High Residual Feed Intake Groups Research Articles

198 Discovery of key functional SNP markers associated with feed efficiency in beef cattle

Abstract Beef production contributes to approximately 2.4% of the total Greenhouse Gas emissions in Canada. Improving beef cattle feed efficiency (FE) may lead to improved energy partitioning and resource use, thereby improving the sustainability of the beef industry. Our objective was to identify differentially expressed key regulatory genes and associated novel functional SNP markers linked to FE in Canadian beef cattle using RNA-Sequencing (RNA-Seq) of rumen tissue collected from 48 beef cattle [n = 16 Angus, n = 16 Charolais, n = 16 Kinsella (Composite Hybrid including Angus, Charolais, Galloway, Hereford, Holstein, Brown Swiss, and Simmental)] selected for extreme FE phenotypes. In total, 11 key regulatory genes (MYH1, MYL2, MYLPF, TNNC2, EIF4B, RHOD, TCEANC, CKM, ENSBTAG00000040518, SERPINB2, and USP43) were significantly differentially expressed (DE) between extreme Residual Feed Intake (RFI) groups (low-RFI n = 8, high-RFI n = 8 per breed) using CLC Genomics Workbench (FDR < 0.05; |FC| >2). Using an optimized RNA-Seq variant calling pipeline using STAR and BCFtools, a total of [total (unique to low-RFI, unique to high-RFI)] 75 (36, 39), 78 (42, 36), and 53 (35, 18) uniquely fixed functional SNPs were located within coding regions of these 11 functional candidate genes, in low- and high-RFI animals in the Angus, Charolais, and Kinsella breeds, respectively. Considering all functional SNPs uniquely identified in low- or high-RFI groups for all breed comparisons, the majority of SNPs were identified in MYH1, EIF4B, and SERPINB2 genes, which function together in metabolically demanding biological processes (P < 0.05) related to muscle contraction, muscle system, and muscle filament function processes. Additionally, EIF4B and SERPINB2 genes were found to have a role in signaling pathways that coordinate cell growth and immune function, respectively. Using RNA-Seq to identify key regulatory genes and associated functional SNPs linked to FE may uncover important genetic markers that influence the regulation of FE in beef cattle.

Transcriptomic profiling reveals potential regulatory genes and molecular mechanisms of residual feed intake in Jian carp (Cyprinus carpio var. Jian)

Feed efficiency is one of the most important economic traits in animal production. Improving feed efficiency through genetic selection or other approaches will reduce production costs and mitigate environmental impacts. Residual feed intake (RFI) has some advantages over traditional feed efficiency metrics as a selection criterion for improving feed efficiency, because it is not a ratio and unrelated to growth. In this study, high RFI (HRFI) and low RFI (LRFI) Jian carp (Cyprinus carpio var. Jian) were tested for feed efficiency traits and serum biochemical indices. No significant differences were observed in the growth rates between HRFI and LRFI group, but daily feed intake of LRFI was significantly lower than that of the HRFI group. The results indicated that significantly higher content of triglyceride (TG) and total cholesterol (T-CHO) in the LRFI group was significantly correlated with RFI. We also selected HRFI and LRFI carp for transcriptomic analysis to determine differentially expressed genes (DEGs) in the liver tissues of 12 individuals. A total of 830 DEGs were identified between HRFI and LRFI group, of which 486 genes were up-regulated and 344 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that DEGs were mainly enriched in fatty acid metabolism, ErbB signaling pathway, phosphatidylinositol signaling system, and autophagy. Lipid metabolism and autophagy-related genes, were considered candidate genes that played a crucial role in regulating feed efficiency. Taken together, these results indicated that differences in RFI affect Jian carp metabolism and cell fate, and that alterations in fatty acid metabolism and autophagy are key physiological modes of regulation in low RFI Jian carp. Our data provide valuable candidate genes and candidate pathways, which will help to study the molecular mechanisms of feed efficiency in carp.

Metabolomics Profiling of Serum and Urine from Chuanzang Black Pigs with Different Residual Feed Intake.

This study was conducted to evaluate associations of blood variables and urine variables with different residual feed intakes (RFIs) in growing Chuanzang black (CB) pigs. A total of 228 growing CB boars from 99 days were used. The same basal diet was offered ad libitum and individual feed intake and body weight were measured over a period of 181 d. The CB pigs were categorized based on their residual feed intake values, with six individuals each from the high and low ends selected and divided into two groups: the low residual feed intake group (LS) and the high residual feed intake group (HS). Serum and urine samples were collected at the end of the experiment for determination of metabolomics profiling. Results showed that there were significantly different metabolites in serum and urine of different RFI groups (fold-change, FC > 2.0 or FC < 0.5, and p < 0.05), and 21 metabolites were identified in serum and 61 in urine. Cluster analysis showed that 20 metabolites were up-regulated and one metabolite was down-regulated in serum; 44 metabolites were up-regulated and 17 metabolites were down-regulated in urine. Kyoto Encyclopedia of Genes and Genomes analysis showed that the differential metabolites of serum were enriched in linoleic acid metabolism, and the differential metabolites of urine were enriched in steroid hormone biosynthesis, taurine and hypotaurine metabolism, and primary bile acid biosynthesis. The correlations between serum metabolites and urine metabolites indicated a significant positive correlation between all fatty acyls in serum metabolites and L-glutamate in urine. However, no compelling genetic or blood biomarkers have been found to explain the differences in RFI, suggesting multiple approaches to effective feed use in pigs. This study provides new insights into the subsequent assessment of RFI by metabolomics profiling, as well as the development of novel feed additives for the factors that will facilitate future research directions in CB pigs.

Feed efficiency and enteric methane emissions indices are inconsistent with the outcomes of the rumen microbiome composition

The correlation between enteric methane emissions (eME) and feed efficiency (FE) in cattle is linked to the anaerobic fermentation of feedstuffs that occurs in the rumen. Several mathematical indices have been developed to predict feed efficiency and identify low methane emitters in herds. To investigate this, the current study aimed to evaluate the rumen microbial composition in the same group of animals ranked according to six different indices (three indices for FE and three for eME). Thirty-three heifers were ranked into three groups, each consisting of 11 animals, based on FE (feed conversion efficiency - FCE, residual weight gain - RG, and residual feed intake - RFI) and eME indices (production, yield, and intensity). Rumen fluids were collected using a stomach tube and analyzed using 16S rRNA and 18S rRNA, targeting rumen bacteria, archaea, and protozoa. The sequencing analysis revealed that the presence of unique microbial species in the rumen varies across animals ranked by the FE and eME indices. The High RG group harbored 17 unique prokaryotic taxa, while the High FCE group contained only seven. Significant differences existed in the microbial profiles of the animals based on the FE and eME indices. For instance, Raoultibacter was more abundant in the Intermediate RFI group but less so in the Intermediate RG and Intermediate FCE groups. The abundance of Entodinium was higher while Diplodinium was lower in the High FCE group, in contrast to the High RG and High RFI groups. Methanobrevibacter exhibited similar abundances across eME indices. However, the heifers did not demonstrate the same production, yield, and intensity of eME. The present findings underscore the importance of standardizing the FE and eME indices. This standardization is crucial for ensuring consistent and reliable assessments of the composition and function of the rumen microbiome across different herds.

Integrated multi-omics reveals the relationship between growth performance, rumen microbes and metabolic status of Hu sheep with different residual feed intakes

Residual feed intake (RFI) is a metric that provides a more accurate measure of feed efficiency. The lower the RFI, the higher the feed efficiency. The changes in the host microbiome and metabolome contribute to the greater feed efficiency of low RFI (LRFI) animals. The aim of this study was to explore the differences in rumen microorganisms, rumen metabolites and plasma metabolites of Hu sheep with differing RFI through the microbiome and metabolome. A total of 80 Hu sheep were used. The experiment consisted of a 15-d pretrial period and a 128-d experimental period. The RFI in the experimental period was calculated for all sheep, and the sheep were screened into high RFI (HRFI, n = 8) and LRFI (n = 8) groups. The HRFI and LRFI sheep did not differ in their initial and final body weights, average daily gain and body measurements, but the dry matter intake of LRFI sheep was significantly decreased (28.4%, P < 0.001). The sheep with LRFI had higher digestibility of crude protein (P = 0.010) and ether extract (P = 0.010) compared to HRFI group. The concentrations of acetate (P = 0.036), propionate (P = 0.010), valerate (P = 0.027) and total volatile fatty acids (P = 0.048) in rumen of LRFI group were higher compared to HRFI group. The results of 16S rDNA sequencing indicated that the sheep with LRFI had higher proportions of Prevotella genus in rumen liquid (P = 0.031). The rumen metabolome and plasma metabolome results showed that the citrate cycle, pyruvate metabolism and alanine, aspartate and glutamate metabolism processes were more active for sheep in LRFI group, which provided more energy substrate such as malic acid, oxoglutaric acid and citric acid. In conclusion, sheep with LRFI can utilize feed more efficiently, and the more active energy metabolism pathway and the production of energy substances may account for the higher feed efficiency.

Performance, nutrient utilization and meat quality traits in Bos indicus cattle: a meta-analysis examining the effect of residual feed intake.

This meta-analysis aims to investigate the effects of residual feed intake (RFI) phenotype on performance, nutrient utilization and meat quality traits in Zebu (Bos indicus) cattle. Twenty-three peer-reviewed publications with 37 treatment means were included in the dataset. Weighted mean difference analysis compared animals categorized into low RFI (more efficient) versus medium or high RFI (less efficient) groups. Data heterogeneity via meta-regression and subgroup analysis, considering variables such as animal age, sex class, experimental duration, RFI group, dietary concentrate, and estimated metabolizable energy intake were also explored. The predominant genetic group of cattle in the dataset was Nellore (89.18%), followed by Brahman (10.81%). More efficient animals (low RFI phenotype) exhibited less dry matter intake (DMI; P < 0.010) than medium or high RFI animals (-0.95kg vs. -0.42kg/d). Cattle dietary crude protein and fiber digestibility were consistent across RFI groups (P > 0.05), while dietary ether extract digestibility tended to decrease (P = 0.050) in low RFI animals (-13.20g/kg DM). Low RFI animals tended to increased (P = 0.065) ribeye area (REA) compared to the high/medium RFI groups, while carcass backfat thickness (BFT) decreased (P = 0.042) compared to high/medium RFI groups. Moreover, there was an increase (P < 0.001) of 0.22kg in Warner-Bratzler shear force (WBSF) and a reduction (P < 0.001) in the myofibrillar fragmentation index (MFI) in low RFI animals. Meat color parameters (lightness [L*] and yellowness [b*]) and visual marbling scores were consistent (P > 0.05) across RFI groups. In conclusion, Zebu cattle classified as efficient (low RFI) exhibited reduced DMI, which improves their feed efficiency. However, BFT and meat quality parameters such as tenderness (WBSF and MFI) and redness [a*] were compromised by low RFI phenotype, highlighting the challenge of enhancing feed efficiency and meat quality traits in Zebu cattle.

1H-NMR-Based Plasma Metabolomic Profiling of Crossbred Beef Cattle with Divergent RFI Phenotype

This study focused on exploring the metabolomic profiles of crossbred beef cattle with varying levels of residual feed intake (RFI), a measure of feed efficiency in beef cattle. Sixty-seven crossbred growing beef steers (BW = 277 ± 29.7 kg) were subjected to a high-forage total mixed ration for 64 days to determine their RFI phenotypes. At the end of the 64d feeding trial, beef steers were divided into two groups based on their RFI values: low (or negative)-RFI beef steers (n = 28; RFI = −1.08 ± 0.88 kg/d) and high (or positive)-RFI beef steers (n = 39; RFI = 1.21 ± 0.92 kg/d). Blood samples were collected, and plasma samples were analyzed using Nuclear Magnetic Resonance spectroscopy, resulting in the identification of 50 metabolites. The study found a distinct metabolomic signature associated with RFI status. Eight metabolites, including amino acids (tyrosine, glycine, valine, leucine, and methionine) and other compounds (dimethyl sulfone, 3-hydroxy isovaleric acid, citric acid, creatine, and L-carnitine), showed differential abundance between low- and high-RFI groups. Specifically, tyrosine, glycine, and dimethyl sulfone exhibited significant specificity and sensitivity, which produced a discriminatory model with an area under the receiver operating characteristic (ROC) curve of 0.7, making them potential markers for RFI. A logistic regression model incorporating these biomarkers effectively distinguished between high- and low-RFI steers, with a threshold cutoff point of 0.48, highlighting a distinctive metabolite profile associated with efficient nutrient utilization in low-RFI cattle. The logistic regression model, incorporating these biomarkers, holds promise for accurately categorizing RFI values, providing insights into the metabolic basis of feed efficiency in beef cattle.

Variability in residual feed intake, nutrient utilisation and blood parametersin Murrah buffalo calves fed on total mixed ration

The present study was conducted on 18 female Murrah buffalo calves divided into two treatment groups to determine the residual feed intake, nutrient digestibility and blood metabolite parameters when fed with ration containing wheat (Triticum aestivum) straw, berseem (Trifolium alexandrinum) fodder as roughages and concentrate mixture to meet their requirements. Regular recording of body weight and feed intake was done during 90-day trial period. Residual feed intake (RFI) values were determined for individual animals based on which they were divided into low and high RFI groups. DM intake was lower in low RFI animals than high RFI animals. The blood glucose level and growth hormone level in low and high RFI group was comparable in both groups. Low RFI group had greater concentration of creatinine (1.62 vs. 1.21 mg/dL) as well as IGF-1 (136.70 vs. 120.38 ng/mL) whereas, concentration of total plasma protein level (6.80 vs 7.43 g/dL), albumin (3.46 vs 3.71 g/dl), aspartate aminotransferase (102.20 vs. 122.60 IU/L) and cortisol (3.48 vs. 5.32 ng/mL) were lesser in low RFI group with respect to high RFI group, indicating a positive correlation of RFI with total plasma protein, albumin, aspartate aminotransferase and cortisol and a negative correlation with plasma creatinine and IGF-1 levels in female Murrah buffalo calves. It was concluded that low RFI group of female Murrah buffalo calves showed better performance when fed with total mixed ration.

Impact of divergence of residual feed intake on triglyceride metabolism-related gene expression in meat-type ducks.

Triglyceride (TG) metabolism is a key factor that affects residual feed intake (RFI); however, few studies have been conducted on the related gene expression in poultry. The aim of the present study was to investigate the expression of genes and their associations with RFI in meat-type ducks. Weight gain and feed intake (FI) at an age 21-42 days were measured and the RFI was calculated. Quantitative PCR was used to test the expression of the six identified genes, namely peroxisome proliferator activated receptor γ (PPARγ), glycerol kinase 2 (GK2), glycerol-3-phosphate dehydrogenase 1 (GPD1), glycerol kinase (GYK), lipase E (LIPE), and lipoprotein lipase (LPL) in the duodenum in the high RFI (HRFI) and low RFI (LRFI) groups. The results demonstrated that daily feed intake, feed conversion ratio (FCR), and RFI were markedly higher in HRFI ducks than those in LRFI ducks. Moreover, the levels of expression of PPARγ, GK2, and LIPE were significantly higher in the LRFI group than those in the HRFI group. Correlation analysis showed that PPARγ, GK2, and LIPE were significantly negatively associated with FCR and RFI. Furthermore, gene expression levels were negatively associated with the measured phenotype. The association of GK2 with PPARγ, GPD1, LPL, and LIPE was positive. The relationship between the TG related gene and RFI was further verified to potentially develop pedigree poultry breeding programs. The results of this study suggested that the expression of genes correlated with TG metabolism and transport is up-regulated in the duodenum of ducks with high feed efficiency. PPARγ, GK2, and LIPE are important genes that affect RFI. The results of the present study provide information that could facilitate further explorations of the mechanism of RFI and potential markers at the molecular and cellular levels.

Combined transcriptome and metabolome analysis reveal key regulatory genes and pathways of feed conversion efficiency of oriental river prawn Macrobrachium nipponense

BackgroundOriental river prawn Macrobrachium nipponense is an economically important aquaculture species in China, Japan, and Vietnam. In commercial prawn farming, feed cost constitutes about 50 to 65% of the actual variable cost. Improving feed conversion efficiency in prawn culture will not only increase economic benefit, but also save food and protect the environment. The common indicators used for feed conversion efficiency include feed conversion ratio (FCR), feed efficiency ratio (FER), and residual feed intake (RFI). Among these, RFI is much more suitable than FCR and FER during the genetic improvement of feed conversion efficiency for aquaculture species.ResultsIn this study, the transcriptome and metabolome of hepatopancreas and muscle of M. nipponense from high RFI low RFI groups, which identified after culture for 75 days, were characterized using combined transcriptomic and metabolomic analysis. A total of 4540 differentially expressed genes (DEGs) in hepatopancreas, and 3894 DEGs in muscle were identified, respectively. The DEGs in hepatopancreas were mainly enriched in KEGG pathways including the metabolism of xenobiotics by cytochrome P450 (down-regulated), fat digestion and absorption (down-regulated) and aminoacyl-tRNA biosynthesis (up-regulated), etc. The DEGs in muscle were mainly enriched in KEGG pathways including the protein digestion and absorption (down-regulated), glycolysis/gluconeogenesis (down-regulated), and glutathione metabolism (up-regulated), etc. At the transcriptome level, the RFI of M. nipponense was mainly controlled in biological pathways such as the high immune expression and the reduction of nutrients absorption capacity. A total of 445 and 247 differently expressed metabolites (DEMs) were identified in the hepatopancreas and muscle, respectively. At the metabolome level, the RFI of M. nipponense was affected considerably by amino acid and lipid metabolism.ConclusionsM. nipponense from higher and lower RFI groups have various physiological and metabolic capability processes. The down-regulated genes, such as carboxypeptidase A1, 6-phosphofructokinase, long-chain-acyl-CoA dehydrogenase, et. al., in digestion and absorption of nutrients, and the up-regulated metabolites, such as aspirin, lysine, et. al., in response to immunity could be potential candidate factors contributed to RFI variation for M. nipponense. Overall, these results would provide new insights into the molecular mechanism of feed conversion efficiency and assist in selective breeding to improve feed conversion efficiency in M. nipponense.

Metagenomic insights into the relationship between gut microbiota and residual feed intake of small-sized meat ducks.

The objective of this study was to determine the regulatory effects of gut microbiota on the feed efficiency (FE) of small-sized meat ducks by evaluating correlations between gut microbiota and residual feed intake (RFI). A total of 500 21-day-old healthy male ducks with similar initial body weights (645 ± 15.0 g) were raised contemporaneously in the same experimental facility until slaughter at 56 days of age. In total, nine low-RFI (LR) and nine high-RFI (HR) birds were selected for further gut microbiota composition and functional analyses based on the production performance, and the RFI was calculated from 22 to 56 days of age. Growth performance results indicated a significantly lower RFI, feed conversion ratio, feed intake, and average daily feed intake in the LR ducks (P < 0.05). Taxonomy results of gut microbiota showed the identification of 19 kinds of phyla and more than 250 kinds of genera in all samples. No significant discrepancies in cecal bacterial α-diversity were discovered between the LR and HR groups, which indicated that the microbial modulatory effects on RFI may be attributed to the bacterial composition, rather than the species diversity. Differential analysis of bacterial communities between the LR and HR groups showed a significant increment of Firmicutes and a significant decline of Bacteroidetes in the LR group (P < 0.05). Specifically, genera of Erysipelatoclostridium, Parasutterella, Fournierella, and Lactococcus significantly proliferated, while Bacteroides significantly decreased in the LR group (P < 0.05). Furthermore, correlation analysis showed that the RFI was significantly correlated with carbohydrate metabolism-related bacteria including Bacteroides, Alistipes, Bifidobacterium, Ruminiclostridium_9, Sellimonas, Oscillibacter, Escherichia-Shigella, Lactococcus, and Streptococcus. In conclusion, the communities related to carbohydrate metabolism had positive regulatory effects on the FE of small-sized meat ducks, promoting it by improving the relative abundance and utilization of these communities. The present study provides valuable insight into the dynamics of gut microbiota underlying the variations in the FE of small-sized meat ducks.

Identification and characterization of hypothalamic circular RNAs associated with bovine residual feed intake

Residual feed intake (RFI) is crucial economic indicator used for calculating the feed efficiency of growing beef cattle. circRNA plays an important biological role in gene transcriptional regulation, but little is known about its potential functional regulation underlying RFI phenotypic variation. As the core center of regulation of animal feeding, the hypothalamus is closely associated with RFI. Therefore, the present study aimed to identify the key genes and functional pathways contributing to variance in cattle RFI phenotypes using RNA sequencing from hypothalamic tissue samples, in order to gain insight into the potential regulatory role of circRNAs in bovine RFI phenotypic variation. Differentially expressed genes were detected by RNA sequencing for beef cattle in the high and low RFI groups, followed by GO, KEGG enrichment, and circRNA-miRNA co-expression network analysis. A total of 257 circRNAs were differentially expressed between the two groups, with 128 significantly upregulated and 129 significantly downregulated genes in H group compared to L group. Among them, 9 unique circRNAs were present in group L and 4 unique circRNAs were present in group H. GO and KEGG enrichment analysis of the source genes of the differentially expressed circRNAs revealed that they were mainly involved in metabolic processes, such as cellular metabolic processes, cellular macromolecular metabolic processes, and regulatory pathways related to nutrient metabolism, including protein and amino acid metabolism, as well as vitamin metabolism and pancreatic secretion associated with the animal feeding behavior. The circRNAs detected in this study were mostly novel, and have not been investigated directly to be associated with the RFI phenotype. Interestingly, most miRNAs of differentially expressed circRNAs predicted based on the circRNA-miRNA co-expression network analysis by using top 50 differentially expressed circRNAs and 13 unique circRNAs, have been reported to be related to animal RFIs, implying that circRNAs in bovine hypothalamic tissue may regulate phenotypic variation in RFI through miRNAs. The study results illustrate the complex biological functions of the hypothalamus in regulating feed efficiency and showing the potential role of circRNAs in the feeding behavior regulation of livestock, which would contributing to expanding the understanding of circRNA.

Effects of residual feed intake divergence on growth performance, carcass traits, meat quality, and blood biochemical parameters in small-sized meat ducks

Feed efficiency (FE) is a major economic trait of meat duck. This study aimed to evaluate the effects of residual feed intake (RFI) divergence on growth performance, carcass traits, meat quality, and blood biochemical parameters in small-sized meat ducks. A total of 500 healthy 21-day-old male ducks were housed in individual cages until slaughter at 63 d of age. The growth performance was determined for all the ducks. The carcass yield, meat quality, and blood biochemical parameters were determined for the selected 30 high-RFI (HRFI) and 30 low-RFI (LRFI) ducks. In terms of growth performance, the RFI, feed conversion ratio (FCR), and average daily feed intake (ADFI) were found to be significantly lower in the LRFI group (P < 0.01), whereas no differences were observed in the BW and body weight gain (P > 0.05). For slaughter performance, no differences were observed in the carcass traits between the LRFI and HRFI groups (P > 0.05). For meat quality, the shear force of breast muscle was significantly lower in the LRFI group (P < 0.05), while the other meat quality traits of breast and thigh muscles demonstrated no differences (P > 0.05). For blood biochemical parameters, the serum concentrations of triglycerides (TG) and glucose (GLU) were significantly lower in the LRFI group (P < 0.05), while the other parameters showed no differences (P > 0.05). The correlation analysis demonstrated a high positive correlation between RFI, FCR, and ADFI (P < 0.01). The RFI demonstrated a negative effect on the breast muscle and lean meat yields, but a positive effect on the shear force of breast muscle (P < 0.05). Further, the RFI demonstrated a positive effect on the TG and GLU levels (P < 0.05). These results indicate that the selection for low RFI could improve the FE of small-sized meat ducks without affecting the production performance. This study provides valuable insight into the biological processes underlying the variations in FE in small-sized meat ducks.

Small Intestine Microbiome and Metabolome of High and Low Residual Feed Intake Angus Heifers.

The gastrointestinal tract (GIT) contains complex microbial communities and plays an essential role in the overall health of the host. Previous studies of beef cattle feed efficiency have primarily concentrated on the ruminal microbiota because it plays a key role in energy production and nutrient supply in the host. Although the small intestine is the important site of post-ruminal digestion and absorption of nutrients, only a few studies have explored the relationship between the microbial populations in the small intestine and feed efficiency. Moreover, variations in GIT metabolites contribute to differences in feed efficiency. The objective of this study was to investigate relationships among bacterial populations of duodenum, jejunum, ileum; microbial metabolites; and RFI phenotype of beef cattle. We carried out by using Illumina MiSeq sequencing of the 16S rRNA V3-V4 region and liquid chromatography-mass spectrometry (LC–MS). In the duodenum, the relative abundances of Firmicutes ( p < 0.01), Lachnospiraceae, Ruminococcaceae, Family_XIII, Christensenellaceae, Christensenellaceae_R-7_group ( p < 0.05), and Lachnospiraceae_NK3A20_group ( p < 0.05) were higher in the low residual feed intake (LRFI) group compared with the high residual feed intake (HRFI) group, whereas the HRFI group had higher abundances of Proteobacteria and Acinetobacter ( p < 0.01). In the jejunum, the relative abundances of Lachnospiraceae and Lachnospiraceae_NK3A20_group were higher in the LRFI group ( p < 0.05). In the ileum, the relative abundances of Ruminococcaceae ( p < 0.01), Christensenellaceae, Christensenellaceae_R-7_group, and Ruminococcus_2 were also higher in the LRFI group ( p < 0.05). Moreover, the genera Lachnospiraceae_NK3A20_group, Christensenellaceae_R-7_group, and Ruminococcus_2 were negatively associated with RFI, while the genus Acinetobacter was positively associated with RFI. The metabolomics analysis revealed that the LRFI group significantly improved protein digestion and absorption, as well as glycerophospholipid metabolism in the duodenum, jejunum, ileum. The correlation between intestinal microorganisms and metabolites revealed that some microorganisms play an important role in amino acid metabolism, glycerophospholipid metabolism, nutrient digestion and absorption, and antioxidant enhancement. The present study provides a better understanding of the small intestinal microbiota and metabolites of beef cattle with different RFI phenotypes and the relationships among them, which are potentially important for the improvement of beef cattle feed efficiency.

Rumen Microbiome and Metabolome of High and Low Residual Feed Intake Angus Heifers.

Feed cost is the greatest expense during cattle production; therefore, reducing it is critical to increasing producer profits. In ruminants, the microbial population is important to nutrient digestion and absorption in the rumen. The objective of this study was to investigate the relationships among rumen bacteria, rumen metabolites, and the residual feed intake (RFI) phenotype of beef cattle. Twelve Angus heifers were selected to be sampled and divided into high RFI (HRFI; n = 6) group and low RFI (LRFI; n = 6) group according to their RFI classification determined during the feedlot-finishing period. After the ruminal liquid samples were collected at slaughter, Illumina MiSeq sequencing of the 16S rRNA V3-V4 region and liquid chromatography-mass spectrometry (LC-MS) were performed to determine their bacterial composition and metabolites, respectively. At the phylum level, the relative abundance of Proteobacteria was higher in the LRFI group than in the HRFI group (P < 0.01). At the family level, the relative abundances of Rikenellaceae (P < 0.01), Ruminococcaceae, Bacteroidales_S24-7_group, and Lachnospiraceae (P < 0.05) were significantly higher in the LRFI group. At the genus level, the relative abundances of Rikenellaceae_RC9_gut_group and Ruminiclostridium_1 were higher in the LRFI group (P < 0.01), as were the relative abundances of norank_f__Bacteroidales_S24-7_group, Lachnospiraceae_ND3007_group, and Lachnospiraceae_NK3A20_group (P < 0.05). Moreover, the genera Rikenellaceae_RC9_gut_group, Ruminococcaceae_NK4A214_group, Christensenellaceae_R-7_group, Ruminococcaceae_UCG-010, Lachnospiraceae_ND3007_group, Ruminiclostridium_1, and Lachnospiraceae_NK3A20_group were negatively associated with the RFI; both foundational and key species are associated with feed efficiency phenotype. In addition, rumen metabolomics analysis revealed that the RFI was associated with significantly altered concentrations of rumen metabolites involved in protein digestion and absorption, Linoleic acid metabolism, Lysine degradation, and Fatty acid degradation. Correlation analysis revealed the potential relationships between the significantly differential ruminal metabolites and the genera ruminal bacteria. The present study provides a better understanding of rumen bacteria and metabolites of beef cattle with different RFI phenotypes and the relationships among them, which are potentially important for the improvement of beef cattle feed efficiency.

Metagenomics reveals differences in microbial composition and metabolic functions in the rumen of dairy cows with different residual feed intake

BackgroundRumen microbial composition and functions have vital roles in feed digestion and fermentation and are linked to feed efficiency in cattle. This study selected Holstein cows, which are high in both milk protein content and milk yield, to analyse the relationship between the rumen microbiota and residual feed intake (RFI). Eighteen multiparous lactating cows were divided into low RFI (LRFI, high efficiency, n = 9) and high RFI (HRFI, low efficiency, n = 9) groups to investigate the differences in microbial composition and functions.ResultsThe relative abundances of butyrate producers, including the Clostridium, Butyrivibrio, Eubacterium and Blautia genera, were higher in HRFI cows than in LRFI cows (P < 0.05). Four carbohydrate metabolic pathways (glycolysis/gluconeogenesis, pentose phosphate pathway, fructose and mannose metabolism, and butanoate metabolism) and one energy metabolism pathway (methane metabolism), were more abundant in HRFI animals (P < 0.05). Quorum sensing and DNA replication pathways were more abundant in HRFI cows. For CAZyme profiles, 14 out of 19 genes encoding carbohydrates-deconstructing enzymes were more abundant in HRFI cows (P < 0.05). Seven Lachnospiraceae species associated with carbohydrate metabolism and quorum sensing may contribute to the difference in feed efficiency. Moreover, the LRFI cows had lower abundances of Methanosphaera (P < 0.01), Methanobrevibacter ruminantium (P = 0.09) and methanogenesis functions (P = 0.04).ConclusionsThe rumen microbiota of low-efficiency cows has stronger abilities to degrade carbohydrates and produce methane, and quorum sensing pathways could also be associated with differences in feed efficiency. This study provides a deeper understanding of the microbial ecology of dairy cows with different feed efficiencies and highlights the possibility of modulating the rumen microbiome or microbial functions to improve the feed efficiency of dairy cows.

Individual Feed Efficiency Monitoring of Charolaise Candidate Young Bulls in Relation to Feeding Behavior and Self-Performance Test Results.

Simple SummaryNowadays, in beef cattle breeding programs considerable interest lies in selecting animals that require fewer feed inputs without negatively impacting performance traits, thereby improving the profitability. This study has shown that the feeding behavior of Charolaise candidate young bulls mainly depend on residual feed intake (RFI), whilst RFI had no effect on phenotypic body composition and performance test results (except for feed intake/dry matter intake and gain to feed). Skeletal traits, including back-loin length and rump length as well as frame and muzzle width showed negative associations with RFI value, indicating that the longer, taller, higher frame size bulls were more efficient. At the same time, bulls with better RFI values were associated with forelegs/hind legs weakness. The close relationship of dry matter intake and feed efficiency in Charolaise candidate bulls suggests that measures are relevant and may have an application in the performance test. Performance from individual dry matter intake information may be the most cost-effective way to test a greater number of animals annually.This study evaluated the effect of differences in residual feed intake (RFI) of Charolaise candidate young bulls on feeding behavior and self-performance test results. Bulls were classified into high and low RFI (H-RFI, L-RFI) groups. Bulls were fed in a HOKOFARM system to measure individual animal intake and behavior. L-RFI bulls had significantly lower feed intakes (p = 0.002) and higher gain to feed ratio (p = 0.001), lower intake per day/kg DM (dry matter) (p = 0.002) and lower intake g/body weight/day (p < 0.001). L-RFI animals had lower visits number per day (p = 0.02), but spent longer time per visit (p = 0.02), and tended to have higher intake g/visit (p = 0.06) on feeders. The correlation between RFI and DMI (dry matter intake)/bodyweight/day as well as intake per day/kg were large and positive. Back-loin length and rump length, and moreover muzzle width and frame, showed negative correlations with RFI value. However, bulls with better RFI values associated with lower legs score. Results reveal that RFI was shown beneficial correlations with economically relevant self-performance traits. Further investigations are needed to seek additional indicator traits that are predictive for RFI.

Characterization and Duodenal Transcriptome Analysis of Chinese Beef Cattle With Divergent Feed Efficiency Using RNA-Seq.

Residual feed intake (RFI) is an important measure of feed efficiency for agricultural animals. Factors associated with cattle RFI include physiology, dietary factors, and the environment. However, a precise genetic mechanism underlying cattle RFI variations in duodenal tissue is currently unavailable. The present study aimed to identify the key genes and functional pathways contributing to variance in cattle RFI phenotypes using RNA sequencing (RNA-seq). Six bulls with extremely high or low RFIs were selected for detecting differentially expressed genes (DEGs) by RNA-seq, followed by conducting GO, KEGG enrichment, protein-protein interaction (PPI), and co-expression network (WGCNA, n = 10) analysis. A total of 380 differentially expressed genes was obtained from high and low RFI groups, including genes related to energy metabolism (ALDOA, HADHB, INPPL1), mitochondrial function (NDUFS1, RFN4, CUL1), and feed intake behavior (CCK). Two key sub-networks and 26 key genes were detected using GO analysis of DEGs and PPI analysis, such as TPM1 and TPM2, which are involved in mitochondrial pathways and protein synthesis. Through WGCNA, a gene network was built, and genes were sorted into 27 modules, among which the blue (r = 0.72, p = 0.03) and salmon modules (r = −0.87, p = 0.002) were most closely related with RFI. DEGs and genes from the main sub-networks and closely related modules were largely involved in metabolism; oxidative phosphorylation; glucagon, ribosome, and N-glycan biosynthesis, and the MAPK and PI3K-Akt signaling pathways. Through WGCNA, five key genes, including FN1 and TPM2, associated with the biological regulation of oxidative processes and skeletal muscle development were identified. Taken together, our data suggest that the duodenum has specific biological functions in regulating feed intake. Our findings provide broad-scale perspectives for identifying potential pathways and key genes involved in the regulation of feed efficiency in beef cattle.

Differential gene expression in liver of colored broiler chicken divergently selected for residual feed intake.

Feed constitutes about 60-70% of the total cost of poultry production. So maximizing the feed efficiency will reduce production cost. The rapid growth in the juvenile period is essential to achieve higher body weight. Therefore, identifying the genes and pathways involved in rapid growth at an early age with a lesser requirement of feed is of utmost importance to further economize the broiler production. The efficiency of feed utilization was measured using RFI (residual feed intake). The present study aimed to estimate the RFI (0-5week) in a population of indigenously developed colored broiler sire line chicken as well as identifying the differentially expressed genes influencing RFI in high and low RFI groups. The liver samples of high and low RFI broiler chicken aged 35days were used for microarray analysis. A total of 2798 differentially expressed genes (DEGs) were identified, out of which 913 genes were downregulated and 1885 were upregulated. The fold change varied from - 475.17 to 552.94. A subset of genes was confirmed by qRT-PCR, and outcomes were matched well with microarray data. In the functional annotation study of DEGs, the highest significant GO (Gene Ontology) terms in the biological process included protein transport, protein localization, regulation of apoptosis, and mitochondrial transport. Gene network analysis of these DEGs plays an important role to understand the interaction among genes. Study of the important genes which were differentially expressed and the related molecular pathways in this population may hold the potential for future breeding strategies for augmenting feed efficiency.

Feeding efficiency and behavior of young Simmental bulls selected for high growth capacity: Comparison of bulls with high vs. low residual feed intake

Thex objectives of this study were to evaluate the variability of residual feed intake (RFI) in young Simmental bulls and to study the potential use of certain feeding behavioral traits as indicators of feed efficiency. At an average age of 9 months, multiple groups of 6 young bulls were moved from the same pen to a pen equipped for monitoring of intake and feeding behaviors. For the first part of the study, 272 young bulls subjected to performance tests at the Genetic Center of Italian Simmental were considered. The overall ADG was 1.57 kg/day and the overall dry matter intake (DMI) was 10.35 kg/day. The RFI values ranged from −2.55 to +1.86 kg DM/day. Bulls visited the trough 49.5 times/day and the total feeding time (FT) was 113.1 min/day. There were 8.65 missing events (MEv) per day for a total time of 5.98 min/day. The base model, which considered metabolic body weight and ADG, explained 50.5% of the variability in DMI. Addition of feeding behaviors to the analysis explained an additional 5% of the variation in DMI (P < 0.05). In a dataset restricted to bulls with an average daily gain (ADG) greater than the overall average (1.57 kg/day), we selected two groups of bulls, a Low RFI group (n = 66) and a High RFI group (n = 79). As expected, the High RFI and Low RFI groups had the same ADG (1.77 kg/day) and significantly different DMI (P < 0.01). The different feed efficiency resulted in a significant reduction in excretions (P < 0.01), which were approximately 11% lower for methane, 9% lower for fecal N, and 13% lower for urinary N in the high efficiency group. The High RFI group had a higher feeding events number than the Low RFI group (P = 0.02), but the groups had similar daily FT (overall average: 115.3 min/day). The Low RFI group had a feeding rate that was 9.8 g DM/min lower than the High RFI group (P = 0.01). Most likely, the longer time of mastication and the slower feed intake allowed more efficient digestion in the Low RFI group. The two groups had no significant differences in MEv, in number or total time (both P > 0.05). This study is the first to evaluate feeding efficiency in an Italian Simmental breed. Although some behavioral traits differed significantly between the Low and High RFI groups, their inclusion in the DMI prediction model only had a small effect.