Feed-efficient pigs exhibit molecular patterns allowing a timely circulation of hormones and nutrients

Gut-brain bidirectional determination in regulating the residual feed intake of small-sized meat ducks

The gut-brain axis is essential in maintaining the homeostasis of neuronal system, endocrine system, and intestinal microbiota in both the afferent and efferent directions. This axis is considered to be a key mechanism that regulates feed efficiency (FE). This study aimed to investigate the regulatory mechanisms of gut-brain axis-related genes on the residual feed intake (RFI) in H-strain small-sized meat ducks. A total of 500 ducks with similar initial BW (635.2 ± 15.1 g) were selected and reared in the same experimental facility until slaughter at 42 d of age. RFI was calculated from the average daily gain (ADG), average daily feed intake (ADFI), and metabolic body weight (MBW0.75). Thirty high-RFI (H-RFI) and 30 low-RFI (L-RFI) birds were selected for further evaluation of growth performance, carcass characteristics, and blood biochemical parameter measurements. Six L-RFI and 6 H-RFI birds were then subjected to hypothalamic transcriptomic and cecal microbial sequencing analyses. Results indicated that L-RFI birds exhibited lower production performance (ADFI, FCR, and RFI) and blood biochemical indices (total cholesterol and ghrelin content) compared with H-RFI birds (P < 0.05). Gene expression differed significantly between the L-RFI and H-RFI birds, with 70 upregulated and 50 downregulated genes. The bacterial communities of L-RFI birds showed higher abundances of Bacteroides, Bifidobacterium, and Lactococcus, and lower abundances of Erysipelatoclostridium, Parasutterella, Fournierella, and Blautia compared with H-RFI birds (P < 0.05). Interactive analysis revealed bacterial communities associated with FE were significantly correlated with hypothalamic genes (P < 0.05), for example, Bacteroides was positively correlated with DGKH and LIPT2, while negatively correlated with CAPN9, GABRD, and PDE1A. Bifidobacterium showed significant correlations with ATP2A3, CALHM6, and TMEM121B. Overall, RFI was a crucial indicator of FE, regulated by interactions between brain gene expression and gut microbiota through cAMP signaling, neuroactive ligand-receptor interaction, and calcium signaling pathways. Notably, increased expression of hypothalamic genes and abundance of carbohydrate-utilization microbiota in L-RFI meat ducks improved FE by enhancing energy metabolism and volatile fatty acids absorption.

Genetic architecture and correlations between the gut microbiome and gut gene transcription in Chinook salmon (Oncorhynchus tshawytscha)

Population divergence through selection can drive local adaptation in natural populations which has implications for the effective restoration of declining and extirpated populations. However, adaptation to local environmental conditions is complicated when both the host and its associated microbiomes must respond via co-evolutionary change. Nevertheless, for adaptation to occur through selection, variation in both host and microbiome traits should include additive genetic effects. Here we focus on host immune function and quantify factors affecting variation in gut immune gene transcription and gut bacterial community composition in early life-stage Chinook salmon (Oncorhynchus tshawytscha). Specifically, we utilized a replicated factorial breeding design to determine the genetic architecture (sire, dam and sire-by-dam interaction) of gut immune gene transcription and microbiome composition. Furthermore, we explored correlations between host gut gene transcription and microbiota composition. Gene transcription was quantified using nanofluidic qPCR arrays (22 target genes) and microbiota composition using 16 S rRNA gene (V5-V6) amplicon sequencing. We discovered limited but significant genetic architecture in gut microbiota composition and transcriptional profiles. We also identified significant correlations between gut gene transcription and microbiota composition, highlighting potential mechanisms for functional interactions between the two. Overall, this study provides support for the co-evolution of host immune function and their gut microbiota in Chinook salmon, a species recognized as locally adapted. Thus, the inclusion of immune gene transcription profile and gut microbiome composition as factors in the development of conservation and commercial rearing practices may provide new and more effective approaches to captive rearing.

Animal board invited review: Heritability of nitrogen use efficiency in fattening pigs: Current state and possible directions

Pork, an important component of human nutrition worldwide, contributes considerably to anthropogenic nitrogen and greenhouse gas emissions. Reducing the environmental impact of pig production is therefore essential. This can be achieved through system-level strategies, such as optimising resource use, improving manure management and recycling leftovers from human food production, and at the individual animal level by maintaining pig health and fine-tuning dietary protein levels to individual requirements. Breeding, coupled with nutritional strategies, offers a lasting solution to improve nitrogen use efficiency (NUE) - the ratio of nitrogen retained in the body to nitrogen ingested. With a heritability as high as 0.54, incorporating NUE into breeding programmes appears promising. Nitrogen use efficiency involves multiple tissues and metabolic processes, and is influenced by the environment and individual animal characteristics, including its genetic background. Heritable genetic variation in NUE may therefore occur in many different processes, including the central nervous regulation of feed intake, the endocrine system, the gastrointestinal tract where digestion and absorption take place, and the composition of the gut microbiome. An animal's postabsorptive protein metabolism might also harbour important genetic variation, especially in the maintenance requirements of tissues and organs. Precise phenotyping, although challenging and costly, is essential for successful breeding. Various measurement techniques, such as imaging techniques and mechanistic models, are being explored for their potential in genetic analysis. Despite the difficulties in phenotyping, some studies have estimated the heritability and genetic correlations of NUE. These studies suggest that direct selection for NUE is more effective than indirect methods through feed efficiency. The complexity of NUE indicates a polygenic trait architecture, which has been confirmed by genome-wide association studies that have been unable to identify significant quantitative trait loci. Building sufficiently large reference populations to train genomic prediction models is an important next step. However, this will require the development of truly high-throughput phenotyping methods. In conclusion, breeding pigs with higher NUE is both feasible and necessary but will require increased efforts in high-throughput phenotyping and improved genome annotation.

A Co-Culture Model of IPEC-J2 and Swine PBMC to Study the Responsiveness of Intestinal Epithelial Cells: The Regulatory Effect of Arginine Deprivation

Simple Summary

The interest in amino acids comes from their involvement in research on alternative strategies for the utilization of antibiotics on farms. Among several substances used to replace antibiotics, there is arginine, an essential amino acid in newborns and piglets. This amino acid has a protective role in intestinal immune cells and improves intestinal immunity. The purpose of this research was to define a co-culture model, in which intestinal epithelial cells can communicate with peripheral blood mononuclear cells (PBMC) to deepen the effects of arginine deprivation on intestinal epithelial cells over time. The main finding was that the lack of arginine highly impacts on intestinal and immune cells by way of immuno-regulation mediated by the expression of pro- and anti-inflammatory cytokines. The use of this experimental model could allow us to investigate the impact of and interactions between specific nutrients and the complex intestinal environment and, in addition, to assess feed additives to improve health and animal production.

Abstract

Arginine is a semi-essential amino acid, supplementation with which induces a reduction of intestinal damage and an improvement of intestinal immunity in weaned piglets, but the mechanism is not yet entirely clear. The aim of this study was to characterise a co-culture model by measuring changes in gene expression over time (24 and 48 h) in intestinal IPEC-J2 cells in the presence of immune cells activated with phytohemagglutinin and, consequently, to assess the effectiveness of arginine deprivation or supplementation in modulating the expression of certain cytokines related to the regulation of intestinal cells’ function. The main results show the crucial role of arginine in the viability/proliferation of intestinal cells evaluated by an MTT assay, and in the positive regulation of the expression of pro-inflammatory (TNF-α, IL-1α, IL-6, IL-8) and anti-inflammatory (TGF-β) cytokines. This experimental model could be important for analysing and clarifying the role of nutritional conditions in intestinal immune cells’ functionality and reactivity in pigs as well as the mechanisms of the intestinal defence system. Among the potential applications of our in vitro model of interaction between IEC and the immune system there is the possibility of studying the effect of feed additives to improve animal health and production.

Variations in Microbial Diversity and Metabolite Profiles of Female Landrace Finishing Pigs With Distinct Feed Efficiency

To enhance pig production, feed efficiency (FE) should be improved; however, the mechanisms by which gut microbes affect FE in pigs have not been fully elucidated. To investigate the differences between the composition and functionality of the gut microbiota associated with low and high FE, microbial compositions were characterized using 16S rRNA sequencing, functional annotations were performed by shotgun metagenomics, and metabolomic profiles were created by GC-TOF-MS from female Landrace finishing pigs with low and high feed conversion ratios (FCRs). Lactobacillus was enriched in the gut microbiota of individuals with low FCRs (and thus high FE), while Prevotella abundance was significantly higher in individuals with high FCRs (and thus low FE). This may be linked to carbohydrate consumption and incomplete digestion. The activity of pathways involved in the metabolism of cofactors and vitamins was greater in pigs with lower FE. We also identified differences in pyruvate-related metabolism, including phenylalanine and lysine metabolism. This suggests that pyruvate metabolism is closely related to microbial fermentation in the colon, which in turn affects glycolysis. This study deepens our understanding of how gut microbiota are related to pig growth traits, and how regulating microbial composition could aid in improving porcine FE. However, these results need to be validated using a larger pig cohort in the future.

Genome-wide association and transcriptome studies identify candidate genes and pathways for feed conversion ratio in pigs

Background

The feed conversion ratio (FCR) is an important productive trait that greatly affects profits in the pig industry. Elucidating the genetic mechanisms underpinning FCR may promote more efficient improvement of FCR through artificial selection. In this study, we integrated a genome-wide association study (GWAS) with transcriptome analyses of different tissues in Yorkshire pigs (YY) with the aim of identifying key genes and signalling pathways associated with FCR.

Results

A total of 61 significant single nucleotide polymorphisms (SNPs) were detected by GWAS in YY. All of these SNPs were located on porcine chromosome (SSC) 5, and the covered region was considered a quantitative trait locus (QTL) region for FCR. Some genes distributed around these significant SNPs were considered as candidates for regulating FCR, including TPH2, FAR2, IRAK3, YARS2, GRIP1, FRS2, CNOT2 and TRHDE. According to transcriptome analyses in the hypothalamus, TPH2 exhibits the potential to regulate intestinal motility through serotonergic synapse and oxytocin signalling pathways. In addition, GRIP1 may be involved in glutamatergic and GABAergic signalling pathways, which regulate FCR by affecting appetite in pigs. Moreover, GRIP1, FRS2, CNOT2, and TRHDE may regulate metabolism in various tissues through a thyroid hormone signalling pathway.

Conclusions

Based on the results from GWAS and transcriptome analyses, the TPH2, GRIP1, FRS2, TRHDE, and CNOT2 genes were considered candidate genes for regulating FCR in Yorkshire pigs. These findings improve the understanding of the genetic mechanisms of FCR and may help optimize the design of breeding schemes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07570-w.

Impact of Intestinal Microbiota on Growth and Feed Efficiency in Pigs: A Review

This review summarises the evidence for a link between the porcine intestinal microbiota and growth and feed efficiency (FE), and suggests microbiota-targeted strategies to improve productivity. However, there are challenges in identifying reliable microbial predictors of host phenotype; environmental factors impact the microbe–host interplay, sequential differences along the intestine result in segment-specific FE- and growth-associated taxa/functionality, and it is often difficult to distinguish cause and effect. However, bacterial taxa involved in nutrient processing and energy harvest, and those with anti-inflammatory effects, are consistently linked with improved productivity. In particular, evidence is emerging for an association of Treponema and methanogens such as Methanobrevibacter in the small and large intestines and Lactobacillus in the large intestine with a leaner phenotype and/or improved FE. Bacterial carbohydrate and/or lipid metabolism pathways are also generally enriched in the large intestine of leaner pigs and/or those with better growth/FE. Possible microbial signalling routes linked to superior growth and FE include increased intestinal propionate production and reduced inflammatory response. In summary, the bacterial taxa and/or metabolic pathways identified here could be used as biomarkers for FE/growth in pigs, the taxa exploited as probiotics or the taxa/functionality manipulated via dietary/breeding strategies in order to improve productivity in pigs.

Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle

Long non-coding RNA (lncRNA) can regulate several aspects of gene expression, being associated with complex phenotypes in humans and livestock species. In taurine beef cattle, recent evidence points to the involvement of lncRNA in feed efficiency (FE), a proxy for increased productivity and sustainability. Here, we hypothesized specific regulatory roles of lncRNA in FE of indicine cattle. Using RNA-Seq data from the liver, muscle, hypothalamus, pituitary gland and adrenal gland from Nellore bulls with divergent FE, we submitted new transcripts to a series of filters to confidently predict lncRNA. Then, we identified lncRNA that were differentially expressed (DE) and/or key regulators of FE. Finally, we explored lncRNA genomic location and interactions with miRNA and mRNA to infer potential function. We were able to identify 126 relevant lncRNA for FE in Bos indicus, some with high homology to previously identified lncRNA in Bos taurus and some possible specific regulators of FE in indicine cattle. Moreover, lncRNA identified here were linked to previously described mechanisms related to FE in hypothalamus-pituitary-adrenal axis and are expected to help elucidate this complex phenotype. This study contributes to expanding the catalogue of lncRNA, particularly in indicine cattle, and identifies candidates for further studies in animal selection and management.

Host-Microbiota Interactions in Ileum and Caecum of Pigs Divergent in Feed Efficiency Contribute to Nutrient Utilization

The composition of the intestinal microbiota plays an important role in the digestion and utilization of nutrients and for gut health. Low-fiber diets stimulate digestion and absorption processes, predominantly in the upper region of the gastrointestinal tract, thereby increasing the conversion of feed into body weight. As a consequence, the chemical composition of digesta after duodenal and jejunal absorption processes and passage has a limited complexity affecting colonization and molecular profiles of enterocytes in the hind gut. To decipher ileal and caecal microbial ecosystems and host transcriptional profiles that are beneficial for effective use of the remaining nutrients, pigs differing in feeding efficiency were studied. Biological functions that were consistently enriched at both the gene and microbiota levels comprise immunity-related processes, which ensure the integrity of the gastrointestinal tract. In addition, the differential abundance of certain genera, including Rothia, Subdoligranulu, Leeia and Cellulosilyticum, reflects the establishment of a microbial profile that supports the digestion of endogenously indigestible dietary components in highly feed-efficient pigs. Overall, the results indicate the potential to promote these beneficial functions and further improve feed efficiency through manipulation of dietary and probiotic strategies.

Indirect genetic effects on the relationships between production and feeding behaviour traits in growing Duroc pigs

Performance and feeding behaviour traits in growing pigs could be affected by social interaction effects when animals are raised in group. So, properly knowing the genetic correlations between direct and social interaction effects among performance and feeding behaviour traits could improve the accuracy of the genetic evaluations. Our aim was to explore the role of feeding behaviour traits (FBT) and indirect genetic effects (IGEs) in the genetic evaluations of growing pigs. Thus, genetic parameters were estimated for production traits (PT): average daily gain, average daily feed consumption, feed conversion ratio and backfat thickness; as well as for FBT: average daily feeding rate, average daily feeding frequency, average daily occupation time and average daily time between consecutive visits. Traits were recorded in 1144 Duroc pigs during the fattening period. Two bivariate models were fitted: classic animal model and an animal model fitting IGE. Estimations were done following Bayesian procedures. Heritability estimates obtained with classic animal model for all studied traits were medium-high. The additional heritable variation captured by IGE supposed that the ratios of total genetic variance to phenotypic variance (T2) were higher than the heritability estimates obtained with the classic model, except for occupation time trait, when a lower value (0.20 ± 0.19) was estimated. This is due to a high and negative correlation between IGE and direct genetic effects (DGEs) of this particular trait (-0.78 ± 0.27). Results from classic animal model do not evidence a clear role of FBT to improve the accuracy of breeding value predictions for PT; only average daily feeding rate seems to show a positive correlation (around 0.50 to 0.60) with average daily gain, average daily feed consumption and backfat thickness. However, when IGE model was fitted, the number of estimates of genetic correlations between FBT and PT showing a relevant magnitude increased, generally for the correlations between IGE of FBT and DGE of PT; or particularly for the correlations between IGE of average daily feeding frequency, and the IGE of all the PT, except average daily gain. Thus, in evaluations using the animal model with IGE fitted, the inclusion of FBT could aid the improvement of the accuracy of breeding value predictions for PT. This is a consequence of the improved genetic relationships between traits that can be fitted when considering such models.

A Transcriptome Analysis Identifies Biological Pathways and Candidate Genes for Feed Efficiency in DLY Pigs

Feed cost accounts for approximately 65–75% of overall commercial pork production costs. Therefore, improving the feed efficiency of pig production is important. In this study, 12 individuals with either extremely high (HE) or low (LE) feed efficiency were selected from 225 Duroc × (Landrace × Yorkshire) (DLY) pigs. After the pigs were slaughtered, we collected small intestine mucosal tissue. Next, RNA sequencing (RNA-seq) analysis was used to reveal the presence and quantity of genes expressed between these extremely HE- and LE-groups. We found 433 significantly differentially expressed genes (DEGs) between the HE- and LE-groups. Of these, 389 and 44 DEGs were upregulated and downregulated in the HE-group, respectively. An enrichment analysis showed that the DEGs were mainly enriched in functions related to apical plasma membrane composition, transporter activity, transport process and hormone regulation of digestion and absorption. Protein network interaction and gene function analyses revealed that SLC2A2 was an important candidate gene for FE in pigs, which may give us a deeper understanding of the mechanism of feed efficiency. Furthermore, some significant DEGs identified in the current study could be incorporated into artificial selection programs for increased feeding efficiency in pigs.

Investigation of muscle transcriptomes using gradient boosting machine learning identifies molecular predictors of feed efficiency in growing pigs

Background

Improving feed efficiency (FE) is a major challenge in pig production. This complex trait is characterized by a high variability. Therefore, the identification of predictors of FE may be a relevant strategy to reduce phenotyping efforts in breeding and selection programs. The aim of this study was to investigate the suitability of expressed muscle genes in prediction of FE traits in growing pigs. The approach considered different transcriptomics experiments to cover a large range of FE values and identify reliable predictors.

Results

Microarrays data were obtained from longissimus muscles of two lines divergently selected for residual feed intake (RFI). Pigs (n = 71) from three experiments belonged to generations 6 to 8 of selection, were fed either a diet with a standard composition or a diet rich in fiber and lipids, received feed ad libitum or at restricted level, and weighed between 80 and 115 kg at slaughter. For each pig, breeding value for RFI was estimated (RFI-BV), and feed conversion ratio (FCR) and energy-based feed conversion ratio (FCRe) were calculated during the test periods. Gradient boosting algorithms were used on the merged muscle transcriptomes to identify very important predictors of FE traits. About 20,405 annotated molecular probes were commonly expressed in longissimus muscle across experiments. Six to 267 expressed muscle genes covering a variety of biological processes were found as important predictors for RFI-BV (R² = 0.63–0.65), FCR (R² = 0.61–0.70) and FCRe (R² = 0.49–0.52). The error of prediction was less than 8% for FCR. Altogether, 56 predictors were common to RFI-BV and FCR. Expression levels of 24 target genes were further measured by qPCR. Linear regression confirmed the good accuracy of combining mRNA levels of these genes to fit FE traits (RFI-BV: R² = 0.73, FRC: R² = 0.76; FCRe: R² = 0.75). Stepwise regression procedure highlighted 10 genes (FKBP5, MUM1, AKAP12, FYN, TMED3, PHKB, TGF, SOCS6, ILR4, and FRAS1) in a linear combination predicting FCR and FCRe. In addition, FKBP5 and expression levels of five other genes (IGF2, SERINC3, CSRNP3, EZR and RPL16) significantly contributed to RFI-BV.

Conclusion

It was possible to identify few genes expressed in muscle that might be reliable predictors of feed efficiency.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-6010-9) contains supplementary material, which is available to authorized users.