2Improving feed efficiency by understanding the intestinal bacterial network in pigs and poultry Dr. Stefan G. BuzoianuDr. Peadar G. LawlorMs. Ursula McCormackMoorepark Research Centre,Teagasc, IrelandDr. Barbara Metzler-ZebeliMr. Andor MolnarMs. Janine ScholzUniversity of Veterinary Medicine Vienna
4ECO-FCE overview Feb 2013 – Feb 2017 17 partners 7 WPs Overall objectivesimprove food security by optimising the feed efficiency in pigs and broilers without negatively affecting animal welfare and meat qualityreduce the ecological footprint of the pig and broiler production systemsWP 3 objectiveto examine the gut structure, function, microbiota and metagenomics in animals divergent for feed efficiency
5RFI Work Package 3 Intestinal structure & function Intestinal health Intestinal microbiotaAnimal performanceGeneticsGenomicsRFILowMediumHighHealth & welfareMeat quality
6Determination of feed efficiency Selection of high and low feed efficient animals - based on Residual Feed IntakeResidual Feed Intake (RFI) = difference between observed and predicted feed intake, with lower RFI values indicating greater energy efficiencyRFI = 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 efficiencyFeed 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)
7Feed efficiency in monogastric livestock species GeneticsDietRearing environmentAgeGut commensal microbiotaSubstantial variation in feed efficiency between individual animals.Great variation in gut commensal microbiota between individuals.
8Role of the intestinal microbiota Benefits to the hostintestinal maturationinhibition of pathogen growthnutrient salvagingdetoxificationproduction of vitaminsCosts to the hostcompetition for nutrientsimmune activationproduction of toxinsopportunistictoxin reabsorptionmucolytic activity
9Effect 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
10Effect of gut microbiota composition on body weight Obese humans & mice:Firmicutes Bacteroidetes Low-calorie dietFirmicutes Bacteroidetes wikipedia.orgActinobacteria Bacteroidetes no difference in FirmicutesChanges in Lactobacillus and Bifidobacterium speciesMethanogenic archaea Requena et al. (2013) Trends Food Sci Tech 34:44Meat-producing monogastric livestock species are young, fast growing and lean animalsAre the key players the same as in human obesity models ?
12Diet-related cecal microbiota and performance in male chickens Caecal microbial communities by dietCaecal microbial communities identified as being from birds with improved performance or poorer performanceDiet is the most influencing factor affecting feed efficiency.Torok et al. (2011) AEM 77: 5868
13Batch to batch variation in caecal microbiota of chickens 3 different batches of chickensPCA plot of caecal microbiota. The plot is based on between groups (trials) analysis.Very different microbiota profiles across chicken batchesVery different feed use efficiencies across chicken batchesStanley et al. (2013) PloS ONE 8(12): e84290High variation in caecal microbiota partly due to lack of colonisation of the chickens by maternally derived bacteriaHigh hygiene levels in modern commercial hatcheries remove natural bacteriaEnvironmental microbiota from transport boxes, first feed and staff people
14Fecal community of high and low feed efficient broiler chickens Singh et al. (2014) J Appl Genet 55: 145
15Characterisation of differences in gut microbiota and gut function of chickens with good and poor feed efficiencyExperimental design:2 partner institutions (AFBI & Vetmeduni) performed identical chicken experiments with 3 batches of 50/64 chicksSimilar chicken genetic: Cobb 500FFSimilar maize-soybean meal diets (starter, grower, and finisher diets)No in-feed antibiotics and any other gut health-related additivesChickens were individually housedBest and worst feed efficient chickens were identified using Residual Feed IntakeOn day 42, samples were collected for:Ileal and caecal digesta for metagenomics and microbial metabolitesTissue of duodenum, jejunum, ileum, caeca for gut function and structure
16Residual feed intake of good and poor feed efficient broiler chickens Great variation in residual feed intake and thus in feed use efficiency.
17Microbial metagenome of good and poor feed efficient chickens Shotgun sequencing using MiSeq Technology (Illumina)Under construction
18Influencing factors: Host genome or gut microbiota ? Jejunal electrophysiological characteristics of good and poor feed efficient broiler chickensGut 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 mucosaInfluencing factors: Host genome or gut microbiota ?
20Literature 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 profilemice (Antunes et al., 2011)pigs (Mulder et al., 2009)
21Screening on feed efficiency in pigs Teagasc × 3 AFBI Vetmeduni46 littersCommon geneticsCommon & site-specific boarsCommon dietsCommon protocolsPigs divergent for RFIweaningd 42d 84d 112F – faecalI – ileal digestaC – caecal digestaP – performancePPFFF I C
22Compositional analysis Microbiota profilingd 0 (weaning)d 42d 84d 126d 139PPPPFFFFF I CCompositional analysis16S rRNA gene sequencingFunctionalityShotgun metagenomicsIlluminaF – faecal; I – ileal digesta; C – caecal digesta; P – performance
23Progress on microbiota profiling Samples collectedDNA extracted16S rRNA gene sequencing – results being analysedShotgun metagenomicssamples being preparedresults ~ Oct 2014
24Manipulation of GIT microbial profile inoculationNutritionManagementLow RFIAdditives
25Inoculation with faecal inoculum from good feed converters Anaerobically processeddiluted 1:6strainedcentrifuged (6000 × G for 15 minutes)frozen at -80°C in 10% glycerolNo inoculumSingle inoculationMultiple inoculationInoculumNo inoculumSingle inoculationMultiple inoculationSowsOffspring
26Nutritional intervention Optimum strategy – inoculumPrebiotics – alone or in combinationMonitoring and sampling of offspring through their lifetimeperformancehealthintestinal microbiota
27AcknowledgementsECO-FCE has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration (FP7 2007/2013) under grant agreement NoTeagasc Walsh Fellowship Programme
30ECO-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.
31Nutrient digestibility Interactions between gut microbiome and host physiology and healthMucus secretionNF-kBBarrier functionMucosal immunityCommensalmicrobiotaGrowth &feed efficiencyGut morphologyNutrient digestibilityNutrienttransportersBäckhed (2011) Ann Nutr Metab 58(suppl 2): 44; Twarziok et al. (2014) Mol Inf 33: 171