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Dysbiosis in the Development of Type I Diabetes and Associated Complications: From Mechanisms to Targeted Gut Microbes Manipulation Therapies
Get PDFPublication history: Accepted - 8 March 2021; Published online - 9 March 2021Globally, we are facing a worrying increase in type 1 diabetes mellitus (T1DM) incidence, with onset at younger age shedding light on the need to better understand the mechanisms of disease and step-up prevention. Given its implication in immune system development and regulation of metabolism, there is no surprise that the gut microbiota is a possible culprit behind T1DM pathogenesis. Additionally, microbiota manipulation by probiotics, prebiotics, dietary factors and microbiota transplantation can all modulate early host–microbiota interactions by enabling beneficial microbes with protective potential for individuals with T1DM or at high risk of developing T1DM. In this review, we discuss the challenges and perspectives of translating microbiome data into clinical practice. Nevertheless, this progress will only be possible if we focus our interest on developing numerous longitudinal, multicenter, interventional and double-blind randomized clinical trials to confirm their efficacy and safety of these therapeutic approachesThis research was funded by UEFISCDI, project ID PN-III-P1-1.1-PD-2019-0499, grant number 224/2021
Investigation of the Effect of Slurry, Combined with Inorganic N Rate and Timing, on the Yield of Spring Barley Post Cover Crop of Stubble Turnips
Get PDFPublication history: Accepted - 19 January 2021; Published online - 27 January 2021ntegration of cover crops into arable rotations over winter results in difficulty in determining the nitrogen (N) requirement for the following commercial crop. The region of Northern Ireland (NI) has had no previous field research on cover crops and how they may affect N supply to the following commercial crop. Stubble turnips (Brassica rapa oleifera L.) were sown as a cover crop, after the harvest of winter barley (Hordeum vulgare L.) and retained over winter. Prior to planting the stubble turnips, pig slurry was applied to maximise cover crop growth. The stubble turnips accumulated 111 and 150 kg N/ha in their biomass. This equates to 79 and 107% of the N requirement of a 5 t/ha spring barley crop, if this N is released sufficiently. In this experiment, the cover crop of stubble turnips was over-sown with spring barley and supplemented with different rates of organic manures (either applied at 50 m3/ha of pig slurry or not applied), and inorganic N fertiliser (0, 70 and 140 kg N/ha), at two different timings (early or late). In the two experimental years, additional N supplied in the form of inorganic N or organic manures, did not significantly enhance spring barley yields. No control area of fallow was included in this trial. However, this study demonstrates that in this region there may be a greater rate of N release from the cover crop of stubble turnips than estimated due to agronomic management practices applied and conducive climatic conditions. This means that in this study location, a reduced N rate programme supplemented to the spring barley is possible, which lead to considerable financial savingsThis research was supported and funded by AFBI (Agri-Food and Biosciences Institute) in conjunction with DAERA (Department of Agriculture, Environment and Rural Affairs)
Relationships between metabolic profiles and gene expression in liver and leukocytes of dairy cows in early lactation.
Get PDFPublication history: Accepted - 11 October 2020; Published online - 15 January 2021Homeorhetic mechanisms assist dairy cows in the transition from pregnancy to lactation. Less successful cows develop severe negative energy balance (NEB), placing them at risk of metabolic and infectious diseases and reduced fertility. We have previously placed multiparous Holstein Friesian cows from 4 herds into metabolic clusters, using as biomarkers measurements of plasma nonesterified fatty acids, β-hydroxybutyrate, glucose and IGF-1 collected at 14 and 35 d in milk (DIM). This study characterized the global transcriptomic profiles of liver and circulating leukocytes from the same animals to determine underlying mechanisms associated with their metabolic and immune function. Liver biopsy and whole-blood samples were collected around 14 DIM for RNA sequencing. All cows with available RNA sequencing data were placed into balanced (BAL, n = 44), intermediate (n = 44), or imbalanced (IMBAL, n = 19) metabolic cluster groups. Differential gene expression was compared between the 3 groups using ANOVA, but only the comparison between BAL and IMBAL cows is reported. Pathway analysis was undertaken using DAVID Bioinformatic Resources (https://david.ncifcrf.gov/). Milk yields did not differ between BAL and IMBAL cows but dry matter intake was less in IMBAL cows and they were in greater energy deficit at 14 DIM (−4.48 v −11.70 MJ/d for BAL and IMBAL cows). Significantly differentially expressed pathways in hepatic tissue included AMPK signaling, glucagon signaling, adipocytokine signaling, and insulin resistance. Genes involved in lipid metabolism and cholesterol transport were more highly expressed in IMBAL cows but IGF1 and IGFALS were downregulated. Leukocytes from BAL cows had greater expression of histones and genes involved in nucleosomes and cell division. Leukocyte expression of heat shock proteins increased in IMBAL cows, suggesting an unfolded protein response, and several key genes involved in immune responses to pathogens were upregulated (e.g., DEFB13, HP, OAS1Z, PTX3, and TLR4). Differentially expressed genes upregulated in IMBAL cows in both tissues included CD36, CPT1, KFL11, and PDK4, all central regulators of energy metabolism. The IMBAL cows therefore had greater difficulty maintaining glucose homeostasis and had dysregulated hepatic lipid metabolism. Their energy deficit was associated with a reduced capacity for cell division and greater evidence of stress responses in the leukocyte population, likely contributing to an increased risk of infectious disease.This project received funding from the European Union's Seventh Framework Programme (Brussels, Belgium) for research, technological development, and demonstration under grant agreement no. 61368
Development of polymorphic markers in the immune gene complex loci of cattle
Get PDFPublication history: Accepted - 18 January 2021; Published online - 6 March 2021The addition of cattle health and immunity traits to genomic selection indices holds promise to increase individual animal longevity and productivity, and decrease economic losses from disease. However, highly variable genomic loci that contain multiple immune-related genes were poorly assembled in the first iterations of the cattle reference genome assembly and underrepresented during the development of most commercial genotyping platforms. As a consequence, there is a paucity of genetic markers within these loci that may track haplotypes related to disease susceptibility. By using hierarchical assembly of bacterial artificial chromosome inserts spanning 3 of these immune-related gene regions, we were able to assemble multiple full-length haplotypes of the major histocompatibility complex, the leukocyte receptor complex, and the natural killer cell complex. Using these new assemblies and the recently released ARS-UCD1.2 reference, we aligned whole-genome shotgun reads from 125 sequenced Holstein bulls to discover candidate variants for genetic marker development. We selected 124 SNPs, using heuristic and statistical models to develop a custom genotyping panel. In a proof-of-principle study, we used this custom panel to genotype 1,797 Holstein cows exposed to bovine tuberculosis (bTB) that were the subject of a previous GWAS study using the Illumina BovineHD array. Although we did not identify any significant association of bTB phenotypes with these new genetic markers, 2 markers exhibited substantial effects on bTB phenotypic prediction. The models and parameters trained in this study serve as a guide for future marker discovery surveys particularly in previously unassembled regions of the cattle genome.Hammond, Heimeier, and Schwartz were supported by United Kingdom Research and Innovation, Biotechnology and Biological Sciences Research Council (UKRI-BBSRC) funding awards BB/M027155/1, BBS/E/I/00007031, BBS/E/I/00007038, BBS/E/I/00007039, BBS/OS/GC/000015B, and BBS/OS/GC/200016. Glass was supported by UKRI-BBSRC funding awards BB/J004227/1, BB/J004235/1, and BB/P013740; Glass, Skuce, and Allen were also supported by UKRI-BBSRC BB/E018386/1, BB/E018335/1 and 2, and BB/L004054/1; Glass was also supported by UKRI-BBSRC award BB/M027155/1 and BB/P013740/1. Wilkinson was supported by UKRI-BBSRC BB/L004054/1. We gratefully acknowledge the Agri-Food and Biosciences Institute (AFBI, Northern Ireland) who collected and provided samples in the form of phenotyped bTB case/control samples for use within this project. Bickhart, Bakshy, McClure, and Null were supported by appropriated projects 5090-31000-026-00-D, Investigating Microbial, Digestive, and Animal Factors to Increase Dairy Cow Performance and Nutrient Use Efficiency, and 8042-31000-001-00-D, Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection, of the Agricultural Research Service (ARS) of the USDA. Cole and Null were supported by appropriated project 8042-31000-002-00-D, “Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals of ARS-USDA. Cole was also partially supported by the grant “Reducing Mastitis in the Dairy Cow by Increasing the Prevalence of Beneficial Polymorphisms in Genes Associated with Mastitis Resistance” from the Minnesota Agricultural Experiment Station Rapid Agricultural Response Fund. Smith was supported by appropriated project 3040-31000-100-00-D, “Developing a Systems Biology Approach to Enhance Efficiency and Sustainability of Beef and Lamb Production,” of ARS-USDA. Bickhart, Bakshy, Young, and Smith were supported by USDA NIFA grant number 2015-67015-22970, “US-UK Collaborative project: “Reassembly of cattle immune gene clusters for quantitative analysis.
Probiotics and potential applications for alternative poultry production systems
Get PDFPublication history: Accepted - 17 March 2021; Published online - 26 March 2021.Concerns over animal welfare continue to
be a critical component of law and policies associated
with commercial food animal production. Social and market
pressures are the driving forces behind the legislation
and result in the change of poultry production management
systems. As a result, the movement toward cagefree
and aviary-based egg production systems has become
standard practices. Cage-based systems being replaced
by alternative methods that offer a suitable housing environment
to meet or exceed poultry welfare needs and
require different management, including the ban of
antibiotics in poultry diets. For broiler production, pasture-
raised and free-range management systems have
become more popular. However, challenges remain from
exposure to disease-causing organisms and foodborne
pathogens in these environments. Consequently, probiotics
can be supplemented in poultry diets as commercial
feed additives. The present review discusses the impacts
of these probiotics on the performance of alternative poultry
production systems for improving food safety and
poultry health by mitigating pathogenic organisms and
improving egg and meat quality and production.Dr. El Jeni was generously supported by a Fulbright
Fellowship through the U.S. Department of State
Effect of space allowance and mixing on growth performance and body lesions of grower-finisher pigs in pens with a single wet-dry feeder
Get PDFPublicationhistory: Accepted - 17 December 2020; Published online - 6 January 2021.Background: Low space allowance (SA) and mixing may result in reduced growth performance (GP) and animal
welfare issues because of adverse social behaviours directed to pen mates. This could be exacerbated in pens with
single space feeders owing to social facilitation of feeding behaviour. The present study aimed to investigate the
effect of SA and mixing on GP and body lesions (BL) in pens with one single space wet-dry feeder.
Results: Two experiments were conducted on grower-finisher pigs from 10 to 21 weeks of age. In Exp1, pigs (N =
216) were assigned to three SA; 0.96m2/pig (n = 6 pens; 10 pigs/pen; SA96), 0.84m2/pig (n = 6; 12 pigs/pen; SA84)
and 0.72m2/pig (n = 6; 14 pigs/pen; SA72), in a randomized design. In Exp2, pigs (N = 230) were used in a 2 × 2
factorial randomized design considering SA and mixing as treatments. Pigs were assigned to two SA; 0.96m2/pig
(n = 10 pens; 10 pigs/pen; SA96) and 0.78 m2/pig (n = 10; 13 pigs/pen; SA78) and were either mixed or not at the
entry to the finishing facility. GP was not affected by SA (P > 0.05) in either experiment. In Exp2, non-mixed pigs
were 5.4 kg heavier (P < 0.001), gained 74 g more per day (P = 0.004), consumed 101.8 g more of feed per day (P =
0.007) and tended to have higher feed efficiency (P = 0.079) than mixed pigs from 11 to 21 weeks of age. Number
of BL was affected by SA in both experiments. In Exp1, SA72 pigs had 74.4 and 97.4% more BL than SA96 and SA84
pigs at 20 weeks of age respectively (P < 0.01). In Exp2, SA78 pigs had 48.6, 43.6 and 101.3% more BL than SA96
pigs at 12, 16 and 21 weeks of age respectively (P < 0.05). Mixing did not affect the number of BL from 12 to 21
weeks of age in Exp2 (P > 0.05).
Conclusion: Mixing had a considerable effect on growth performance thus, strategies to avoid or mitigate mixing
should be considered. Although space allowance had no effect on growth performance, high number of body
lesions in the lower space allowance indicates that space allowances equal or below 0.78 m2/pig are detrimental to
the welfare of pigs despite following the EU legislation.Jordi Camp Montoro was supported by the Teagasc Walsh Scholarship
Scheme grant-in-aid project Introducing new feeding programs and facilities
for Irish finishing pigs ref. 0415. The funders had no role in the study design,
data collection and analysis, decision to publish, or preparation of the
manuscript
Editorial: Developments in Campylobacter, Helicobacter & Related Organisms Research – CHRO 2019
Get PDFPublication history: Accepted - 14 December 2020; Published - 8 January 2021
Review of two mechanical separation technologies for the sustainable management of agricultural phosphorus in nutrient-vulnerable zones
Get PDFPublication history: Accepted - 20 April 2021; Published online - 23 April 2021This work reviews two mechanical separation technologies (screw press and decanting centrifuge) which could be used in the dairy, beef, pig and anaerobic digestion sectors in nutrient-vulnerable zones in order to improve the sustainability of manure and anaerobic digestate management by decreasing agricultural phosphorus loss and reducing environmental impact on water quality. Capital and operating costs, separation efficiency and throughput, and management and processing of separated fractions, including transport costs, environmental impacts and the biosecurity of separated solids for export, were considered. Of the two technologies reviewed, screw press separation is a more cost-effective option (5-fold cheaper per tonne of feedstock) when lower amounts of export of phosphorus off farm are acceptable. For farms and those with anaerobic digesters managing larger volumes of manure/digestate, screw press separation is possible. However if higher levels of phosphorus removal are required, the use of decanting centrifugation is a viable option. Centralised processing facilities could also make use of decanting centrifuge technology to act as processing hubs for local farms within a distance that makes it economical for transport of manure/treated manure to/from the processor (the maximum distance for economical transport of raw manure and separated solids is approximately 70 km and 84 km, respectively). Both separation technologies could be integrated into agricultural manure and digestate management systems in order to provide a more sustainable approach to managing agricultural phosphorus loss and its associated impact on water quality. Screw press and decanting centrifuge separation could reduce phosphorous loss to water bodies by 34% and from 30 to 93%, respectively.The authors wish to acknowledge support from the Department of Agriculture, Environment and Rural Affairs for Northern Ireland for funding Evidence and Innovation Project 18-04-01
An investigation of the potential adoption of anaerobic digestion for energy production in Irish farms
Get PDFPublished online: Accepted - 20 January 2021; Published online - 27 January 2021Anaerobic digestion (AD) has been recognised as an effective means of simultaneously producing energy while reducing greenhouse gas (GHG) emissions. Despite having a large agriculture sector, Ireland has experienced little uptake of the technology, ranking 20th within the EU-28. It is, therefore, necessary to understand the general opinions, willingness to adopt, and perceived obstacles of potential adopters of the technology. As likely primary users of this technology, a survey of Irish cattle farmers was conducted to assess the potential of on-farm AD for energy production in Ireland. The study seeks to understand farmers’ motivations, perceived barriers, and preferred business model. The study found that approximately 41% of the 91 respondents were interested in installing AD on their farming enterprise within the next five years. These Likely Adopters tended to have a higher level of education attainment, and together, currently hold 4379 cattle, potentially providing 37,122 t year−1 of wastes as feedstock, resulting in a potential CO2 reduction of 800.65 t CO2-eq. year−1. Moreover, the results indicated that the primary consideration preventing the implementation of AD is a lack of information regarding the technology and high investment costs. Of the Likely Adopters and Possible Adopters, a self-owned and operated plant was the preferred ownership structure, while 58% expressed an interest in joining a co-operative scheme. The findings generated provide valuable insights into the willingness of farmers to implement AD and guidance for its potential widespread adoption.The research leading to these results has received funding from the European Union’s
INTERREG VA Programme, managed by the Special EU Programmes Body (SEUPB), with match
funding provided by the Department for the Economy (Northern Ireland) and Department of
Enterprise, Trade and Employment (Republic of Ireland), grant number IVA5033. The views and
opinions expressed in this article do not necessarily reflect those of the European Commission or the
Special EU Programmes Body (SEUPB)
Does Mycobacterium tuberculosis var. bovis survival in the environment confound bovine tuberculosis control and eradication? A literature review
Get PDFPublication history: Accepted - 25 January 2021; Published online - 5 February 2021.Bovine tuberculosis (bTB) is one of the globe’s most common, multihost zoonoses and results in substantial socioeconomic costs
for governments, farming industries, and tax payers. Despite decades of surveillance and research, surprisingly, little is known
about the exact mechanisms of transmission. In particular, as a facultative intracellular pathogen, to what extent does survival of
the causative agent, Mycobacterium tuberculosis var. bovis (M. bovis), in the environment constitute an epidemiological risk for
livestock and wildlife? Due largely to the classical pathology of cattle cases, the received wisdom was that bTB was spread by direct
inhalation and exchange of bioaerosols containing droplets laden with bacteria. Other members of the Mycobacterium tuberculosis
complex (MTBC) exhibit differing host ranges, an apparent capacity to persist in environmental fomites, and they favour a range
of different transmission routes. It is possible, therefore, that infection from environmental sources of M. bovis could be a disease
transmission risk. Recent evidence from GPS-collared cattle and badgers in Britain and Ireland suggests that direct transmission
by infectious droplets or aerosols may not be the main mechanism for interspecies transmission, raising the possibility of indirect
transmission involving a contaminated, shared environment. &e possibility that classical pulmonary TB can be simulated and
recapitulated in laboratory animal models by ingestion of contaminated feed is a further intriguing indication of potential
environmental risk. Livestock and wildlife are known to shedM. bovis onto pasture, soil, feedstuffs, water, and other fomites; field
and laboratory studies have indicated that persistence is possible, but variable, under differing environmental conditions. Given
the potential infection risk, it is timely to review the available evidence, experimental approaches, and methodologies that could be
deployed to address this potential blind spot and control point. Although we focus on evidence from Western Europe, the
concepts are widely applicable to other multihost bTB episystems.This work was commissioned and funded by the
Department of Agriculture, Environment and Rural Affairs
for Northern Ireland (DAERA-NI) under Evidence and
Innovation Project 18/03/01