Honey bees occupy a pivotal role in safeguarding ecological balance and bolstering the global agricultural economy through their indispensable pollination services. As the foremost commercial pollinator and producer of bee products, the western honey bees, Apis mellifera, have been extensively domesticated and managed worldwide. To harness their potential and enhance production traits, selective breeding practices are commonly implemented under human management. Nevertheless, despite the significance of these efforts, the foundational theories and concepts that underpin honey bee breeding remain fragmented. In this paper, we discuss the biological taxonomy of A. mellifera and the pertinent issues therein, emphasizing the necessity to recognize it as a domesticated animal and elucidate the concepts associated with livestock breeding. Drawing upon recent advances in the studies of honey bees and other domesticated species, we review the progress and challenges encountered in utilizing traditional breeding methods, which rely on phenotypic selection and natural mating, as well as marker-assisted selections integrating modern biotechnological tools at the molecular level. Moreover, the utilization of gene-editing tools in honey bee breeding is prospected, and the importance of reconciling bee breeding practices with conservation strategies is highlighted. Future research endeavors are anticipated to decipher the intricate genetic architecture underlying honey bee traits and develop precise genetic markers while weighing the ecological consequences of these breeding interventions. Through interdisciplinary collaboration and relentless innovation, robust technological support can be established to restore and protect honey bee populations, thereby ensuring the sustained vitality and contribution of this precious natural resource to our planet.

The dynamic interaction between the gut microbiota and the host significantly affects host biological processes and disease progression. In recent years, the regulatory mechanisms underlying these intricate interactions have been widely studied. Noncoding RNAs (ncRNAs) are a class of functional RNAs that, despite not being translated into proteins, play critical roles in mediating host–gut microbiota interactions. In this review, we systematically elucidate the mechanisms of action and influence of ncRNAs derived from both hosts and microorganisms. Specifically, certain host ncRNAs depend on the microbiota to modulate gene expression and function, whereas other host ncRNAs can alter the composition and functionality of the gut microbiota. Conversely, bacterial small RNAs (sRNAs) can infiltrate host cells and modulate the expression and functions of host genes. These interactions reveal the complex communication modes between the host and microbiota, providing a new perspective for investigating the occurrence and development of intestinal diseases. Consequently, through the intervention of ncRNAs, host‒microbe interaction dynamics can be effectively regulated, thereby providing potential theoretical and technical foundations for the prevention and treatment of intestinal diseases.

Rapid body weight gain in broilers overloads the metabolic system of the organism, resulting in leg abnormalities, which seriously affects animal welfare and industry economics. In this study, broilers with normal and deformed leg bones were examined. Serum biochemical indices showed that the serum calcium to phosphorus ratio was extremely decreased in leg deformed group. In addition, abnormal serum lipid levels suggested a disruption in lipid metabolism. Based on widely targeted metabonomic analysis of serum and cartilage tissues, a total of nine differential metabolites (DMs) significantly associated with leg abnormalities and serum calcium and phosphorus levels were screened, including carnitine C16:0, carnitine C18:1, 3-hydroxymethyl-L-tyrosine, cis-4-hydroxy-D-proline, cis-L-3-hydroxyproline, trans-4-hydroxy-L-proline, and so on. Pathway analysis revealed that fatty acid degradation and arachidonic acid metabolism were enriched. Analysis of DMs in these two pathways showed that prostaglandin D₂, prostaglandin J₂, prostaglandin A₂, 15-keto prostaglandin F_2α, and Δ12-prostaglandin J₂ significantly differed between the normal and abnormal groups. It was hypothesized that these important metabolic pathways and metabolites were involved in the metabolic regulation of leg abnormalities.

Enterococcus faecalis is known for its ability to form strong biofilms and its role as an opportunistic pathogen. In this study, we screened and characterized a multidrug-resistant (MDR) and strong biofilm-forming E. faecalis isolate obtained from a shrimp sample to determine its genetic diversity, molecular epidemiology, and underlying factors associated with antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs). The E. faecalis MTR_EFS01 strain was isolated using culturing, staining, and biochemical tests and MALDI-TOF methods. The MDR profile of the strain was determined through the disk diffusion test. The complete genomic sequence of E. faecalis MTR_EFS01 was obtained using the Illumina NextSeq2000 platform. The de novo assembly of the E. faecalis MTR_EFS01 genome revealed a total length of 2,862,301 bp with 80.0 × coverage. This genome comprised 38 contigs, a G + C content of 37.4%, and identified two CRISPR arrays, seven prophages, and 55 RNA genes. The E. faecalis MTR_EFS01 strain was classified as ST862 with a high pathogenicity index of 0.896. The strain harbored eight ARGs conferring resistance to tetracycline, erythromycin, trimethoprim, and MDR efflux pumps. Furthermore, 27 VFGs were identified in this strain, linked to antiphagocytosis, adherence, biofilm formation, enzymes, and immune invasion. Metabolic functional analysis revealed that our strain had 243 subsystems, with the most abundant genes associated with carbohydrate metabolism, amino acids and derivatives, and protein metabolism. The findings in this study underscore the importance of continuous monitoring, research, and collaborative efforts to address the growing threat of MDR and biofilm-forming pathogens in diverse settings.

Supplementation of sodium butyrate (SB) has been proved to be beneficial for improving the growth performance and health of animals, but its effects on rabbits have not been well understood. Therefore, this study aimed to investigate the effects of SB supplementation on growth performance, meat quality, and intestinal health of rabbits by evaluating feed intake and efficiency, diarrhea index, blood and cecum metabolites, cecal pH and short-chain fatty acids (SCFAs), histological staining, nutritional composition of meat, and gene expression profile of cecum. A total of 14 weaned male New Zealand White rabbits (35 ± 2 days, 1.70 ± 0.09 kg) were randomly divided into two groups: rabbits in Control group were fed normally with the basal diet, and rabbits in Butyrate group were supplemented with 0.75 g/kg SB on the basis of the basal diet. After a 1-week acclimatization period, the formal trial lasted for 10 weeks. Results suggest that dietary SB reduced the feed conversion ratio and diarrhea index of rabbits (p < 0.05). SB treatment significantly increased serum glutamyl transpeptidase, total bile acid, total cholesterol, triglyceride, and glucose levels and decreased tCO₂ content relative to the Control group (p < 0.05). Meanwhile, crude ash content in rabbits' meat was significantly increased by SB treatment (p < 0.05). Furthermore, SB treatment significantly increased the integrity of epithelial villi and number of goblet cells in the cecum and decreased cecal pH compared with the Control group. Dietary SB also upregulated levels of Na⁺-K⁺ ATPase, Ca²⁺-Mg²⁺ ATPase, total superoxide dismutase, and glutathione peroxidase in cecum. SCFAs analysis revealed that dietary supplementation with SB increases butyric acid in the cecum contents. Furthermore, SB supplementation is demonstrated to stimulate the proliferation and migration of cecal epithelial cells through activating Wnt/β-catenin pathways in rabbits both in vitro and in vivo by using transcriptome sequencing and gene function verification technologies. Taken together, our findings provide a theoretical basis for the application of SB as an alternative to antibiotics in livestock production.

China boasts an abundance of indigenous chicken genetic resources, where the exploitation of whole-genome single nucleotide polymorphism (SNP) information offers significant potential for their development. However, the current chicken SNP chips are primarily designed for commercial chickens or a few local breeds. To address this gap, we have developed “Shennong 1 chicken 40K” liquid chip utilizing the genotyping by targeted sequencing. This chip integrates SNPs and present/absent variants and is specifically crafted for Chinese indigenous chickens. It encompasses 44,849 target sites, selected through an integration of whole-genome resequencing data, pan-genome data, genome-wide association study data, and previously reported functional data for economic traits. Compared to published gene chips, this chip contains a higher number of polymorphic loci in Chinese indigenous chickens, demonstrating enhanced applicability. Our validation of the chip on 204 individuals from seven different breeds yielded a mean capture ratio of 99.474% for the target sites, with minor allele frequencies > 0.05 accounting for 98.557% of the total sites. This chip effectively classifies different breeds, aligning clustering results from population structure analysis with actual breed groupings, thereby demonstrating the chip's excellent applicability. Additionally, we identified genes associated with production and environmental adaptation in chickens through selection signal analysis (IGF1, SOX5, CACNA1G, and CXCR4). Importantly, the chip's functional sites allow for precise evaluation, aiding in understanding the economic traits of specific breeds for informed decision-making. Overall, the chip provides essential technical support for the conservation, breeding, identification, and evaluation of Chinese indigenous chicken genetic resources.

Age has an important effect on the aroma of chicken meat. In this study, we systematically analyzed the patterns of aroma changes with increasing age and the key aroma-contributing compounds and metabolites that lead to aroma differences with age. Electronic nose (e-nose) and gas chromatography-mass spectrometry analyses showed that the overall aroma intensity and the types and levels of volatile aroma compounds increased with age. Eight key aroma-contributing compounds were identified by GC-olfactometry (GC-O) and odor activity value analyses, and their content increased with age. The e-nose and GC-O results revealed that 315-day-old chickens had the strongest aroma. Thus, taking 315-day-old chickens as reference, we found that the contents of key aroma-contributing compounds and metabolites at 140 days of age were most similar to those at 315 days of age. Due to low feed cost, yellow chickens around 140 days of age were more suitable for marketing in terms of volatile aroma substances. It was found that hexanal, 1-octen-3-ol, and (E,E)-2,4-decadienal contributed the most to chicken aroma. Additionally, small peptides were found to be the main types of metabolites responsible for the aroma difference in chickens due to age. Weighted gene co-expression network analysis identified Ile-Ser, Ile-Thr, and Phe-Ile as metabolic markers of hexanal and 1-octen-3-ol, respectively. Further analysis revealed that Ile-Ser, Ile-Thr, and Phe-Ile may promote the Maillard reaction by acting as substrates on the one hand, and facilitating the uptake of amino acids on the other hand, which in turn increases the contents of hexanal and 1-octen-3-ol.

Wheat as a kind of diet material can be used for broiler production. However, due to non-starch polysaccharides in wheat, wheat may lead to lower growth performance and worth health. To reverse the negative effect, solid-state fermentation pro-enzymes were added. In this experiment, growth performance, intestinal health-related genes, short chain fatty acids (SCFAs) and intestinal microbiota were detected to find the effects of wheat meal and combined with enzymes on broiler chickens from 15 to 42 days of age. A total of 432 1-day-old Arbor Acres broiler chickens were fed corn-based diet (CD) for 14 days as the preparation stage of the experiment. Then, they were randomly divided into three groups and fed three different kinds of diets which were corn-based diet (CD group), wheat-based diet (WD group), and SFP enzymes supplementation in WD (Enzymes+Wheat-based diet group). The results showed that compared with broilers in CD group, broilers in WD group had lower weight gain and higher Feed conversion ratio (p < 0.05) during the whole experimental period especially from day 15 to day 21, but there was no significant effect on feed intake (p > 0.05). Moreover, SFP enzymes decreased the spleen index (p < 0.05). Wheat also had trends to decrease the expression of ZO-1 (p = 0.096) and increase the concentrations of acetate (p < 0.05), butyrate (p < 0.05) and total SCFAs (p < 0.05), in which SFP enzymes caused the opposite results except for butyrate, and SFP enzymes even increased the expression of ZO-1 (p < 0.001) and OCCLUDIN (p = 0.075) and decreased the expression of TNF-α (p < 0.01). Meanwhile, wheat enhanced the abundances of Barnesiella and Bifidobacterium (p < 0.05) and inhibited the abundances of Flavonifractor, Sellimonas, Lachnospiraceae_NK4A136_group, Subdoligranulum, and Ruminococcus_gauvreauii_group (p < 0.05), and SFP enzymes could reverse the negative effects, and the changes in microbiota could explain the other different parameters. Collectively, wheat results in inflammation and worse growth performance, but SFP enzymes supplementation in WD benefits chickens' growth performance by improving intestinal barrier function, decreasing inflammation, modulating cecal microbiota and SCFAs production.

The aim was to evaluate the ingestive behavior and body development of backgrounded heifers from three genotypes in the Brazilian Pantanal. Twenty-two heifers with an average body weight of 180 kg and 15 months of age were used, distributed into three genotype groups: eight Nelore (N), seven Nelore × Angus (½ Angus, NA), and seven Nelore × Pantaneiro (½ Pantaneiro, NP). Nelore and NP heifers exhibited similar grazing times, which were higher compared with NA heifers. It was observed that chest depth, heart girth, rump width between ischia, and hook width between ilia values were higher in NA heifers and similar among the other genotypes. The total and average daily gain of NA heifers was higher than N and NP heifers. It is concluded that there are significant differences in ingestive behavior and body development among genotypes, suggesting variations in the capacity of genotypes to adapt to the Pantanal environment. These results suggest that the crossbreeding between Nelore and Angus maximizes the benefits derived from heterosis, as individuals from this cross are more efficient in weight gain and have body development with desirable characteristics. The crossbreeding of the Pantaneiro breed with Nelore resulted in low body development in the NP heifers, indicating limited heterosis gains from this cross, even in the breed's native environment.