This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
Improving feed efficiency by
understanding the intestinal bacterial
network in pigs and poultry
Dr. Barbara Metzler-Zebeli
Mr. Andor Molnar
Ms. Janine Scholz
Dr. Stefan G. Buzoianu
Dr. Peadar G. Lawlor
Ms. Ursula McCormack
University of Veterinary Medicine
Vienna
Moorepark Research Centre,
Teagasc, Ireland
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
Introduction
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
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
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
Work Package 3
Intestinal
structure &
function
Genomics
Low
Genetics
Intestinal
health
RFI
High
Medium
Health &
welfare
Meat quality
Animal
performance
Intestinal
microbiota
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
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 * BW0.75 + 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 * BW0.75 + b2 * FI]
RIG = (RG/SD RG) - (RFI/SD RFI)
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
Feed efficiency in monogastric livestock species
Feed
efficiency
Genetics
Diet
Rearing
environment
Age
Gut commensal microbiota
Substantial variation in feed efficiency between individual animals.
Great variation in gut commensal microbiota between individuals.
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
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
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
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
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
Effect of gut microbiota composition on body
weight
Obese humans & mice:
Firmicutes 
Bacteroidetes 
Firmicutes 
Bacteroidetes 
wikipedia.org
Low-calorie diet
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 ?
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
Chickens
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
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
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
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
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
Fecal community of high and low feed efficient
broiler chickens
High efficient chickens
Low efficient chickens
7
18
12
Proteobacteria (%)
79
Firmicutes (%)
52
Bacteroidetes (%)
28
Singh et al. (2014) J Appl Genet 55: 145
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
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
Weighing
d1
d7
Weighing
d14
Ammonia
emission
Metagenomics
(faeces) (faeces)
Metagenomics
(faeces)
Metagenomics
(faeces)
Weighing
Weighing
Weighing
d21
d28
d35
Weighing
d42
Daily 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
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
Residual feed intake of good and poor feed efficient
broiler chickens
300
200
Residual feed intake
Male
Female
(g)
100
Great variation in residual
feed intake and thus in
feed use efficiency.
0
-100
-200
Feed efficiency, P< 0.001
Batch, P>0.1
-300
Good
Average
Poor
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
Microbial metagenome of good and poor feed efficient
chickens
Shotgun sequencing using MiSeq Technology
(Illumina)
Under construction
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
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.
Tissue resistance (Ω/cm2)
200
a
a
Females
Tissue conductance (mS x cm2)
14
1.6
a
Females
12
Feed efficiency, P=0.020
150
Feed efficiency, P=0.002
b
b
8
100
a
Females
1.4
Feed efficiency, P=0.076
1.2
10
b
Short-circuit current (Isc; µEq/cm2 x hour)
ab
1.0
b
0.8
6
0.6
4
50
0.4
2
0
0.2
0.0
0
Good
Average
Poor
Good
Average
Poor
Good
Average
Poor
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 ?
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
Pigs
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
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)
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
Screening on feed efficiency in pigs
46 litters
Pigs
divergent
for RFI
Common
genetics
Teagasc × 3
AFBI
Vetmeduni
Common
& sitespecific
boars
Common
protocols
Common
diets
weaning
d 42
d 84
P
F
d 112
P
F – faecal
I – ileal digesta
C – caecal digesta
P – performance
This project has received funding from the European Union‘s Seventh Framework Programme for
F
research, technological development and demonstration under grant agreement No. 311794.
FIC
Microbiota profiling
d 0 (weaning)
d 42
P
F
d 84
P
F
Compositional analysis
16S rRNA gene sequencing
d 126
P
F
Illumina
F
d 139
P
Functionality
Shotgun metagenomics
F – faecal; I – ileal digesta; C – caecal digesta; P – performance
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
F IC
Progress on microbiota profiling
• Samples collected
• DNA extracted
• 16S rRNA gene sequencing – results being analysed
• Shotgun metagenomics
• samples being prepared
• results ~ Oct 2014
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
Manipulation of GIT microbial profile
Additives
Low RFI
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
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
No
inoculum
Single
inoculation
Sows
Multiple
inoculation
Offspring
Inoculum
No
inoculum
Single
inoculation
Multiple
inoculation
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
Nutritional intervention
• Optimum strategy – inoculum
• Prebiotics – alone or in combination
• Monitoring and sampling of offspring through their lifetime
• performance
• health
• intestinal microbiota
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
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. 311794
• Teagasc Walsh Fellowship Programme
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
Thank you
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
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:
1. 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.
2. Using this improved understanding, strategies to improve feed conversion efficiency
through gut microbiome manipulation in embryonic and subsequent developmental
stages will be developed.
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
Interactions between gut microbiome and host
physiology and health
NF-kB
This project has received funding from the European Union‘s Seventh Framework Programme for
research, technological development and demonstration under grant agreement No. 311794.
Bäckhed (2011) Ann Nutr Metab 58(suppl 2): 44; Twarziok et al. (2014) Mol Inf 33: 171