Feeding Frequency Modulates the Intestinal Transcriptome Without Affecting the Gut Microbiota in Pigs With the Same Daily Feed Intake
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ABSTRACT:
SUBMITTER: Zhang H
PROVIDER: S-EPMC8589026 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND: Feed efficiency is one of the major components determining costs of animal production. Residual feed intake (RFI) is defined as the difference between the observed and the expected feed intake given a certain production. Residual feed intake 1 (RFI1) was calculated based on regression of individual daily feed intake (DFI) on initial test weight and average daily gain. Residual feed intake 2 (RFI2) was as RFI1 except it was also regressed with respect to backfat (BF). It has been shown to be a sensitive and accurate measure for feed efficiency in livestock but knowledge of the genomic regions and mechanisms affecting RFI in pigs is lacking. The study aimed to identify genetic markers and candidate genes for RFI and its component traits as well as pathways associated with RFI in Danish Duroc boars by genome-wide associations and systems genetic analyses. RESULTS: Phenotypic and genotypic records (using the Illumina Porcine SNP60 BeadChip) were available on 1,272 boars. Fifteen and 12 loci were significantly associated (p < 1.52 × 10-6) with RFI1 and RFI2, respectively. Among them, 10 SNPs were significantly associated with both RFI1 and RFI2 implying the existence of common mechanisms controlling the two RFI measures. Significant QTL regions for component traits of RFI (DFI and BF) were detected on pig chromosome (SSC) 1 (for DFI) and 2 for (BF). The SNPs within MAP3K5 and PEX7 on SSC 1, ENSSSCG00000022338 on SSC 9, and DSCAM on SSC 13 might be interesting markers for both RFI measures. Functional annotation of genes in 0.5 Mb size flanking significant SNPs indicated regulation of protein and lipid metabolic process, gap junction, inositol phosphate metabolism and insulin signaling pathway are significant biological processes and pathways for RFI, respectively. CONCLUSIONS: The study detected novel genetic variants and QTLs on SSC 1, 8, 9, 13 and 18 for RFI and indicated significant biological processes and metabolic pathways involved in RFI. The study also detected novel QTLs for component traits of RFI. These results improve our knowledge of the genetic architecture and potential biological pathways underlying RFI; which would be useful for further investigations of key candidate genes for RFI and for development of biomarkers.
| S-EPMC3929553 | biostudies-literature
Project description:Microbes and microbial components potentially impact the performance of pigs through immune stimulation and altered metabolism. These immune modulating factors can include endotoxin from gram negative bacterial outer membrane component, commonly referred to as lipopolysaccharide (LPS). In this study, our objective was to examine the relationship between intestinal barrier integrity, endotoxin and inflammation with feed efficiency (FE), using pig lines divergently selected for residual feed intake (RFI) as a model. Twelve gilts (62 ± 3 kg BW) from the low RFI (LRFI, more efficient) and 12 from the high RFI (HRFI, less efficient) were used. Individual performance data was recorded for 5 wk. At the end of the experimental period, ADFI of LRFI pigs was less (P < 0.001), ADG not different between the 2 lines (P = 0.72) but the G:F of LRFI pigs was greater than for HRFI pigs (P = 0.019). Serum endotoxin concentration (P < 0.01) and the acute phase protein haptoglobin (P < 0.05) were greater in HRFI pigs. Transepithelial resistance of the ileum, transport of fluorescein isothiocyanate labeled-Dextran and-LPS in ileum and colon, as well as tight junction protein mRNA expression in ileum, did not differ between the lines, indicating the 2 lines did not differ in transport characteristics at the intestinal level. Ileum inflammatory markers, myeloperoxidase (P < 0.05) and IL-8 (P < 0.10), were found to be greater in HRFI pigs. Alkaline phosphatase (ALP) activity was significantly increased in the LRFI pigs in ileum and liver tissues and negatively correlated with blood endotoxin (P < 0.05). Lysozyme activity in the liver was not different between the lines; however, the LRFI pigs had a twofold greater lysozyme activity in ileum (P < 0.05). Despite the difference in their activity, ALP or lysozyme mRNA expression was not different between the lines in either tissue. Decreased endotoxin and inflammatory markers and the enhanced activities of antimicrobial enzymes in the LRFI line may not fully explain the difference in the FE between the lines, but they have the potential to prevent the growth potential in HRFI pigs. Further studies are needed to identify the other mechanisms that may contribute to the greater endotoxin and acute phase proteins in the HRFI pigs and the greater FE in the LRFI pigs.
| S-EPMC7109995 | biostudies-literature
Project description:A biphasic feeding regimen exerts an improvement effect on feed efficiency of pigs. While gut microbiome and metabolome are known to affect the host phenotype, so far the effects of reduced feeding frequency on fecal microbiota and their metabolism in pigs remain unclear. Here, the combination of 16S rRNA sequencing technique as well as untargeted and targeted metabolome analyses was adopted to investigate the fecal microbiome and metabolome of growing–finishing pigs in response to a biphasic feeding [two meals per day (M2)] pattern. Sixty crossbred barrows were randomly assigned into two groups with 10 replicates (three pigs/pen), namely, the free-access feeding group (FA) and the M2 group. Pigs in the FA group were fed free access while those in the M2 group were fed ad libitum twice daily for 1 h at 8:00 and 18:00. Results showed that pigs fed biphasically exhibited increased feed efficiency compared to FA pigs. The Shannon and Simpson indexes were significantly increased by reducing the feeding frequency. In the biphasic-fed pigs, the relative abundances of Subdoligranulum, Roseburia, Mitsuokella, and Terrisporobacter were significantly increased while the relative abundances of unidentified_Spirochaetaceae, Methanobrevibacter, unidentified_Bacteroidales, Alloprevotella, Parabacteroides, and Bacteroides were significantly decreased compared to FA pigs. Partial least-square discriminant analysis (PLS-DA) analysis revealed an obvious variation between the FA and M2 groups; the differential features were mainly involved in arginine, proline, glycine, serine, threonine, and tryptophan metabolism as well as primary bile acid (BA) biosynthesis. In addition, the changes in the microbial genera were correlated with the differential fecal metabolites. A biphasic feeding regimen significantly increased the abundances of primary BAs and secondary BAs in feces of pigs, and the differentially enriched BAs were positively correlated with some specific genera. Taken together, these results suggest that the improvement effect of a reduced feeding frequency on feed efficiency of pigs might be associated with the altered fecal microbial composition and fecal metabolite profile in particular the enlarged stool BA pool.
| S-EPMC8546368 | biostudies-literature
Project description:The timing of feed intake can alter circadian rhythms of peripheral tissues. Milk synthesis displays a daily rhythm across several species, but the effect of feeding time on these rhythms is poorly characterised. The objective of this experiment was to determine if the time of feed intake modifies the daily patterns of milk synthesis, plasma metabolites and body temperature in dairy cows. Sixteen lactating Holstein dairy cows were randomly assigned to one of the two treatment sequences in a cross-over design with 17 d periods. Treatments included day-restricted feeding (DRF; feed available from 07.00 to 23.00 hours) and night-restricted feeding (NRF; feed available from 19.00 to 11.00 hours). Cows were milked every 6 h on the last 7 d of each period, and blood samples were collected to represent every 4 h over the day. Peak milk yield was shifted from morning in DRF to evening in NRF, while milk fat, protein and lactose concentration peaked in the evening in DRF and the morning in NRF. Plasma glucose, insulin, NEFA and urea nitrogen concentration fit daily rhythms in all treatments. Night feeding increased the amplitude of glucose, insulin and NEFA rhythms and shifted the daily rhythms by 8 to 12 h (P < 0·05). Night feeding also phase-delayed the rhythm of core body temperature and DRF increased its amplitude. Altering the time of feed availability shifts the daily rhythms of milk synthesis and plasma hormone and metabolite concentrations and body temperature, suggesting that these rhythms may be entrained by food intake.
| S-EPMC7154010 | biostudies-literature
Project description:This study was conducted to evaluate the effect of genetic selection (Lines A and B; Line A pigs have a greater proportion of Pietrain genes than those from Line B and therefore, selected for improved lean tissue accretion) on the feeding behavior of group-housed pigs exposed to daily cyclic high ambient temperatures. Feeding behavior of 78 barrows housed together in a single room was recorded in real time by five automatic feeders. The feeders registered each visit of each pig (day, hour, min, and second) and the amount of feed requested. Daily cyclic high ambient temperature was induced exposing pigs at 22°C from 18.00 to 10.00 h and 30°C from 10.01 to 17.59 h. From this temperature variation, day-period was divided into: 22°C(06-10h), from 6.00 to 10.00 h; 30°C(10-18h), from 10.01 to 17.59 h; and 22°C(18-06h), from 18.00 to 5.59 h. Meal criteria was estimated based on the probability of animals starting a new feeding event within the next minute since the last visit (Pstart). After defining the meal criteria, the number of meals (n), feed intake rate (g/min), feed intake (g/meal), feeder occupancy (min/meal), and interval between meals (min) of each animal were calculated. Greatest probability of starting to feed was observed at 22°C(06-10h), followed by 30°C(10-18h) and then 22°C(18-06h). Regardless of time period, pigs from line A had greater feed intake rate and lower feed intake, feed occupancy per meal and probability of starting a meal when compared with line B pigs. Only line A pigs had greater feed intake and feeder occupancy per meal at 22°C(18-06h) than remainder of the day. This indicates that pig feeding pattern is strongly related to the circadian rhythm. However, the genetic selection for improved lean tissue accretion may modulate pigs feeding behavior under daily cyclic high ambient temperatures.
| S-EPMC8786115 | biostudies-literature
Project description:To identify a proper strategy for future feed-efficient pig farming, it is required to evaluate the ongoing selection scenarios. Tools are lacking for the evaluation of pig selection scenarios in terms of environmental impacts to provide selection guidelines for a more sustainable pig production. Selection on residual feed intake (RFI) has been proposed to improve feed efficiency and potentially reduce the associated environmental impacts. The aim of this study was thus to develop a model to account for individual animal performance in life cycle assessment (LCA) methods to quantify the responses to selection. Experimental data were collected from the fifth generation of pig lines divergently selected for RFI (low line, more efficient pigs, LRFI; high line, less efficient pigs, HRFI). The average feed conversion ratio (FCR) and daily feed intake of LRFI pigs were 7% lower than the average of HRFI pigs (P < 0.0001). A parametric model was developed for LCA based on the dietary net energy fluxes in a pig system. A nutritional pig growth tool, InraPorc®, was included as a module in the model to embed flexibility for changes in feed composition, animal performance traits and housing conditions and to simulate individual pig performance. The comparative individual-based LCA showed that LRFI had an average of 7% lower environmental impacts per kilogram live pig at farm gate compared to HRFI (P < 0.0001) on climate change, acidification potential, freshwater eutrophication potential, land occupation and water depletion. High correlations between FCR and all environmental impact categories (>0.95) confirmed the importance of improvement in feed efficiency to reduce environmental impacts. Significant line differences in all impact categories and moderate correlations with impacts (>0.51) revealed that RFI is an effective measure to select for improved environmental impacts, despite lower correlations compared to FCR. Altogether more optimal criteria for efficient environment-friendly selection can then be expected through restructuring the selection indexes from an environmental point of view.
| S-EPMC7645311 | biostudies-literature
Project description:The objective of this study was to evaluate the feasibility of using the dry matter intake of first 2 h after feeding (DMI-2h), body weight (BW), and milk yield to estimate daily DMI in mid and late lactating dairy cows with fed ration three times per day. Our dataset included 2840 individual observations from 76 cows enrolled in two studies, of which 2259 observations served as development dataset (DDS) from 54 cows and 581 observations acted as the validation dataset (VDS) from 22 cows. The descriptive statistics of these variables were 26.0 ± 2.77 kg/day (mean ± standard deviation) of DMI, 14.9 ± 3.68 kg/day of DMI-2h, 35.0 ± 5.48 kg/day of milk yield, and 636 ± 82.6 kg/day of BW in DDS and 23.2 ± 4.72 kg/day of DMI, 12.6 ± 4.08 kg/day of DMI-2h, 30.4 ± 5.85 kg/day of milk yield, and 597 ± 63.7 kg/day of BW in VDS, respectively. A multiple regression analysis was conducted using the REG procedure of SAS to develop the forecasting models for DMI. The proposed prediction equation was: DMI (kg/day) = 8.499 + 0.2725 × DMI-2h (kg/day) + 0.2132 × Milk yield (kg/day) + 0.0095 × BW (kg/day) (R2 = 0.46, mean bias = 0 kg/day, RMSPE = 1.26 kg/day). Moreover, when compared with the prediction equation for DMI in Nutrient Requirements of Dairy Cattle (2001) using the independent dataset (VDS), our proposed model shows higher R2 (0.22 vs. 0.07) and smaller mean bias (-0.10 vs. 1.52 kg/day) and RMSPE (1.77 vs. 2.34 kg/day). Overall, we constructed a feasible forecasting model with better precision and accuracy in predicting daily DMI of dairy cows in mid and late lactation when fed ration three times per day.
| S-EPMC7825592 | biostudies-literature
Project description:Greater feed efficiency (FE) is critical in increasing profitability while reducing the environmental impact of pig production. Previous studies that identified swine FE-associated bacterial taxa were limited in either sampling sites or sequencing methods. This study characterized the microbiomes within the intestine of FE contrasting Duroc × (Landrace × Yorkshire) (DLY) pigs with a comprehensive representation of diverse sampling sites (ileum, cecum, and colon) and a metagenomic sequencing approach. A total of 226 pigs were ranked according to their FE between weaning to 140 day old, and six with extreme phenotypes were selected, three for each of the high and low groups. The results revealed that the cecum and colon had similar microbial taxonomic composition and function, and had higher capacity in polysaccharide metabolism than the ileum. We found in cecum that the high FE pigs had slightly higher richness and evenness in their micriobiota than the low FE pigs. We identified 12 phyla, 17 genera, and 39 species (e.g., Treponema porcinum, Treponema bryantii, and Firmicutes bacterium CAG:110) that were potentially associated with swine FE variation in cecum microbiota through LEfSe analysis. Species enriched in the cecum of the high FE pigs had a greater ability to utilize dietary polysaccharides and dietary protein according to the KEGG annotation. Analysis of antibiotic resistance based on the CARD database annotation indicated that the macB resistant gene might play an important role in shaping the microbial community in the cecum of pigs with contrasting FE. The bacteria from the genus Prevotella was highly enriched in the cecum of low FE pigs, which may impair the establishment of a more effective nutrient harvesting microbiota because of the interaction between Prevotella and other benefical microbes. These findings improved our understanding of the microbial compositions in the different gut locations of DLY pigs and identified many biomarkers associated with FE variation wich may be used to develop strategies to improve FE in pigs.
| S-EPMC6989599 | biostudies-literature
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.
| S-EPMC7058701 | biostudies-literature
Project description:Differences in chickens' feed intake may be the underlying factor influencing feed-efficiency (FE)-associated variation in intestinal microbiota and physiology. In chickens eating the same amount of feed, quantitative feed restriction may create similar intestinal conditions and help clarify this cause-and-effect relationship. This study investigated the effect of ad libitum versus restrictive feeding (85% of ad libitum) on ileal and cecal microbiota, concentrations of short-chain fatty acids, visceral organ size, intestinal morphology, permeability, and expression of genes related to nutrient uptake, barrier function, and innate immune response in broiler chickens with divergent residual feed intake (RFI; metric for FE). On day 30 posthatch, 28 low-RFI (good FE) and 29 high-RFI (poor FE) chickens across both feeding-level groups (n?=?112) were selected. Supervised multigroup data integration and relevance network analyses showed that especially Lactobacillus (negative) in ileal digesta, Turicibacter (positive) in cecal digesta, and Enterobacteriaceae (positive) in both intestinal segments depended on chicken's feed intake, whereas the level of Anaerotruncus in cecal digesta was most discriminative for high RFI. Moreover, shallower crypts and fewer goblet cells in ceca indicated host-related energy-saving mechanisms with low RFI, whereas greater tissue resistance suggested a stronger jejunal barrier function in low-RFI chickens. Values corresponding to feed intake level × RFI interactions indicated larger pancreas and lower levels of ileal and cecal short-chain fatty acids in restrictively fed high-RFI chickens than in the other 3 groups, suggesting host physiological adaptations to support greater energy and nutrient needs of high-RFI chickens compensating for the restricted feeding. IMPORTANCE The impact of the FE-associated differences in feed intake on intestinal bacterial and host physiological parameters has so far not been clarified. Understanding the underlying principles is essential for the development of cost-effective strategies to improve FE in chicken production. Under conditions of quantitative feed restriction, low- and high-RFI chickens ate the same amount of feed. Therefore, this research helps in distinguishing intestinal bacterial taxa and functions that were highly reliant on feed intake from those that were associated with physiological adaptations to RFI-associated differences in host nutritional needs and intestinal nutrient availability. This work provides a background for further research to assess manipulation of the intestinal microbiota, host physiology, and FE in chickens by dietary intervention.
| S-EPMC6351724 | biostudies-literature