Variations in Microbial Diversity and Metabolite Profiles of Female Landrace Finishing Pigs With Distinct Feed Efficiency.
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ABSTRACT:
SUBMITTER: Wang Z
PROVIDER: S-EPMC8299115 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Feed efficiency (FE) appears to vary even within closely related pigs, and may be partly affected by the diversity in the composition and function of gut microbes. To investigate the components and functional differences of gut microbiota of low and high FE pigs, high throughput sequencing and de novo metagenomics were performed on pig cecal contents. Pigs were selected in pairs with low and high feed conversion ratio. The microorganisms of individuals with different FE were clustered according to diversity. The genus Prevotella was the most enriched in both groups, and the abundance of species Prevotella sp. CAG:604 was significantly increased in low efficiency individuals compared to that in animals showing high efficiency. In contrast, other differential species, including lactic acid bacteria, were all enriched in the group with good feeding characteristics. Functional analysis based on the Kyoto Encyclopedia of Genes and Genomes databases demonstrated that differential genes for the metabolism of carbohydrates were most abundant in both groups, but pathways of pyruvate-related metabolism were more intense in pigs with higher FE. All these data indicated that the microbial environment was closely related to the growth traits of pigs, and regulating microbial composition could aid developing strategies to improve FE for pigs.
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Project description:The goal of this study was to evaluate the microbial communities in the gut and feces from female finishing Landrace pigs with high and low feed conversion ratio (FCR) by 16S rRNA gene amplicon sequencing. Many potential biomarkers can distinguish between high and low FCR groups in the duodenum, ileum, cecum, colon, and rectum, according to linear discriminant analysis effect sizes. The relative abundance of microbes were tested by Mann-Whitney test between the high and low FCR groups in different organs: Campylobacter, Prevotella and Sphaerochaeta were different in the duodenum (P < 0.05); Sanguibacter, Kingella and Anaeroplasma in jejunum; Anaeroplasma, Arthrobacter, Kingella, Megasphaera and SMB53 in the ileum; Butyricicoccus, Campylobacter, Mitsuokella, and Coprobacillus in the cecum; Lactococcus and Peptococcus in the colon; Staphylococcus in the rectum; and Rothia in feces. The prevalence of microbial genera in certain locations could potentially be used as biomarkers to distinguish between high and low FCR. Functional prediction clustering analysis suggested that bacteria in the hindgut mainly participated in carbohydrate metabolism and amino acid metabolism, and different in the relative abundance of metabolic pathways, as predicted from the microbial taxa present, were identified by comparing the high and low groups of each location. The results may provide insights for the alteration of the intestinal microbial communities to improve the growth rate of pigs.
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Project description:Interactions among genomic loci have often been overlooked in genome-wide association studies, revealing the combinatorial effects of variants on phenotype or disease manifestation. Unexplained genetic variance, interactions among causal genes of small effects, and biological pathways could be identified using a network biology approach. The main objective of this study was to determine the genome-wide epistatic variants affecting feed efficiency traits [feed conversion ratio (FCR) and residual feed intake (RFI)] based on weighted interaction SNP hub (WISH-R) method. Herein, we detected highly interconnected epistatic SNP modules, pathways, and potential biomarkers for the FCR and RFI in Duroc and Landrace purebreds considering the whole population, and separately for low and high feed efficient groups. Highly interacting SNP modules in Duroc (1,247 SNPs) and Landrace (1,215 SNPs) across the population and for low feed efficient (Duroc-80 SNPs, Landrace-146 SNPs) and high feed efficient group (Duroc-198 SNPs, Landrace-232 SNPs) for FCR and RFI were identified. Gene and pathway analyses identified ABL1, MAP3K4, MAP3K5, SEMA6A, KITLG, and KAT2B from chromosomes 1, 2, 5, and 13 underlying ErbB, Ras, Rap1, thyroid hormone, axon guidance pathways in Duroc. GABBR2, GNA12, and PRKCG genes from chromosomes 1, 3, and 6 pointed towards thyroid hormone, cGMP-PKG and cAMP pathways in Landrace. From Duroc low feed efficient group, the TPK1 gene was found involved with thiamine metabolism, whereas PARD6G, DLG2, CRB1 were involved with the hippo signaling pathway in high feed efficient group. PLOD1 and SETD7 genes were involved with lysine degradation in low feed efficient group in Landrace, while high feed efficient group pointed to genes underpinning valine, leucine, isoleucine degradation, and fatty acid elongation. Some SNPs and genes identified are known for their association with feed efficiency, others are novel and potentially provide new avenues for further research. Further validation of epistatic SNPs and genes identified here in a larger cohort would help to establish a framework for modelling epistatic variance in future methods of genomic prediction, increasing the accuracy of estimated genetic merit for FE and helping the pig breeding industry.
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Project description:Feed efficiency (FE) traits in pigs are of utmost economic importance. Genetic improvement of FE related traits in pigs might significantly reduce production cost and energy consumption. Hence, our study aimed at identifying SNPs and candidate genes associated with FE related traits, including feed conversion ratio (FCR), average daily gain (ADG), average daily feed intake (ADFI), and residual feed intake (RFI). A genome-wide association study (GWAS) was performed for the four FE related traits in 296 Landrace pigs genotyped with PorcineSNP50 BeadChip. Two different single-trait methods, single SNP linear model GWAS (LM-GWAS) and single-step GWAS (ssGWAS), were implemented. Our results showed that the two methods showed high consistency with respect to SNP identification. A total of 32 common significant SNPs associated with the four FE related traits were identified. Bioinformatics analysis revealed eight common QTL regions, of which three QTL regions related to ADFI and RFI traits were overlapped. Gene ontology analysis revealed six common candidate genes (PRELID2, GPER1, PDX1, TEX2, PLCL2, ICAM2) relevant for the four FE related traits. These genes are involved in the processes of fat synthesis and decomposition, lipid transport process, insulin metabolism, among others. Our results provide, new insights into the genetic mechanisms and candidate function genes of FE related traits in pigs. However, further investigations to validate these results are warranted.
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Project description:The present study investigated the effects of fermented complete feed (FCF) on fecal microbial composition during the grower-finisher period. A total of 20 pigs (Duroc × Landrace × Yorkshire, 48.74± 1.49 kg) were divided randomly into two groups: the CN group (pigs fed with a basal diet) and the FCF group (pigs fed with FCF). After a 60-day trial period, 3 pigs with middle-weight from each treatment were selected for fecal sampling and fecal microbiota analysis. The results showed that the FCF significantly increased operational taxonomic units (OUT) numbers, alpha diversity (Simpson index and Shannon index), and beta diversity, which means that FCF increased the fecal microbiota diversity. At the phylum level, the abundance of Tenericutes, Spirochaetae, Verrucomicrobia, and Cyanobacteria were changed in pigs fed with FCF; and at the genus level, the abundance of Christensenellaceae_R-7_group, Treponema_2, Ruminococcaceae_UCG-005, Prevotellaceae_UCG-003, Phascolarctobacterium, Roseburia, and Prevotella_9 were changed in pigs fed with FCF. The linear discriminant analysis effect size (LEfSe) analysis showed that Roseburia and Prevotella_9 genera were increased, while Tenericutes phyla and Streptococcus, Christensenellaceae_R-7_group, and Lactobacillus genera were decreased in the FCF group compared to the CN group. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) results predicted that the relative abundance of infectious diseases: parasitic associated genes, xenobiotics biodegradation, and metabolism-associated genes were significantly reduced in the FCF group when compared with the CN group, and the relative abundance of signal transduction associated genes, amino acid metabolism-related genes, and replication and repair associated genes were significantly higher in the FCF group when compared with the CN group. In addition, the relative abundance of transport and catabolism-associated genes, membrane transport-associated genes, and biosynthesis of other secondary metabolite-associated genes tended to be higher in the FCF group when compared with the CN group; and the relative abundance of immune diseases associated genes tended to be lower in the FCF group when compared with the CN group. In conclusion, the FCF influenced the alpha and beta diversity of the fecal microbiota of pigs.
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Project description:The optimum proportion of water for preparing liquid feed to maximize growth and optimize feed efficiency (FE) in growing-finishing pigs is not known. The aim of the current study was, using an automatic short-trough sensor liquid feeding system, to identify the water-to-feed ratio at which growth was maximized and feed was most efficiently converted to live-weight. Two experiments were conducted in which four commercially used water-to-feed ratios were fed: 2.4:1, 3.0:1, 3.5:1, and 4.1:1 on a dry matter (DM) basis (the equivalent of 2:1, 2.5:1, 3.0:1, and 3.5:1 on a fresh matter basis). Each experiment comprised 216 pigs, penned in groups of 6 same sex (entire male and female) pigs/pen with a total of 9 pen replicates per treatment. The first experiment lasted 62 days (from 40.6 to 102.2 kg at slaughter) and the second experiment was for 76 days (from 31.8 to 119.6 kg at slaughter). Overall, in Exp. 1, FE was 0.421, 0.420, 0.453, and 0.448 (s.e. 0.0081 g/g; P < 0.01) for pigs fed at 2.4:1, 3.0:1, 3.5:1, and 4.1:1, respectively. Overall, in Exp. 2, average daily gain was 1,233, 1,206, 1,211, and 1,177 (s.e. 12.7 g/day; P < 0.05) for pigs fed at 2.4:1, 3.0:1, 3.5:1, and 4.1:1, respectively. At slaughter, in Exp. 1, dressing percentage was 76.7, 76.6, 76.7, and 75.8 (s.e. 0.17%; P < 0.01) for 2.4:1, 3.0:1, 3.5:1, and 4.1:1, respectively. There were no differences between treatment groups for DM, organic matter, nitrogen, gross energy, or ash digestibilities. These findings indicate that liquid feeding a diet prepared at a water-to-feed ratio of 3.5:1 maximizes FE of growing-finishing pigs without negatively affecting dressing percentage. Therefore, preparing liquid feed for growing-finishing pigs at a water-to-feed ratio of 3.5:1 DM is our recommendation for a short-trough liquid feeding system.
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Project description:An experiment was conducted to examine the effect of meal frequency on growth performance, nutrient digestibility, carcass quality, and lipid metabolism in growing−finishing pigs. Sixty-four Duroc × Landrace × Yorkshire barrows and gilts (26.40 ± 2.10 kg initial body weight) were used in a 112-d experiment in a randomized complete blocked design. The two treatments were the free-access feed group (FA) and the three meals per day group (M3), respectively. The result showed that the average daily feed intake (ADFI) and F: G of the FA group were significantly higher than that in the M3 group during the whole experiment (p < 0.05). Reducing meal frequency also decreased the concentration of triglycerides and urea nitrogen but increased the concentration of insulin and free fatty acids in the blood (p < 0.05). Reducing meal frequency decreased compositions of backfat, belly, and fatty pieces but increased compositions of ham, longissimus muscle, and lean pieces in the carcass (p < 0.05). Greater enzyme activities of ME and FAS and higher mRNA expression of FAS and PPARγ were found in the LM of FA pigs compared with M3 pigs (p < 0.05). In summary, a lower meal frequency improves feed efficiency by regulating lipid metabolism and reducing fat deposition.
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Project description:Interactions among genomic loci have often been overlooked in genome-wide association studies, revealing the combinatorial effects of variants on phenotype or disease manifestation. Unexplained genetic variance, interactions amongst causal genes of small effects, and biological pathways could be identified using a network biology approach. The main objective of this study was to determine the genome-wide epistatic variants affecting feed efficiency traits [feed conversion ratio (FCR) and residual feed intake (RFI)] based on weighted interaction SNP hub (WISH-R) method. Herein, we detected highly interconnected epistatic SNP modules, pathways, and potential biomarkers for the FCR and RFI in Duroc and Landrace purebreds considering the whole population, and separately for low and high feed efficient groups. Highly interacting SNP modules in Duroc (1,247 SNPs) and Landrace (1,215 SNPs) across the population and for low feed efficient (Duroc - 80 SNPs, Landrace - 146 SNPs) and high feed efficient group (Duroc - 198 SNPs, Landrace - 232 SNPs) for FCR and RFI were identified. Gene and pathway analyses identified ABL1, MAP3K4, MAP3K5, SEMA6A, KITLG, and KAT2B from chromosomes 1, 2, 5, and 13 underlying ErbB, Ras, Rap1, thyroid hormone, axon guidance pathways in Duroc. GABBR2, GNA12, and PRKCG genes from chromosomes 1, 3, and 6 pointed towards thyroid hormone, cGMP-PKG and cAMP pathways in Landrace. From Duroc low feed efficient group, the TPK1 gene was found involved with thiamine metabolism, whereas PARD6G, DLG2, CRB1 were involved with the hippo signaling pathway in high feed efficient group. PLOD1 and SETD7 genes were involved with lysine degradation in low feed efficient group in Landrace, while high feed efficient group pointed to genes underpinning valine, leucine, isoleucine degradation, and fatty acid elongation. Some SNPs and genes identified are known for their association with feed efficiency, others are novel and potentially provide new avenues for further research. Further validation of epistatic SNPs and genes identified here in a larger cohort would help to establish a framework for modelling epistatic variance in future methods of genomic prediction, increasing the accuracy of estimated genetic merit for FE and helping the pig breeding industry.
2020-03-23 | GSE144064 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2018-12-21 | GSE109335 | GEO
Project description:Improving feed efficiency (FE) is a major goal of pig breeding, reducing production costs and providing sustainability to the pig industry. Reliable predictors for FE could assist pig producers. We carried out untargeted blood metabolite profiling in uncastrated males from Danbred Duroc (n?=?59) and Danbred Landrace (n?=?50) pigs at the beginning and end of a FE testing phase to identify biomarkers and biological processes underlying FE and related traits. By applying linear modeling and clustering analyses coupled with WGCNA framework, we identified 102 and 73 relevant metabolites in Duroc and Landrace based on two sampling time points. Among them, choline and pyridoxamine were hub metabolites in Duroc in early testing phase, while, acetoacetate, cholesterol sulfate, xanthine, and deoxyuridine were identified in the end of testing. In Landrace, cholesterol sulfate, thiamine, L-methionine, chenodeoxycholate were identified at early testing phase, while, D-glutamate, pyridoxamine, deoxycytidine, and L-2-aminoadipate were found at the end of testing. Validation of these results in larger populations could establish FE prediction using metabolomics biomarkers. We conclude that it is possible to identify a link between blood metabolite profiles and FE. These results could lead to improved nutrient utilization, reduced production costs, and increased FE.
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