Background: Efficiency is characterized by maximum productivity with lower inputs and minimal waste, resulting in greater output with the same or even fewer resources. In livestock, more efficient animals in converting food into protein may improve the economic efficiency of production systems, as feed costs represent a significant expense in beef production. Thus, the present study aimed to use imputed whole-genome sequencing (WGS) data to perform a genome-wide association study (GWAS) in order to identify genomic regions and potential candidate genes involved in the biological processes and metabolic pathways associated with feed efficiency-related traits (RFI: residual feed intake, DMI: dry matter intake, FE: feed efficiency, FC: feed conversion, and RWG: residual weight gain) in Nellore cattle.
Results: The GWAS identified significant SNPs associated with feed efficiency traits in Nellore cattle. A total of 42 SNPs were detected for RFI, 10 for DMI, 99 for FC, 15 for FE, and 3 for RWG, distributed in different autosomes. Annotation analysis identified several candidate genes, and the prioritization highlighted 21, 9, 68, 23, and 8 key genes for RFI, DMI, FC, FE, and RWG, respectively. The prioritized candidate genes are involved in muscle development, lipid metabolism, response to oxidative stress, nutrient metabolism, neurotransmission, and oxidative phosphorylation. Additionally, enrichment analysis indicated that these genes act in several signaling pathways related to signal transduction, the nervous system, the endocrine system, energy metabolism, the digestive system, and nutrient metabolism.
Conclusion: The use of imputed WGS data in GWAS analyses enabled the broad identification of regions and candidate genes throughout the genome that regulate expression of feed efficiency-related traits in Nellore cattle. Our results provide new perspectives into the molecular mechanisms underlying feed efficiency in Nellore cattle, offering a genetic basis to guide the breeding of efficient animals, thereby optimizing resource utilization and the profitability of production systems.
Background: Zearalenone (ZEN), a common mycotoxin in ruminant diets, could disturb the rumen ecosystem and impair rumen fermentation. Noticeably, ZEN has been shown to reduce the relative abundances of specific bacterial taxa that potentially possess quorum sensing (QS) functions, which are deemed essential for the microbial interactions and adaptations during rumen fermentation. Nonetheless, whether QS communications participate in the responses of rumen microbial fermentation to ZEN remains unknown. Therefore, the present trial was performed to explore the potential roles of QS during the alterations of rumen microbial fermentation by ZEN through a rumen simulation technique (RUSITEC) system, in a replicated 4 × 4 Latin square design.
Results: ZEN significantly (P < 0.05) reduced QS signal autoinducer-2 (AI-2), and tended to (P = 0.051) downregulate QS signal C4-homoserine lactone (HSL). ZEN also significantly (P < 0.05) decreased total volatile fatty acid (TVFA), acetate, propionate, isobutyrate, isovalerate, organic matter disappearance (OMD), neutral detergent fiber disappearance (NDFD), and acid detergent fiber disappearance (ADFD) in different manners. The linear discriminant analysis effect size (LEfSe) analysis indicated significantly (P < 0.05) differential enrichments of a series of bacterial taxa such as Butyrivibrio_sp_X503, Rhizobium daejeonense, Hoylesella buccalis, Ezakiella coagulans, Enterococcus cecorum, Ruminococcus_sp_zg-924, Polystyrenella longa, and Methylacidimicrobium fagopyrum across different treatments. The phylogenetic investigation of communities by reconstruction of unobserved states 2 (PICRUSt2) analysis suggested that QS were predicted to be significantly (P < 0.05) affected by ZEN. The metabolomics analysis detected considerable significantly (P < 0.05) differing metabolites and implied that ZEN challenge significantly (P < 0.05) influenced the indole alkaloid biosynthesis, biosynthesis of alkaloids derived from shikimate pathway, and sesquiterpenoid and triterpenoid biosynthesis. Significant (P < 0.05) interconnections of QS molecules with the differential rumen fermentation traits, differential bacterial taxa, and differential metabolites were exhibited by Spearman analysis.
Conclusions: ZEN negatively affected the QS signals of AI-2 and C4-HSL, which was found to correlate with the fluctuations in specific rumen fermentation characteristics, ruminal bacterial populations, and ruminal metabolisms. These interrelationships implied the potential involvement of QS in the reactions of rumen microbiota to ZEN contamination, and probably contributed to the inhibition of rumen fermentation.
Background: The rapid emergence of multidrug-resistant Salmonella in poultry demands alternative control strategies beyond conventional antibiotics. In this study, we evaluated a combination of lytic Salmonella-infecting bacteriophages (SLAM_phiST45 and SLAM_phiST56) and a probiotic bacterium Limosilactobacillus reuteri (SLAM_LAR11) in a chick model challenged with Salmonella enterica serovar Typhimurium infection.
Results: Co-administration with two-phage cocktail and a probiotic showed markedly reduced Salmonella colonization in the gut and systemic organs of chicks, comparable to the effect of phage-only treatment. In contrast with phage-only treatment, the combined therapy significantly improved the rate of body-weight change from the day of infection to necropsy (P < 0.0001) and alleviated infection-associated splenomegaly (P = 0.028) and hepatomegaly (P = 0.011). In the ileum, the villus height-to-crypt depth ratio (VH/CD) increased significantly (P = 0.044). In the colon, expression of tight-junction genes OCLN (P = 0.014), TJP1 (P < 0.0001), and MUC2 (P = 0.011) was elevated, whereas the pro-inflammatory cytokine IL6 was reduced (P = 0.018). These improvements were accompanied, in the cecum, by trends toward decreases in Escherichia-Shigella (P = 0.09) and Clostridium (P = 0.16) and a trend toward an increase in Blautia (P = 0.11); additionally, in the ileum, Lactobacillus (P = 0.037) and Blautia (P = 0.016) increased significantly, yielding a more balanced microbiota than with phage-only treatment. Consistently, levels of functional metabolites, including acetic acid (LDA = 3.32) and lactic acid (LDA = 5.29), were increased.
Conclusion: Taken together, these findings demonstrate that phage-probiotic co-administration not only enhances the clearance of multidrug-resistant Salmonella more effectively than phage treatment alone but also promotes intestinal health, highlighting its potential as an antibiotic-alternatives strategy to improve intestinal health and ensure food safety in poultry production systems.

