Transcriptomic analysis of genes in the nitrogen recycling pathway of meat-type chickens divergently selected for feed efficiency

Chinese Herbal Extracts Mitigate Ammonia Generation in the Cecum of Laying Hens: An In Vitro Study

The objectives of the study were to screen one or several Chinese herbal extracts with good ammonia emission reduction effects using an in vitro gas production study. The study consisted of a control (without Chinese herbal extract), and 11 experimental groups with added cinnamon extract (CE), Osmanthus extract (OE), tangerine peel extract (TPE), dandelion extract (DE), Coptis chinensis extract (CCE), honeysuckle extract (HE), Pulsatilla root extract (PRE), yucca extract (YE), licorice extract (LE), Ginkgo biloba extract (GBE), or astragalus extract (AE). The results showed that HE, PRE, YE, LE, GBE, and AE significantly reduced ammonia production (p ≤ 0.05). The most significant ammonia inhibition was achieved via AE, resulting in a 26.76% reduction. In all treatments, Chinese herbal extracts had no significant effect on pH, conductivity, or uric acid, urea, and nitrate-nitrogen concentrations (p > 0.05). However, AE significantly reduced urease activity and the relative activity of uricase (p ≤ 0.05). AE significantly increased the relative abundance of Bacteroides and decreased the relative abundance of Clostridium, Desulfovibrio, and Prevotell (p ≤ 0.05). Astragalus extract inhibited ammonia emission from laying hens by changing the gut microbial community structure, reducing the relative abundance of ammonia-producing bacteria, and reducing microorganisms' uricase and urease activities.

Sodium butyrate reduces ammonia production in the cecum of laying hens by regulating ammonia-producing bacteria

Sodium butyrate is a commonly used feed additive and can reduce ammonia (NH₃) emissions from laying hens, but the mechanism of this effect is unknown. In this study, the sodium butyrate and cecal content of Lohmann pink laying hens were measured, and in vitro fermentation experiments and NH₃-producing bacteria coculture experiments were carried out to explore the relationship between NH₃ emissions and its associated microbiota metabolism. Sodium butyrate was found to significantly reduce NH₃ emission from the cecal microbial fermentation of Lohmann pink laying hens (P < 0.05). The concentration of NO₃^--N in the fermentation broth of the sodium butyrate-supplemented group increased significantly, and the concentration of NH₄⁺-N decreased significantly (P < 0.05). Moreover, sodium butyrate significantly reduced the abundance of harmful bacteria and increased the abundance of beneficial bacteria in the cecum. The culturable NH₃-producing bacteria consisted mainly of Escherichia and Shigella, such as Escherichia fergusonii, Escherichia marmotae and Shigella flexnerii. Among them, E. fergusonii had the highest potential for NH₃ production. The coculture experiment showed that sodium butyrate can significantly downregulate the expression of the lpdA, sdaA, gcvP, gcvH and gcvT genes of E. fergusonii (P < 0.05), thus reducing the NH₃ emission produced by the bacteria during metabolism. In general, sodium butyrate regulated NH₃-producing bacteria to reduce NH₃ production in the cecum of laying hens. These results are of great significance for NH₃ emission reduction in the layer breeding industry and for future research.

Comparative proteomics revealed duodenal metabolic function associated with feed efficiency in slow-growing chicken

The Korat chicken (KR), developed in Thailand, is a slow-growing breed developed as an alternative breed for Thai chicken producers. The growing interest in slow-growing chicken meat, due to its unique taste, distinct texture, health benefits, and higher broiler welfare have led to higher market demand for KR. However, its low feed efficiency (FE) has a significant negative impact on farm profitability. Understanding the molecular mechanism regulating FE allows for designing a suitable selection program and contributing to breeding more efficient chicken for poultry production. Thus, the objective of our study was to investigate the proteome differences and possible pathways associated with FE in male KR using a label-free quantitative proteomic approach. Seventy-five KR males were individually evaluated for FE, and duodenum samples from 6 animals (3 high-FE and 3 low-FE chickens) were collected at 10 wk of age for differential abundant proteins (DAPs), protein networks, functional enrichment, and pathway analyses. In this study, we found 40 DAPs significantly associated with FE pathways, including glycolysis/gluconeogenesis, peroxisome, oxidative phosphorylation, tight junction, and cysteine and methionine metabolism. Thus, variations in observed DAPs or genes related to DAPs could be interesting biomarker candidates for selection for higher feed utilization efficiency in chicken.

Ammonia reduction by the gdhA and glnA genes from bacteria in laying hens

Ammonia emissions are a high-focus pollution issue in the livestock industry. Ammonia-degrading bacteria can assimilate ammonia nitrogen as a nitrogen source to promote their growth and reproduction, providing an environmentally friendly, low-cost and safe biological way to reduce ammonia emissions from livestock. However, it remains unclear how ammonia-degrading bacteria reduce ammonia emissions from animals and what are the key ammonia assimilation genes. In the present study, two strains with ammonia nitrogen-degrading abilities (Enterococcus faecium strain C2 and Bacillus coagulans strain B1) were screened from laying chicken caecal and faecal samples and reduced ammonia emission rates by 53.60% and 31.38%, respectively. The expression levels of the ammonia assimilation genes gdhA, glnA, and GMPS increased significantly. On this basis, we successfully constructed three clone strains (PET-GDH, PET-GS, and PET-GMPS) that expressed the gdhA, glnA and GMPS genes in E. coli, respectively, to verify their ammonia-reducing activities. The results of an in vitro fermentation study showed that the ammonia production of the PET-GDH and PET-GS groups was significantly lower than that of the empty vector group (p < 0.05), with ammonia emission reduction rates of 55.5% and 54.8%, respectively. However, there was no difference between the PET-GMPS and empty vector groups. These results indicate that gdhA and glnA may be key genes involved in the bacterial-mediated regulation of ammonia emissions by laying hens, and ammonia emissions may be reduced by regulating their expression. The results of the present study provide a theoretical basis for the construction of engineered bacteria to reduce ammonia production in animals.

Natural 15N abundance in specific amino acids indicates associations between transamination rates and residual feed intake in beef cattle

Improving the ability of animals to convert feed resources into food for humans is needed for more sustainable livestock systems. Genetic selection for animals eating less while maintaining their performance (i.e., low residual feed intake [RFI]) appears a smart strategy but its effectiveness relies on high-throughput animal phenotyping. Here, we explored plasma nitrogen (N) isotope ratios in an attempt to identify easily superior young bulls in terms of RFI. For this, 48 Charolais young bulls fed two contrasting diets (corn vs. grass silage diets) were selected from a larger population as extreme RFI animals (24 low-RFI vs. 24 high-RFI) and their plasma analyzed for natural ¹⁵N abundance (δ¹⁵N) in the whole protein (bulk protein) and in the individual protein-bound amino acids (PbAA). For the first time, we showed that the δ ¹⁵N in plasma bulk protein differed (P = 0.007) between efficient (low-RFI) and inefficient (high-RFI) cattle regardless of diet. Furthermore, most analyzed PbAA followed the same trend as the bulk protein, with lower (P < 0.05) δ ¹⁵N values in more efficient (low-RFI) compared with less efficient (high-RFI) cattle, again regardless of diet. The only three exceptions were Phe, Met, and Lys (P > 0.05) for which the first metabolic reaction before being catabolized does not involve transamination, a pathway known naturally to enrich AAs in ¹⁵N. The contrasted isotopic signatures across RFI groups only in those PbAA undergoing transamination are interpreted as differences in transamination rates and N-use efficiency between low- and high-RFI phenotypes. Natural isotopic N signatures in bulk proteins and specific PbAA can be proposed as biomarkers of RFI in growing beef cattle fed different diets. However, the current study cannot delineate whether this effect only occurs post-absorption or to some extent also in the rumen. Our data support the conclusion that most efficient cattle in terms of RFI upregulate N conservation mechanisms compared with less efficient cattle and justify future research on this topic.

Dietary methionine level alters growth, digestibility, and gene expression of amino acid transporters in meat-type chickens

Imbalance in nutrients can affect digestibility of amino acids by altering gene expression of amino acid transporters. We investigated digestibility and molecular transporters of essential amino acids in chickens fed a methionine-deficient diet. A total of 40 chicks (23 D old) were randomly assigned to either a control (0.49% methionine) or a deficient (0.28%) diet until 41 D when they were sampled for Pectoralis (P.) major, kidney, ileum, and hypothalamus for mRNA expression analysis. The ileal content was collected for apparent ileal digestibility (AID) analysis. Birds fed the deficient diet had reduced growth and worse feed efficiency compared to control. The AID of methionine was similar between both groups. The AID of other essential amino acids was higher in the deficient group than control. mRNA expression of b0,+ AT and LAT4 were upregulated in the ileum and kidney but LAT1 was downregulated only in kidney of the deficient group compared to control. In the P. major, SNAT1, SNAT2, and CAT1 were upregulated in the deficient group compared to control. A diet deficiency in methionine affects digestibility of essential amino acids and cysteine, but not the digestibility of methionine. The change in digestibility is reflected in the mRNA expression of amino acid transporters across different tissues.

Effect of host genotype and Eimeria acervulina infection on the metabolome of meat-type chickens

Objective

A study was conducted to identify metabolic biochemical differences between two chicken genotypes infected with Eimeria acervulina and to ascertain the underlying mechanisms for these metabolic alterations and to further delineate genotype-specific effects during merozoite formation and oocyst shedding.

Methods

Fourteen day old chicks of an unimproved (ACRB) and improved (COBB) genotype were orally infected with 2.5 x 10⁵ sporulated E. acervulina oocysts. At 4 and 6 day-post infection, 5 birds from each treatment group and their controls were bled for serum. Global metabolomic profiles were assessed using ultra performance liquid chromatography/tandem mass spectrometry (metabolon, Inc.,). Statistical analyses were based on analysis of variance to identify which biochemicals differed significantly between experimental groups. Pathway enrichment analysis was conducted to identify significant pathways associated with response to E. acervulina infection.

Results

A total of 752 metabolites were identified across genotype, treatment and time post infection. Altered fatty acid (FA) metabolism and β-oxidation were identified as dominant metabolic signatures associated with E. acervulina infection. Key metabolite changes in FA metabolism included stearoylcarnitine, palmitoylcarnitine and linoleoylcarnitine. The infection induced changes in nucleotide metabolism and elicited inflammatory reaction as evidenced by changes in thromboxane B2, 12-HHTrE and itaconate.

Conclusions

Serum metabolome of two chicken genotypes infected with E. acervulina demonstrated significant changes that were treatment-, time post-infection- and genotype-dependent. Distinct metabolic signatures were identified in fatty acid, nucleotide, inflammation and oxidative stress biochemicals. Significant microbial associated product alterations are likely to be associated with malabsorption of nutrients during infection.

Feed Restriction Modulates the Fecal Microbiota Composition, Nutrient Retention, and Feed Efficiency in Chickens Divergent in Residual Feed Intake

There is a great interest to understand the impact of the gut microbiota on host's nutrient use and FE in chicken production. Both chicken's feed intake and gut bacterial microbiota differ between high and low-feed efficient chickens. To evaluate the impact of the feed intake level on the feed efficiency (FE)-associated variation in the chicken intestinal microbiota, differently feed efficient chickens need to eat the same amount of feed, which can be achieved by feeding chickens restrictively. Therefore, we investigated the effect of restrictive vs. ad libitum feeding on the fecal microbiome at 16 and 29 days posthatch (dph), FE and nutrient retention in chickens of low and high residual feed intake (RFI; metric for FE). Restrictively fed chickens were provided the same amount of feed which corresponded to 85% of the ad libitum fed group from 9 dph. FE was determined for the period between 9 and 30 dph and feces for nutrient retention were collected on 31 to 32 dph. From the 112 chickens (n = 56 fed ad libitum, and n = 56 fed restrictively), 14 low RFI and 15 high RFI ad libitum fed chickens, and 14 low RFI (n = 7 per sex) and 14 high RFI restrictively fed chickens were selected as the extremes in RFI and were retrospectively chosen for data analysis. Bray-Curtis dissimilarity matrices showed significant separation between time points, and feeding level groups at 29 dph for the fecal bacterial communities. Relevance networking indicated positive associations between Acinetobacter and feed intake at 16 dph, whereas at 29 dph Escherichia/Shigella and Turicibacter positively and Lactobacillus negatively correlated to chicken's feed intake. Enterobacteriaceae was indicative for low RFI at 16 dph, whereas Acinetobacter was linked to high RFI across time points. However, restrictive feeding-associated changes in the fecal microbiota were not similar in low and high RFI chickens, which may have been related to the higher nutrient retention and thus lower fecal nutrient availability in restrictively fed high RFI chickens. This may also explain the decreased RFI value in restrictively fed high RFI chickens indicating improved FE, with a stronger effect in females.

Transcriptional shifts account for divergent resource allocation in feed efficient broiler chickens

Considerable variation in feed efficiency (FE) has been observed in indigenous and selected meat-type chicken populations. Although this variation could be partially linked to extrinsic factors like diet, housing environment and microbiota, it further illustrates the existence of strong molecular mechanisms enabling the differential allocation of resources for various physiological processes. To further deepen the molecular basis of individual allocation capacity in male and female broilers, an RNA-seq experiment was conducted which based on a phenotyped chicken population divergent in FE. Transcriptional differences linked to FE were pronounced in intestinal and muscular tissue sites of male animals. Specifically, signalling pathways of farnesoid X receptor (FXR) and retinoid X receptor (RXR) might contribute to mediate individual FE. The transcriptional profiles suggested ACSBG2 (muscular lipid utilisation), ASBT (intestinal bile salt transport), CLEC2B (natural killer cell activation), HMGCS2 (jejunal, duodenal and muscular ketogenesis), and SCARB1 (jejunal lipid uptake) as potential mediators driving FE. Results indicate that improvements in FE exploit shifts in resource allocation which might occur at the expense of general immune responsiveness in high efficient male chickens. Consequently, to further improve FE traits and to explore causative molecular patterns, effects originating from sex-dimorphism in chickens need to be taken into consideration.

Differences in intestinal size, structure, and function contributing to feed efficiency in broiler chickens reared at geographically distant locations

The contribution of the intestinal tract to differences in residual feed intake (RFI) has been inconclusively studied in chickens so far. It is also not clear if RFI-related differences in intestinal function are similar in chickens raised in different environments. The objective was to investigate differences in nutrient retention, visceral organ size, intestinal morphology, jejunal permeability and expression of genes related to barrier function, and innate immune response in chickens of diverging RFI raised at 2 locations (L1: Austria; L2: UK). The experimental protocol was similar, and the same dietary formulation was fed at the 2 locations. Individual BW and feed intake (FI) of chickens (Cobb 500FF) were recorded from d 7 of life. At 5 wk of life, chickens (L1, n = 157; L2 = 192) were ranked according to their RFI, and low, medium, and high RFI chickens were selected (n = 9/RFI group, sex, and location). RFI values were similar between locations within the same RFI group and increased by 446 and 464 g from low to high RFI in females and males, respectively. Location, but not RFI rank, affected growth, nutrient retention, size of the intestine, and jejunal disaccharidase activity. Chickens from L2 had lower total body weight gain and mucosal enzyme activity but higher nutrient retention and longer intestines than chickens at L1. Parameters determined only at L1 showed increased crypt depth in the duodenum and jejunum and enhanced paracellular permeability in low vs. high RFI females. Jejunal expression of IL1B was lower in low vs. high RFI females at L2, whereas that of TLR4 at L1 and MCT1 at both locations was higher in low vs. high RFI males. Correlation analysis between intestinal parameters and feed efficiency metrics indicated that feed conversion ratio was more correlated to intestinal size and function than was RFI. In conclusion, the rearing environment greatly affected intestinal size and function, thereby contributing to the variation in chicken RFI observed across locations.

Feed conversion ratio, residual feed intake and cholecystokinin type A receptor gene polymorphisms are associated with feed intake and average daily gain in a Chinese local chicken population

Background

The feed conversion ratio (FCR) and residual feed intake (RFI) are common indexes in measuring feed efficiency for livestock. RFI is a feed intake adjusted for requirements for maintenance and production so these two traits are related. Similarly, FCR is related to feed intake and weight gain because it is their ratio. Cholecystokinin type A receptor (CCKAR) plays an important role in animal digestive process. We examined the interplay of these three parameters in a local Chinese chicken population.

Results

The feed intake (FI) and body weights (BW) of 1,841 individuals were monitored on a daily basis from 56 to 105 d of age. There was a strong correlation between RFI and average daily feed intake (ADFI) and a negative correlation between the FCR and daily gain (r_g = − 0.710). Furthermore, we identified 51 single nucleotide polymorphisms (SNPs) in the CCKAR and 4 of these resulted in amino acid mutations. The C334A mutation was specifically associated with FI and the expected feed intake (EFI) (P <  0.01) and significantly associated with the average daily gain (ADG) (P <  0.05). G1290A was significantly associated with FI and EFI (P < 0.05).

Conclusion

FCR is apply to weight selecting, and RFI is more appropriate if the breeding focus is feed intake. And C334A and G1290A of the CCKAR gene can be deemed as candidate markers for feed intake and weight gain.

Electronic supplementary material

The online version of this article (10.1186/s40104-018-0261-1) contains supplementary material, which is available to authorized users.

Assessing serum metabolite profiles as predictors for feed efficiency in broiler chickens reared at geographically distant locations

1. The objective of this study was to investigate differences in growth performance, serum intermediary metabolites, acute-phase proteins and white blood cells in low, medium and high-residual feed intake (RFI) chickens. It was also assessed if the environment affects the feed efficiency (FE) and FE-related performance and serum profiles of chickens. 2. Individual body weight (BW) and feed intake (FI) were recorded from d 7 of life. At 5 weeks of age, female and male broiler chickens (Cobb 500) were selected according to their RFI (L1: Austria; L2: UK; n = 9/RFI group, sex and locatity -45on) and blood samples were collected. 3. Chickens at L1 had similar FI but a 15% higher BW gain compared to chickens at L2. The RFI values of female chickens were -231, 8 and 215 g and those of male chickens -197, 0 and 267 g for low, medium and high RFI, respectively. 4. Location affected serum glucose, urea, cholesterol, non-esterified fatty acids (NEFA) and ovotransferrin in females, and serum glucose and triglycerides in male chickens. Serum uric acid and NEFA linearly increased from low to high RFI in females, whereas in males, cholesterol showed the same linear response from low to high RFI. Serum alpha-1-acid glycoprotein and blood heterophil-to-lymphocyte ratio linearly increased by 35% and 68%, respectively, from low to high RFI but only in male chickens at L1. 5. Regression analysis showed significant positive relationships between RFI and serum uric acid (R² = 0.49) and cholesterol (R² = 0.13). 6. It was concluded that RFI-related variation in serum metabolites of chickens was largely similar for the two environments and that serum metabolite patterns could be used to predict RFI in chickens.