archaea. A distinct clustering of healthy udder skin versus UCD lesion samples was shown by applying principal component analysis and (sparse) partial least squares analysis on the metagenomic data. Proteobacteria, Bacillota, and Actinomycetota were among the most abundant phyla in healthy udder skin samples. In UCD samples, Bacteroidota was the most abundant phylum. At genus level, Bifidobacterium spp. had the highest relative abundance in healthy skin samples, whereas Porphyromonas spp. and Corynebacterium spp. had the highest relative abundance in UCD samples. In the differential abundance analysis, Porphyromonas spp. and Bacteroides spp. were significantly differentially abundant in UCD samples, whereas Bifidobacterium spp., Staphylococcus sp. AntiMn-1, and Staphylococcus equorum were more commonly found in healthy samples. Moreover, the abundance of several treponeme phylotypes was significantly higher in lesion samples. The streptococcal cysteine protease speB was among the most abundant virulence factors present in severe UCD lesions, while a plethora of virulence factors such as the antitoxin relB were downregulated, possibly contributing to creating the ideal wound climate for the dysbiotic community. Network analysis showed healthy lesion samples had a large network ofpositive, correlations between the abundances of beneficial species such as Aerococcus urinaeequi and Bifidobacterium angulatum, indicating that the healthy skin microbiome forms an active protective bacterial network, which is disrupted in case of UCD. In UCD samples, a smaller microbial network mainly consisting of positive correlations between the abundances of Bacteroides fragilis and anaerobic Bacteroidota was exposed. Moreover, a high correlation between the taxonomic data and virulence factors was revealed, concurrently with 2 separate networks of microbes and virulence factors. One network, matching with the taxonomic findings in the healthy udder skin samples, showcased a community of harmless or beneficial bacteria, such as Bifidobacterium spp. and Butyrivibrio proteoclasticus, associated with hcnB, hcnC, relB, glyoxalase, and cupin 2. The other network, corresponding to UCD samples, consisted of pathogenic or facultative pathogenic and mainly anaerobic bacteria such as Treponema spp., Mycoplasmopsis spp., and bovine gammaherpesvirus 4, that correlated with virulence factors SpvB, fhaB, and haemagglutination activity domain-associated factor. Our results point toward a dysbiotic community with a notable decrease in diversity and evenness, with a loss of normal skin inhabitants and innocuous or useful species making way for predominantly anaerobic, facultative pathogens. The shift in the abundance of virulence factors such as fhaB and SpvB could play a role in the manifestation of a local micro-environment favorable to the microbiome associated with udder skin lesions. Lastly, the presence of specific networks between microbial species, and between microbes and virulence factors was shown.

Severe udder cleft dermatitis lesion transcriptomics points to an impaired skin barrier, defective wound repair and a dysregulated inflammatory response as key elements in the pathogenesis

This study is the first to investigate the transcriptomic changes occurring in severe udder cleft dermatitis lesions (UCD) in Holstein-Friesian cows. An examination of the gene expression levels in natural UCD lesions and healthy udder skin through RNA Seq-Technology provided a deeper insight into the inflammatory pathways associated with this disease. A clear distinction between the gene expression patterns of UCD lesions and healthy skin was shown in the principal component analysis. Genes coding for inflammatory molecules were upregulated such as the chemokines C-X-C motif ligand 2 (CXCL2), 5 (CXCL5) and 8 (CXCL8), and C-C motif ligand 11 (CCL11). Moreover, the genes coding for the multifunctional molecules ADAM12 and SLPI were amongst the highest upregulated ones, whereas the most downregulated genes included the ones coding for keratins and keratin-associated molecules. Predominantly inflammatory pathways such as the chemokine signaling, cytokine receptor interaction and IL-17 signaling pathway were significantly upregulated in the pathway analysis. These results point towards a fulminant, dysregulated inflammatory response concomitant with a disruption of the skin barrier integrity and a hampered wound repair mechanism in severe UCD lesions.

Prevalence and clinical relevance of udder thigh dermatitis in dairy cows

Objective Udder thigh dermatitis (UTD) is especially common in heifers. Skin alterations and necrosis of muscle tissue characterise this condition and, although the disease is well understood, systematic analysis concerning prevalence, risk factors and consequences of UTD is lacking. The aim of this study, therefore were such systematic clinical examinations.

Material and methods Statistical analyses of data were performed to objectively evaluate the supposed higher risk of heifers developing UTD. The study included a total of 317 animals that were examined and classified as UTD positive or negative on the day of calving. The size of skin alterations and the severity of tissue damage were assessed on days 7, 14 and 21 p. p.

Results The overall prevalence resulted in 18 % UTD with a higher risk in heifers (36.8 %) than in cows (4.3 %; P < 0.0001). A significant link was found between the size of tissue lesions and severity of UTD (day 7: P = 0.007; day 14: P = 0.002; day 21: P = 0.011). Peripartal udder oedemas were strongly associated with UTD (P < 0.05). The milk yield and the concentration of milk protein was found to have decreased.

Conclusion UTD appears to be a multi-factorial disease that is supposed to be painful due to the obvious avoidant behaviour in affected animals. In respect to the reduction in daily milk yield and an enhancement of pain related stress, neither the economic impact of UTD, nor the adverse effects on animal welfare should be underestimated.

Clinical relevance Heifers with udder oedema are advised to be examined for the presence of UTD in order to start an early treatment and diminish disease related negative impacts.

An Observational Study Investigating Potential Risk Factors and Economic Impact for Bovine Ischaemic Teat Necrosis on Dairy Farms in Great Britain

Bovine ischaemic teat necrosis (ITN) is an emerging disease of unknown aetiology that affects the teats of dairy cattle. It causes economic and animal welfare issues with many animals being culled. No effective treatments or epidemiological data to inform control strategies are currently available. The aim of this observational study was to investigate farmer-reported experiences and identify potential farm-level risk factors. In January 2018, a questionnaire was sent to a random sample of 1,855 Great Britain (GB) dairy farmers. A usable response rate of 12.3% was obtained. Fifty-one per cent [95% confidence interval (CI): 44.4–57.8%] of farmers reported having experienced ITN on their farm between 1985 and 2018. Rising numbers of farms indicated that ITN is an emerging disease with 46.3% of farmers reporting the first case in the 3 years up to 2018. At the animal level, 47.3% (95% CI: 38.7–55.9%) of the cases occurred during the first lactation and 78.9% (95% CI: 75.2–82.6%) within the first 90 days in milk. Only 20.8% (95% CI: 15.9–26.4%) of the cases were reported to recover, whereas 22.8% (95% CI: 17.8–28.5%) of the cases required culling. The remaining cases experienced complications such as loss of a teat and/or mastitis. From these data, the cost of ITN, through production losses and expenditure, was estimated to be £1,121 per farm per year. The costs were estimated at £720, £860 and £2,133 for recovered, complicated and culled cases, respectively. Univariable and multivariable logistic regression models were used to explore the associations between the presence of ITN on farm and various risk factors. The presence of udder cleft dermatitis (UCD) (odds ratio 2.80; 95% CI: 1.54–5.07; p &lt; 0.01) and chapped teats (odds ratio 6.07; 95% CI: 1.96–18.76; p &lt; 0.01) in the milking herd was associated with the presence of ITN at the farm level. This is the first national questionnaire of ITN within GB and highlights the association of UCD and chapped teats with ITN at the farm level. While there are many limitations and potential bias around farmer questionnaires, these findings highlight several key areas for further disease investigation and possible intervention.

Understanding microbial networks of farm animals through genomics, metagenomics and other meta-omic approaches for livestock wellness and sustainability

The association of microorganisms with livestock as endosymbionts, opportunists, and pathogens has been a matter of debate for a long time. Several livestock-associated bacterial and other microbial species have been identified and characterized through traditional culture-dependent genomic approaches. However, it is imperative to understand the comprehensive microbial network of domestic animals for their wellness, disease management, and disease transmission control. Since it is strenuous to provide a niche replica to any microorganisms while culturing them, thus a substantial number of microbial communities remain obscure. Metagenomics has laid out a powerful lens for gaining insight into the hidden microbial diversity by allowing the direct sequencing of the DNA isolated from any livestock sample like the gastrointestinal tract, udder, or genital system. Through metatranscriptomics and metabolomics, understanding gene expression profiles of the microorganisms and their molecular phenotype has become unchallenging. With large data sets emerging out of the genomic, metagenomic, and other meta-omics methods, several computational tools have also been developed for curation, assembly, gene prediction, and taxonomic profiling of the microorganisms. This review provides a detailed account of the beneficial and pathogenic organisms that dwell within or on farm animals. Besides, it highlights the role of meta-omics and computational tools in a comprehensive analysis of livestock-associated microorganisms.

Recovery from udder cleft dermatitis in dairy cows

Udder cleft dermatitis (UCD) is a common skin problem in dairy cows, localized at the fore udder attachment or between the udder halves. The main objectives of this study were to investigate spontaneous recovery from UCD in a longitudinal study and to investigate the treatment effect on UCD of a topical spray containing chelated copper and zinc in an additional treatment trial. Spontaneous recovery was investigated during a 1-yr longitudinal study in which 7 Swedish dairy herds were visited 9 times each, at 6-wk intervals. During the visits, all cows milked in the milking parlor were examined for mild and severe UCD, udder conformation traits, hygiene, and hock lesions. Additional cow and herd data were obtained from the Swedish official milk recording scheme. Recovery was defined as 2 consecutive observations of no UCD after a UCD case (1 or more consecutive observations of UCD). The recovery rate was calculated and factors associated with recovery were analyzed using discrete-time survival analysis. A treatment study was conducted in 4 of the herds after completion of the longitudinal study. Cows with UCD were allocated to treatment or a control group, and cows in the treatment group were treated once every day for 14 to 28 d. At follow-up visits on d 14, 28, and 56, all cows were scored for UCD. To investigate the effect of treatment, an ordered logistic regression model was used, with UCD score on d 56 (no, mild, or severe) as the outcome. Other potential explanatory variables were also included in the model. A total of 38% (126 of 329) of the cows in the longitudinal study made a spontaneous recovery from UCD. A long duration of UCD, severe lesions and higher parity reduced the chance of recovery. Among the recovered cows, 47% (59 of 126 cows) had a recurrent case of UCD after the recovery. In the treatment study, there was no difference in UCD score on d 56 between the treatment and control groups. Factors that affected the UCD score on d 56 were the duration of UCD before the treatment study started, UCD score on d 1 and udder conformation. Our findings emphasize the importance of further studies to identify effective treatment regimens as well as further studies to unravel the pathophysiology of UCD to improve the recommendations on how to prevent these lesions.

Spatial and temporal organization of jejunal microbiota in goats during animal development process

AIMS

This research aimed to investigate the temporal bacterial colonization relating to non-rumination, transition and rumination phases, together with the spatial organization of microbial community in the jejunal mucosa and digesta of goats.

METHODS AND RESULTS

This study explored the colonization programme of the jejunal microbiota by employing 16S rRNA amplicon sequencing. The colonization pattern of jejunal bacterial community exhibited an age- and gut region-dependent progression during animal development process. Approximately 268 bacterial signatures contributed to the discrimination between gut regions, with Lactobacillus, Ruminococcus, Eubacterium and Clostridium_sensu_stricto were enriched in the jejunal digesta, and Bacteroides and unclassified bacteria were enriched in the jejunal mucosa. Intriguingly, a shift from Lactobacillus to Butyrivibrio, Eubacterium and Ruminococcus after d 20 was observed for jejunal digesta. In mucosa, Bifidobacterium, Corynebacterium, Faecalibacterium and Roseburia increased with age (P < 0·05) while Arcobacter, Bacteroides and Porphyromonas peaked at d 10.

CONCLUSIONS

The jejunal bacterial community was settled after solid starter provision, which may mark the potential boundary of a timeframe for intervention in goats. The spatial heterogeneity highlighted the complicacy of ecological niches during manipulation of gut microbiota.

SIGNIFICANCE AND IMPACT OF THE STUDY

The present study extended the understanding of microbial programming and niche specific in the jejunum among different life stages and the basal cognition of persistent enhancement of nutrient utilization and decline of enteric diseases in ruminants.

A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows

Udder cleft dermatitis (UCD) is a skin condition affecting the fore udder attachment of dairy cows. UCD may be defined as mild (eczematous skin changes) or severe (open wounds, large skin changes). Our aims were to compare the microbiota of mild and severe UCD lesions with the microbiota of healthy skin from the fore udder attachment of control cows, and to investigate whether mastitis-causing pathogens are present in UCD lesions. Samples were obtained from cows in six dairy herds. In total, 36 UCD samples categorized as mild (n = 17) or severe (n = 19) and 13 control samples were sequenced using a shotgun metagenomic approach and the reads were taxonomically classified based on their k-mer content. The Wilcoxon rank sum test was used to compare the abundance of different taxa between different sample types, as well as to compare the bacterial diversity between samples. A high proportion of bacteria was seen in all samples. Control samples had a higher proportion of archaeal reads, whereas most samples had low proportions of fungi, protozoa and viruses. The bacterial microbiota differed between controls and mild and severe UCD samples in both composition and diversity. Subgroups of UCD samples were visible, characterized by increased proportion of one or a few bacterial genera or species, e.g. Corynebacterium, Staphylococcus, Brevibacterium luteolum, Trueperella pyogenes and Fusobacterium necrophorum. Bifidobacterium spp. were more common in controls compared to UCD samples. The bacterial diversity was higher in controls compared to UCD samples. Bacteria commonly associated with mastitis were uncommon. In conclusion, a dysbiosis of the microbiota of mild and severe UCD samples was seen, characterized by decreased diversity and an increased proportion of certain bacteria. There was no evidence of a specific pathogen causing UCD or that UCD lesions are important reservoirs for mastitis-causing bacteria.

Bacterial flora associated with udder cleft dermatitis in Dutch dairy cows

Udder cleft dermatitis (UCD) or udder sores is a skin lesion, characteristically located around the anterior junction between the udder and abdomen of dairy cows. It is a worldwide problem in dairy herds with a large effect on animal welfare. The etiology and possible infectious origins of UCD are largely unknown; however, specific bacterial or parasitic causes are suggested in the literature. Therefore the aim of this study was to investigate the possible bacteriological, mycological, or parasitic involvement in clinically scored UCD lesions. Bacteriological culture was performed on subcutaneous tissue samples taken postmortem at a depth of 5 to 10 mm of 87 mild or severe UCD lesions or from the same place in healthy cows. Fungal culture was performed on a subset of 22 subcutaneous tissue samples of severe UCD postmortem. To investigate the superficial flora, swabs were taken from normal skin or skin lesions of 15 live animals equally divided over 3 groups: healthy skin or mild and severe UCD lesions. Histopathology, to describe and classify the lesions and to assess the presence of mites, fungi, or bacteria, was performed on 128 tissue samples, taken separately. In severe UCD lesions, Trueperella pyogenes and Bacteroides pyogenes were more frequently present in deep tissue layers and in superficial layers, compared with the same layers in mild UCD lesions or healthy skin. Culturing and histopathology indicated no sign of involvement of treponemes, Staphylococcus aureus, Escherichia coli, fungi, or mites in the UCD lesions. Histopathological examination showed that the majority of the lesions were characterized by chronic aspecific inflammation. Severe UCD lesions more frequently showed chronic active inflammation on histopathology, compared with mild UCD lesions. Due to the cross-sectional character of this study, it is difficult to differentiate cause and effect; however, future preventive and curative measures against UCD should take into account the chronic and anaerobic nature of this illness.

Incidence of udder cleft dermatitis (UCD) in dairy cows and risk factors for transitions to UCD

Udder cleft dermatitis (UCD) is a common skin condition in Swedish dairy cows, affecting the anterior parts of the udder. The main objective of this study was to investigate incidence rate and duration of UCD in a 1-yr longitudinal study. Other objectives were to investigate risk factors for transitions from being healthy to having mild or severe UCD, and from having mild UCD to having severe UCD, and associations between UCD and clinical mastitis, somatic cell count (SCC) and hock lesions. Seven herds were included in the study and visited 9 times each at 6-wk intervals. At the visits, mild and severe UCD lesions, hock lesions, udder conformation traits, and hygiene scores were registered for each cow milked in the milking parlor. Information on breed, parity, days in milk (DIM), results from test milkings (milk production, SCC, and urea level), and veterinary treatments was also obtained. A UCD case was defined as one or several consecutive observations of UCD. The incidence and duration of UCD were described. Mixed-effect logistic regression models were used to analyze associations between potential risk factors and transitions to any type of UCD. Separate risk factor analyses were performed for transitions to mild and severe UCD. Associations with SCC, mastitis, and hock lesions were also analyzed with mixed-effect logistic regression models. The mean overall incidence of new UCD cases for all visits and herds was 0.5 cases per cow-year at risk. Risk factors associated with a higher risk of a transition to any type of UCD and mild UCD were breed (Swedish Red vs. Swedish Holstein), an indentation or fold at the fore udder attachment, and increasing DIM. In addition, a low milk urea level was associated with a lower risk of transition to any type of and mild UCD. Cows with previous mild UCD and high-yielding cows had increased risk for a transition to severe UCD. Cows that had an observed transition to severe UCD had an increased risk of veterinary-treated clinical mastitis within 6 wk after the UCD observation. No associations were found between UCD and SCC or hock lesions. The median observed duration of a UCD case was 12 wk, but most cases did not have an observed start or end during the study period. The observed duration of cases including severe UCD was longer than for cases involving only mild UCD. The high incidence and often long duration of UCD emphasize the need for preventive measures and treatment strategies.