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Feed Restriction Modulates the Fecal Microbiota Composition, Nutrient Retention, and Feed Efficiency in Chickens Divergent in Residual Feed Intake
Get PDFPublication histroy: Accepted - 23 October 2018; Published - 19 November 2019.There is a great interest to understand the impact of the gut microbiota on host’s
nutrient use and FE in chicken production. Both chicken’s feed intake and gut bacterial
microbiota differ between high and low-feed efficient chickens. To evaluate the impact
of the feed intake level on the feed efficiency (FE)-associated variation in the chicken
intestinal microbiota, differently feed efficient chickens need to eat the same amount of
feed, which can be achieved by feeding chickens restrictively. Therefore, we investigated
the effect of restrictive vs. ad libitum feeding on the fecal microbiome at 16 and 29
days posthatch (dph), FE and nutrient retention in chickens of low and high residual
feed intake (RFI; metric for FE). Restrictively fed chickens were provided the same
amount of feed which corresponded to 85% of the ad libitum fed group from 9 dph.
FE was determined for the period between 9 and 30 dph and feces for nutrient retention
were collected on 31 to 32 dph. From the 112 chickens (n = 56 fed ad libitum, and
n = 56 fed restrictively), 14 low RFI and 15 high RFI ad libitum fed chickens, and
14 low RFI (n = 7 per sex) and 14 high RFI restrictively fed chickens were selected
as the extremes in RFI and were retrospectively chosen for data analysis. Bray-Curtis
dissimilarity matrices showed significant separation between time points, and feeding
level groups at 29 dph for the fecal bacterial communities. Relevance networking
indicated positive associations between Acinetobacter and feed intake at 16 dph,
whereas at 29 dph Escherichia/Shigella and Turicibacter positively and Lactobacillus
negatively correlated to chicken’s feed intake. Enterobacteriaceae was indicative for
low RFI at 16 dph, whereas Acinetobacter was linked to high RFI across time points.
However, restrictive feeding-associated changes in the fecal microbiota were not similar
in low and high RFI chickens, whichmay have been related to the higher nutrient retention
and thus lower fecal nutrient availability in restrictively fed high RFI chickens. Thismay also
explain the decreased RFI value in restrictively fed high RFI chickens indicating improved
FE, with a stronger effect in females.This project (ECO-FCE) has received funding from the
European Union’s Seventh Framework Programme for research,
technological development and demonstration under grant
agreement No. 311794
A Novel Natural Antimicrobial Can Reduce the in vitro and in vivo Pathogenicity of T6SS Positive Campylobacter jejuni and Campylobacter coli Chicken Isolates
Get PDFPublication history: Accepted - 21 August 2018; Published - 07 September 2018.Human campylobacteriosis is considered one of the most common foodborne diseases
worldwide with poultry identified as the main source of infection accounting for 50–
80% of human cases. Highly virulent Campylobacter spp., positive for the Type VI
secretion system (T6SS), which have an increased ability to adhere to and invade
the host gastrointestinal epithelium are highly prevalent in poultry. Multidrug resistant
strains of bacteria are rapidly evolving and therefore, new antimicrobials to supplement
animal feed that are able to control Campylobacter species, are in great need. The
work presented herein indicates that a novel phenolic antimicrobial, Auranta 3001, is
able to reduce the adhesion and invasion of human intestinal epithelial cells (HCT-
8) by two T6SS positive chicken isolates, C. jejuni RC039 (p < 0.05) and C. coli
RC013 (p < 0.001). Exposure of C. jejuni RC039 and C. coli RC013 to Auranta 3001
downregulated the expression of hcp and cetB genes, known to be important in the
functionality of T6SS. Furthermore, the reduced adhesion and invasion is associated
with a significant decrease in bacterial motility of both isolates (p < 0.05–p < 0.001)
in vitro. Most importantly our in vivo results show that Auranta 3001 is able to reduce
cecum colonization levels from log 8 CFU/ml to log 2 CFU/ml for C. jejuni RC039
and from log 7 CFU/ml to log 2 CFU/ml for C. coli RC013. In conclusion, this novel
antimicrobial is able to reduce the pathogenic properties of T6SS campylobacters in vitro
and also to decrease colonization in vivo.This work has been funded through a research grant awarded to
NC by Auranta, Nova UCD, Belfield Innovation Park, Belfield,
Dublin 4, Ireland
Relationship between the structure and composition of rumen microorganisms and the digestibility of neutral detergent fibre in goats
Get PDFPublication history: Accepted - 7 June 2018; Published online - 26 July 2018; Published print - January 2019.Objective: This experiment was conducted to compare the structure and composition of ruminal microorganisms in goats with high and low neutral detergent fibre (NDF) digestibility.
Methods: Nineteen crossbred goats were used as experimental animals and fed the same total mixed rations during the 30-day pre-treatment and 6-day digestion trialperiods. All faeces were collected during the digestion period for measuring the NDF digestibility. Then, high and the low NDF digestibility individuals were chosen for the high NDF digestibility group (HFD) and low NDF digestibility group (LFD), respectively. Rumen contents were collected for total microbial DNA extraction. The V4 region of the bacterial 16S rRNA gene was amplified using universal primers of bacteria and sequenced using high-throughput sequencer. The sequences were mainly analysed by QIIME 1.8.0.
Results: A total of 18,694 operational taxonomic units were obtained, within 81.98% belonged to bacteria, 6.64% belonged to archaea and 11.38% was unassigned microorganisms. Bacteroidetes, Firmicutes, and Proteobacteria were the predominant microbial phyla in both groups. At the genus level, the relative abundance of fifteen microorganisms were significantly higher (p<0.05) and six microorganisms were extremely significantly higher (p<0.01) in LFD than HFD. Overall, 176 core shared genera were identified in the two groups. The relative abundance of 2 phyla, 5 classes, 10 orders, 13 families and 15 genera had a negative correlation with NDF digestibility, but only the relative abundance of Pyramidobacter had a positive correlation with NDF digestibility.
Conclusion: There were substantial differences in NDF digestibility among the individual goats, and the NDF digestibility had significant correlation with the relative abundance of some ruminal microorganisms.The authors would like to thank the National Key R&D Program of China (grant number: 2017YFD0502005) and Sichuan Beef Cattle Innovation Team (grant number: 035Z389) for the financial support
Bovine Tuberculosis in Britain and Ireland – A Perfect Storm? the Confluence of Potential Ecological and Epidemiological Impediments to Controlling a Chronic Infectious Disease
Get PDFPublication history: Accepted - 3 May 2018; Published online - 5 June 2018Successful eradication schemes for bovine tuberculosis (bTB) have been implemented
in a number of European and other countries over the last 50 years. However, the
islands of Britain and Ireland remain a significant aberration to this trend, with the recent
exception of Scotland. Why have eradication schemes failed within these countries, while
apparently similar programs have been successful elsewhere? While significant socioeconomic and political factors have been discussed elsewhere as key determinants of
disease eradication, here we review some of the potential ecological and epidemiological
constraints that are present in these islands relative to other parts of Europe. We argue
that the convergence of these potential factors may interact additively to diminish the
potential of the present control programs to achieve eradication. Issues identified include
heterogeneity of diagnostic testing approaches, the presence of an abundant wildlife
reservoir of infection and the challenge of sustainably managing this risk effectively;
the nature, size, density and network structure of cattle farming; potential effects of
Mycobacterium bovis strain heterogeneity on disease transmission dynamics; possible
impacts of concurrent endemic infections on the disclosure of truly infected animals;
climatological differences and change coupled with environmental contamination. We
further argue that control and eradication of this complex disease may benefit from an
ecosystem level approach to management. We hope that this perspective can stimulate a
new conversation about the many factors potentially impacting bTB eradication schemes
in Britain and Ireland and possibly stimulate new research in the areas identified.Authors' work is funded by the Department of Agriculture, Environment and Rural Affairs, Northern Ireland (DAERA-NI
Assessments of Composite and Discrete Sampling Approaches for Water Quality Monitoring
Get PDFPublication history: Accepted - 26 March 2018; Published online - 14 April 2018.Achieving an operational compromise between spatial coverage and temporal resolution in national scale river water quality monitoring is a major challenge for regulatory authorities, particularly where chemical concentrations are hydrologically dependent. The efficacy of flow-weighted composite sampling (FWCS) approaches for total phosphorus (TP) sampling (n = 26–52 analysed samples per year), previously applied in monitoring programmes in Norway, Sweden and Denmark, and which account for low to high flow discharges, was assessed by repeated simulated sampling on high resolution TP data. These data were collected in three research catchments in Ireland over the period 2010–13 covering a base-flow index range of 0.38 to 0.69. Comparisons of load estimates were also made with discrete (set time interval) daily and sub-daily sampling approaches (n = 365 to >1200 analysed samples per year). For all years and all sites a proxy of the Norwegian sampling approach, which is based on re-forecasting discharge for each 2-week deployment, proved most stable (median TP load estimates of 87–98%). Danish and Swedish approaches, using long-term flow records to set a flow constant, were only slightly less effective (median load estimates of 64–102% and 80–96%, respectively). Though TP load estimates over repeated iterations were more accurate using the discrete approaches, particularly the 24/7 approach (one sample every 7 h in a 24 bottle sampler - median % load estimates of 93–100%), composite load estimates were more stable, due to the integration of multiple small samples (n = 100–588) over a deployment
Exploring the oxidative, antimicrobial and genomic properties of Campylobacter jejuni strains isolated from poultry
Get PDFPublication history: Accepted - 13 June 2018; Published online - 19 June 2018.Campylobacter jejuni is the leading cause of food-borne bacterial enteritis in humans, with contaminated poultry
products considered the main source of infection. To survive the food chain, C. jejuni utilizes multiple defense
mechanisms that counter oxidative and aerobic stresses. In this study, we phenotypically characterised 63 C.
jejuni strains with oxidative stress survival and antimicrobial susceptibility testing to investigate correlations
between these two phenotypes against the source of the strains and the presence of the MarR regulators RrpA
and RrpB which have a role in regulating the response to oxidative and aerobic stress. C. jejuni strains isolated
from meat and neck skin displayed the highest resistance to oxidative stress. In addition, C. jejuni strains that
have an rrpA+rrpB− profile exhibit increased resistance to oxidative stress and to antimicrobials. Here we establish
a preliminary link between the distribution of RrpA and RrpB and the increased resistance to antimicrobials.
This study provides insight into how the genotypic make up of C. jejuni can influence the ability of
the bacterium to survive within areas of high oxygen stress, such as the food chain, and subsequently can have a
potential negative impact on human health.This work was partially supported by the Ministry of Science and
Innovation (AGL2009-07550; AGL2012-39028) and by the
Autonomous Community of Madrid, Spain (S2009/AGR-1489; S2013/
ABI-2747). M. Ugarte-Ruiz was supported by the FPU programme (AP2009-
1747) from the Spanish Ministry of Education, Culture and Sports
during her stage at London School of Hygiene & Tropical Medicine
(2013)
Multi-country loss rates of honey bee colonies during winter 2016/2017 from the COLOSS survey
Get PDFPublication history: Accepted - 5 March 2018; Published online - 8 May 2018.In this short note we present comparable loss rates of honey bee colonies during winter 2016/2017 from 27 European
countries plus Algeria, Israel and Mexico, obtained with the COLOSS questionnaire. The 14,813 beekeepers providing
valid loss data collectively wintered 425,762 colonies, and reported 21,887 (5.1%, 95% confidence interval 5.0–5.3%)
colonies with unsolvable queen problems and 60,227 (14.1%, 95% CI 13.8–14.4%) dead colonies after winter. Additionally
we asked for colonies lost due to natural disaster, which made up another 6,903 colonies (1.6%, 95% CI 1.5–1.7%).
This results in an overall loss rate of 20.9% (95% CI 20.6–21.3%) of honey bee colonies during winter 2016/2017, with
marked differences among countries. The overall analysis showed that small operations suffered higher losses than larger
ones (p < 0.001). Overall migratory beekeeping had no significant effect on the risk of winter loss, though there
was an effect in several countries. A table is presented giving detailed results from 30 countries. A map is also included,
showing relative risk of colony winter loss at regional level.The authors are also grateful to various national funding
sources for their support of some of the monitoring surveys
[including, in the Republic of Serbia, MPNTR-RS, through grant
number III46002]. The authors acknowledge the financial support
by the University of Graz for open access publication
Decision support beyond total savings—Eligibility and potential savings for individual participants from changes in the national surveillance strategy for bovine viral diarrhoea (BVD) in Ireland
Get PDFPublication history: Accepted - 9 April 2018; Published online - 11 April 2018Surveillance and management of livestock diseases is often evaluated with reference to expected sector-wide costs. In contrast, we calculate losses or savings for individual herd owners of a change in monitoring strategy during a national cattle disease eradication programme: bovine viral diarrhoea (BVD) in Ireland. The alternative strategy differs in how the disease is identified; by its sample- rather than census-based approach; and by its greater cost per test. We examined the costs faced by each breeding herd if testing were conducted using serology on a sample of young stock, in contrast to the current method of tissue-tag testing of all newborn calves. Following best knowledge of the likely costs, the following input values were used: i) €2.50 per test for tissue-tag testing and €7.66 for serology, ii) serology conducted on a sample of 10 young stock per management group from either the 6–12 month or 9–18 month cohorts; iii) 3 scenarios for the number of management groups: one per herd (M∞), one per 100 cows (M100) and one per 50 cows (M50). We found that many herds would often not be able to supply a suitable sample of young stock for serology or would face higher testing costs than when using tissue tag testing. The largest number (25%) of herds would benefit from participating in the change if sampling were done in October. These could annually save between €2.1 million under M∞ and €0.8 million under M50 (€108 - €49 per herd). However, analysing herd-level data we found that 90% of all Irish breeding herds would save less than €1.42 per cow or €99 in total per annum under M∞, and €0.59 per cow or €36 in total under M50. In a sensitivity analysis, we allowed serology costs to vary between €2 and €10 per animal. Herds at the 10 t h percentile of most savings made from switching would save at most €155 (M∞ at €2 per serology test) but would not save anything under M50 at costs ≥ €10. We conclude that, under these assumptions, the expected reduction in testing costs for the majority of beneficiaries would barely outweigh the practical implications of the strategy switch or the risks to the eradication programme associated with sample based surveillance. This study does not assess the cost-effectiveness of alternatives post-eradication.This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors
Achieving Sustainable Phosphorus Use in Food Systems through Circularisation
Get PDFPublication history: Accepted - 28 May 2018; Published - 30 May 2018.The notion of a phosphorus (P) circular economy provides the philosophy, framework,
and opportunity to enable food production systems to become more efficient, sustainable,
and resilient to a future P scarcity or sudden price shock. Whilst P recovery and recycling are central
strategies for closing the P cycle, additional gains in environmental performance of food systems
can be obtained by further minimising the amounts of P (a) introduced into the food system by
lowering system P demand and (b) lost from the system by utilising legacy P stores in the landscape.
This minimisation is an important cascading component of circularisation because it reduces the
amounts of P circulating in the system, the amounts of P required to be recycled/recovered and
the storage of unused P in the landscape, whilst maintaining agricultural output. The potential
for circularisation and minimisation depends on regional differences in these P flow dynamics.
We consider incremental and transformative management interventions towards P minimisation
within circular economies, and how these might be tempered by the need to deliver a range of
ecosystem services. These interventions move away from current production philosophies based on
risk-averse, insurance-based farming, and current consumption patterns which have little regard
for their environmental impact. We argue that a greater focus on P minimisation and circularisation
should catalyse different actors and sectors in the food chain to embrace P sustainability and should
empower future research needs to provide the confidence for them to do so without sacrificing future
regional food security.This paper was produced as part of the RePhoKUs project (The role of phosphorus in the
sustainability and resilience of the UK food system) funded by BBSRC, ESRC, NERC, and the Scottish Government
under the UK Global Food Security research programme (Grant No. BB/R005842/1)
Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future
Get PDFPublication history: Accepted - 23 August 2018; Published - 25 September 2018.The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi,
methanogenic archaea and phages. These microbes interact closely to breakdown
plant material that cannot be digested by humans, whilst providing metabolic energy
to the host and, in the case of archaea, producing methane. Consequently, ruminants
produce meat and milk, which are rich in high-quality protein, vitamins and minerals,
and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy
global protein demand is necessary, despite limited land availability, and whilst ensuring
environmental impact is minimized. Although challenging, these goals can be met,
but depend on our understanding of the rumen microbiome. Attempts to manipulate
the rumen microbiome to benefit global agricultural challenges have been ongoing for
decades with limited success, mostly due to the lack of a detailed understanding of this
microbiome and our limited ability to culture most of these microbes outside the rumen.
The potential to manipulate the rumen microbiome and meet global livestock challenges
through animal breeding and introduction of dietary interventions during early life have
recently emerged as promising new technologies. Our inability to phenotype ruminants
in a high-throughput manner has also hampered progress, although the recent increase
in “omic” data may allow further development of mathematical models and rumen
microbial gene biomarkers as proxies. Advances in computational tools, high-throughput
sequencing technologies and cultivation-independent “omics” approaches continue to
revolutionize our understanding of the rumen microbiome. This will ultimately provide the
knowledge framework needed to solve current and future ruminant livestock challenges.SH, DM, MP, RM-T, SW, IT, HS, JE, SK, GA, and CC
acknowledge the support of ERA-net gas co-fund for funding
(Project name: RumenPredict). SH, HM and CC acknowledge
support from BBSRC (BBL/L026716/1 and BBL/L026716/2)
and a British Council Newton Institutional Links funding
(Grant 172629373). IM acknowledges funding from the
European Research Council under the European Union’s
Horizon 2020 research and innovation program (Grant 640384).
JE acknowledges funding from an EU H2020 Marie Curie
Fellowship (706899). CC, AK-S, and EH were supported by
the Biotechnology and Biological Sciences Research Council
(Grants BBS/OS/GC/000011B and BBS/E/W/0012843D). CN
and OM acknowledge the support of the British Council
Newton Institutional Links funding (Grant 216425215). SRUC
receives financial support from the Scottish Government’s Rural
and Environment Science and Analytical Services Division
(RESAS). RD and RR acknowledge financial support from the
Biotechnology and Biological Sciences Research Council (BBSRC
BB/N01720X/1). DY-R and AB acknowledge funding from
MINECO, Spain (Grant AGL2017-86938-R). GS acknowledges
funding from the U.S. Department of Agriculture National
Institute of Food and Agriculture foundational (Grant 2015-
67015-23246). EP acknowledges funding from CNPq (Grant
401590/2014-3). All authors are also members of the Global
Research Alliance Rumen Microbial Genomics network