• Effects of Different Rearing Methods on Health Status, Immunity and Performance of Artificially Reared Calves

      Earley, Bernadette (Biomed Central, 2003-03-31)
      Morbidity and mortality of the young calf represent a major cause of economic concern for producers [1]. The objective of the study was to evaluate the performance and immune status of calves reared in the presence or absence of quartz linear heating lamps (CD 3000) and fed calf milk replacer either by bucket or by teat. Mart-purchased Holstein/Friesian calves were approximately 21 days of age at arrival at the research centre. The calves were allocated randomly to one of the following four treatments (n = 16 calves per treatment) using a 2 × 2 factorial design; 1). Teat fed + quartz linear lamp (QLL) (2). Bucket fed + QLL; 3). Teat fed + no QLL and 4). Bucket fed + no QLL. For the 42-day experimental period, 8 groups of 8 calves were penned (2.4 × 10.0 m) on straw in a naturally ventilated Monopitch calf house. A quartz linear heating lamp (3 k output) was positioned in the centre of the individual sheds, 10 feet above the floor of the straw bedded pens for these on QLL treatments, and remained switched on for the duration of the study. The calves received an individual allowance of 25 kg of milk replacer powder offered warm (38°C) by bucket and had ad libitum access to a concentrate ration. Individual disease episodes were determined by the requirement to treat with antibiotics for either enteric disease or respiratory disease. Serum immunoglobulins (IgG1) were measured quantitatively by single radial immunodiffusion standard and calculated via an internal Ig standard (100 mg/L) on days 1, 14 and 28 of the study. Haematological parameters were measured on days 1, 14 and 42 of the study and included red blood cell number, haemoglobin, packed cell volume, mean cell volume and total white cell counts. The data were analysed using a model appropriate to factorial design, with terms for QLL and teat in the main plot. The average temperature and relative humidity of the shed compartments with and without the QLL heating lamps were recorded continuously and were 11.3°C and 81% and 10.5°C and 86%, respectively. There was no significant difference (P > 0.05) between treatments with respect to liveweight gain from day of arrival (day 1) to day 42 of the study. There was no significant interaction between QLL, no QLL, teat fed and bucket fed treatments with respect to serum IgG1 concentrations and haematological parameters throughout the study period (P > 0.05). The incidence of respiratory disease and enteric disease was similar across the treatment groups (P > 0.05). It is concluded that the rearing of calves indoors, in the presence of quartz linear heating lamps, and either fed calf milk replacer by teat or bucket had no beneficial effect on calf health and performance when compared with calves reared in a natural ventilated environment.
    • Temporal trends in reproductive performance in Irish dairy herds and associated risk factors

      Mee, John F (Biomed Central, 2004-03-01)
      Irish dairy herd fertility has been declining since the 1980s. The extent, nature and causes of this decline in fertility and the current status of Irish dairy herd fertility were described. An increase in calving interval of approximately one day per year has been recorded. The principal components of this trend have been an increased incidence of postpartum endocrinopathies, reduced expression of oestrus and a fall in conception rate. Both submission rate and calving-to-service interval have increased slightly over time. Significant risk factors associated with these trends have been strain substitution within the Holstein-Friesian breed and single trait selection for milk production. Critically, these changes have been reflected in loss of body condition. Contributory factors included increased herd size and possibly increased use of DIYAI. The most recent Irish study showed that 48% of cows conceived to first service and 14% of cows were not pregnant at the end of the industry-average 15-week spring breeding season. However, the top quartile of herds achieved a first-service conception rate of 59%, illustrating the wide variation between herds. These phenotypic trends were attributed to both genetic and environmental factors and their interactions. Recent Irish dairy herd fertility performance falls short of the targets set for seasonal compact calving.
    • Prevalence of antibodies to Leptospira interrogans serovar hardjo in bulk tank milk from unvaccinated irish dairy herds

      Leonard, Nola; Mee, John F; Snijders, Sylvia; Mackie, Dermot (Biomed Central, 2004-04-01)
      Bulk tank milk samples, collected from 347 herds throughout the Republic of Ireland using a sampling frame based on seven milk-recording organisations, were tested by ELISA for antibodies to Leptospira interrogans serovar hardjo. These herds, which had not been vaccinated against leptospirosis within the previous five years, were categorised according to their province, milk-recording organisation and size. Two-hundred-and-seventy-three herds (79%) had a positive ELISA titre. Both the probability of a herd being seropositive and the antibody level in the herd milk sample were affected by the province (P < 0.05 and P < 0.01, respectively) and the herd size category (P < 0.05 and P < 0.01, respectively). Larger herds were significantly more likely to have positive reactions and higher mean concentrations of antibody. It was concluded that a high proportion of unvaccinated Irish dairy herds have been exposed to infection with Leptospira hardjo.
    • Effect of liner design, pulsator setting, and vacuum level on bovine teat tissue changes and milking characteristics as measured by ultrasonography

      Gleeson, David E; O'Callaghan, Edmond J; Rath, Myles V (Biomed Central, 2004-05-01)
      Friesian-type dairy cows were milked with different machine settings to determine the effect of these settings on teat tissue reaction and on milking characteristics. Three teat-cup liner designs were used with varying upper barrel dimensions (wide-bore WB = 31.6 mm; narrow-bore NB = 21.0 mm; narrow-bore NB1 = 25.0 mm). These liners were tested with alternate and simultaneous pulsation patterns, pulsator ratios (60:40 and 67:33) and three system vacuum levels (40, 44 and 50 kPa). Teat tissue was measured using ultrasonography, before milking and directly after milking. The measurements recorded were teat canal length (TCL), teat diameter (TD), cistern diameter (CD) and teat wall thickness (TWT). Teat tissue changes were similar with a system vacuum level of either 50 kPa (mid-level) or 40 kPa (low-level). Widening the liner upper barrel bore dimension from 21.0 mm (P < 0.01) or 25.0 mm (P < 0.001) to 31.6 mm increased the magnitude of changes in TD and TWT after machine milking. Milk yield per cow was significantly (P < 0.05) higher and cluster-on time was reduced (P < 0.01) with the WB cluster as compared to the NB1 cluster. Minimum changes in teat tissue parameters were achieved with system vacuum level of 40 kPa and 50 kPa using NB and WB clusters, respectively. Similar changes in teat tissue and milk yield per cow were observed with alternate and simultaneous pulsation patterns. Widening pulsator ratio from 60:40 to 67:33 did not have negative effects on changes in teat tissue and had a positive effect on milk yield and milking time. Milk liner design had a bigger effect on teat tissue changes and milking characteristics than pulsation settings.
    • Dry cow therapy with a non-antibiotic intramammary teat seal - a review

      Crispie, Fiona; Flynn, James; Ross, R Paul; Hill, Colin; Meaney, William J (Biomed Central, 2004-07-01)
      Dry cow antibiotic therapy is used to eliminate existing intramammary infections and to prevent new infections in the dry period. It is implemented as part of a total management system known as the 'Five-Point Plan' for mastitis control. Recent public concerns over the widespread prophylactic use of antibiotics, coupled with an increasing interest in organic farming, have lead to a re-evaluation of the treatment of cows at drying-off. As a result, attention has focussed on the use of novel alternatives to antibiotic therapy at the end of lactation. One such therapy involves the application of a non-antibiotic bismuth-based intramammary teat seal designed for use in cows with low cell counts at the end of lactation. Like the keratin plug that forms naturally in teats of cows that have been dried-off, teat seal forms a physical barrier to invading pathogens. To date, a number of independent studies have shown that teat seal is as effective as traditional dry cow antibiotic products in preventing the occurrence of new infection during the dry period in cows with somatic cell counts of ≤200,000 cells ml-1 at drying-off. This paper reviews the efficacy of teat seal in preventing dry period mastitis in both conventional and organic dairying systems.
    • Update on the development of a novel dry cow therapy using a bismuth-based intramammary teat seal in combination with the bacteriocin lacticin 3147

      Crispie, Fiona; Flynn, James; Ross, R Paul; Hill, Colin; Meaney, William J (Biomed Central, 2004-11-01)
      Public concerns over the widespread prophylactic use of antibiotics have led to a search for alternatives to dry cow therapy for the prevention of intramammary infections. A popular alternative is to infuse a teat seal at drying-off. The teat seal is a viscous non-antibiotic formulation and when it is infused into the teat canal and the teat sinus it forms an internal seal that provides a physical barrier to invasion by mastitis-causing pathogens. Enhancement of teat seal formulations may be achieved using non-antibiotic additives such as bacteriocins, potent proteins produced by some bacteria that have the ability to kill other microorganisms. This paper traces the history of investigations at Moorepark Research Centre into the efficacy of teat seal plus lacticin 3147, a bacteriocin produced by Lactococcus lactis DPC3147, in the prevention of intramammary infections in dry cows. Indications from on-going investigations are that a dry cow formulation combining the two products has considerable potential as a non-antibiotic prophylactic product.
    • 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.
    • A general method for selection of riboflavin-overproducing food grade micro-organisms

      Burgess, Catherine M; Smid, Eddy J; Rutten, Ger; van Sinderen, Douwe (Biomed Central, 2006-07-18)
      Background: This study describes a strategy to select and isolate spontaneous riboflavin-overproducing strains of Lactobacillus (Lb.) plantarum, Leuconostoc (Lc.) mesenteroides and Propionibacterium (P.) freudenreichii. Results: The toxic riboflavin analogue roseoflavin was used to isolate natural riboflavin-overproducing variants of the food grade micro-organisms Lb. plantarum, Lc. mesenteroides and P. freudenreichii strains. The method was successfully employed for strains of all three species. The mutation(s) responsible for the observed overproduction of riboflavin were identified for isolates of two species. Conclusion: Selection for spontaneous roseoflavin-resistant mutants was found to be a reliable method to obtain natural riboflavin-overproducing strains of a number of species commonly used in the food industry. This study presents a convenient method for deriving riboflavin-overproducing strains of bacterial starter cultures, which are currently used in the food industry, by a non-recombinant methodology. Use of such starter strains can be exploited to increase the vitamin content in certain food products.
    • Relatedness between the two-component lantibiotics lacticin 3147 and staphylococcin C55 based on structure, genetics and biological activity

      O'Connor, Eileen B; Cotter, Paul D.; O'Connor, Paula M.; O'Sullivan, Orla; Tagg, John R; Ross, R Paul; Hill, Colin (Biomed Central, 2007-04-02)
      Background: Two component lantibiotics, such as the plasmid-encoded lacticin 3147 produced by Lactococcus lactis DPC3147 and staphylococcin C55 produced by Staphylococcus aureus C55, represent an emerging subgroup of bacteriocins. These two bacteriocins are particularly closely related, exhibiting 86% (LtnA1 and C55α) and 55% (LtnA2 and C55β) identity in their component peptides. The aim of this study was to investigate, for the first time for any two component bacteriocins, the significance of the relatedness between these two systems. Results: So close is this relatedness that the hybrid peptide pairs LtnA1:C55β and C55α:LtnA2 were found to have activities in the single nanomolar range, comparing well with the native pairings. To determine whether this flexibility extended to the associated post-translational modification/processing machinery, the staphylococcin C55 structural genes were directly substituted for their lacticin 3147 counterparts in the ltn operon on the large conjugative lactococcal plasmid pMRC01. It was established that the lacticin LtnA1 post-translational and processing machinery could produce functionally active C55α, but not C55β. In order to investigate in closer detail the significance of the differences between LtnA1 and C55α, three residues in LtnA1 were replaced with the equivalent residues in C55α. Surprisingly, one such mutant LtnA1-Leu21Ala was not produced. This may be significant given the positioning of this residue in a putative lipid II binding loop. Conclusion: It is apparent, despite sharing striking similarities in terms of structure and activity, that these two complex bacteriocins display some highly dedicated features particular to either system.
    • A review of factors influencing litter size in Irish sows

      Lawlor, Peadar G; Lynch, P Brendan (Biomed Central, 2007-06-01)
      Many factors influence litter size. These include genetics, gilt management, lactation length, parity distribution, disease, stress and boar fertility. In the past 20 years, litter size in Irish sows has increased by only one pig. Born alive figures now average at 11.2 pigs per litter. In this regard, Ireland is falling behind our European competitors who have made significant advances over this time. Denmark, for example, has an average figure of 12.7 pigs born alive per litter and France an average of 12.5. The single area that could be improved immediately is sow feeding. It is important that sows are fed correctly throughout pregnancy. If over-fed during pregnancy, sows will have depressed appetite during lactation. If underfed in pregnancy, sows will be too thin at farrowing. The correct way to feed a pregnant sow is to match her feed allocation to her requirement for maintenance, body growth and growth of her developing foetuses. During lactation, sows should be given as much feed as they can eat to prevent excessive loss of body condition. Liquid-feed curves should be such that lactating sows are provided with a minimum mean daily feed supply of 6.2 kg. A small proportion of sows will eat more and this could be given as supplementary dry feed. Where dry feeding is practised in the farrowing house, it is difficult to hand-feed sows to match their appetite. Ideally ad libitum wet/dry feeders should be used. From weaning to service, sows should once again be fed ad libitum. If liquid feeding, this means giving at least 60 MJ DE (digestible energy) per day during this period. If dry feeding, at least 4 kg of lactation diet should be fed daily. The effort spent perfecting sow feeding management on units should yield high dividends in the form of increased pigs born alive per litter.
    • Effect of restricting silage feeding prepartum on time of calving, dystocia and stillbirth in Holstein-Friesian cows

      Gleeson, David E; O'Brien, Bernadette; Mee, John F (Biomed Central, 2007-11-01)
      A study was carried out to investigate the effect of restricting silage feeding on time of calving and calving performance in Holstein-Friesian cows. In the treatment group (n = 1,248 cows, 12 herds) silage feeding commenced in the evening (17:00 to 20:00 h), after a period of restricted access (2 to 10 h) while in the control group ad-libitum access to silage was provided over the 24 h period (n = 1,193 cows, 12 herds). Daytime and nighttime calvings were defined as calvings occurring between the hours of 06:30 and 00:29 and between 00:30 and 06:29, respectively. Restricting access to silage resulted in less calvings at night compared to cows with ad-libitum access to silage (18 vs 22%, P < 0.05). Cows with restricted access to silage had a higher percentage of difficult calvings (11 vs 7%, P < 0.001) and stillbirths (7 vs 5%, P < 0.05) compared to cows in the control group. The percentage of calvings at night was lower (13%) when access to silage was restricted for 10 h compared to 2, 4 or 6 h (22, 18, 25%, respectively) (P < 0.001). Calf sire breed, calf gender or cow parity did not influence time of calving. In conclusion, offering silage to pregnant Holstein-Friesian cows in the evening, after a period of restricted access, reduced the incidence of nighttime calvings, but increased the incidence of dystocia and stillbirth.
    • 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 (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.
    • Development of a real-time multiplex PCR assay for the detection of multiple Salmonella serotypes in chicken samples.

      O'Regan, Edel; McCabe, Evonne; Burgess, Catherine M; McGuinness, Sheila; Barry, Thomas; Duffy, Geraldine; Whyte, Paul; Fanning, Seamus (Biomed Central, 2008-09-21)
      Background: A real-time multiplex PCR assay was developed for the detection of multiple Salmonella serotypes in chicken samples. Poultry-associated serotypes detected in the assay include Enteritidis, Gallinarum, Typhimurium, Kentucky and Dublin. The traditional cultural method according to EN ISO 6579:2002 for the detection of Salmonella in food was performed in parallel. The real-time PCR based method comprised a pre-enrichment step in Buffered Peptone Water (BPW) overnight, followed by a shortened selective enrichment in Rappaport Vasilliadis Soya Broth (RVS) for 6 hours and subsequent DNA extraction. Results: The real-time multiplex PCR assay and traditional cultural method showed 100% inclusivity and 100% exclusivity on all strains tested. The real-time multiplex PCR assay was as sensitive as the traditional cultural method in detecting Salmonella in artificially contaminated chicken samples and correctly identified the serotype. Artificially contaminated chicken samples resulted in a detection limit of between 1 and 10 CFU per 25 g sample for both methods. A total of sixty-three naturally contaminated chicken samples were investigated by both methods and relative accuracy, relative sensitivity and relative specificity of the real-time PCR method were determined to be 89, 94 and 87%, respectively. Thirty cultures blind tested were correctly identified by the real-time multiplex PCR method. Conclusion: Real-time PCR methodology can contribute to meet the need for rapid identification and detection methods in food testing laboratories.
    • Farm management factors associated with bulk tank total bacterial count in Irish dairy herds during 2006/07

      Kelly, PT; O'Sullivan, K; Berry, Donagh P.; More, Simon J; Meaney, William J; O'Callaghan, Edmond J; O'Brien, Bernadette (Biomed Central, 2009-01-01)
      Research has shown that total bacterial count (TBC), which is the bacterial growth per ml of milk over a fixed period of time, can be decreased by good hygiene and farm management practices. The objective of the current study was to quantify the associations between herd management factors and bulk tank TBC in Irish spring calving, grass-based dairy herds. The relationship between bulk tank TBC and farm management and infrastructure was examined using data from 400 randomly selected Irish dairy farms where the basal diet was grazed grass. Herd management factors associated with bulk tank TBC were identified using linear models with herd annual total bacterial score (i.e., arithmetic mean of the natural logarithm of bulk tank TBC) included as the dependent variable. All herd management factors were individually analysed in a separate regression model, that included an adjustment for geographical location of the farm. A multiple stepwise regression model was subsequently developed. Median bulk tank TBC for the sample herds was 18,483 cells/ml ranging from 10,441 to 130,458 cells/ml. Results from the multivariate analysis indicated that the following management practices were associated with low TBC; use of heated water in the milking parlour; participation in a milk recording scheme; and tail clipping of cows at a frequency greater than once per year. Increased level of hygiene of the parlour and cubicles were also associated with lower TBC. Herd management factors associated with bulk tank TBC in Irish grazing herds were generally in agreement with most previous studies from confinement systems of milk production.
    • Purging of inbreeding depression within the Irish Holstein-Friesian population

      McParland, Sinead; Kearney, Francis; Berry, Donagh P. (Biomed Central, 2009-01-21)
      The objective of this study was to investigate whether inbreeding depression in milk production or fertility performance has been partially purged due to selection within the Irish Holstein-Friesian population. Classical, ancestral (i.e., the inbreeding of an individual's ancestors according to two different formulae) and new inbreeding coefficients (i.e., part of the classical inbreeding coefficient that is not accounted for by ancestral inbreeding) were computed for all animals. The effect of each coefficient on 305-day milk, fat and protein yield as well as calving interval, age at first calving and survival to second lactation was investigated. Ancestral inbreeding accounting for all common ancestors in the pedigree had a positive effect on 305-day milk and protein yield, increasing yields by 4.85 kg and 0.12 kg, respectively. However, ancestral inbreeding accounting only for those common ancestors, which contribute to the classical inbreeding coefficient had a negative effect on all milk production traits decreasing 305-day milk, fat and protein yields by -8.85 kg, -0.53 kg and -0.33 kg, respectively. Classical, ancestral and new inbreeding generally had a detrimental effect on fertility and survival traits. From this study, it appears that Irish Holstein-Friesians have purged some of their genetic load for milk production through many years of selection based on production alone, while fertility, which has been less intensely selected for in the population demonstrates no evidence of purging.
    • Estimation of prediction error variances via Monte Carlo sampling methods using different formulations of the prediction error variance

      Hickey, John M; Veerkamp, Roel F; Calus, M. P. L.; Mulder, Han A; Thompson, Robin (Biomed Central, 2009-02-09)
      Calculation of the exact prediction error variance covariance matrix is often computationally too demanding, which limits its application in REML algorithms, the calculation of accuracies of estimated breeding values and the control of variance of response to selection. Alternatively Monte Carlo sampling can be used to calculate approximations of the prediction error variance, which converge to the true values if enough samples are used. However, in practical situations the number of samples, which are computationally feasible, is limited. The objective of this study was to compare the convergence rate of different formulations of the prediction error variance calculated using Monte Carlo sampling. Four of these formulations were published, four were corresponding alternative versions, and two were derived as part of this study. The different formulations had different convergence rates and these were shown to depend on the number of samples and on the level of prediction error variance. Four formulations were competitive and these made use of information on either the variance of the estimated breeding value and on the variance of the true breeding value minus the estimated breeding value or on the covariance between the true and estimated breeding values.
    • Comparative genomics of lactic acid bacteria reveals a niche-specific gene set

      O'Sullivan, Orla; O'Callaghan, John; Sangrador-Vegas, Amaia; McAuliffe, Olivia; Slattery, Lydia; Kaleta, Pawel; Callanan, Michael J.; Fitzgerald, Gerald F; Ross, R Paul; Beresford, Tom (Biomed Central, 2009-03-05)
      Background: The recently sequenced genome of Lactobacillus helveticus DPC4571 1 revealed a dairy organism with significant homology (75% of genes are homologous) to a probiotic bacteria Lb. acidophilus NCFM 2. This led us to hypothesise that a group of genes could be determined which could define an organism's niche. Results: Taking 11 fully sequenced lactic acid bacteria (LAB) as our target, (3 dairy LAB, 5 gut LAB and 3 multi-niche LAB), we demonstrated that the presence or absence of certain genes involved in sugar metabolism, the proteolytic system, and restriction modification enzymes were pivotal in suggesting the niche of a strain. We identified 9 niche specific genes, of which 6 are dairy specific and 3 are gut specific. The dairy specific genes identified in Lactobacillus helveticus DPC4571 were lhv_1161 and lhv_1171, encoding components of the proteolytic system, lhv_1031 lhv_1152, lhv_1978 and lhv_0028 encoding restriction endonuclease genes, while bile salt hydrolase genes lba_0892 and lba_1078, and the sugar metabolism gene lba_1689 from Lb. acidophilus NCFM were identified as gut specific genes. Conclusion: Comparative analysis revealed that if an organism had homologs to the dairy specific geneset, it probably came from a dairy environment, whilst if it had homologs to gut specific genes, it was highly likely to be of intestinal origin. We propose that this "barcode" of 9 genes will be a useful initial guide to researchers in the LAB field to indicate an organism's ability to occupy a specific niche.
    • Paratuberculosis sero-status and milk production, SCC and calving interval in Irish dairy herds

      Hoogendam, K; Richardson, E; Mee, John F (Biomed Central, 2009-04-01)
      The objective of this study was to investigate the impact of paratuberculosis sero-status on milk yield, fat, protein, somatic cell count and calving interval in Irish dairy herds. Serum from all animals over 12 months of age (n = 2,602) in 34 dairy herds was tested for antibodies to Mycobacterium avium subsp. paratuberculosis using an ELISA. Herds were categorised by sero-status into positive, non-negative and negative, where a positive herd contained two or more positive cows, a non-negative herd contained only one positive cow and a negative herd contained no positive cows. Data at animal, parity and herd-level were analysed by multiple regression using general linear models. Positive herds (mean herd size = 129 cows) and non-negative herds (81 cows) were larger than negative herds (72 cows) (P < 0.01). Negative herds had the highest economic breeding index (EBI), while positive herds had the highest estimated breeding value (EBV) for milk yield. There was no significant effect of paratuberculosis sero-status at animal, parity or herd-level on milk yield, milk fat or protein production, somatic cell count score (SCCS) or calving interval. Negative herds tended to have a lower SCCS than positive and nonnegative herds (P = 0.087). This study only examined the effects of paratuberculosis sero-status but did not examine the clinical effects of Johne's disease at the farm or dairy industry levels.
    • Farm management factors associated with bulk tank somatic cell count in Irish dairy herds

      Kelly, PT; O'Sullivan, K; Berry, Donagh P.; More, Simon J; Meaney, William J; O'Callaghan, Edmond J; O'Brien, Bernadette (Biomed Central, 2009-04-01)
      The relationship between bulk tank somatic cell count (SCC) and farm management and infrastructure was examined using data from 398 randomly selected, yet representative, Irish dairy farms where the basal diet is grazed grass. Median bulk tank SCC for the farms was 282,887 cells/ml ranging from 82,209 to 773,028 cells/ml. Two questionnaires were administered through face-to-face contact with each farmer. Herd-level factors associated with bulk tank SCC were determined using linear models with annual somatic cell score (i.e., arithmetic mean of the natural logarithm of bulk tank SCC) included as the dependent variable. All herd level factors were analysed individually in separate regression models, which included an adjustment for geographical location of the farm; a multiple regression model was subsequently developed. Management practices associated with low SCC included the use of dry cow therapy, participation in a milk recording scheme and the use of teat disinfection post-milking. There was an association between low SCC and an increased level of hygiene and frequency of cleaning of the holding yard, passageways and cubicles. Herd management factors associated with bulk tank SCC in Irish grazing herds are generally in agreement with most previous studies from confinement systems of milk production.
    • Demographics of cattle positive for Mycobacterium avium subspecies paratuberculosis by faecal culture, from submissions to the Cork Regional Veterinary Laboratory

      Richardson, EKB; Mee, John F; Sánchez-Miguel, C; Crilly, J; More, Simon J (Biomed Central, 2009-06-01)
      The demography of bovine infections caused by Mycobacterium avium subspecies paratuberculosis (MAP) in Ireland is poorly defined. The objective of this study was to describe the demographics of cattle positive to MAP on faecal culture, based on submissions to the Cork Regional Veterinary Laboratory (Cork RVL) from 1994 to 2006. The study focused on all available faecal samples from adult cattle with non-responsive chronic diarrhoea that were submitted by private veterinary practitioners to Cork RVL for MAP culture. For each MAP-positive by faecal culture animal, data were collated from Cork RVL and Cattle Movement Monitoring Scheme (CMMS) records. Johne's disease (JD) was confirmed in 110 animals from 86 herds by the Cork RVL between 1994 and 2006, with a rate of positive cases between 15% and 18% over last four years of the study. Two breeds (Holstein/Friesian or Limousin) made up 78% of submissions. Movements were assessed for the 57 study animals with available movement information, 90% died within one year of the test and 26% tested positive in the herd they were born into. The study provides preliminary information about movement trends and demographics of animals with MAP positive submissions. Although the study area is restricted, it includes the most intensive (and economically-important) dairy region in Ireland. The demographics of JD infection from the study area are in agreement with international reports. Further work is required to determine demographic trends, incidence and prevalence of JD throughout Ireland. It is hoped this work may contribute to the development of a surveillance strategy for MAP by regional veterinary laboratories.