• Irish pig farmer's perceptions and experiences of tail and ear biting.

      Haigh, Amy; O'Driscoll, Keelin; Department of Agriculture, Food and the Marine (Biomed Central, 2019-01-01)
      Abnormal behaviours such as ear and tail biting of pigs is of significant welfare and economic concern. Currently, pig welfare legislation is under renewed focus by the EU commission and is likely to be enforced more thoroughly. The legislation prohibits routine tail docking and requires adequate enrichment to be provided. In Ireland, tail-docking is still the most utilised control mechanism to combat tail biting, but biting is still widespread even in tail-docked pigs. In addition, as pig farms are almost all fully slatted, bedding type material cannot be provided. Thus, the opinions, and practices of farmers in countries like Ireland, which may need to make significant adaptations to typical pig management systems soon, need to be considered and addressed. We carried out a survey of pig farmers during 2015 in order to gain a greater understanding of the extent of biting on Irish farms, perception on the most important preventive measures, current enrichment use and actions following outbreaks. Fifty-eight farmers from 21 Counties responded with an average herd size of 710 ± 597 sows (range 90–3000 sows). Only two farms had experienced no biting in the last year. Of the farms that had experienced tail biting (88%), 86% had also experienced ear biting. The most common concerns relating to biting were condemnation and reduced productivity of bitten pigs with both receiving an average score of 4 (most serious). Ear biting occurred most commonly in the 2nd stage (approximately 47–81 days from weaning) weaner and tail biting in the finishing stage. The most important preventive measures were felt to be taking care of animal health, restricting density, maintaining an even quality of feed/content and maintaining good air movement. Sixty-five percent of respondents added additional enrichment following an outbreak. Chains were the most common form of enrichment currently used (83%). Those not using chains favoured wood, toys and rope (17%). Identification of the most effective and accessible control and prevention measures both for the animals and for the farming community is thus essential. Improved understanding of the concerns and practices of producers, which this survey contributes to, is a first step towards this aim.
    • Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

      Guerin, Emma; Shkoporov, Andrey N; Stockdale, Stephen R; Comas, Joan C; Khokhlova, Ekaterina V; Clooney, Adam G; Daly, Karen M; Draper, Lorraine A; Stephens, Niamh; Scholz, Dimitri; et al. (Biomed Central, 2021-04-12)
      Background The gut phageome comprises a complex phage community of thousands of individual strains, with a few highly abundant bacteriophages. CrAss-like phages, which infect bacteria of the order Bacteroidales, are the most abundant bacteriophage family in the human gut and make an important contribution to an individual’s core virome. Based on metagenomic data, crAss-like phages form a family, with four sub-families and ten candidate genera. To date, only three representatives isolated in pure culture have been reported: ΦcrAss001 and two closely related phages DAC15 and DAC17; all are members of the less abundant candidate genus VI. The persistence at high levels of both crAss-like phage and their Bacteroidales hosts in the human gut has not been explained mechanistically, and this phage-host relationship can only be properly studied with isolated phage-host pairs from as many genera as possible. Results Faeces from a healthy donor with high levels of crAss-like phage was used to initiate a faecal fermentation in a chemostat, with selected antibiotics chosen to inhibit rapidly growing bacteria and selectively enrich for Gram-negative Bacteroidales. This had the objective of promoting the simultaneous expansion of crAss-like phages on their native hosts. The levels of seven different crAss-like phages expanded during the fermentation, indicating that their hosts were also present in the fermenter. The enriched supernatant was then tested against individual Bacteroidales strains isolated from the same faecal sample. This resulted in the isolation of a previously uncharacterised crAss-like phage of candidate genus IV of the proposed Alphacrassvirinae sub-family, ΦcrAss002, that infects the gut commensal Bacteroides xylanisolvens. ΦcrAss002 does not form plaques or spots on lawns of sensitive cells, nor does it lyse liquid cultures, even at high titres. In keeping with the co-abundance of phage and host in the human gut, ΦcrAss002 and Bacteroides xylanisolvens can also co-exist at high levels when co-cultured in laboratory media. Conclusions We report the isolation and characterisation of ΦcrAss002, the first representative of the proposed Alphacrassvirinae sub-family of crAss-like phages. ΦcrAss002 cannot form plaques or spots on bacterial lawns but can co-exist with its host, Bacteroides xylanisolvens, at very high levels in liquid culture without impacting on bacterial numbers. Video abstract
    • Lactobacillus mucosae DPC 6426 as a bile-modifying and immunomodulatory microbe

      Ryan, Paul M; Stolte, Ellen H; London, Lis E E; Wells, Jerry M; Long, Sarah L; Joyce, Susan A; Gahan, Cormac G M; Fitzgerald, Gerald F; Ross, R Paul; Caplice, Noel M; et al. (Biomed Central, 2019-02-08)
      Background Lactobacillus mucosae DPC 6426 has previously demonstrated potentially cardio-protective properties, in the form of dyslipidaemia and hypercholesterolemia correction in an apolipoprotein-E deficient mouse model. This study aims to characterise the manner in which this microbe may modulate host bile pool composition and immune response, in the context of cardiovascular disease. Lactobacillus mucosae DPC 6426 was assessed for bile salt hydrolase activity and specificity. The microbe was compared against several other enteric strains of the same species, as well as a confirmed bile salt hydrolase-active strain, Lactobacillus reuteri APC 2587. Results Quantitative bile salt hydrolase assays revealed that enzymatic extracts from Lactobacillus reuteri APC 2587 and Lactobacillus mucosae DPC 6426 demonstrate the greatest activity in vitro. Bile acid profiling of porcine and murine bile following incubation with Lactobacillus mucosae DPC 6426 confirmed a preference for hydrolysis of glyco-conjugated bile acids. In addition, the purified exopolysaccharide and secretome of Lactobacillus mucosae DPC 6426 were investigated for immunomodulatory capabilities using RAW264.7 macrophages. Gene expression data revealed that both fractions stimulated increases in interleukin-6 and interleukin-10 gene transcription in the murine macrophages, while the entire secretome was necessary to increase CD206 transcription. Moreover, the exopolysaccharide elicited a dose-dependent increase in nitric oxide and interleukin-10 production from RAW264.7 macrophages, concurrent with increased tumour necrosis factor-α secretion at all doses. Conclusions This study indicates that Lactobacillus mucosae DPC 6426 modulates both bile pool composition and immune system tone in a manner which may contribute significantly to the previously identified cardio-protective phenotype.
    • Lactobacillus ruminis strains cluster according to their mammalian gut source

      O'Donnell, Michelle M.; Harris, Hugh; Lynch, Denise B; Ross, R Paul; O'Toole, Paul W.; Science Foundation Ireland; 07/IN.1/B1780 (Biomed Central, 01/04/2015)
      Background Lactobacillus ruminis is a motile Lactobacillus that is autochthonous to the human gut, and which may also be isolated from other mammals. Detailed characterization of L. ruminis has previously been restricted to strains of human and bovine origin. We therefore sought to expand our bio-bank of strains to identify and characterise isolates of porcine and equine origin by comparative genomics. Results We isolated five strains from the faeces of horses and two strains from pigs, and compared their motility, biochemistry and genetic relatedness to six human isolates and three bovine isolates including the type strain 27780T. Multilocus sequence typing analysis based on concatenated sequence data for six individual loci separated the 16 L. ruminis strains into three clades concordant with human, bovine or porcine, and equine sources. Sequencing the genomes of four additional strains of human, bovine, equine and porcine origin revealed a high level of genome synteny, independent of the source animal. Analysis of carbohydrate utilization, stress survival and technological robustness in a combined panel of sixteen L. ruminis isolates identified strains with optimal survival characteristics suitable for future investigation as candidate probiotics. Under laboratory conditions, six human isolates of L. ruminis tested were aflagellate and non-motile, whereas all 10 strains of bovine, equine and porcine origin were motile. Interestingly the equine and porcine strains were hyper-flagellated compared to bovine isolates, and this hyper-flagellate phenotype correlated with the ability to swarm on solid medium containing up to 1.8% agar. Analysis by RNA sequencing and qRT-PCR identified genes for the biosynthesis of flagella, genes for carbohydrate metabolism and genes of unknown function that were differentially expressed in swarming cells of an equine isolate of L. ruminis. Conclusions We suggest that Lactobacillus ruminis isolates have potential to be used in the functional food industry. We have also identified a MLST scheme able to distinguish between strains of L. ruminis of different origin. Genes for non-digestible oligosaccharide metabolism were identified with a putative role in swarming behaviour.
    • Lameness prevalence and management practices on Irish pasture-based dairy farms

      Browne, N.; Hudson, C. D.; Crossley, R. E.; Sugrue, K.; Kennedy, Emer; Huxley, J. N.; Conneely, Muireann; Teagasc Walsh Scholarship Programme; Dairy Research Ireland (Biomed Central, 2022-06-08)
      Background Lameness is a painful disease, which negatively impacts dairy cow production and welfare. The aim of this observational study was to determine herd lameness prevalence, describe current lameness management practices and identify the presence of established risk factors for lameness on Irish pasture-based dairy farms. Farms were visited once during grazing (99 farms) and again during housing (85 farms). Lameness scoring was carried out at each visit (AHDB 0–3 scale); cows were classified as lame if they scored two or three. Farm management practices and infrastructure characteristics were evaluated via farmer questionnaires and direct measurements of farm infrastructure. Results Median herd-level lameness prevalence was 7.9% (interquartile range = 5.6 – 13.0) during grazing and 9.1% (interquartile range = 4.9 – 12.0) during housing; 10.9% of cows were lame at a single visit and 3.5% were lame at both visits (chronically lame or had a repeat episode of lameness). Fifty-seven percent of farmers were not familiar with lameness scoring and only one farm carried out lameness scoring. Only 22% of farmers kept records of lame cows detected, and 15% had a lameness herd health plan. Twenty-eight percent of farmers waited more than 48 h to treat a lame cow, and 21% waited for more than one cow to be identified as lame before treating. Six percent of farmers carried out routine trimming and 31% regularly footbathed (> 12 times per year). Twelve percent put severely lame cows in a closer paddock and 8% stated that they used pain relief to treat severely lame cows. Over 50% of farms had at least one cow track measurement that was classified as rough or very rough, and cow tracks were commonly narrow for the herd size. On 6% of farms, all cubicle beds were bare concrete (no matting or bedding) and on a further 6% of farms, there was a combination of cubicles with and without matting or bedding. On 56% of farms, all pens contained less than 1.1 cubicles per cow and on 28% of farms, a proportion of pens contained less than 1.1 cubicles per cow. Conclusions Overall, this study identified infrastructure and management practices which could be improved upon. The comparatively low lameness prevalence demonstrated, compared to fully housed systems, also highlights the benefits of a pasture-based system for animal welfare; however, there remains scope for improvement.
    • Length of metacarpal and metatarsal bones in five Iranian sheep breeds and their associations with ungula measurements

      Azarpajouh, Samaneh; Munita, María P.; Calderón Díaz, Julia A. (2021-12-06)
      Background This study aimed to measure the length of metacarpal and metatarsal bones in five Iranian sheep breeds and to correlate the length of the bones with ungula measurements. Thoracic and pelvic limbs of 2-year-old, previously untrimmed, pastured Afshari, Moghani, Kurdi, Makoui, and Lori–Bakhtiari ewes, (n = 20 ewes per breed) were collected after slaughter. The following lengths were recorded in the metacarpal and metatarsal bones: from the margo proximalis lateralis to the lateral (L1) and medial (D1) cartilago physialis; from the margo proximalis lateralis to the margo abaxialis of the lateral (L2) and medial (D2) caput; from the cartilago physialis lateralis to the margo abaxialis of the lateral caput (X1); from the cartilago physialis medialis to the margo distalis of the caput ridge (X2) and from the margo axialis of cartilago physialis to the margo axialis of the lateral caput (X3). Additionally, measurements of the ungula including pars dorsalis length, pars mobilis lateralis and medialis height, pars dorsalis height to the ground and to the solea cornea, thickness of the solea in the pars dorsalis, pars mobilis lateralis and medialis, solea cornea length and angulus dorsalis were recorded in the medial and lateral digits of the thoracic and pelvic limbs. Data on length of the metatarsal and metacarpal bones were analysed using mixed model equations while Pearson correlations were calculated between metacarpal and metatarsal bones and ungula measurements. Results Lori- Bakhtiari and Moghani ewes had greater L1, L2, and D1 and D2 while X1, X2 and X3 was greater in Kurdi ewes (P < 0.05). Measurements such as L1, L2, D1 and D2 were greater in the metatarsal than in metacarpal bones (P < 0.05) and the opposite was observed for X1, X2 and X3 (P < 0.05). No asymmetry was observed between the lateral and medial measurements (P > 0.05). Low to moderate correlations were observed between bone and ungula measurements (P < 0.05). Conclusion Under the conditions of this study, differences in metacarpal and metatarsal bone measurements were observed between breeds but no asymmetry was observed between lateral and medial bones. Results indicate an association between metacarpal and metatarsal bones ungula measurements. This could provide baseline information for the development and/or improvement of current ungula health protocols in the studied sheep breeds.
    • Liver fluke in Irish sheep: prevalence and associations with management practices and co-infection with rumen fluke.

      Munita, Maria Pia; Rea, Rosemary; Martinez-Ibeas, Ana Maria; Byrne, Noel; McGrath, Guy; Munita-Corbalan, Luis Enrique; Sekiya, Mary; Mulcahy, Grace; Sayers, Riona; Department of Agriculture, Food and the Marine (Biomed Central, 2019-11-06)
      Background The present study aimed to identify the national prevalence of Fasciola hepatica in Irish sheep and to conduct a risk analysis assessment based on management and treatment practices in participating flocks. Also, co-infection with rumen fluke was quantified and its association with liver fluke and management practices was assessed. Methods A total of 305 sheep flocks were selected ensuring even national representation of the sheep population. Participating farms were asked to complete a survey questionnaire on farm management practices and submit faecal samples during the winter of 2014–2015. Pooled faecal samples were analysed for the presence of F. hepatica and co-infection with rumen fluke. Apparent and true prevalence were calculated, additionally, the rate of co-infection with rumen fluke was also obtained. Correlation and regression analyses were used for assessing associations between management practices, liver fluke infection and co-infection with rumen fluke. Results The national true prevalence of F. hepatica was 50.4% (n = 305). Regional prevalence varied from 41% in the east to 52% in the south. Co-infection with rumen fluke was observed in 40% of the studied population and correlated with increased F. hepatica egg counts (OR = 2.9; P ≤ 0.001). Predominant breeds were Suffolk, Texel and Horned Mountain breeds. Beef cattle were the most frequent type of other livestock present on farms and mixed species grazing was frequently reported (73%). More than half of the flocks reported a mid-to-late lambing period (March-April). Use of mountain land for grazing was of 32%. Flukicides were most commonly used twice over the autumn-winter period. Regression analyses highlighted significant association of F. hepatica status, with the presence of other livestock on farm, frequency of flukicides used during the winter and clinical presentation of liver fluke. A significant increase in eggs per gram of faeces was observed in Charollais sheep in comparison with all other breeds. Co-infection with F. hepatica and Calicophoron daubneyi was also significantly associated with the presence of other livestock on the farm, type of flukicide used and clinical fasciolosis. Conclusions The present study provides up-to-date information on the prevalence of F. hepatica in Irish sheep and adds insight to the epidemiology of the disease. These findings will be useful for designing new holistic control measures for F. hepatica infection.
    • Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) prevalence in humans in close contact with animals and measures to reduce on-farm colonisation

      Crespo-Piazuelo, Daniel; Lawlor, Peadar G.; Irish Health Research Board; JPIAMR-2017–1-A (Biomed Central, 2021-08-06)
      Since the 1940s, Staphylococcus aureus has adapted to the use of different antimicrobials to treat infections. Although S. aureus can act as a commensal bacterium, some strains are facultative pathogens and acquiring them can be fatal. In particular, treating infections caused by S. aureus with acquired antimicrobial resistance is problematic, as their treatment is more difficult. Some of these S. aureus variants are methicillin-resistant S. aureus (MRSA) with prevalence across the globe in health-care facilities, community settings and on livestock farms. Apart from humans, MRSA can colonise other animal species, and because of this, resistance to new antimicrobials can appear and jump between species. Livestock and companion animals are particularly important in this regard considering the relatively high usage of antimicrobials in these species. There is a risk to humans who come into direct contact with animals acquiring MRSA but there is also the risk of animals acquiring MRSA from colonised humans. In this review, we summarise studies conducted worldwide to characterise the prevalence of MRSA in veterinarians, farmers and other personnel who come into close contact with animals. Finally, alternative treatment, preventive measures and on-farm strategies to reduce MRSA introduction to a farm and carriage within a herd are discussed.
    • Long-term stability of RNA in post-mortem bovine skeletal muscle, liver and subcutaneous adipose tissues

      Bahar, Bojlul; Monahan, Frank J; Moloney, Aidan P; Schmidt, Olaf; MacHugh, David E; Sweeney, Torres; National Development Plan 2000-2006; Teagasc Walsh Fellowship Programme (Biomed Central, 2007-11-29)
      Background: Recovering high quality intact RNA from post-mortem tissue is of major concern for gene expression studies in animals and humans. Since the availability of post-mortem tissue is often associated with substantial delay, it is important that we understand the temporal variation in the stability of total RNA and of individual gene transcripts so as to be able to appropriately interpret the data generated from such studies. Hence, the objective of this experiment was to qualitatively and quantitatively assess the integrity of total and messenger RNA extracted from bovine skeletal muscle, subcutaneous adipose tissue and liver stored at 4°C at a range of time points up to 22 days post-mortem. These conditions were designed to mimic the environment prevailing during the transport of beef from the abattoir to retail outlets. Results: The 28S and 18S rRNA molecules of total RNA were intact for up to 24 h post-mortem in liver and adipose tissues and up to 8 days post-mortem in skeletal muscle. The mRNA of housekeeping genes (GAPDH and ACTB) and two diet-related genes (RBP5 and SCD) were detectable up to 22 days post-mortem in skeletal muscle. While the mRNA stability of the two housekeeping genes was different in skeletal muscle and liver, they were similar to each other in adipose tissue. After 22 days post-mortem, the relative abundance of RBP5 gene was increased in skeletal muscle and in adipose tissue and decreased in liver. During this period, the relative abundance of SCD gene also increased in skeletal muscle whereas it decreased in both adipose tissue and liver. Conclusion: Stability of RNA in three tissues (skeletal muscle, subcutaneous adipose tissue and liver) subjected to long-term post-mortem storage at refrigeration temperature indicated that skeletal muscle can be a suitable tissue for recovering biologically useful RNA for gene expression studies even if the tissue is subjected to post-mortem storage for weeks, whereas adipose tissue and liver should be processed within 24 hours post-mortem.
    • Managing variability in decision making in swine growing-finishing units

      Agostini, Piero D.S.; Manzanilla, Edgar G; de Blas, Carlos; Fahey, Alan G.; da Silva, Caio A; Gasa, Josep; Spanish Ministerio de Ciencia e Innovación; Agencia Española de Cooperación Internacional para el Desarrollo; AGL2011-29960 (Biomed Central, 2015-09-01)
      Analysis of data collected from pig farms may be useful to understand factors affecting pig health and productive performance. However, obtaining these data and drawing conclusions from them can be done at different levels and presents several challenges. In the present study, information from 688 batches of growing-finishing (GF) pigs (average initial and final body weight of 19.1 and 108.5 kg respectively) from 404 GF farms integrated in 7 companies was obtained between July 2008 and July 2010 in Spain by survey. Management and facility factors associated with feed conversion ratio (FCR) and mortality were studied by multiple linear regression analysis in each single company (A to G) and in an overall database (OD). Factors studied were geographic location of the farm, trimester the pigs entered the farm, breed of sire and sex segregation in pens (BREGENSEG), use of circovirus vaccine, number of origins the pigs were obtained from, age of the farm, percentage of slatted floor, type of feeder, drinker and ventilation, number of phases and form of feed, antibiotic administration system, water source, and number and initial weight of pigs. Results In two or more companies studied and/or in OD, the trimester when pigs were placed in the farm, BREGENSEG, number of origins of the pigs, age of the farm and initial body weight were factors associated with FCR. Regarding mortality, trimester of placement, number of origins of the pigs, water source in the farm, number of pigs placed and the initial body weight were relevant factors. Age of the farm, antibiotic administration system, and water source were only provided by some of the studied companies and were not included in the OD model, however, when analyzed in particular companies these three variables had an important effect and may be variables of interest in companies that do not record them. Conclusions Analysing data collected from farms at different levels helps better understand factors associated with productive performance of pig herds. Out of the studied factors trimester of placement and number of origins of the pigs were the most relevant factors associated with FCR and mortality.
    • MAP, Johne’s disease and the microbiome; current knowledge and future considerations

      Matthews, Chloe; Cotter, Paul D; O’ Mahony, Jim; Department of Agriculture, Food and the Marine; 15/S/651 (Biomed Central, 2021-05-07)
      Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne’s disease in ruminants. As an infectious disease that causes reduced milk yields, effects fertility and, eventually, the loss of the animal, it is a huge financial burden for associated industries. Efforts to control MAP infection and Johne’s disease are complicated due to difficulties of diagnosis in the early stages of infection and challenges relating to the specificity and sensitivity of current testing methods. The methods that are available contribute to widely used test and cull strategies, vaccination programmes also in place in some countries. Next generation sequencing technologies have opened up new avenues for the discovery of novel biomarkers for disease prediction within MAP genomes and within ruminant microbiomes. Controlling Johne’s disease in herds can lead to improved animal health and welfare, in turn leading to increased productivity. With current climate change bills, such as the European Green Deal, targeting livestock production systems for more sustainable practices, managing animal health is now more important than ever before. This review provides an overview of the current knowledge on genomics and detection of MAP as it pertains to Johne’s disease.
    • Markers associated with heading and aftermath heading in perennial ryegrass full-sib families

      Arojju, Sai Krishna; Barth, Susanne; Milbourne, Dan; Conaghan, Patrick; Velmurugan, Janaki; Hodkinson, Trevor R; Byrne, Stephen L.; Department of Agriculture, Food and the Marine, Ireland; Teagasc Walsh Fellowship Programme; EU Marie-Sklodowska-Curie Fellowship; et al. (Biomed Central, 16/07/2016)
      Background Heading and aftermath heading are important traits in perennial ryegrass because they impact forage quality. So far, genome-wide association analyses in this major forage species have only identified a small number of genetic variants associated with heading date that overall explained little of the variation. Some possible reasons include rare alleles with large phenotypic affects, allelic heterogeneity, or insufficient marker density. We established a genome-wide association panel with multiple genotypes from multiple full-sib families. This ensured alleles were present at the frequency needed to have sufficient statistical power to identify associations. We genotyped the panel via partial genome sequencing and performed genome-wide association analyses with multi-year phenotype data collected for heading date, and aftermath heading. Results Genome wide association using a mixed linear model failed to identify any variants significantly associated with heading date or aftermath heading. Our failure to identify associations for these traits is likely due to the extremely low linkage disequilibrium we observed in this population. However, using single marker analysis within each full-sib family we could identify markers and genomic regions associated with heading and aftermath heading. Using the ryegrass genome we identified putative orthologs of key heading genes, some of which were located in regions of marker-trait associations. Conclusion Given the very low levels of LD, genome wide association studies in perennial ryegrass populations are going to require very high SNP densities. Single marker analysis within full-sibs enabled us to identify significant marker-trait associations. One of these markers anchored proximal to a putative ortholog of TFL1, homologues of which have been shown to play a key role in continuous heading of some members of the rose family, Rosaceae.
    • Marriage exchanges, seed exchanges, and the dynamics of manioc diversity

      Deletrea, Marc; McKey, Doyle B.; Hodkinson, Trevor R (National Academy of Sciences, 2012-07-02)
      The conservation of crop genetic resources requires understanding the different variables-cultural, social, and economic-that impinge on crop diversity. In small-scale farming systems, seed exchanges represent a key mechanism in the dynamics of crop genetic diversity, and analyzing the rules that structure social networks of seed exchange between farmer communities can help decipher patterns of crop genetic diversity. Using a combination of ethnobotanical and molecular genetic approaches, we investigated the relationships between regional patterns of manioc genetic diversity in Gabon and local networks of seed exchange. Spatially explicit Bayesian clustering methods showed that geographical discontinuities of manioc genetic diversity mirror major ethnolinguistic boundaries, with a southern matrilineal domain characterized by high levels of varietal diversity and a northern patrilineal domain characterized by low varietal diversity. Borrowing concepts from anthropology-kinship, bridewealth, and filiation-we analyzed the relationships between marriage exchanges and seed exchange networks in patrilineal and matrilineal societies. We demonstrate that, by defining marriage prohibitions, kinship systems structure social networks of exchange between farmer communities and influence the movement of seeds in metapopulations, shaping crop diversity at local and regional levels.
    • Measurements of the acid-binding capacity of ingredients used in pig diets

      Lawlor, Peadar G; Lynch, P Brendan; Caffrey, Patrick J.; O'Reilly, James J; O'Connell, M. Karen (Biomed Central, 2005-08-01)
      Some feed ingredients bind more acid in the stomach than others and for this reason may be best omitted from pig starter foods if gastric acidity is to be promoted. The objective of this study was to measure the acid-binding capacity (ABC) of ingredients commonly used in pig starter foods. Ingredients were categorised as follows: (i) milk products (n = 6), (ii) cereals (n = 10), (iii) root and pulp products (n = 5), (iv) vegetable proteins (n = 11), (v) meat and fish meal (n = 2), (vi) medication (n = 3), (vii) amino acids (n = 4), (viii) minerals (n = 16), (ix) acid salts (n = 4), (x) acids (n = 10). A 0.5 g sample of food was suspended in 50 ml distilled de-ionised water with continuous stirring. This suspension was titrated with 0.1 mol/L HCl or 0.1 mol/L NaOH so that approximately 10 additions of titrant was required to reach pH 3.0. The pH readings after each addition were recorded following equilibration for three minutes. ABC was calculated as the amount of acid in milliequivalents (meq) required to lower the pH of 1 kg food to (a) pH 4.0 (ABC-4) and (b) pH 3.0 (ABC-3). Categories of food had significantly different (P < 0.01) ABC values. Mean ABC-4 and ABC-3 values of the ten categories were: (i) 623 (s.d. 367.0) and 936 (s.d. 460.2), (ii) 142 (s.d. 79.2) and 324 (s.d. 146.4), (iii) 368 (s.d. 65.3) and 804 (s.d. 126.7), (iv) 381 (s.d. 186.1) and 746 (s.d. 227.0), (v) 749 (s.d. 211.6) and 1508 (s.d. 360.8), (vi) 120 (s.d. 95.6) and 261 (s.d. 163.2), (vii) 177 (s.d. 60.7) and 1078 (s.d. 359.0), (viii) 5064 (s.d. 5525.1) and 7051 (s.d. 5911.6), (ix) 5057 (s.d. 1336.6) and 8945 (s.d. 2654.1) and (x) -5883 (s.d. 4220.5) and -2591 (s.d. 2245.4) meq HCl per kg, respectively. Within category, ABC-3 and ABC- 4 values were highly correlated: R2 values of 0.80 and greater for food categories i, iv, v, vi, vii and viii. The correlation between predicted and observed ABC values of 34 mixed diets was 0.83 for ABC-4 and 0.71 for ABC-3. It was concluded that complete diets with low ABC values may be formulated through careful selection of ingredients. The final pH to which ABC is measured should matter little as ABC-3 and ABC-4 are highly correlated.
    • Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity

      Cobo-Díaz, José F.; Alvarez-Molina, Adrián; Alexa, Elena A.; Walsh, Calum J.; Mencía-Ares, Oscar; Puente-Gómez, Paula; Likotrafiti, Eleni; Fernández-Gómez, Paula; Prieto, Bernardo; Crispie, Fiona; et al. (Biomed Central, 2021-10-14)
      Background The microorganisms that inhabit food processing environments (FPE) can strongly influence the associated food quality and safety. In particular, the possibility that FPE may act as a reservoir of antibiotic-resistant microorganisms, and a hotspot for the transmission of antibiotic resistance genes (ARGs) is a concern in meat processing plants. Here, we monitor microbial succession and resistome dynamics relating to FPE through a detailed analysis of a newly opened pork cutting plant over 1.5 years of activity. Results We identified a relatively restricted principal microbiota dominated by Pseudomonas during the first 2 months, while a higher taxonomic diversity, an increased representation of other taxa (e.g., Acinetobacter, Psychrobacter), and a certain degree of microbiome specialization on different surfaces was recorded later on. An increase in total abundance, alpha diversity, and β-dispersion of ARGs, which were predominantly assigned to Acinetobacter and associated with resistance to certain antimicrobials frequently used on pig farms of the region, was detected over time. Moreover, a sharp increase in the occurrence of extended-spectrum β-lactamase-producing Enterobacteriaceae and vancomycin-resistant Enterococcaceae was observed when cutting activities started. ARGs associated with resistance to β-lactams, tetracyclines, aminoglycosides, and sulphonamides frequently co-occurred, and mobile genetic elements (i.e., plasmids, integrons) and lateral gene transfer events were mainly detected at the later sampling times in drains. Conclusions The observations made suggest that pig carcasses were a source of resistant bacteria that then colonized FPE and that drains, together with some food-contact surfaces, such as equipment and table surfaces, represented a reservoir for the spread of ARGs in the meat processing facility. Video Abstract
    • Microbiome and metabolome modifying effects of several cardiovascular disease interventions in apo-E−/− mice

      Ryan, Paul M; London, Lis E E; Bjorndahl, Trent C; Mandal, Rupasri; Murphy, Kiera; Fitzgerald, Gerald F; Shanahan, Fergus; Ross, R Paul; Wishart, David S; Caplice, Noel M; et al. (Biomed Central, 13/03/2017)
      Background There is strong evidence indicating that gut microbiota have the potential to modify, or be modified by the drugs and nutritional interventions that we rely upon. This study aims to characterize the compositional and functional effects of several nutritional, neutraceutical, and pharmaceutical cardiovascular disease interventions on the gut microbiome, through metagenomic and metabolomic approaches. Apolipoprotein-E-deficient mice were fed for 24 weeks either high-fat/cholesterol diet alone (control, HFC) or high-fat/cholesterol in conjunction with one of three dietary interventions, as follows: plant sterol ester (PSE), oat β-glucan (OBG) and bile salt hydrolase-active Lactobacillus reuteri APC 2587 (BSH), or the drug atorvastatin (STAT). The gut microbiome composition was then investigated, in addition to the host fecal and serum metabolome. Results We observed major shifts in the composition of the gut microbiome of PSE mice, while OBG and BSH mice displayed more modest fluctuations, and STAT showed relatively few alterations. Interestingly, these compositional effects imparted by PSE were coupled with an increase in acetate and reduction in isovalerate (p < 0.05), while OBG promoted n-butyrate synthesis (p < 0.01). In addition, PSE significantly dampened the microbial production of the proatherogenic precursor compound, trimethylamine (p < 0.05), attenuated cholesterol accumulation, and nearly abolished atherogenesis in the model (p < 0.05). However, PSE supplementation produced the heaviest mice with the greatest degree of adiposity (p < 0.05). Finally, PSE, OBG, and STAT all appeared to have considerable impact on the host serum metabolome, including alterations in several acylcarnitines previously associated with a state of metabolic dysfunction (p < 0.05). Conclusions We observed functional alterations in microbial and host-derived metabolites, which may have important implications for systemic metabolic health, suggesting that cardiovascular disease interventions may have a significant impact on the microbiome composition and functionality. This study indicates that the gut microbiome-modifying effects of novel therapeutics should be considered, in addition to the direct host effects.
    • Microbiome definition re-visited: old concepts and new challenges

      Berg, Gabriele; Rybakova, Daria; Fischer, Doreen; Cernava, Tomislav; Vergès, Marie-Christine C; Charles, Trevor; Chen, Xiaoyulong; Cocolin, Luca; Eversole, Kellye; Corral, Gema H; et al. (Biomed Central, 2020-06-30)
      Abstract The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term “microbiome.” Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract
    • The miRNAome of the postpartum dairy cow liver in negative energy balance

      Fatima, Attia; Lynn, David J; O'Boyle, Padraic; Seoighe, Cathal; Morris, Dermot G.; Teagasc Walsh Fellowship Programme (Biomed Central, 2014-04-12)
      Background: Negative energy balance (NEB) is an altered metabolic state in high yielding cows that occurs during the first few weeks postpartum when energy demands for lactation and maintenance exceed the energy supply from dietary intake. NEB can, in turn, lead to metabolic disorders and to reduced fertility. Alterations in the expression of more than 700 hepatic genes have previously been reported in a study of NEB in postpartum dairy cows. miRNAs (microRNA) are known to mediate many alterations in gene expression post transcriptionally. To study the hepatic miRNA content of postpartum dairy cows, including their overall abundance and differential expression, in mild NEB (MNEB) and severe NEB (SNEB), short read RNA sequencing was carried out. To identify putative targets of differentially expressed miRNAs among differentially expressed hepatic genes reported previously in dairy cows in SNEB computational target identification was employed. Results: Our results indicate that the dairy cow liver expresses 53 miRNAs at a lower threshold of 10 reads per million. Of these, 10 miRNAs accounted for greater than 95% of the miRNAome (miRNA content). Of the highly expressed miRNAs, miR-122 constitutes 75% followed by miR-192 and miR-3596. Five out of thirteen let-7 miRNA family members are also among the highly expressed miRNAs. miR-143, down-regulated in SNEB, was found to have 4 putative up-regulated gene targets associated with SNEB including LRP2 (low density lipoprotein receptor-related protein 2), involved in lipid metabolism and up-regulated in SNEB. Conclusions: This is the first liver miRNA-seq profiling study of moderate yielding dairy cows in the early postpartum period. Tissue specific miR-122 and liver enriched miR-192 are two of the most abundant miRNAs in the postpartum dairy cow liver. miR-143 is significantly down-regulated in SNEB and putative targets of miRNA-143 which are up-regulated in SNEB, include a gene involved in lipid metabolism.
    • Modelling phosphorus loss from agricultural catchments : a comparison of the performance of SWAT, HSPF and SHETRAN for the Clarianna catchment

      Nasr, Ahmed Elssidig; Bruen, Michael; Parkin, Geoff; Birkinshaw, Steve; Moles, Richard; Byrne, Paul; Environmental Protection Agency (IWA Publishing, 02/07/2012)
      Much research in Europe at present has been directed at generating and assessing modelling tools for use in catchment management, driven by the requirements and schedule of the Water Framework Directive. A logical first step is to assess the suitability of existing models for this task so that any resources used in generating new models can be targeted at actual modelling needs. Crucial questions, relating to the model structure and complexity and spatial and temporal scales required must also be addressed. This paper reports a comparison of the performance and suitability of three "off-the-shelf" distributed catchment models, each with a different level of complexity, applied to modelling phosphorous losses from the Clarianna catchment in Ireland. In this paper, the performance of three such models (SWAT, HSPF and SHETRAN/GOPC) is compared, both in estimating discharges and phosphorous loads in the Clarianna catchment. The flow comparison has showed that the HSPF model was the best in simulating the mean daily discharges. However, the best calibration results for daily total phosphorus loads in the study catchment has been achieved by the SWAT model.
    • Moderate-intensity aerobic and resistance exercise is safe and favorably influences body composition in patients with quiescent Inflammatory Bowel Disease: a randomized controlled cross-over trial

      Cronin, Owen; Barton, Wiley; Moran, Carthage; Sheehan, Donal; Whiston, Ronan; Nugent, Helena; McCarthy, Yvonne; Molloy, Catherine B; O’Sullivan, Orla; Cotter, Paul D.; et al. (2019-02-12)
      Background Overweight and metabolic problems now add to the burden of illness in patients with Inflammatory Bowel Disease. We aimed to determine if a program of aerobic and resistance exercise could safely achieve body composition changes in patients with Inflammatory Bowel Disease. Methods A randomized, cross-over trial of eight weeks combined aerobic and resistance training on body composition assessed by Dual Energy X-ray Absorptiometry was performed. Patients in clinical remission and physically inactive with a mean age of 25 ± 6.5 years and Body Mass Index of 28.9 ± 3.8 were recruited from a dedicated Inflammatory Bowel Disease clinic. Serum cytokines were quantified, and microbiota assessed using metagenomic sequencing. Results Improved physical fitness was demonstrated in the exercise group by increases in median estimated VO2max (Baseline: 43.41mls/kg/min; post-intervention: 46.01mls/kg/min; p = 0.03). Improvement in body composition was achieved by the intervention group (n = 13) with a median decrease of 2.1% body fat compared with a non-exercising group (n = 7) (0.1% increase; p = 0.022). Lean tissue mass increased by a median of 1.59 kg and fat mass decreased by a median of 1.52 kg in the exercising group. No patients experienced a deterioration in disease activity scores during the exercise intervention. No clinically significant alterations in the α- and β-diversity of gut microbiota and associated metabolic pathways were evident. Conclusions Moderate-intensity combined aerobic and resistance training is safe in physically unfit patients with quiescent Inflammatory Bowel Disease and can quickly achieve favourable body compositional changes without adverse effects. Trial registration The study was registered at ClinicalTrials.gov; Trial number: NCT02463916 .