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Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter
Get PDFPublication history: Accepted - 17 August 2020; Published online - 9 September 2020Background
The factors affecting host-pathogen ecology in terms of the microbiome remain poorly studied. Chickens are a key source of protein with gut health heavily dependent on the complex microbiome which has key roles in nutrient assimilation and vitamin and amino acid biosynthesis. The chicken gut microbiome may be influenced by extrinsic production system parameters such as Placement Birds/m2 (stocking density), feed type and additives. Such parameters, in addition to on-farm biosecurity may influence performance and also pathogenic bacterial numbers such as Campylobacter. In this study, three different production systems ‘Normal’ (N), ‘Higher Welfare’ (HW) and ‘Omega-3 Higher Welfare’ (O) were investigated in an industrial farm environment at day 7 and day 30 with a range of extrinsic parameters correlating performance with microbial dynamics and Campylobacter presence.
Results
Our data identified production system N as significantly dissimilar from production systems HW and O when comparing the prevalence of genera. An increase in Placement Birds/m2 density led to a decrease in environmental pressure influencing the microbial community structure. Prevalence of genera, such as Eisenbergiella within HW and O, and likewise Alistipes within N were representative. These genera have roles directly relating to energy metabolism, amino acid, nucleotide and short chain fatty acid (SCFA) utilisation. Thus, an association exists between consistent and differentiating parameters of the production systems that affect feed utilisation, leading to competitive exclusion of genera based on competition for nutrients and other factors. Campylobacter was identified within specific production system and presence was linked with the increased diversity and increased environmental pressure on microbial community structure. Addition of Omega-3 though did alter prevalence of specific genera, in our analysis did not differentiate itself from HW production system. However, Omega-3 was linked with a positive impact on weight gain.
Conclusions
Overall, our results show that microbial communities in different industrial production systems are deterministic in elucidating the underlying biological confounders, and these recommendations are transferable to farm practices and diet manipulation leading to improved performance and better intervention strategies against Campylobacter within the food chain.OG and NC acknowledge research funding from Moy Park. UZI is funded by NERC Independent Research Fellowship (NE/L011956/1)
What is the current significance of low birthweight pigs on commercial farms in Northern Ireland in terms of impaired growth and mortality?
Get PDFPublication history: Accepted - 25 July 2020; Published - 31 July 2020.There is little modern data addressing the differential lifetime growth of commercially reared low and average birthweight pigs born into large litters (>14 piglets). As such, the main aim of this study was to quantify the lifetime growth and mortality rate of low and average birthweight pigs on commercial farms in Northern Ireland. It was also aimed to analyse the level, stage and cause of mortality within each birthweight category. A total of 328 low birthweight (LOW BW; 0.05). The alimentary tract (27%) and respiratory tract (27%) were the most commonly implicated body systems following post-mortem examination of post-weaning deaths. In conclusion, this study quantified the inferior weight, growth rate and mortality of Low BW pigs, identifying the lactation and immediate post-weaning periods as having greatest potential in reducing this birthweight associated growth differential
Grazing cattle exposure to neighbouring herds and badgers in relation to bovine tuberculosis risk
Get PDFPublication history: Accepted - 28 September 2020; Published online - 30 September 2020.Bovine tuberculosis (bTB) can be spread between and among cattle and wildlife hosts e.g. European badger
(Meles meles). The majority of cattle in the UK and Ireland are grazed during the summer, potentially exposing
them to Mycobacterium bovis. 18 farms were surveyed (39% dairy, 61% beef; fields n = 697) for one grazing
season (May-November 2016, n = 148,461 field days) to quantify the co-occurrence of cattle with badger setts
and latrines and adjacency to neighbouring cattle herds. 3% (n = 24) of the fields had a badger sett or latrine
recorded, dairy cattle were significantly more likely to co-occur with badger setts and latrines than beef cattle.
Most farms (89%) grazed cattle adjacent to a neighbouring herd, which accounted for 18% of the grazing season.
Potential exposure to neighbouring herds did not differ between production systems but did vary between life
stages. A significant positive association between the proportion of time cattle spent grazing fields with setts
present and the historic 1-, 3- and 5- year bTB status (p = 0.007, p = 0.013 and p = 0.013 respectively) was
found. However, when cattle were grazed in fields with latrines, a significant negative association was found
between the proportion of time cattle spent grazing fields with latrines present and the historic 3- and 5- year
bTB status (p = 0.033 and p = 0.012 respectively). Historic bTB status and percentage of days spent beside a
neighbouring herd was unrelated. Idiosyncrasies at farm-level and between risk factors indicated that individual
farm assessments would be beneficial to understand potential exposure risk.This research was funded as part of a PhD studentship by the
Department of Agriculture, Environment and Rural Affair
Microbiological assessments in a cut flower crop polytunnel field trial adopting soil covering and microbiocides for Fusarium wilt suppression
Get PDFPublication history: Published online - 4 September 2020Cut flower Matthiola incana were raised by local commercial cultivators in a polytunnel. The field soil beds were either left uncovered as normal or covered with polythene sheets (except a hole for plant plug space). Average temperatures in the top 5 cm soil under cover dropped from 28 oC to 18 oC compared to its spiking up to 37 oC in uncovered counterparts. Microbiological analyses indicated that soil covering induced two log10 folds reduction of the wilt causal fungi Fusarium oxysporum and concomitantly increased one log10 fold wilt antagonistic natural soil inhabiting fungi populations. Standard dip/drench mixtures of commercial and local isolates microbiocides (bacteria) applied to M. incana plug roots improved plant health assessed by visible scores of the level of damage or wilt symptoms under soil covered treatments. Scanning electron microscopy, cultural and 16S rRNA PCR analyses revealed potent antifungal bacteria attached to the hyphal surfaces of F. oxysporum as ectosymbionts that may have implications for virulence regulation and host plants’ wilt disease control. Our microbiological data support the prospects of combining physiological and microbiological interventions upon covering the soil surface that offers the local horticulturists an evidence based sustainable means of Fusarium wilt control suppression in polytunnel crops.Department of Agriculture, Environment and Rural Affairs
(DAERA) directed Evidence and Innovation project 16/3/11,
and the support of a EU FP7–BIOFECTOR grant (JRR, CF,
TM) for this stud
Genomic characterization, formulation and efficacy in planta of a siphoviridae and podoviridae protection cocktail against the bacterial plant pathogens
Get PDFPublication history: Accepted - 25 January 2020; Published online - 28 January 2020.: In the face of global human population increases, there is a need for efficacious integrated pest
management strategies to improve agricultural production and increase sustainable food production.
To counteract significant food loses in crop production, novel, safe and efficacious measures should
be tested against bacterial pathogens. Pectobacteriaceae species are one of the causative agents of the
bacterial rot of onions ultimately leading to crop losses due to ineffective control measures against
these pathogens. Therefore, the aim of this study was to isolate and characterize bacteriophages
which could be formulated in a cocktail and implemented in planta under natural environmental
conditions. Transmission electron microscopy (TEM) and genome analysis revealed Siphoviridae and
Podoviridae family bacteriophages. To test the protective effect of a formulated phage cocktail against
soft rot disease, three years of field trials were performed, using three different methods of treatment
application. This is the first study to show the application of a phage cocktail containing Podoviridae
and Siphoviridae bacteriophages capable of protecting onions against soft rot in field conditions.The M.A.Z-M. was funded by Department of Agriculture, Environment and Rural Affairs (DAERA),
Northern Ireland by PhD studentship
Occupational Injury and Working Days Lost in Northern Ireland’s Farming Sector
Get PDFPublication history: Accepted - 21 October 2020Agriculture is one of the most hazardous sectors in terms of occupational injuries resulting in 29 more working days being lost. This paper employs a dataset of 7,500 Northern Irish farms 30 over the period 2015-2019 to investigate what factors affect the number of working days lost 31 in agriculture. Results indicate that public policies aimed to improve farm safety should focus 32 on dairy farms, young workers, family members different from the main farmer, and 33 dangerous working practices related to machineries and vehicles. Besides, results indicate 34 that more than 18,000 workdays are lost every year in Northern Irish farms
Impact of sow lactation feed intake on the growth and suckling behavior of low and average birthweight pigs to 10 weeks of age
Get PDFPublication history: Accepted - 2 May 2020; Published online - 9 May 2020.Improved genetics in commercial
pig production have resulted in larger litter sizes.
However this has increased the prevalence of compromised
pigs exhibiting inferior birthweights,
weaning weights, and lifetime performance. This
study aimed to determine the effects of increased
sow lactation feed intake on growth of low and
average birthweight piglets until 10 wk of age. Low
(Low BW; <1 kg) and average (Av BW; 1.3–1.7 kg)
birthweight animals were reared in uniformly
weighted litters comprising 14 piglets on a foster
mother offered either a low (Low FA; max 7.5 kg/d)
or high (High FA; max 11 kg/d) feed allowance over
a 28- ± 1-d lactation. Piglet performance was monitored
from birth until 10 wk of age. Sows offered
a High FA consumed 42.4 kg more feed on average
than those offered Low FA, resulting in a greater
derived milk yield (P < 0.05). Animals of Av BW
remained heavier than Low BW pigs throughout
the trial (P < 0.05). Piglets reared by High FA sows
were heavier at weeks 3, 4, 5, and 7 (P < 0.05) but
not week 10 (P > 0.05). Growth rate of piglets relative
to their birthweight was significantly greater
for Low BW piglets than those of Av BW during
lactation (P < 0.001). Piglets reared by sows offered
a High FA expressed greater relative growth preweaning
(P < 0.05); however, postweaning relative
growth for piglets reared on sows offered a Low FA
was greater (P < 0.05) suggesting compensatory
growth. Neither birthweight nor sow feed allowance
significantly affected preweaning mortality (P
> 0.05). However, Low BW animals on sows with
a High FA recorded half the preweaning mortality
of Low BW pigs on sows with a Low FA. During
week 1 of lactation, Av BW litters recorded a
greater total suckling duration compared to Low
BW litters (P < 0.05) but there was no difference
in suckling frequency (P > 0.05). During week 3 of
lactation, High FA litters displayed a significantly
lower suckling frequency (P < 0.05) yet a greater
total suckling duration (P < 0.001). Average daily
gain was greater for Av BW pigs during weeks 4–7
(P < 0.001) but no difference was recorded between
weeks 7 and 10 (P > 0.05). Average daily feed intake
was greater for Av BW pigs throughout the nursery
period (P < 0.05) but feed–conversion ratio did not
differ compared to Low BW pens (P>0.05). In conclusion,
offering sows a High FA increased weaning
weight of all animals; however, birthweight was the
major determinant of postweaning performance
River lamprey present an unusual predation threat to Atlantic salmon smolts in Lough Neagh, Northern Ireland.
Get PDFPublication history: Accepted - 28 July 2020;A new monitoring programme on the Lough Neagh catchment has documented a high incidence of river lamprey, Lampetra fluviatilis L., predation on Atlantic salmon smolts, Salmo salar L.,. In total 470 smolts were examined during the 2020 emigration period with 168 fish (36%) exhibiting lamprey scars of which 57 were lightly scarred and 111 were classed as heavily scarred. Lamprey predation was not size selective on Lough Neagh S. salar smolts.This work was funded by Department of Agriculture, Environment and Rural Affairs for N. Ireland
Long term retention of dummy acoustic transmitters in adult brown trout
Get PDFPublication history: Accepted - 12 August 2020; Published online - 13 October 2020.A group of 36 1+ age class Salmo trutta were surgically implanted with dummy acoustic tags and monitored for 370 days. In total 13 tags were expelled through-out the experiment with an overall tag loss rate of c. 0.035 tag/d. Fish length was the only explanatory variable which had a significant association with subsequent tag expulsion. The estimated probability of retaining a tag for a year for a fish of length 32 cm was 0.76, 34 cm was 0.60 and 36 cm was 0.38. The long term tag loss patterns were examined and discussed
Nitrogen surplus – a unified indicator for water pollution in for Europe?
No full textPublication history: Accepted - 15 April 2020; Published online - 22 April 2020Pollution of ground-and surface waters with nitrates from agricultural sources poses a risk to drinking water quality and has negative impacts on the environment. At the national scale, the gross nitrogen budget (GNB) is accepted as an indicator of pollution caused by nitrates. There is, however, little common EU-wide knowledge on the budget application and its comparability at the farm level for the detection of ground-and surface water pollution caused by nitrates and the monitoring of mitigation measures. Therefore, a survey was carried out among experts of various European countries in order to assess the practice and application of fertilization planning and nitrogen budgeting at the farm level and the differences between countries within Europe. While fertilization planning is practiced in all of the fourteen countries analyzed in this paper, according to current legislation, nitrogen budgets have to be calculated only in Switzerland, Germany and Romania. The survey revealed that methods of fertilization planning and nitrogen budgeting at the farm level are not unified throughout Europe. In most of the cases where budgets are used regularly (Germany, Romania, Switzerland), standard values for the chemical composition of feed, organic fertilizers, animal and plant products are used. The example of the Dutch Annual Nutrient Cycling Assessment (ANCA) tool (and partly of the Suisse Balance) shows that it is only by using farm-specific “real” data that budgeting can be successfully applied to optimize nutrient flows and increase N efficiencies at the farm level. However, this approach is more elaborate and requires centralized data processing under consideration of data protection concerns. This paper concludes that there is no unified indicator for nutrient management and water quality at the farm level. A comparison of regionally calculated nitrogen budgets across European countries needs to be interpreted carefully, as methods as well as data and emission factors vary across countries. For the implementation of EU nitrogen-related policies—notably, the Nitrates Directive—nutrient budgeting is currently ruled out as an entry point for legal requirements. In contrast, nutrient budgets are highlighted as an environment indicator by the OECD and EU institutions.This project was funded from the European Union’s Horizon 2020 project FAIRWAY (https://www.
fairway-project.eu/) under grant agreement No. 727984