The gastric isthmus from D+ and D- broiler lines divergently selected for digestion efficiency shows histological and morphological differences

Implication of digestive functions and microbiota in the establishment of muscle glycogen differences between divergent lines for ultimate pH

Both the quality of chicken meat and the quality of chicks are influenced by the level of breast muscle glycogen reserves. In order to study the role of digestive metabolism in establishing this muscular phenotype, we compared two divergent chicken lines for the ultimate pH (pHu) of the breast meat, a proxy for glycogen reserves. Males aged 4 weeks had twice the breast muscle glycogen content in the pHu- line (low pHu) than in the pHu +  line (high pHu). The increase in glycogen reserves (pHu-) was associated with a higher relative weight of the proventriculus and gizzard, as well as better apparent ileal digestibility of nitrogen and calcium. The diversity of the cecal microbiota was comparable, but three bacterial genera (Lachnospira, Lachnospiraceae UCG-010, Caproiciproducens) varied between the lines. The differences observed could lead to down-regulation of carbon fixation in prokaryotes and of the citrate cycle in the pHu + line. RNA-seq analysis of the jejunum, the major site of nutrient absorption, revealed 149 genes differentially expressed (DE) between the lines, including several genes linked to immunity, hormonal response and circadian rhythms that are less expressed in pHu + animals. Others involved in cell migration and proliferation, and more generally tissue morphogenesis, also differed between the lines. Among the DE genes, several co-localized with Quantitative Trait Loci (QTL) controlling pHu and selection signatures identified in the divergent lines, such as the gene coding for ghrelin, a hormone regulating appetite.

A comparative study on the effect of limestone particle size on performance, ileal digestibility of calcium and phosphorus, and bone characteristics in broilers and pullets

1. The effects of limestone particle size on growth performance, gastrointestinal tract (GIT) traits, ileal morphology, duodenal gene expression of calbindin, apparent ileal digestibility coefficients (AIDC) of calcium (Ca) and phosphorus (P) and tibia characteristics in broilers and pullets were assessed in broilers and pullets. These birds have different growth rates and likely different responses to parameters, such as particle size.2. A total of 240 chicks aged one day, 120 Ross 308 female broilers, and 120 Hy-Line pullets were allocated randomly into four treatments in a 2 × 2 factorial arrangement with two bird types (broilers vs. pullets) and two limestone particle sizes (<0.5 mm versus 1-2 mm) to give six replicates containing 10 chicks in each from 1 to 21 d of age.3. Feed intake and weight gain were greater (P < 0.001) and feed per gain (FCR) was better (P < 0.001) in broilers compared to pullets from 1 to 21 d of age. Greater villus width (P < 0.01), villus height (P < 0.001) and crypt depth (P < 0.01) were seen for broilers compared to pullets.4. Pullets fed coarse Ca particles had higher calbindin gene expression at 21 d of age (P = 0.05). Both AIDC of Ca and P were higher (P < 0.001) in broilers compared to pullets. The AIDC of Ca from 0.463 to 0.516 was increased (P < 0.05) by feeding coarse limestone particles. A significant interaction was found between bird type and limestone particle size (P < 0.01), where pullets fed coarse Ca particles had higher bone P concentration in tibia than broilers.5. Broilers had better ileum absorptive capacity and growth performance compared to pullets. The AIDC of Ca and P was higher in broilers than in pullets. Increased limestone particle size elevated villus height, AIDC of Ca and concentration of P in the tibia.

Comparative analysis of the characteristics of digestive organs in broiler chickens with different feed efficiencies

Improving feed efficiency is one of the main goals of chicken breeding and production. The function of the digestive system, where feed is digested and nutrients are absorbed, is closely related to feed efficiency. However, the association between feed efficiency and the development of different digestive organs in chickens remains unclear. Here, we investigated the individual feed efficiency of 207 broilers during the fast-growing period with an electronic feeder and examined the characteristics of 8 organs of their digestive system (the liver, bile, proventriculus, gizzard, duodenum, jejunum, ileum, and cecum) at market age. Both the feed conversion ratio (FCR) and residual feed intake (RFI) were significantly negatively correlated with the gizzard weight (GW) and significantly positively correlated with the relative weight of the liver (RLW). Additionally, we found an obvious negative relationship between the FCR and cecal length (CL). A two-tailed t test further confirmed these correlation analysis results. Specifically, compared to birds with the lowest feed efficiencies, the GW of broilers with the highest feed efficiencies (the lowest FCR or RFI) was 22.74% and 17.97% higher, respectively. The RLW of chickens with the highest feed efficiencies was 10.82 to 13.73% less than that of chickens with the lowest feed efficiencies. In addition, we found that increased CL (5.42–12.09%) was significantly associated with better feed efficiency. Thus, our study showed that the feed efficiency of broilers was related to the development of the gizzard, liver, and cecum. These findings provide new insight into the genetic and physiological regulation of feed efficiency in broilers.

Phenotypic timeline of gastrointestinal tract development in broilers divergently selected for digestive efficiency

Sustainability of poultry farming relies on the development of more efficient and autonomous production systems in terms of feed supply. This implies a better integration of adaptive traits in breeding programs, including digestive efficiency, to favor the use of a wider variety of feedstuffs. The objective of the study was to better characterize the kinetics of development of the digestive tract in broilers, in relationship with digestive efficiency by measuring various digestive parameters as well as serum color. Absolute and relative growth of gastrointestinal tract organs were compared between 2 divergent chicken lines selected on digestive efficiency (AMEn) during 7 wk of development. We show that as early as 7 d of age, these 2 lines differs for several organs developments and that these differences remain visible later on. In addition, the allometry of the gizzard and intestine segments is different between the 2 lines, with efficient birds putting more effort in the upper part of the digestive tract during postnatal development and less-efficient birds putting more effort in the lower part of the gastrointestinal tract. Interestingly, we also showed that differences in serum pigmentation, which is a good biomarker for digestive capacity, could be a convenient diagnostic tool to discriminate between chickens with high or low digestive efficiency at early stages of development. In conclusion, this study showed that selection of chickens for AMEn had large impacts in gastrointestinal development including at early stages and is a valuable resource for further studies on the genetic and physiological control of the response of the animal to feed variations.

Broilers divergently selected for digestibility differ for their digestive microbial ecosystems

Improving the digestive efficiency of broiler chickens (Gallus gallus) could reduce organic waste, increase the use of alternative feed not used for human consumption and reduce the impact of feed in production costs. By selecting chicken lines divergently for their digestive efficiency, we showed previously that digestive efficiency is under genetic control and that the two resulting divergent lines, D+ (high digestive efficiency or “digestibility +”) and D- (low digestive efficiency or “digestibility -”), also differ for the abundance of specific bacteria in their caeca. Here we perform a more extensive census of the bacteria present in the digestive microbiota of 60 chickens selected for their low apparent metabolizable energy corrected for nitrogen balance (AMEn-) or high (AMEn+) digestive efficiency in a [D+ x D-] F8 progeny of 200 individuals. We sequenced the 16S rRNA genes of the ileal, jejunal and caecal microbiotas, and compared the compositions and predicted functions of microbiotas from the different intestinal segments for 20 AMEn+ and 19 AMEn- birds. The intestinal segment of origin was the main factor structuring the samples. The caecal microbiota was the most impacted by the differences in digestive efficiency, with 41 bacterial species with abundances differing between highly and poorly efficient birds. Furthermore, we predicted that the caecal microbiota of efficient birds might be enriched in genes contributing to the degradation of short chain fatty acids (SCFA) from non-starch polysaccharides. These results confirm the impact of the genetic selection led on digestibility on the caecal microbiota taxonomic composition. They open the way toward the identification of specific, causal genes of the host controlling variations in the abundances of bacterial taxons.

Functional genomics of the digestive tract in broilers

Background

The sustainability of poultry farming relies on the development of more efficient and autonomous production systems in terms of feed supply. This implies a better integration of adaptive traits in breeding programs, including digestive efficiency, in order to favor the use of a wider variety of feedstuffs. The aim of the project was to improve the understanding of genes involved in digestive functions by characterizing the transcriptome of different sections of the digestive tract: the junction between the proventriculus and the gizzard, the gizzard, the gastroduodenal junction, and the jejunum.

Results

Total RNA from the four tissues were sequenced on a HiSeq2500 for six 23-day-old chickens from a second generation (F2) cross between two lines that were divergent for their digestive efficiency (D+/D-). Bioinformatics and biostatistics analyses of the RNA-seq data showed a total of 11,040 differentially expressed transcripts between the four tissues. In total, seven clusters of genes with markedly different expression profiles were identified. Functional analysis on gene groups was performed using “Gene Ontology” and semantic similarity. It showed a significant enrichment of body immune defenses in the jejunum, and an enrichment of transcriptional activity in the gizzard. Moreover, an interesting enrichment for neurohormonal control of muscle contraction was found for the two gizzard’s junctions.

Conclusion

This analysis allows us to draw the first molecular portrait of the different sections of the digestive tract, which will serve as a basis for future studies on the genetic and physiological control of the response of the animal to feed variations.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5344-z) contains supplementary material, which is available to authorized users.

Relationships between digestive efficiency and metabolomic profiles of serum and intestinal contents in chickens

The increasing cost of conventional feedstuffs has bolstered interest in genetic selection for digestive efficiency (DE), a component of feed efficiency, assessed by apparent metabolisable energy corrected to zero nitrogen retention (AMEn). However, its measurement is time-consuming and constraining, and its relationship with metabolic efficiency poorly understood. To simplify selection for this trait, we searched for indirect metabolic biomarkers through an analysis of the serum metabolome using nuclear magnetic resonance (¹H NMR). A partial least squares (PLS) model including six amino acids and two derivatives from butyrate predicted 59% of AMEn variability. Moreover, to increase our knowledge of the molecular mechanisms controlling DE, we investigated ¹H NMR metabolomes of ileal, caecal, and serum contents by fitting canonical sparse PLS. This analysis revealed strong associations between metabolites and DE. Models based on the ileal, caecal, and serum metabolome respectively explained 77%, 78%, and 74% of the variability of AMEn and its constitutive components (utilisation of starch, lipids, and nitrogen). In our conditions, the metabolites presenting the strongest associations with AMEn were proline in the serum, fumarate in the ileum and glucose in caeca. This study shows that serum metabolomics offers new opportunities to predict chicken DE.

Impact of Selection for Digestive Efficiency on Microbiota Composition in the Chicken

Objectives

Feed efficiency and its digestive component, digestive efficiency, are key factors in the environmental impact and economic output of poultry production. The interaction between the host and intestinal microbiota has a crucial role in the determination of the ability of the bird to digest its food and to the birds’ feed efficiency. We therefore investigated the phenotypic and genetic relationships between birds’ efficiency and the composition of the cecal microbiota in a F2 cross between broiler lines divergently selected for their high or low digestive efficiency.

Methods

Analyses were performed on 144 birds with extreme feed efficiency values at 3 weeks, with feed conversion values of 1.41±0.05 and 2.02±0.04 in the efficient and non-efficient groups, respectively. The total numbers of Lactobacillus, L. salivarius, L. crispatus, C. coccoides, C. leptum and E. coli per gram of cecal content were measured.

Results

The two groups mainly differed in larger counts of Lactobacillus, L. salivarius and E. coli in less efficient birds. The equilibrium between bacterial groups was also affected, efficient birds showing higher C. leptum, C. coccoides and L. salivarius to E. coli ratios. The heritability of the composition of microbiota was also estimated and L. crispatus, C. leptum, and C. coccoides to E. coli ratios were moderately but significantly heritable (0.16 to 0.24). The coefficient of fecal digestive use of dry matter was genetically and positively correlated with L. crispatus, C. leptum, C. coccoides (0.50 to 0.76) and negatively with E. coli (-0.66). Lipid digestibility was negatively correlated with E. coli (-0.64), and AMEn positively correlated with C. coccoides and with the C. coccoides to Lactobacillus ratio (0.48 to 0.64). We also detected 14 Quantitative Trait Loci (QTL) for microbiota on the host genome, mostly on C. leptum and Lactobacillus. The QTL for C. leptum on GGA6 was close to genome-wide significance. This region mainly includes genes involved in anti-inflammatory responses and in the motility of the gastrointestinal tract.