RSS 1.0Teagasc publications in Biomed Central
This collection contains articles published in the Open Access Biomed Central journals by Teagasc authors.
Recent Submissions
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Temporal trends in biosecurity in Irish pig herds using a standardized scoring systemAbstract Background Biosecurity measures are crucial to the introduction and spread of pathogens both within and between farms. External biosecurity focuses on preventing pathogens from entering or leaving the farm, while internal biosecurity aims to limit or stop the spread of pathogens within the farm. Implementing biosecurity measures not only protects animals from disease but also has positive effects on productivity, welfare and farm profitability. By reducing the need for antimicrobials, biosecurity measures also contribute to combating antimicrobial resistance. To assess and improve biosecurity, tools like Biocheck.UGent have been developed. In Ireland, the Biocheck.UGent tool has been widely used in pig farms since 2018. The aims of this study were firstly to assess temporal trends on biosecurity scores in Irish pig farms from 2018 to 2023 using the Biocheck.UGent tool and secondly to identify areas for improvement. Results There was an increase in the number of annual assessments over the study period, with the majority of farms being assessed multiple times. Overall, external biosecurity scores were higher than internal scores. Improvements in the scores were observed over time for most of the subcategories for external and internal biosecurity and across the different farm types. Analysis of the subcategories within the scoring system revealed areas with lower scores, including disease management, cleaning and disinfection, and measures between compartments. Weaner-to-finisher farms tended to have lower scores compared to other farm types. Conclusions While external biosecurity in Irish pig farms is generally high, there is room for improvement in internal biosecurity. This study highlights the importance of continuous efforts to improve biosecurity. The data obtained will aid in estimating the cost–benefit of implementing biosecurity measures, crucial for decision-making and better returns on investments.
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Observational study: effect of varying transport durations and feed withdrawal on the physiological status and health of dairy calvesAbstract Long-distance transport and associated fasting of unweaned calves have the potential to compromise the animals’ welfare. This observational study aimed to determine how transport and fasting durations impacted the physiology and health of 115 transported calves in three transport groups; IRE (n = 20, mean age 29.8d; short road transport (~ 29 h incl. resting time) and short feed deprivation (~ 11 h)), INT (n = 65, mean age 24.9d; long road/ferry transport (~ 79 h incl. resting times) and long feed deprivation (~ 28 h and 25 h)), and NLD (n = 30, mean age 17.7d; short road transport (~ 28 h incl. resting time) and long feed deprivation (> 18 h)). All calves travelled through an assembly centre. Each calf was blood sampled (arrival at destination farm, 1-week and 3-weeks post-arrival), health scored (arrival, 1, 3, 7, 8, 20d post-arrival) and weighed (farm/mart of origin [IRE and INT only], arrival, and 3-weeks post-arrival). (Generalised) linear mixed models were used to analyse differences in blood variables, weight, and health scores on arrival and during recovery (all other timepoints). Despite differing transport durations, both INT and NLD calves exhibited glucose, beta-hydroxy-butyrate, non-esterified-fatty-acids and sodium levels outside reference limits upon arrival, which were different from values observed in IRE calves (p < 0.05). Lactate and potassium were above reference range for INT calves on arrival, and higher than in IRE and NLD groups (p < 0.05). One- and three-weeks post arrival, most variables returned to within reference ranges, and differences between groups were minimal and not clearly associated with either transport duration or fasting during transport. Health scores did not differ between transport groups at arrival, and differences were minimal during the three-week recovery period. INT calves lost more weight during the journey than IRE calves (p < 0.01), while INT and NLD calves gained similar weight in the 3-weeks post-arrival, but less than IRE calves (both p < 0.01). Overall, changes in the physiological status of calves post transport appeared to relate more to the duration of feed deprivation than to the duration of transport, except for potassium and lactate (muscle fatigue), which were impacted more for INT calves. Most variables showed clear signs of recovery to within reference levels for all groups within three weeks. Minimizing the duration of feed deprivation during transport should be a key consideration for the dairy industry to reduce the impact of transport on calf welfare.
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Relationship between the rumen microbiome and liver transcriptome in beef cattle divergent for feed efficiencyAbstract Background Feed costs account for a high proportion of the variable cost of beef production, ultimately impacting overall profitability. Thus, improving feed efficiency of beef cattle, by way of determining the underlying genomic control and selecting for feed efficient cattle provides a method through which feed input costs may be reduced whilst also contributing to the environmental sustainability of beef production. The rumen microbiome dictates the feed degradation capacity and consequent nutrient supply in ruminants, thus potentially impacted by feed efficiency phenotype. Equally, liver tissue has been shown to be responsive to feed efficiency phenotype as well as dietary intake. However, although both the rumen microbiome and liver transcriptome have been shown to be impacted by host feed efficiency phenotype, knowledge of the interaction between the rumen microbiome and other peripheral tissues within the body, including the liver is lacking. Thus, the objective of this study was to compare two contrasting breed types (Charolais and Holstein-Friesian) divergent for residual feed intake (RFI) over contrasting dietary phases (zero-grazed grass and high-concentrate), based on gene co-expression network analysis of liver transcriptome data and microbe co-abundance network of rumen microbiome data. Traits including RFI, dry matter intake (DMI) and growth rate (ADG), as well as rumen concentrations of volatile fatty acids were also included within the network analysis. Results Overall, DMI had the greatest number of connections followed by RFI, with ADG displaying the fewest number of significant connections. Hepatic genes related to lipid metabolism were correlated to both RFI and DMI phenotypes, whilst genes related to immune response were correlated to DMI. Despite the known relationship between RFI and DMI, the same microbes were not directly connected to these phenotypes, the Succiniclasticum genus was however, negatively connected to both RFI and ADG. Additionally, a stepwise regression analysis revealed significant roles for both Succiniclasticum genus and Roseburia.faecis sp. in predicting RFI, DMI and ADG. Conclusions Results from this study highlight the interactive relationships between rumen microbiome and hepatic transcriptome data of cattle divergent for RFI, whilst also increasing our understanding of the underlying biology of both DMI and ADG in beef cattle.
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Sowing seeds of awareness: a cross-sectional analysis of mental health literacy and help-seeking in Irish farmersAbstract Background Farmers around the world are at risk of depression, anxiety, and suicidal ideation yet many avoid seeking help. In Ireland, farmers’ mental health is a national concern, as farmers face barriers of masculine norms around help-seeking. This study aimed to examine the prevalence and relationship between mental health literacy and mental health help-seeking in the Irish farming community. It also aimed to identify if mental health literacy or mental health help-seeking differed depending on gender, age, education, health status and income level. Methods We conducted a cross-sectional assessment of 351 Irish farmers’ mental health literacy and help-seeking using validated psychometric measures: the Mental Help Seeking Intention Scale (MHSIS), the Attitudes Toward Seeking Professional Psychological Help Short Form (ATSPPH-SF), and the Multicomponent Mental Health Literacy Measure (MMHL). Results Irish farmers’ mental health literacy and help-seeking scores were interrelated. Though low, farmers’ scores were comparable to the general population and higher than some European samples. Despite broadly favourable attitudes towards seeking professional mental health help, Irish farmers perceived significant barriers to accessing care and exhibited stoic health attitudes. Farmers with less education and men were particularly at risk. Conclusion Irish farmers’ stoic attitudes may be a response to their perceived lack of services. Interventions providing mental health literacy education and improving access to existing mental health services are particularly important for this population of farmers.
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Shotgun metagenomic sequencing reveals the influence of artisanal dairy environments on the microbiomes, quality, and safety of Idiazabal, a raw ewe milk PDO cheeseAbstract Background Numerous studies have highlighted the impact of bacterial communities on the quality and safety of raw ewe milk-derived cheeses. Despite reported differences in the microbiota among cheese types and even producers, to the best of our knowledge, no study has comprehensively assessed all potential microbial sources and their contributions to any raw ewe milk-derived cheese, which could suppose great potential for benefits from research in this area. Here, using the Protected Designation of Origin Idiazabal cheese as an example, the impact of the environment and practices of artisanal dairies (including herd feed, teat skin, dairy surfaces, and ingredients) on the microbiomes of the associated raw milk, whey, and derived cheeses was examined through shotgun metagenomic sequencing. Results The results revealed diverse microbial ecosystems across sample types, comprising more than 1300 bacterial genera and 3400 species. SourceTracker analysis revealed commercial feed and teat skin as major contributors to the raw milk microbiota (45.6% and 33.5%, respectively), being a source of, for example, Lactococcus and Pantoea, along with rennet contributing to the composition of whey and cheese (17.4% and 41.0%, respectively), including taxa such as Streptococcus, Pseudomonas_E or Lactobacillus_H. Functional analysis linked microbial niches to cheese quality- and safety-related metabolic pathways, with brine and food contact surfaces being most relevant, related to genera like Brevibacterium, Methylobacterium, or Halomonas. With respect to the virulome (virulence-associated gene profile), in addition to whey and cheese, commercial feed and grass were the main reservoirs (related to, e.g., Brevibacillus_B or CAG-196). Similarly, grass, teat skin, or rennet were the main contributors of antimicrobial resistance genes (e.g., Bact-11 or Bacteriodes_B). In terms of cheese aroma and texture, apart from the microbiome of the cheese itself, brine, grass, and food contact surfaces were key reservoirs for hydrolase-encoding genes, originating from, for example, Lactococcus, Lactobacillus, Listeria or Chromohalobacter. Furthermore, over 300 metagenomic assembled genomes (MAGs) were generated, including 60 high-quality MAGs, yielding 28 novel putative species from several genera, e.g., Citricoccus, Corynebacterium, or Dietzia. Conclusion This study emphasizes the role of the artisanal dairy environments in determining cheese microbiota and, consequently, quality and safety. Video Abstract
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Effect of enhanced plane of nutrition in early life on the transcriptome and proteome of the anterior pituitary gland in Angus heifer calvesAbstract Background Enhanced nutrition during the early calfhood period has been shown to lead to earlier pubertal development in heifer calves. This is of interest as earlier pubertal onset can subsequently facilitate earlier calving which can economically benefit production systems. Reproductive development in heifers is regulated by the hypothalamic-pituitary-ovarian signalling pathway. In particular the anterior pituitary gland is central to reproductive development, through the dynamics of gonadotropic pulsatility. However, despite clear knowledge of the influence of enhanced dietary intake on subsequent reproductive development, the molecular control governing this response in the pituitary gland within the hypothalamic-pituitary-ovarian signalling axis in heifer calves is not fully understood. The objective of this study was to examine the effect of an enhanced plane of nutrition during early life on the anterior pituitary gland of heifer calves through both transcriptomic and proteomic analyses. Between 3 and 21 weeks of age, heifer calves were offered either a high (HI, n = 14) or moderate (MOD, n = 14) plane of nutrition, designed to elicit target growth rates of 1.2 and 0.5 kg/d for HI and MOD groups, respectively. All calves were euthanised at 21 weeks of age and anterior pituitary tissue harvested for subsequent use in global transcriptomic and proteomic analyses. Results Average daily gain was affected by diet (P < 0.001) and was 1.18 and 0.50 kg/day, for HI and MOD calves, respectively. RNAseq analysis resulted in the identification of 195 differentially expressed genes (Padj<0.05; fold change > 1.5), with 277 proteins identified as differentially abundant (Padj<0.05; fold change > 1.5) between contrasting dietary treatment groups. Biochemical pathway analysis of differentially affected genes and proteins revealed an enrichment for both growth hormone and GnRH signalling pathways (Padj.<0.05). Additionally, pathway analysis predicted an effect of enhanced dietary intake on endocrine function within the anterior pituitary gland as well as on reproductive system development and function (Padj.<0.05). Conclusions Results from this study show that an enhanced dietary intake during early calfhood affected the molecular control of the anterior pituitary gland in heifer calves in early life.
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Summer scour syndrome in weaned dairy calves: case seriesAbstract Background Summer scour syndrome (SSS) is a recently identified pathological condition affecting weaned dairy and dairy-beef calves during their first grazing season in Ireland. The syndrome is characterised by diarrhoea, weight loss, weakness, and can ultimately lead to death in some calves. Oral and oesophageal ulcerations are present in some cases. This study aimed to characterise a series of SSS cases in weaned dairy-bred calves on Irish commercial farms. Results Five farms with calves having unexplained diarrhoea at grass were referred by private veterinary practitioners (PVP) following preliminary testing to exclude coccidiosis and parasitic gastroenteritis. Farms were visited within 2 to 5 days following PVP’s referrals, or 2 days to 3 weeks relative to the onset of clinical signs. Farm management data, grass and concentrate samples, and biological samples from 46 calves (8 to 10 calves/farm) displaying clinical signs were collected. Two farms were subsequently found positive for coccidiosis and/or had chronic pneumonia problems after a thorough herd investigation and were designated as non-case farms (NCF). The remaining three farms were deemed typical SSS outbreaks (case farms; CF). Mean rumen fluid pH per farm ranged from 6.67 to 7.09 on CF, and 6.43–6.88 on NCF. Mean rumen fluid ammonia concentrations ranged from 17.6 to 29.6 mg/L and 17.2–45.0 mg/L on CF and NCF, respectively. Corresponding blood ammonia concentrations ranged from 129 to 223 µmol/L and 22–25 µmol/L. Mean blood copper and molybdenum concentrations were within normal range on all farms. Grass crude protein concentrations on the paddocks where the calves had grazed, and were currently grazing on the day of visit ranged from 137 to 148 g/kg DM and 106–177 g/kg DM, respectively on CF, and 160–200 g/kg DM and 151–186 g/kg DM, respectively on NCF. On CF, inorganic nitrogen fertiliser was applied 1 to 3 weeks pre-grazing, whereas on the two NCF, inorganic nitrogen fertiliser was applied 2 to 3 weeks pre-grazing on one farm and no fertiliser was applied on the other. Conclusion These findings suggest that copper or molybdenum toxicity, and ruminal acidosis are not the primary causes of SSS. High blood ammonia concentrations and the timing and level of inorganic nitrogen fertiliser application to paddocks pre-grazing, warrant further investigation.
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Description of patterns of ear and tail lesions during the grower-finisher period in a commercial pig farmBackground Ear and tail lesions are prevalent indicators of impaired welfare observed in pig production with different multifactorial causes. Understanding the progression of ear and tail lesions over time is important to implement preventative strategies on commercial pig farms. Therefore, this case study aimed to provide a detailed account of patterns of ear and tail lesions in pigs on a single commercial farm during the grower-finisher period. Case presentation A total of 1,676 12-week old pigs (n = 773 females and n = 903 males, all tail docked) were followed from arrival to the grower facilities until transferred to the finisher stage on a commercial pig farm in Ireland. Pigs were individually weighed and inspected for the severity of fresh ear and tail lesions (score 0–4) on transfer to the first grower (24.9 ± 5.33 kg, 12 weeks of age, n = 1,676 pigs), second grower (33.3 ± 7.04 kg, 14 weeks of age, n = 1,641 pigs), and finisher stage (60.2 ± 7.74 kg, 18 weeks of age, n = 1,626 pigs). Due to the low number of pigs with high scores, ear lesions were classified as no (score 0), mild (score 1), moderate (score 2) and severe (score ≥ 3) and tail lesions were classified as no (score 0), mild (score 1), and moderate-to-severe (score ≥ 2). Ear lesions were more prevalent than tail lesions at each inspection. There were approx. 19% of pigs with ear lesions at all three inspections but no pigs presented with tail lesions at all three inspections. When considering the specific severity categories, we observed 32 different ear lesion score combinations and 15 different tail lesion score combinations across the three inspections. Conclusion The high number of observed patterns of ear and tail lesions suggest large individual variability in lesion progression. Ear lesions were more of an issue than tail lesions and little is known about this health and welfare problem indicating that further research into causes and management strategies is needed.
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Development of an animal health testing tool to reduce antimicrobial use on farms: perceptions, implications, and needs of Irish dairy farmers and farm veterinariansAbstract Background The threat of antimicrobial resistance is triggering the need for behavioural change towards antimicrobial use on Irish farms. Newly introduced veterinary medicine regulations are mandating the restricted and more prudent use of antimicrobials in the animal health sector. The need to reduce antimicrobials has placed a greater emphasis on the importance of animal health testing, however, issues with current testing practices are affecting diagnosis and subsequent drug usage. There is potential for digital technologies to address these issues and reduce antimicrobial use on farms, however, for these tools to be successful, they would need to be developed in collaboration with future end users. Results Using qualitative approaches (focus groups), this study engages with dairy farmers and farm veterinary practitioners to detail current challenges with animal health diagnosis and to explore the initial development of a rapid, on-farm animal health testing tool to address these challenges. Issues with timing and testing, the role of knowledge and experience, and veterinarian availability all affect the ability of farmers and veterinarians to diagnose animal health issues on farm. These issues are having negative implications including the increased and unnecessary use of antimicrobials. An on-farm testing tool would help mitigate these effects by allowing veterinarians to achieve rapid diagnosis, facilitating the timely and targeted treatment of animal illnesses, helping to reduce overall antimicrobial use on farms. However, engagement with end users has highlighted that if a tool like this is not developed correctly, it could have unintended negative consequences such as misdiagnosis, increased antimicrobial use, challenges to farmer-veterinarian relationships, and data misuse. This study outlines initial end user needs and requirements for a testing tool but suggests that in order to successfully design and develop this tool, co-design approaches such as Design Thinking should be applied; to mitigate future negative impacts, and to ensure a testing tool like this is designed specifically to address Irish dairy farmers and farm veterinarians’ values and needs, ensuring responsible and successful uptake and use. Conclusions Digital tools can be effective in reducing antimicrobial use on farms, however, to be successful, these tools should be designed in a user centred way.
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Effect of suckler cow breed type and parity on the development of the cow-calf bond post-partum and calf passive immunityAbstract Background Development of the cow-calf bond post-partum and passive immunity of calves from spring-calving beef × beef (B×B) and beef × dairy (B×D) cow genotypes was determined using primiparous and multiparous (Experiment 1), and primiparous and second-parity (Experiment 2) animals. In Experiment 1, calves either suckled colostrum naturally (‘natural-suckling’) (n = 126), or were fed colostrum, using an oesophageal-tube (‘artificially-fed’) (n = 26), from their dam within 1-h post-partum. In Experiment 2, all calves (n = 60) were artificially-fed colostrum from their dam. Prior to colostrum suckling/feeding, colostrum was sampled for IgG analysis. The cow-calf bond was assessed using CCTV recordings during the first 4-h post-partum. Calves were blood sampled at 48-h post-partum to determine IgG and total protein (TP) concentrations, and zinc sulphate turbidity (ZST) units. Results There was no difference (P > 0.05) in cow licking behaviours and calf standing and suckling behaviours between the genotypes, except in Experiment 2 where B×D calves had more attempts to suckle before suckling occurred (P ≤ 0.05) compared to B×B calves. In Experiment 1, multiparous cows licked their calves sooner (P ≤ 0.05) and for longer (P < 0.01), and their calves had fewer attempts to stand (P < 0.001), stood for longer (P = 0.05), and had fewer attempts to suckle before suckling occurred (P < 0.001) than primiparous cows; there was no parity effect on cow-calf behaviour in Experiment 2. Colostrum IgG concentrations and measures of calf passive immunity did not differ (P > 0.05) between the genotypes in either Experiment. In Experiment 1, colostrum IgG concentrations were greater (P ≤ 0.05) in multiparous compared to primiparous cows and their calves had superior (P ≤ 0.05) passive immunity; no effect of parity was found in Experiment 2. Passive immunity did not differ (P > 0.05) between suckled and artificially-fed calves in Experiment 1. Conclusions Cow genotype had little effect on cow-calf behaviours, but under ‘natural-suckling’ conditions primiparous cows expressed maternal inexperience and their calves were less vigorous than multiparous cows. Colostrum IgG concentration and calf passive immunity measures were unaffected by genotype, but under ‘natural-suckling’ conditions calves from primiparous cows had lower passive immunity.
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Relationships between pig farm management and facilities and lung lesions' scores and between lung lesions scores and carcass characteristicsAbstract Background The objective of this study was to examine the inter-relationships between pig farm management and facilities (as assessed by questionnaire) and post-mortem lung lesion (lung score assesment), which are the result of respiratory infections. The relationships between carcass characteristics and post-mortem lung lesion scores were also investigated. Results Questionnaire responses were collected from 22 self-selecting pig farmers about their farm facilities/management and health condition of the respiratory system of pigs, including the occurrence of clinical respiratory signs, results of laboratory testing for respiratory pathogens, and the use of respiratory vaccines. When fatteners were sent to the abattoir, their carcasses (n = 1,976) were examined for evidence of respiratory disease by lung lesion (pleuritis pneumonia-like (PP-like) and enzootic pneumonia-like (EP-like) lesions) scoring and the Actinobacillus pleuropneumoniae Index (APPI) was calculated. Carcass characteristics were recorded and, retrospectively, the prevalence of cachectic pigs was calculated. Using these variables, the relationships between farm facilities/management and lung lesions scores and the relationships between the latter and carcass characteristics and cachexia were explored. The key findings relating farm facilities and management to lung lesions were: slatted floors were associated with significantly higher EP-like lesions scores than litter bedding in weaners, single-stage fattening in the same building was associated with significantly higher EP-like lesions scores than two-stage fattening, but herd size, stocking density, use of all-in/all-out (AIAO) rule, technological break duration and variation in daily temperature did not affect lung lesions scores. The key findings relating lung lesion scores to carcass characteristics were: a significant, negative correlation between EP-like scores and carcass weight but not with other carcass characteristics, a significant positive correlation between PP-like scores and carcass meat content and prevalence of cachectic carcasses and a significant positive correlation between lung APPI and prevalence of cachectic carcasses. Conclusions It can be concluded that both farm facilities and management affect lung lesions scores and that the latter affect carcass characteristics. Lung lesion scoring is an inexpensive technique suitable for rapid monitoring of large numbers of carcasses that can be performed after animal slaughter. It provides useful information to inform producers about possible deficits in farm facilities or management and is a predictor of economic loss due to poorer quality carcasses.
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First reported case in an Irish flock of MCF- like systemic necrotizing vasculitis in sheep associated with ovine herpesvirus 2Abstract Background Ovine gammaherpesvirus 2 (OvHV-2) is the causative agent of sheep associated malignant catarrhal fever (MCF). As sheep are the adapted host for OvHV-2, it is generally presumed that infection is not associated with disease in this species. However, a recent case review combined in-situ hybridisation, PCR and histopathology and correlated the viral distribution with systemic necrotizing vasculitis and concluded OvHV-2 was the likely agent responsible for sporadic, MCF-like vascular disease in sheep. Case presentation Using similar methods this case study reports on the findings of the first reported cases in an Irish Flock of MCF- like systemic necrotizing vasculitis in sheep associated with OvHV-2. Sheep A, a 16-month-old Texel-cross hogget displayed signs of ill- thrift, Sheep B, a nine-month-old Belclare-cross lamb, was found dead having displayed no obvious symptoms. Both cases occurred on the same farm, however the animals were not related. Lymphohistiocytic vasculitis of various tissues was the predominant histopathological finding in both animals. Conclusion By combining histopathology, PCR and in-situ hybridisation results, MCF- like systemic necrotizing vasculitis associated with OvHV-2 has been diagnosed for the first time in an Irish flock.
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The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traitsAbstract Background Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal study assessing the impact of ripening in three natural caves on the microbiome and resistome succession across three different producers of Cabrales blue-veined cheese. Results Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome. Lactococcus and the former Lactobacillus genus, among other taxa, showed high abundance in cheeses at initial stages of ripening, either coming from the raw material, starter culture used, and/or the environment of processing plants. Along cheese ripening in caves, these taxa were displaced by other bacteria, such as Tetragenococcus, Corynebacterium, Brevibacterium, Yaniella, and Staphylococcus, predominantly originating from cave environments (mainly food contact surfaces), as demonstrated by source-tracking analysis, strain analysis at read level, and the characterization of 613 metagenome-assembled genomes. The high abundance of Tetragenococcus koreensis and Tetragenococcus halophilus detected in cheese has not been found previously in cheese metagenomes. Furthermore, Tetragenococcus showed a high level of horizontal gene transfer with other members of the cheese microbiome, mainly with Lactococcus and Staphylococcus, involving genes related to carbohydrate metabolism functions. The resistome analysis revealed that raw milk and the associated processing environments are a rich reservoir of antimicrobial resistance determinants, mainly associated with resistance to aminoglycosides, tetracyclines, and β-lactam antibiotics and harbored by aerobic gram-negative bacteria of high relevance from a safety point of view, such as Escherichia coli, Salmonella enterica, Acinetobacter, and Klebsiella pneumoniae, and that the displacement of most raw milk-associated taxa by cave-associated taxa during ripening gave rise to a significant decrease in the load of ARGs and, therefore, to a safer end product. Conclusion Overall, the cave environments represented an important source of non-starter microorganisms which may play a relevant role in the quality and safety of the end products. Among them, we have identified novel taxa and taxa not previously regarded as being dominant components of the cheese microbiome (Tetragenococcus spp.), providing very valuable information for the authentication of this protected designation of origin artisanal cheese. Video Abstract
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Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigsAbstract Background Post weaning diarrhoea (PWD) causes piglet morbidity and mortality at weaning and is a major driver for antimicrobial use worldwide. New regulations in the EU limit the use of in-feed antibiotics (Ab) and therapeutic zinc oxide (ZnO) to prevent PWD. New approaches to control PWD are needed, and understanding the role of the microbiota in this context is key. In this study, shotgun metagenome sequencing was used to describe the taxonomic and functional evolution of the faecal microbiota of the piglet during the first two weeks post weaning within three experimental groups, Ab, ZnO and no medication, on commercial farms using antimicrobials regularly in the post weaning period. Results Diversity was affected by day post weaning (dpw), treatment used and diarrhoea but not by the farm. Microbiota composition evolved towards the dominance of groups of species such as Prevotella spp. at day 14dpw. ZnO inhibited E. coli overgrowth, promoted higher abundance of the family Bacteroidaceae and decreased Megasphaera spp. Animals treated with Ab exhibited inconsistent taxonomic changes across time points, with an overall increase of Limosilactobacillus reuteri and Megasphaera elsdenii. Samples from non-medicated pigs showed virulence-related functions at 7dpw, and specific ETEC-related virulence factors were detected in all samples presenting diarrhoea. Differential microbiota functions of pigs treated with ZnO were related to sulphur and DNA metabolism, as well as mechanisms of antimicrobial and heavy metal resistance, whereas Ab treated animals exhibited functions related to antimicrobial resistance and virulence. Conclusion Ab and particularly ZnO maintained a stable microbiota composition and functionality during the two weeks post weaning, by limiting E. coli overgrowth, and ultimately preventing microbiota dysbiosis. Future approaches to support piglet health should be able to reproduce this stable gut microbiota transition during the post weaning period, in order to maintain optimal gut physiological and productive conditions.
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An in-depth evaluation of metagenomic classifiers for soil microbiomesAbstract Background Recent endeavours in metagenomics, exemplified by projects such as the human microbiome project and TARA Oceans, have illuminated the complexities of microbial biomes. A robust bioinformatic pipeline and meticulous evaluation of their methodology have contributed to the success of these projects. The soil environment, however, with its unique challenges, requires a specialized methodological exploration to maximize microbial insights. A notable limitation in soil microbiome studies is the dearth of soil-specific reference databases available to classifiers that emulate the complexity of soil communities. There is also a lack of in-vitro mock communities derived from soil strains that can be assessed for taxonomic classification accuracy. Results In this study, we generated a custom in-silico mock community containing microbial genomes commonly observed in the soil microbiome. Using this mock community, we simulated shotgun sequencing data to evaluate the performance of three leading metagenomic classifiers: Kraken2 (supplemented with Bracken, using a custom database derived from GTDB-TK genomes along with its own default database), Kaiju, and MetaPhlAn, utilizing their respective default databases for a robust analysis. Our results highlight the importance of optimizing taxonomic classification parameters, database selection, as well as analysing trimmed reads and contigs. Our study showed that classifiers tailored to the specific taxa present in our samples led to fewer errors compared to broader databases including microbial eukaryotes, protozoa, or human genomes, highlighting the effectiveness of targeted taxonomic classification. Notably, an optimal classifier performance was achieved when applying a relative abundance threshold of 0.001% or 0.005%. The Kraken2 supplemented with bracken, with a custom database demonstrated superior precision, sensitivity, F1 score, and overall sequence classification. Using a custom database, this classifier classified 99% of in-silico reads and 58% of real-world soil shotgun reads, with the latter identifying previously overlooked phyla using a custom database. Conclusion This study underscores the potential advantages of in-silico methodological optimization in metagenomic analyses, especially when deciphering the complexities of soil microbiomes. We demonstrate that the choice of classifier and database significantly impacts microbial taxonomic profiling. Our findings suggest that employing Kraken2 with Bracken, coupled with a custom database of GTDB-TK genomes and fungal genomes at a relative abundance threshold of 0.001% provides optimal accuracy in soil shotgun metagenome analysis.
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Promiscuous, persistent and problematic: insights into current enterococcal genomics to guide therapeutic strategyAbstract Vancomycin-resistant enterococci (VRE) are major opportunistic pathogens and the causative agents of serious diseases, such as urinary tract infections and endocarditis. VRE strains mainly include species of Enterococcus faecium and E. faecalis which can colonise the gastrointestinal tract (GIT) of patients and, following growth and persistence in the gut, can transfer to blood resulting in systemic dissemination in the body. Advancements in genomics have revealed that hospital-associated VRE strains are characterised by increased numbers of mobile genetic elements, higher numbers of antibiotic resistance genes and often lack active CRISPR-Cas systems. Additionally, comparative genomics have increased our understanding of dissemination routes among patients and healthcare workers. Since the efficiency of currently available antibiotics is rapidly declining, new measures to control infection and dissemination of these persistent pathogens are urgently needed. These approaches include combinatory administration of antibiotics, strengthening colonisation resistance of the gut microbiota to reduce VRE proliferation through commensals or probiotic bacteria, or switching to non-antibiotic bacterial killers, such as bacteriophages or bacteriocins. In this review, we discuss the current knowledge of the genomics of VRE isolates and state-of-the-art therapeutic advances against VRE infections.
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Cutaneous application of SecurePig® FLASH, a Pig appeasing pheromone analogue, facilitates adaptation and manages social behavior during feeding in semi-extensive conditionsAbstract Background Farm animals face several challenges throughout their lives, which can affect both their welfare and their productivity. Promoting adaptation in animals is one way of limiting these consequences. In various animal species, the use of maternal appeasing pheromones is efficient to reduce aggressiveness, improve adaptation and thus ensuring better welfare and productivity. This study sought to investigate the efficiency of a treatment with a Pig Appeasing Pheromone (PAP) on the behavior of pigs reared under semi-extensive conditions and exposed to a potential conflict– collective feeding. Animals (n = 14 divided in 2 groups of 7) were subjected to 3 different phases, (A) baseline - no pigs received the PAP, (B) SP − 2 out of the 7 pigs per group received the PAP and (C) AP– all pigs received the PAP. Behaviors related to feeding, aggression and locomotion were compared between the 3 phases of the study. Results Compared to the baseline period, we observed that the number of head knocks was reduced when some pigs (p < 0.001) and all pigs (p < 0.005) received the PAP. Similarly, we observed that the number of fleeing attempts was reduced when some pigs (p < 0.001) and all pigs (p < 0.001) were treated when compared to baseline. This number was lower in the AP phase than in the SP phase (p < 0.001). When all pigs were treated (AP), we also observed that they spent less time investigating the floor than during the two other phases (p < 0.001), but they seemed more likely to leave the feeder due to the presence or behavior of another pig of the group (SP vs. AP, p < 0.05). Conclusions The PAP application improved adaptation in pigs by reducing aggressiveness and promoting conflict avoidance. Those results validate the efficiency of the pheromonal treatment under semi-extensive rearing conditions to help pigs to cope with a challenging situation. Using PAP in the pig industry seems interesting to limit unwanted consequences of farm practices on animal welfare and productivity, by promoting their adaptation.
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An across breed, diet and tissue analysis reveals the transcription factor NR1H3 as a key mediator of residual feed intake in beef cattleAbstract Background Provision of feed is a major determinant of overall profitability in beef production systems, accounting for up to 75% of the variable costs. Thus, improving cattle feed efficiency, by way of determining the underlying genomic control and subsequently selecting for feed efficient cattle, provides a method through which feed input costs may be reduced. The objective of this study was to undertake gene co-expression network analysis using RNA-Sequence data generated from Longissimus dorsi and liver tissue samples collected from steers of two contrasting breeds (Charolais and Holstein-Friesian) divergent for residual feed intake (RFI), across two consecutive distinct dietary phases (zero-grazed grass and high-concentrate). Categories including differentially expressed genes (DEGs) based on the contrasts of RFI phenotype, breed and dietary source, as well as key transcription factors and proteins secreted in plasma were utilised as nodes of the gene co-expression network. Results Of the 2,929 DEGs within the network analysis, 1,604 were reported to have statistically significant correlations (≥ 0.80), resulting in a total of 43,876 significant connections between genes. Pathway analysis of clusters of co-expressed genes revealed enrichment of processes related to lipid metabolism (fatty acid biosynthesis, fatty acid β-oxidation, cholesterol biosynthesis), immune function, (complement cascade, coagulation system, acute phase response signalling), and energy production (oxidative phosphorylation, mitochondrial L-carnitine shuttle pathway) based on genes related to RFI, breed and dietary source contrasts. Conclusions Although similar biological processes were evident across the three factors examined, no one gene node was evident across RFI, breed and diet contrasts in both liver and muscle tissues. However within the liver tissue, the IRX4, NR1H3, HOXA13 and ZNF648 gene nodes, which all encode transcription factors displayed significant connections across the RFI, diet and breed comparisons, indicating a role for these transcription factors towards the RFI phenotype irrespective of diet and breed. Moreover, the NR1H3 gene encodes a protein secreted into plasma from the hepatocytes of the liver, highlighting the potential for this gene to be explored as a robust biomarker for the RFI trait in beef cattle.
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Survey of farm, parlour and milking management, parlour technologies, SCC control strategies and farmer demographics on Irish dairy farmsAbstract Background This cross-sectional study describes a survey designed to fill knowledge gaps regarding farm management practices, parlour management practices and implemented technologies, milking management practices, somatic cell count (SCC) control strategies, farmer demographics and attitudes around SCC management on a sample of Irish dairy farms. Results We categorized 376 complete responses by herd size quartile and calving pattern. The average respondent herd was 131 cows with most (82.2%) operating a seasonal calving system. The median monthly bulk tank somatic cell count for seasonal calving systems was 137,000 cells/ml (range 20,000 – 1,269,000 cells/ml), 170,000 cells/ml for split-calving systems (range 46,000 – 644,000 cells/ml) and 186,000 cells/ml for ‘other’ herds (range 20,000 – 664,000 cells/ml). The most common parlour types were swing-over herringbones (59.1%) and herringbones with recording jars (22.2%). The average number of units across herringbone parlours was 15, 49 in rotary parlours and two boxes on automatic milking system (AMS) farms. The most common parlour technologies were in-parlour feeding systems (84.5%), automatic washers on the bulk tank (72.8%), automatic cluster removers (57.9%), and entrance or exit gates controlled from the parlour pit (52.2%). Veterinary professionals, farming colleagues and processor milk quality advisors were the most commonly utilised sources of advice for SCC management (by 76.9%, 50.0% and 39.2% of respondents respectively). Conclusions In this study, we successfully utilised a national survey to quantify farm management practices, parlour management practices and technology adoption levels, milking management practices, SCC control strategies and farmer demographics on 376 dairy farms in the Republic of Ireland. Rotary and AMS parlours had the most parlour technologies of any parlour type. Technology add-ons were generally less prevalent on farms with smaller herds. Despite finding areas for improvement with regard to frequency of liner changes, glove-wearing practices and engagement with bacteriology of milk samples, we also found evidence of high levels of documentation of mastitis treatments and high use of post-milking teat disinfection. We discovered that Irish dairy farmers are relatively content in their careers but face pressures regarding changes to the legislation around prudent antimicrobial use in their herds.
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Metagenomic comparison of the faecal and environmental resistome on Irish commercial pig farms with and without zinc oxide and antimicrobial usageAbstract Background Antimicrobials and heavy metals such as zinc oxide (ZnO) have been commonly used on Irish commercial pig farms for a 2-week period post-weaning to help prevent infection. In 2022, the prophylactic use of antimicrobials and ZnO was banned within the European Union due to concerns associated with the emergence of antimicrobial resistance (AMR) and contamination of the environment with heavy metals. In this study, faecal and environmental samples were taken from piglets during the weaning period from ten commercial farms, of which five farms used antimicrobial or ZnO prophylaxis (AB-ZnO farms) and five which had not used antimicrobials or ZnO for the previous 3 years (AB-ZnO free farms). A total of 50 samples were compared using a metagenomic approach. Results The results of this study showed some significant differences between AB-ZnO and AB-ZnO free farms and suggested positive selection for AMR under antimicrobial and ZnO treatment. Moreover, strong differences between environmental and faecal samples on farms were observed, suggesting that the microbiome and its associated mobile genetic elements may play a key role in the composition of the resistome. Additionally, the age of piglets affected the resistome composition, potentially associated with changes in the microbiome post-weaning. Conclusions Overall, our study showed few differences in the resistome of the pig and its environment when comparing AB-ZnO farms with AB-ZnO free farms. These results suggest that although 3 years of removal of in-feed antimicrobial and ZnO may allow a reduction of AMR prevalence on AB-ZnO farms, more time, repeated sampling and a greater understanding of factors impacting AMR prevalence will be required to ensure significant and persistent change in on-farm AMR.
