2. Improving feed efficiency by understanding the intestinal bacterial network in pigs and poultry
Dr. Stefan G. Buzoianu
Dr. Peadar G. Lawlor
Ms. Ursula McCormack
Moorepark Research Centre,
Teagasc, Ireland
Dr. Barbara Metzler-Zebeli
Mr. Andor Molnar
Ms. Janine Scholz
University of Veterinary Medicine Vienna

3. Introduction

4. ECO-FCE overview Feb 2013 – Feb 2017 17 partners 7 WPs
Overall objectives
improve food security by optimising the feed efficiency in pigs and broilers without negatively affecting animal welfare and meat quality
reduce the ecological footprint of the pig and broiler production systems
WP 3 objective
to examine the gut structure, function, microbiota and metagenomics in animals divergent for feed efficiency

5. RFI Work Package 3 Intestinal structure & function Intestinal health
Intestinal microbiota
Animal performance
Genetics
Genomics
RFI
Low
Medium
High
Health & welfare
Meat quality

6. Determination of feed efficiency
Selection of high and low feed efficient animals - based on Residual Feed Intake
Residual Feed Intake (RFI) = difference between observed and predicted feed intake, with lower RFI values indicating greater energy efficiency
RFI = FI [a + b1 * BW b2 * BWG]
Where a is the intercept and b1 and b2 are partial regression coefficients of feed intake (FI) on BW0.75 and body weight gain (BWG), respectively.
Other measures of feed efficiency
Feed efficiency = gain (g) / feed intake (g)
Feed conversion ratio (FCR) = feed intake (g) / gain (g)
RG = BWG [a + b1 * BW b2 * FI]
RIG = (RG/SD RG) - (RFI/SD RFI)

7. Feed efficiency in monogastric livestock species
Genetics
Diet
Rearing environment
Age
Gut commensal microbiota
Substantial variation in feed efficiency between individual animals.
Great variation in gut commensal microbiota between individuals.

8. Role of the intestinal microbiota
Benefits to the host
intestinal maturation
inhibition of pathogen growth
nutrient salvaging
detoxification
production of vitamins
Costs to the host
competition for nutrients
immune activation
production of toxins
opportunistic
toxin reabsorption
mucolytic activity

9. Effect of host microbiota on host metabolism and hormone secretion
Intestinal microbiota can redirect energy partitioning to adipose tissue and reduce fatty acid oxidation.
Implications for feed use efficiency and carcass composition in livestock animals?
Bäckhed (2011) Ann Nutr Metab 58(suppl 2):44

10. Effect of gut microbiota composition on body weight
Obese humans & mice:
Firmicutes 
Bacteroidetes 
Low-calorie diet
Firmicutes 
Bacteroidetes 
wikipedia.org
Actinobacteria 
Bacteroidetes 
no difference in Firmicutes
Changes in Lactobacillus and Bifidobacterium species
Methanogenic archaea 
Requena et al. (2013) Trends Food Sci Tech 34:44
Meat-producing monogastric livestock species are young, fast growing and lean animals
Are the key players the same as in human obesity models ?

11. Chickens

12. Diet-related cecal microbiota and performance in male chickens
Caecal microbial communities by diet
Caecal microbial communities identified as being from birds with improved performance or poorer performance
Diet is the most influencing factor affecting feed efficiency.
Torok et al. (2011) AEM 77: 5868

13. Batch to batch variation in caecal microbiota of chickens
3 different batches of chickens
PCA plot of caecal microbiota. The plot is based on between groups (trials) analysis.
Very different microbiota profiles across chicken batches
Very different feed use efficiencies across chicken batches
Stanley et al. (2013) PloS ONE 8(12): e84290
High variation in caecal microbiota partly due to lack of colonisation of the chickens by maternally derived bacteria
High hygiene levels in modern commercial hatcheries remove natural bacteria
Environmental microbiota from transport boxes, first feed and staff people

14. Fecal community of high and low feed efficient broiler chickens
Singh et al. (2014) J Appl Genet 55: 145

15. Characterisation of differences in gut microbiota and gut function of chickens with good and poor feed efficiency
Experimental design:
2 partner institutions (AFBI & Vetmeduni) performed identical chicken experiments with 3 batches of 50/64 chicks
Similar chicken genetic: Cobb 500FF
Similar maize-soybean meal diets (starter, grower, and finisher diets)
No in-feed antibiotics and any other gut health-related additives
Chickens were individually housed
Best and worst feed efficient chickens were identified using Residual Feed Intake
On day 42, samples were collected for:
Ileal and caecal digesta for metagenomics and microbial metabolites
Tissue of duodenum, jejunum, ileum, caeca for gut function and structure

16. Residual feed intake of good and poor feed efficient broiler chickens
Great variation in residual feed intake and thus in feed use efficiency.

17. Microbial metagenome of good and poor feed efficient chickens
Shotgun sequencing using MiSeq Technology (Illumina)
Under construction

18. Influencing factors: Host genome or gut microbiota ?
Jejunal electrophysiological characteristics of good and poor feed efficient broiler chickens
Gut electrophysiology was performed using Ussing chamber technique.
Tissue originated from the distal jejunum.
Good feed efficient females showed lower tissue resistance, higher conductance and short-circuit current indicating a higher ion flux and permeability of the jejunal mucosa
Influencing factors: Host genome or gut microbiota ?

19. Pigs

20. Literature Little data available in pigs
↓ Bacteroidetes & ↑ Firmicutes in obese pigs (Pedersen et al., 2013)
↑ Firmicutes & ↓ β-Proteobacteria in ERS-fed pigs (Haenen et al., 2013)
Protein, CHO and lipid metabolic pathways affected by intestinal microbial profile
mice (Antunes et al., 2011)
pigs (Mulder et al., 2009)

21. Screening on feed efficiency in pigs
Teagasc × 3 AFBI Vetmeduni
46 litters
Common genetics
Common & site-specific boars
Common diets
Common protocols
Pigs divergent for RFI
weaning
d 42
d 84
d 112
F – faecal
I – ileal digesta
C – caecal digesta
P – performance P P F F
F I C

22. Compositional analysis
Microbiota profiling
d 0 (weaning)
d 42
d 84
d 126
d 139 P P P P F F F F
F I C
Compositional analysis
16S rRNA gene sequencing
Functionality
Shotgun metagenomics
Illumina
F – faecal; I – ileal digesta; C – caecal digesta; P – performance

23. Progress on microbiota profiling
Samples collected
DNA extracted
16S rRNA gene sequencing – results being analysed
Shotgun metagenomics
samples being prepared
results ~ Oct 2014

24. Manipulation of GIT microbial profile
inoculation
Nutrition
Management
Low RFI
Additives

25. Inoculation with faecal inoculum from good feed converters
Anaerobically processed
diluted 1:6
strained
centrifuged (6000 × G for 15 minutes)
frozen at -80°C in 10% glycerol
No inoculum
Single inoculation
Multiple inoculation
Inoculum
No inoculum
Single inoculation
Multiple inoculation
Sows
Offspring

26. Nutritional intervention
Optimum strategy – inoculum
Prebiotics – alone or in combination
Monitoring and sampling of offspring through their lifetime
performance
health
intestinal microbiota

27. Acknowledgements
ECO-FCE has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration (FP7 2007/2013) under grant agreement No
Teagasc Walsh Fellowship Programme

28. Thank you

30. ECO-FCE Gut structure, function, microbiota and metagenomics
Hypothesis:
It is assumed that the gut microbiome of pigs and broiler chickens with good and poor feed use efficiency differs in key members, thereby influencing the intestinal and metabolic host response, production efficiency and host health.
Objectives:
To enhance our understanding of the interactions between gut microbiome and host genome in pigs and chickens. This task will be achieved by employing cutting-edge 16S rRNA-specific and shotgun metagenomics.
Using this improved understanding, strategies to improve feed conversion efficiency through gut microbiome manipulation in embryonic and subsequent developmental stages will be developed.

31. Nutrient digestibility
Interactions between gut microbiome and host physiology and health
Mucus secretion
NF-kB
Barrier function
Mucosal immunity
Commensal
microbiota
Growth &
feed efficiency
Gut morphology
Nutrient digestibility
Nutrient
transporters
Bäckhed (2011) Ann Nutr Metab 58(suppl 2): 44; Twarziok et al. (2014) Mol Inf 33: 171