Combined effect of microbially derived cecal SCFA and host genetics on feed efficiency in broiler chickens

BACKGROUND

Improving feed efficiency is the most important goal for modern animal production. The regulatory mechanisms of controlling feed efficiency traits are extremely complex and include the functions related to host genetics and gut microbiota. Short-chain fatty acids (SCFAs), as significant metabolites of microbiota, could be used to refine the combined effect of host genetics and gut microbiota. However, the association of SCFAs with the gut microbiota and host genetics for regulating feed efficiency is far from understood.

RESULTS

In this study, 464 broilers were housed for RFI measuring and examining the host genome sequence. And 300 broilers were examined for cecal microbial data and SCFA concentration. Genome-wide association studies (GWAS) showed that four out of seven SCFAs had significant associations with genome variants. One locus (chr4: 29414391-29417189), located near or inside the genes MAML3, SETD7, and MGST2, was significantly associated with propionate and had a modest effect on feed efficiency traits and the microbiota. The genetic effect of the top SNP explained 8.43% variance of propionate. Individuals with genotype AA had significantly different propionate concentrations (0.074 vs. 0.131 μg/mg), feed efficiency (FCR: 1.658 vs. 1.685), and relative abundance of 14 taxa compared to those with the GG genotype. Christensenellaceae and Christensenellaceae_R-7_group were associated with feed efficiency, propionate concentration, the top SNP genotypes, and lipid metabolism. Individuals with a higher cecal abundance of these taxa showed better feed efficiency and lower concentrations of caecal SCFAs.

CONCLUSION

Our study provides strong evidence of the pathway that host genome variants affect the cecal SCFA by influencing caecal microbiota and then regulating feed efficiency. The cecal taxa Christensenellaceae and Christensenellaceae_R-7_group were identified as representative taxa contributing to the combined effect of host genetics and SCFAs on chicken feed efficiency. These findings provided strong evidence of the combined effect of host genetics and gut microbial SCFAs in regulating feed efficiency traits. Video Abstract.

Full-lactation performance of multiparous dairy cows with differing residual feed intake

Residual feed intake (RFI) is an efficiency trait underpinning profitability and environmental sustainability in dairy production. This study compared performance during a complete lactation of 36 multiparous dairy cows divided into three equal-sized groups with high (HRFI), intermediate (IRFI) or low RFI (LRFI). Residual feed intake was determined by two different equations. Residual feed intake according to the NorFor system was calculated as (RFI_NorFor) = (NE_intake)–(NE_maintenance + NE_gestation + NE_milk—NE_mobilisation + NE_deposition). Residual feed intake according to the USA National Research Council (NRC) (RFI_NRC) was calculated as: RFI = DMI − predicted DMI where predicted_s DMI = [(0.372× ECM)+(0.0968×BW^0.75)]×(1−e^{−0.192×(DIM/7+3.67)}). Cows in the HRFI_NorFor group showed higher daily CH₄ production, CH₄/ECM and CH₄ yield (g/kg DMI) than IRFI_NorFor and LRFI_NorFor cows. Cows characterized by high efficiency (LRFI_NorFor) according to the NorFor system had lower body weight. Dry matter intake and apparent dry matter digestibility were not affected by efficiency group but milk yield was lower in the low efficiency, HRFI_NorFor, group. Cows characterized by high efficiency according to the NRC system (LRFI_NRC) had lower dry matter intake while yield of CH₄ was higher. Daily CH₄ production and CH₄ g/kg ECM did not differ between RFI_NRC groups. Dairy cows characterized by high efficiency (both LRFI_NorFor and LRFI_NRC cows) over a complete lactation mobilized more of their body reserves in early lactation as well as during the complete lactation. The results also indicated great phenotypic variation in RFI between different stages the lactation.

In vitro and in vivo Studies of Soybean Peptides on Milk Production, Rumen Fermentation, Ruminal Bacterial Community, and Blood Parameters in Lactating Dairy Cows

Soybean peptides (SPs), a feed additive derived from soybean, exhibit nutritional function and biological activity in monogastric animals, but limited studies have been conducted in dairy cows. Our experiments were conducted to evaluate the effects of SPs on the nutrient degradability of dry matter (DM), crude protein (CP), neutral detergent fiber (NDF), and acid detergent fiber (ADF) in vitro and milk production, rumen fermentation and bacterial community, and blood parameters of dairy cows. For in vitro experiment, ruminal fluids were collected from three ruminal cannulated Holstein dairy cows. A total of three levels of SPs (0, 0.38, and 1.92 g/kg DM of SPs) were added to the total mixed ration (TMR). Nutrient degradability and fermentation fluid pH were determined at 24 and 48 h using 3.0 g samples of the substrate. Gas production after 48 h was recorded by an automated trace gas recording system using 0.5 g samples of the substrate. The results showed that DM, NDF, ADF (p < 0.01), and CP (p < 0.05) degradabilities were significantly increased at 1.92 g/kg DM of SPs at 24 h, and asymptotic gas production (p = 0.05) was increased at 48 h. For in vivo experiment, 110 lactating Holstein cows (209.7 ± 65.2 DIM; 37.2 ± 6.4 kg/d milk yield) were randomly assigned to 0 (control group, CON) or 50 g/head/day SPs (SP-supplemented group). Yields of milk (p < 0.05), milk protein (p < 0.05), and milk lactose (0.05 < p < 0.10) increased on SPs supplementation; however, the milk fat percentage decreased (p < 0.05). The concentrations of individual volatile fatty acids (VFAs) (p < 0.05) and superoxide dismutase (SOD) (p < 0.01) were also increased. Rumen bacterial diversity in SP-supplemented cows was higher (p < 0.05). The relative abundances of Rikenellaceae_RC9_gut_group, Butyrivibrio, Selenomonas, and Shuttleworthia were significantly increased and that of Coprococcus was decreased (p < 0.05). Our results showed that supplementing 1.92 g/kg DM of SPs could improve the nutrient degradability in vitro and 50 g/head/day of SPs could improve milk production and antioxidant ability of dairy cows. The rumen bacterial diversity was also enhanced by SP supplementation.

Association of Residual Feed Intake With Blood Metabolites and Reproduction in Holstein Cows

The objectives of this study were to evaluate the associations between residual dry matter (DM) intake or residual feed intake (RFI) from 1 to 15 weeks postpartum and concentrations of metabolites in plasma in early lactation and reproduction in Holstein cows. Data from 9 experiments, including 851 cows, were used. Intake of DM, milk yield, and body weight were evaluated daily, whereas milk composition and body condition were evaluated twice weekly for the first 105 days postpartum. Blood was sampled on the day of calving and again on days 7, 14, and 21 postpartum and analyzed for concentrations of non-esterified fatty acids (FA), β-hydroxybutyrate (BHB), and glucose. Reproduction was evaluated for the first 300 days postpartum. Residual DM intake was calculated as the observed minus the predicted intake, with intake predicted based on a model that accounted for major energy sinks. Cows were ranked and categorized into RFI quartiles, from the smallest (Q1) to the largest (Q4) RFI (−1.87, −0.46, 0.39, and 1.90 kg/day). Increasing efficiency (i.e., from Q4 to Q1) resulted in linear decreases in DM intake (Q1 to Q4; 18.9, 20.4, 21.3, and 22.7 kg/day), and median days open (132, 125, 135, and 147 d). Conversely, improving efficiency was associated with a linear increase in pregnancy per artificial insemination (AI, 31.4, 30.6, 31.2, and 24.5%) and quadratic increases in the 21-day cycle pregnancy rate (21.2, 21.1, 22.0, and 16.6%) and the proportion of pregnant cows (79.0, 80.7, 82.4, and 71.5%). The estimated net energy for lactation (NEL) content of diets increased linearly with improved RFI (1.88, 1.76, 1.71, and 1.58 Mcal/kg), resulting in no association between RFI and energy-corrected milk yield or body energy change. Nevertheless, increased feed efficiency was associated with a linear increase in concentrations of blood FA (0.68, 0.63, 0.60, and 0.59 mM), but a quadratic association with BHB (0.75, 0.64, 0.64, and 0.65 mM), with no association with glucose. Collectively, the most feed efficient cows ate 3.8 kg/day less DM, produced the same amount of energy-corrected milk, and had improved reproductive performance compared with the least efficient cows, thus suggesting that the underlying mechanisms responsible for improved feed efficiency might also be linked with improvements in reproduction.

Plasma proteins δ15N vs plasma urea as candidate biomarkers of between-animal variations of feed efficiency in beef cattle: Phenotypic and genetic evaluation

Identifying animals that are superior in terms of feed efficiency may improve the profitability and sustainability of the beef cattle sector. However, measuring feed efficiency is costly and time-consuming. Biomarkers should thus be explored and validated to predict between-animal variation of feed efficiency for both genetic selection and precision feeding. In this work, we aimed to assess and validate two previously identified biomarkers of nitrogen (N) use efficiency in ruminants, plasma urea concentrations and the ¹⁵N natural abundance in plasma proteins (plasma δ¹⁵N), to predict the between-animal variation in feed efficiency when animals were fed two contrasted diets (high-starch vs high-fibre diets). We used an experimental network design with a total of 588 young bulls tested for feed efficiency through two different traits (feed conversion efficiency [FCE] and residual feed intake [RFI]) during at least 6 months in 12 cohorts (farm × period combination). Animals reared in the same cohort, receiving the same diet and housed in the same pen, were considered as a contemporary group (CG). To analyse between-animal variations and explore relationships between biomarkers and feed efficiency, two statistical approaches, based either on mixed-effect models or regressions from residuals, were conducted to remove the between-CG variability. Between-animal variation of plasma δ¹⁵N was significantly correlated with feed efficiency measured through the two criteria traits and regardless of the statistical approach. Conversely, plasma urea was not correlated to FCE and showed only a weak, although significant, correlation with RFI. The response of plasma δ¹⁵N to FCE variations was higher when animals were fed a high-starch compared to a high-fibre diet. In addition, we identified two dietary factors, the metabolisable protein to net energy ratio and the rumen protein balance that influenced the relation between plasma δ¹⁵N and FCE variations. Concerning the genetic evaluation, and despite the moderate heritability of the two biomarkers (0.28), the size of our experimental setup was insufficient to detect significant genetic correlations between feed efficiency and the biomarkers. However, we validated the potential of plasma δ¹⁵N to phenotypically discriminate two animals reared in identical conditions in terms of feed efficiency as long as they differ by at least 0.049 g/g for FCE and 1.67 kg/d for RFI. Altogether, the study showed phenotypic, but non-genetic, relationships between plasma proteins δ¹⁵N and feed efficiency that varied according to the efficiency index and the diet utilised.

Assessing feed efficiency in early and mid lactation and its associations with performance and health in Holstein cows

Objectives were to evaluate the associations between residual dry matter (DM) intake (RFI) and residual N intake (RNI) in early lactation, from 1 to 5 wk postpartum, and in mid lactation, from 9 to 15 wk postpartum, and assess production performance and risk of diseases in cows according to RFI in mid lactation. Data from 4 experiments including 399 Holsteins cows were used in this study. Intakes of DM and N, yields of milk components, body weight, and body condition were evaluated daily or weekly for the first 105 d postpartum. Milk yield by 305 d postpartum was also measured. Incidence of disease was evaluated for the first 90 d postpartum and survival up to 300 d postpartum. Residual DM and N intake were calculated in early and mid lactation as the observed minus the predicted values, which were based on linear models that accounted for major energy or N sinks, including daily milk energy or N output, metabolic body weight, and daily body energy or N changes, and adjusting for parity, season of calving, and treatment within experiment. Cows were ranked by RFI and RNI in mid lactation and categorized into quartiles (Q1 = smallest RFI, to Q4 = largest RFI). Increasing efficiency in mid lactation resulted in linear decreases in RFI (depicted from Q1 to Q4; -0.93, -0.05, -0.04, and 0.98 kg/d), DMI (16.0, 16.9, 17.3, and 18.4 kg/d), net energy for lactation (NE_L) intake (26.8, 28.4, 29.0, and 30.8 Mcal/d), and NE_L balance (-9.0, -8.1, -8.2, and -5.5 Mcal/d) during early lactation, but no differences were observed in body NE_L or N changes or yield of energy-corrected milk in the first 5 wk of lactation. Residual DM intake in mid lactation was associated with RFI (Pearson r = 0.43, and Spearman ρ = 0.32) and RNI (r = 0.44, ρ = 0.36) in early lactation, and with RNI in mid lactation (r = 0.91, ρ = 0.84). Similarly, RNI in mid lactation was associated with RNI in early lactation (r = 0.42, ρ = 0.35). During the first 15 wk postpartum, more efficient cows in mid lactation consumed 3.5 kg/d less DM (Q1 = 19.3 vs. Q4 = 22.8 kg/d) and were more N efficient (Q1 = 31.6 vs. Q4 = 25.8%), at the same time that yields of milk (Q1 = 39.0 vs. Q4 = 39.4 kg/d), energy-corrected milk (Q1 = 38.6 vs. Q4 = 39.3 kg/d), and milk components did not differ compared with the quartile of least efficient cows. Furthermore, RFI in mid lactation was not associated with 305-d milk yield, incidence of diseases in the first 90 d postpartum, or survival by 300 d postpartum. Collectively, rankings of RFI and RNI are associated and repeatable across lactation stages. The most feed-efficient cows were also more N efficient in early and mid lactation. Phenotypic selection of RFI based on measurements in mid lactation is associated with improved efficiency without affecting production or health in dairy cows.

Association of residual feed intake with growth performance, carcass traits, meat quality, and blood variables in native chickens

Improving feed efficiency is a primary goal in poultry breeding strategies. Residual feed intake (RFI) in chickens typically calculated during the growing period is a measure of feed efficiency that is independent of the level of production. The objective of this study was to evaluate phenotypic correlations of growth performance, carcass traits, meat quality, and blood variables with RFI in growing native chickens. A total of 1,008 chickens were selected for the experiment to derive RFI. After the RFI measurement period of 42 d, 25 chickens with low RFI values, 25 chickens with medium RFI values, and 25 chickens with high RFI values were selected. The RFI was significantly positively correlated with feed conversion ratio and average daily feed intake, while it was not significantly correlated with initial body weight (BW), final BW, average daily body weight gain, and metabolic BW0.75. The abdominal fat weight and yield of high RFI group were significantly greater than those of medium and low RFI groups, and the abdominal fat yield was significantly positively correlated with RFI. Moreover, the plasma insulin-like growth factor 1 (IGF-1) content of low RFI group was significantly greater than those of high and medium RFI groups. The plasma concentrations of adrenocorticotropic hormone, triiodothyronine (T3), and cortisol of high RFI birds were significantly greater than that of low RFI birds. RFI was significantly positively correlated with plasma concentrations of T3 and cortisol, while it was significantly negatively correlated with plasma concentration of IGF-1. In addition, the serum levels of glucose and triglyceride of high RFI birds were significantly lower than that of low RFI birds. The serum low-density lipoprotein cholesterol (LDL-C) content of high RFI group was significantly greater than that of medium and low RFI groups, and it was significantly positively correlated with RFI. Our data suggested that selection of chickens with low RFI values may be beneficial to reduce fat deposition in native chickens without affecting the meat quality. Circulating IGF-1, T3, cortisol, and LDL-C concentrations can be used as indirect selection indicators of feed efficiency in native chickens. The effect of IGF-1, T3, cortisol, and LDL-C on feed efficiency of native chickens should be carefully examined and validated in future breeding programs.

miR-497 regulates fatty acid synthesis via LATS2 in bovine mammary epithelial cells

Both mRNA and miRNA play an important role in the regulation of mammary fatty acid metabolism and milk fat synthesis.

GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle

Residual feed intake (RFI), a measure of feed efficiency, is an important economic and environmental trait in beef production. Selection of low RFI (feed efficient) cattle could maintain levels of production, while decreasing feed costs and methane emissions. However, RFI is a difficult and expensive trait to measure. Identification of single nucleotide polymorphisms (SNPs) associated with RFI may enable rapid, cost effective genomic selection of feed efficient cattle. Genome-wide association studies (GWAS) were conducted in multiple breeds followed by meta-analysis to identify genetic variants associated with RFI and component traits (average daily gain (ADG) and feed intake (FI)) in Irish beef cattle (n = 1492). Expression quantitative trait loci (eQTL) analysis was conducted to identify functional effects of GWAS-identified variants. Twenty-four SNPs were associated (P < 5 × 10^-5) with RFI, ADG or FI. The variant rs43555985 exhibited strongest association for RFI (P = 8.28E-06). An eQTL was identified between this variant and GFRA2 (P = 0.0038) where the allele negatively correlated with RFI was associated with increased GFRA2 expression in liver. GFRA2 influences basal metabolic rates, suggesting a mechanism by which genetic variation may contribute to RFI. This study identified SNPs that may be useful both for genomic selection of RFI and for understanding the biology of feed efficiency.

Invited review: Learning from the future-A vision for dairy farms and cows in 2067

The world's population will reach 10.4 billion in 2067, with 81% residing in Africa or Asia. Arable land available for food production will decrease to 0.15 ha per person. Temperature will increase in tropical and temperate zones, especially in the Northern Hemisphere, and this will push growing seasons and dairy farming away from arid areas and into more northern latitudes. Dairy consumption will increase because it provides essential nutrients more efficiently than many other agricultural systems. Dairy farming will become modernized in developing countries and milk production per cow will increase, doubling in countries with advanced dairying systems. Profitability of dairy farms will be the key to their sustainability. Genetic improvements will include emphasis on the coding genome and associated noncoding epigenome of cattle, and on microbiomes of dairy cattle and farmsteads. Farm sizes will increase and there will be greater lateral integration of housing and management of dairy cattle of different ages and production stages. Integrated sensors, robotics, and automation will replace much of the manual labor on farms. Managing the epigenome and microbiome will become part of routine herd management. Innovations in dairy facilities will improve the health of cows and permit expression of natural behaviors. Herds will be viewed as superorganisms, and studies of herds as observational units will lead to improvements in productivity, health, and well-being of dairy cattle, and improve the agroecology and sustainability of dairy farms. Dairy farmers in 2067 will meet the world's needs for essential nutrients by adopting technologies and practices that provide improved cow health and longevity, profitable dairy farms, and sustainable agriculture.