Buffalo heifers selected for lower residual feed intake have lower feed intake, better dietary nitrogen utilisation and reduced enteric methane production

Host genetics and gut microbiota synergistically regulate feed utilization in egg-type chickens

BACKGROUND

Feed efficiency is a crucial economic trait in poultry industry. Both host genetics and gut microbiota influence feed efficiency. However, the associations between gut microbiota and host genetics, as well as their combined contributions to feed efficiency in laying hens during the late laying period, remain largely unclear.

METHODS

In total, 686 laying hens were used for whole-genome resequencing and liver transcriptome sequencing. 16S rRNA gene sequencing was conducted on gut chyme (duodenum, jejunum, ileum, and cecum) and fecal samples from 705 individuals. Bioinformatic analysis was performed by integrating the genome, transcriptome, and microbiome to screen for key genetic variations, genes, and gut microbiota associated with feed efficiency.

RESULTS

The heritability of feed conversion ratio (FCR) and residual feed intake (RFI) was determined to be 0.28 and 0.48, respectively. The ileal and fecal microbiota accounted for 15% and 10% of the FCR variance, while the jejunal, cecal, and fecal microbiota accounted for 20%, 11%, and 10% of the RFI variance. Through SMR analysis based on summary data from liver eQTL mapping and GWAS, we further identified four protein-coding genes, SUCLA2, TNFSF13B, SERTM1, and MARVELD3, that influence feed efficiency in laying hens. The SUCLA2 and TNFSF13B genes were significantly associated with SNP 1:25664581 and SNP rs312433097, respectively. SERTM1 showed significant associations with rs730958360 and 1:33542680 and is a potential causal gene associated with the abundance of Corynebacteriaceae in feces. MARVELD3 was significantly associated with the 1:135348198 and was significantly correlated with the abundance of Enterococcus in ileum. Specifically, a lower abundance of Enterococcus in ileum and a higher abundance of Corynebacteriaceae in feces were associated with better feed efficiency.

CONCLUSIONS

This study confirms that both host genetics and gut microbiota can drive variations in feed efficiency. A small portion of the gut microbiota often interacts with host genes, collectively enhancing feed efficiency. Therefore, targeting both the gut microbiota and host genetic variation by supporting more efficient taxa and selective breeding could improve feed efficiency in laying hens during the late laying period.

Enteric methane research and mitigation strategies for pastoral-based beef cattle production systems

Ruminant livestock play a key role in global society through the conversion of lignocellulolytic plant matter into high-quality sources of protein for human consumption. However, as a consequence of the digestive physiology of ruminant species, methane (CH₄), which originates as a byproduct of enteric fermentation, is accountable for 40% of global agriculture's carbon footprint and ~6% of global greenhouse gas (GHG) emissions. Therefore, meeting the increasing demand for animal protein associated with a growing global population while reducing the GHG intensity of ruminant production will be a challenge for both the livestock industry and the research community. In recent decades, numerous strategies have been identified as having the potential to reduce the methanogenic output of livestock. Dietary supplementation with antimethanogenic compounds, targeting members of the rumen methanogen community and/or suppressing the availability of methanogenesis substrates (mainly H₂ and CO₂), may have the potential to reduce the methanogenic output of housed livestock. However, reducing the environmental impact of pasture-based beef cattle may be a challenge, but it can be achieved by enhancing the nutritional quality of grazed forage in an effort to improve animal growth rates and ultimately reduce lifetime emissions. In addition, the genetic selection of low-CH₄-emitting and/or faster-growing animals will likely benefit all beef cattle production systems by reducing the methanogenic potential of future generations of livestock. Similarly, the development of other mitigation technologies requiring minimal intervention and labor for their application, such as anti-methanogen vaccines, would likely appeal to livestock producers, with high uptake among farmers if proven effective. Therefore, the objective of this review is to give a detailed overview of the CH₄ mitigation solutions, both currently available and under development, for temperate pasture-based beef cattle production systems. A description of ruminal methanogenesis and the technologies used to estimate enteric emissions at pastures are also presented.

Understanding the role of rumen epithelial host-microbe interactions in cattle feed efficiency

Feed efficiency is one of the economically important traits for the cattle industry that affects profit (feed costs) and the environment (production of manure and methane). Due to that feed efficiency is driven by multi-factors, mechanisms contributing to the animal to animal variation in this trait have not been well defined, limiting the development of precision feeding strategies to improve the herd production efficiency. Rumen microbial fermentation and volatile fatty acids (VFA) production have been recently reported to be associated with cattle feed efficiency, however the roles of rumen epithelial function in feed efficiency are less studied although the rumen epithelium has an important function in VFA absorption and metabolism which can affect host feed efficiency. Rumen epithelium is colonized with a diverse microbial population, termed epimural microbiota, which has proposed functions in tissue development, barrier and inflammation, urea transport, and oxygen scavenging, suggesting that they can affect rumen epithelial functions and subsequently cattle feed efficiency. Especially, prospective functions of epimural microbiota, enhanced rumen immunity and increased rumen epithelial thickness, might contribute to less nutritional requirement for tissue recuperation. Thus, the understanding of the functions of rumen epithelium, epimural microbiota, and rumen epithelial host-microbe interactions is essential to identify their roles in contributing to feed efficiency. In this review, we will focus on to date research findings on the structure of rumen epithelium, epimural microbiota, and epithelial host-microbe interactions together with their functions and how these are associated with feed efficiency, aiming to provide insights on future directions to study rumen epithelial host-microbe interactions and improve the rumen functions in cattle.

Identifying the key genes and functional enrichment pathways associated with feed efficiency in cattle

Residual feed intake (RFI) is a measurement of feed efficiency, and is inversely correlated with feed efficiency. The differentially expressed genes (DEGs) associated with RFI vary substantially among studies, posing great challenges in finding the RFI-related marker genes. This study attempted to resolve this issue by integrating and comparing the multiple transcriptome sequencing data associated with RFI in the cattle liver, using differential, functional enrichment, protein-protein interaction (PPI) network, weighted co-expression network (WGCNA), and gene set enrichment analyses (GSEA) to identify the candidate genes and functional enrichment pathways that are closely associated with RFI. Four candidate genes namely SHC1, GPX4, ACADL, and IGF1 were identified and validated as the marker genes for RFI. Four functional enrichment pathways, namely the fatty acid metabolism, sugar metabolism, energy metabolism, and protein ubiquitination were also found to be closely related to RFI. This study identified several genes and signaling pathways with shared characteristics, which will provide new insights into the molecular mechanisms related to the regulation of feed efficiency, and provide basis for molecular markers related to feed efficiency in beef cattle.

Residual feed intake and related biochemical parameters in male Sahiwal calves

This study was conducted to evaluate the differences in efficiency of feed utilisation in Sahiwal calves with low and high residual feed intake (RFI) by comparing feed intake, nutrient digestibility, growth traits and blood biochemical parameters. Eighteen growing male Sahiwal calves (aged 12 months, average body weight 120.04 kg) were selected and fed individually total mixed ration as per their requirements for a period of 60 days. Fifty per cent of maize grains in concentrate mixture containing 33% maize grains were replaced by fresh potatoes (DM basis). Based on linear regression models involving dry matter intake (DMI), average daily gain (ADG) and mid test metabolic body size, calves were assigned into low and high RFI groups. Residual feed intake (RFI) values were calculated for individual calves and the calves were divided into low (–0.20) and high (+0.18) RFI groups. Low RFI animals consumed less dry matter than the expected or predicted one indicating their more efficiency of feed utilization. The intakes of DM and CP were 4.95 and 6.47% lower in low RFI animals compared to high RFI animals while average daily gain was higher in low RFI group. The digestibility of DM, OM, CP, EE, total carbohydrates, NDF and ADF were similar in low and high RFI groups, however, nitrogen retention was higher in low RFI group. Values of alanine amino transferase (25.85 vs. 35.72 IU/L), aspartate amino transferase (80.33 vs. 100.57 IU/L), total protein (7.34 and 8.24 mg/dL), blood urea nitrogen (15.45 and 22.22 mg/dL) and creatinine (1.27 and 1.78 mg/dL) were higher for high RFI as compared to low RFI group. The concentration of growth hormone, insulin and IGF-1 were similar in both the groups. From present study, it could be concluded that low RFI animals were more efficient in feed conversion.

Energy partitioning by broiler breeder hens in conventional daily-restricted feeding and precision feeding systems

An empirical linear mixed model was derived to describe metabolizable energy (ME) partitioning in broiler breeder hens. Its coefficients described ME used for total heat production (HP), growth (ADG), and egg mass (EM). A total of 480 Ross 308 hens were randomly and equally assigned to 2 treatments: precision feeding (PF) and conventional daily-restricted feeding (CON) from 23 to 34 wk of age. The PF system allowed birds to enter feeding stations voluntarily at any time, weighed them, and provided access to feed for 60 s if their BW was less than the breeder-recommended target BW. The CON birds were fed daily each morning. Energetic efficiency of hens was evaluated using residual feed intake (RFI), defined as the difference between observed and predicted ME intake (MEI). The energy partitioning model predicted (P < 0.05): MEI = A × BW0.67 + 1.75 × ADG + 0.75 × EM + ϵ. The coefficient A, a vector of age-specific HP, was 142 kcal/kg0.67/d; the energy requirement for growth and EM was 1.75 and 0.75 kcal/g, respectively. For the CON and the PF hens, respectively, MEI was 366 and 354 kcal/d (P = 0.006); RFI was -5.9 and 6.7 kcal/d (P = 0.009); HP% was 85.5 and 87.7 (P < 0.001); hen-day egg production (HDEP) was 65.5 and 55.2% (P < 0.001). Although the CON hens had higher MEI, the model predicted lower HP%; thus, CON hens had more nutrients available for egg production, increased egg production, and were more energetically efficient than the PF hens. The decreased egg production by the PF hens was likely due to these hens receiving production-related feed increases after an egg was laid. However, feed allocation increases for the CON hens resulted in increasing MEI for all CON hens at the same time. Therefore, the PF hens had lower MEI and lower HDEP than the CON hens.

Identification of key genes and pathways associated with feed efficiency of native chickens based on transcriptome data via bioinformatics analysis

BACKGROUND

Improving feed efficiency is one of the important breeding targets for poultry industry. The aim of current study was to investigate the breast muscle transcriptome data of native chickens divergent for feed efficiency. Residual feed intake (RFI) value was calculated for 1008 closely related chickens. The 5 most efficient (LRFI) and 5 least efficient (HRFI) birds were selected for further analysis. Transcriptomic data were generated from breast muscle collected post-slaughter.

RESULTS

The differently expressed genes (DEGs) analysis showed that 24 and 325 known genes were significantly up- and down-regulated in LRFI birds. An enrichment analysis of DEGs showed that the genes and pathways related to inflammatory response and immune response were up-regulated in HRFI chickens. Moreover, Gene Set Enrichment Analysis (GSEA) was also employed, which indicated that LRFI chickens increased expression of genes related to mitochondrial function. Furthermore, protein network interaction and function analyses revealed ND2, ND4, CYTB, RAC2, VCAM1, CTSS and TLR4 were key genes for feed efficiency. And the 'phagosome', 'cell adhesion molecules (CAMs)', 'citrate cycle (TCA cycle)' and 'oxidative phosphorylation' were key pathways contributing to the difference in feed efficiency.

CONCLUSIONS

In summary, a series of key genes and pathways were identified via bioinformatics analysis. These key genes may influence feed efficiency through deep involvement in ROS production and inflammatory response. Our results suggested that LRFI chickens may synthesize ATP more efficiently and control reactive oxygen species (ROS) production more strictly by enhancing the mitochondrial function in skeletal muscle compared with HRFI chickens. These findings provide some clues for understanding the molecular mechanism of feed efficiency in birds and will be a useful reference data for native chicken breeding.

Residual feed intake divergence during the preweaning period is associated with unique hindgut microbiome and metabolome profiles in neonatal Holstein heifer calves

BACKGROUND

Recent studies underscored that divergence in residual feed intake (RFI) in mature beef and dairy cattle is associated with changes in ruminal microbiome and metabolome profiles which may contribute, at least in part, to better feed efficiency. Because the rumen in neonatal calves during the preweaning period is underdeveloped until close to weaning, they rely on hindgut microbial fermentation to breakdown undigested diet components. This leads to production of key metabolites such as volatile fatty acids (VFA), amino acids, and vitamins that could potentially be absorbed in the hind-gut and help drive growth and development. Whether RFI divergence in neonatal calves is associated with changes in hindgut microbial communities and metabolites is largely unknown. Therefore, the objective of the current study was to determine differences in hindgut microbiome and metabolome in neonatal Holstein heifer calves retrospectively-grouped based on feed efficiency as most-efficient (M-eff) or least-efficient (L-eff) calves using RFI divergence during the preweaning period.

METHODS

Twenty-six Holstein heifer calves received 3.8 L of first-milking colostrum from their respective dams within 6 h after birth. Calves were housed in individual outdoor hutches bedded with straw, fed twice daily with a milk replacer, and had ad libitum access to a starter grain mix from birth to weaning at 42 d of age. Calves were classified into M-eff [n = 13; RFI coefficient = - 5.72 ± 0.94 kg DMI (milk replacer + starter grain)/d] and L-eff [n = 13; RFI coefficient = 5.61 ± 0.94 kg DMI (milk replacer + starter grain)/d] based on a linear regression model including the combined starter grain mix and milk replacer DMI, average daily gain (ADG), and metabolic body weight (MBW). A deep sterile rectal swab exposed only to the rectum was collected immediately at birth before colostrum feeding (i.e., d 0), and fecal samples at d 14, 28, and 42 (prior to weaning) for microbiome and untargeted metabolome analyses using 16S rRNA gene sequencing and LC-MS. Microbiome data were analyzed with the QIIME 2 platform and metabolome data with the MetaboAnalyst 4.0 pipeline.

RESULTS

No differences (P > 0.05) in body measurements including body weight (BW), body length (BL), hip height (HH), hip width (HW), and wither height (WH) were detected between M-eff and L-eff calves at birth and during preweaning. Although milk replacer intake did not differ between groups, compared with L-eff, M-eff heifers had lower starter intake (P < 0.01) between d 18 to 42 of age, whereas no differences (P > 0.05) for ADG, cumulative BWG, or body measurements were observed between RFI groups during the preweaning period. Microbiome and metabolome profiles through the first 42 d of age indicated greater hindgut capacity for the production of energy-generating substrates (butyrate and propionate) and essential nutrients (vitamins and amino acids) in heifers with greater estimated feed efficiency.

CONCLUSION

Despite consuming approximately 54.6% less solid feed (cumulative intake, 10.90 vs. 19.98 ± 1.66 kg) from birth to weaning, the microbiome-metabolome changes in the hindgut of most-efficient heifers might have helped them maintain the same level of growth as the least-efficient heifers.

Associations between residual feed intake and apparent nutrient digestibility, in vitro methane-producing activity, and volatile fatty acid concentrations in growing beef cattle1

The objectives of this study were to examine the relationship between residual feed intake (RFI) and DM and nutrient digestibility, in vitro methane production, and volatile fatty acid (VFA) concentrations in growing beef cattle. Residual feed intake was measured in growing Santa Gertrudis steers (Study 1; n = 57; initial BW = 291.1 ± 33.8 kg) and Brangus heifers (Study 2; n = 468; initial BW = 271.4 ± 26.1 kg) fed a high-roughage-based diet (ME = 2.1 Mcal/kg DM) for 70 d in a Calan-gate feeding barn. Animals were ranked by RFI based on performance and feed intake measured from day 0 to 70 (Study 1) or day 56 (Study 2) of the trial, and 20 animals with the lowest and highest RFI were identified for subsequent collections of fecal and feed refusal samples for DM and nutrient digestibility analysis. In Study 2, rumen fluid and feces were collected for in vitro methane-producing activity (MPA) and VFA analysis in trials 2, 3, and 4. Residual feed intake classification did not affect BW or BW gain (P > 0.05), but low-RFI steers and heifers both consumed 19% less (P < 0.01) DMI compared with high-RFI animals. Steers with low RFI tended (P < 0.1) to have higher DM digestibility (DMD) compared with high-RFI steers (70.3 vs. 66.5 ± 1.6% DM). Heifers with low RFI had 4% higher DMD (76.3 vs. 73.3 ± 1.0% DM) and 4 to 5% higher (P < 0.01) CP, NDF, and ADF digestibility compared with heifers with high RFI. Low-RFI heifers emitted 14% less (P < 0.01) methane (% GE intake; GEI) calculated according to Blaxter and Clapperton (1965) as modified by Wilkerson et al. (1995), and tended (P = 0.09) to have a higher rumen acetate:propionate ratio than heifers with high RFI (GEI = 5.58 vs. 6.51 ± 0.08%; A:P ratio = 5.02 vs. 4.82 ± 0.14%). Stepwise regression analysis revealed that apparent nutrient digestibilities (DMD and NDF digestibility) for Study 1 and Study 2 accounted for an additional 8 and 6%, respectively, of the variation in intake unaccounted for by ADG and mid-test BW0.75. When DMD, NDF digestibility, and total ruminal VFA were added to the base model for Study 2, trials 2, 3, and 4, the R2 increased from 0.33 to 0.47, explaining an additional 15% of the variation in DMI unrelated to growth and body size. On the basis of the results of these studies, differences in observed phenotypic RFI in growing beef animals may be a result of inter-animal variation in apparent nutrient digestibility and ruminal VFA concentrations.

Nitrogen recycling and feed efficiency of cattle fed protein-restricted diets

The ability of cattle to grow and reproduce when ingesting low-protein diets is a crucial attribute for productive beef cattle systems in the seasonally dry tropics and subtropics. Nitrogen (N) recycling to the rumen is an important and known physiological mechanism allowing ruminants to efficiently grow in low-protein diets, but is usually disregarded in the nutritional models. This review discusses the role and magnitude of N recycling to provide additional N as microbial substrate in the rumen and in determining the efficiency of ruminants ingesting low-protein diets, to better understand the major factors regulating N recycling to the rumen. In addition to a review of the literature, study-adjusted regressions were used to evaluate various aspects of crude protein (CP) intake and availability, N recycling and excretion. There is large variation in N excretion and N-use efficiency among diets and among individuals, illustrating the opportunity for improvement in overall efficiency of cattle production. These data indicated that N recycling to the entire gastrointestinal tract supplies from half to twice as much N available for microbial growth as does the diet. Addition of rumen-degradable protein can increase rumen efficiency in using the available energy, as, conversely, the addition of fermentable energy can increase rumen efficiency in using the available CP. The present review has demonstrated that both are possible because of greater N recycling. Also, the importance of preserving the available N for determining individual variation in feed efficiency and the implications for selection are discussed. Nitrogen recycling can be controlled at both the epithelial wall of compartments of the gastrointestinal tract and at the liver, where ureagenesis occurs. Addition of fermentable energy can increase N recycling to the rumen and to post-ruminal tract by acting at both sites, and the mechanisms for this are discussed in the text. Although the effect of altering CP concentration in the diet has been substantially investigated, other factors potentially modulating N recycling, such as total fermentable energy, sources of protein and energy, hormonal modulation, and genetic variance, remain poorly understood. The selection of more efficient animals and development of diets with a lower environmental impact inescapably means further elucidation of the N-recycling mechanism.