Antlers are unique mammalian organs that grow rapidly through extensive cartilage proliferation. Vitamin A (VA), via retinoic acid, is known to influence skeletal development, yet its contribution to antler growth remains unclear. We investigated whether rumen-protected VA supplementation modulates antler biology in sika deer by integrating gut microbiota profiling, fecal and serum metabolomics, antler cartilage transcriptomics, and in vitro chondrocyte assays. VA was associated with compositional shifts in the gut microbiota and altered metabolic profiles in feces and serum. Notably, the melatonin-derived metabolite AMFK increased in both matrices and showed strong associations with antler weight and cartilage-related gene expression. VA-supplemented deer exhibited higher antler weight, and antler transcriptomes indicated changes in pathways consistent with cartilage extracellular matrix and growth signaling. In chondrocytes, AMFK promoted proliferation and upregulated chondrogenic markers. Together, these findings suggest that VA may promote antler growth through a microbiota–metabolite–gene axis rather than by altering systemic retinol alone.

Feed efficiency remains a significant challenge in farmed raccoon dogs, and performance differences can occur even when diets are formulated with similar nutrient levels. Beyond nutrient concentrations, digestion kinetics can alter the timing of carbon and nitrogen availability along the gastrointestinal tract, thereby influencing microbial assembly in a segment-specific way. Twenty 2-month-old male raccoon dogs (Nyctereutes procyonoides) were divided into four dietary groups (n = 5) in a 2 × 2 factorial design. The design combined protein-source formulations containing either soybean cake or dried distillers grains with solubles and starch-source formulations based primarily on either extruded corn or high-amylose corn starch, representing relatively rapid and slow expected digestion characteristics, respectively. The purpose was to assess how digestion-rate synchronization affects jejunal and cecal microbiota structure and whether community state types (CSTs) link diet and feed efficiency. Growth performance varied modestly among treatments, with group B showing the lowest feed-to-gain ratio (F/G) and highest average daily gain (ADG). Starch source significantly affected ADG, while protein and protein × starch interaction influenced F/G. Microbiota profiles were strongly segment-dependent: the cecum had higher richness and diversity than the jejunum. Two-way analyses and Bray–Curtis ordinations showed that the jejunal community was primarily associated with the protein × starch interaction, whereas the cecal community was associated mainly with the protein-source factor and the protein × starch interaction. Network analysis revealed more complex and densely connected microbial communities in the cecum, with core genera occupying central positions. Dirichlet multinomial mixture modeling, performed independently for each intestinal segment, identified two jejunal community states (J-CST1 and J-CST2) and two cecal community states (C-CST1 and C-CST2). J-CST1 and J-CST2 represented alternative lactic acid bacteria-dominated configurations, with J-CST2 enriched in Lactobacillus and J-CST1 characterized by higher abundances of Streptococcus and Bacillus. C-CST2 was represented predominantly by samples from group B and was characterized by higher abundances of Segatella and taxa affiliated with Bacteroidota and Lachnospiraceae. Predicted functional profiles differed between CSTs, involving pathways related to carbohydrate, amino acid, lipid, and bile acid metabolism. Mediation analysis did not provide consistent evidence of significant indirect effects for J-CST membership, whereas C-CST membership was associated with significant estimated indirect effects on final body weight, ADG, and F/G. These findings suggest that dietary protein- and starch-source combinations with different expected digestion characteristics drive segment-specific microbial patterns. Supported by taxonomic, network and functional evidence, cecal CSTs act as an intermediate ecological phenotype that partially explains the variation in growth efficiency, highlighting hindgut community states as potential targets for personalized nutrition of raccoon dogs.

The gut microbiome plays critical roles in nutrient metabolism and host adaptation in ruminants, yet genome-level functional differences in the fecal microbiomes across geographic populations of wild red deer remain underexplored. Here, we integrated 16S rRNA gene sequencing and shotgun metagenomics to characterize the fecal microbiome of wild red deer populations in Inner Mongolia (NMG, n = 16) and Gansu Province (GS, n = 16), China. The NMG population exhibited significantly higher α-diversity and a distinct microbial community compared to GS (adjusted p < 0.05). NMG was enriched in Clostridium, Eubacterium, and Bacillus, while GS harbored higher abundances of Ruminococcus, Oscillospira, and Faecalibacterium (adjusted p < 0.05). Functional profiling revealed that the fecal microbiome in NMG showed greater functional potential associated with amino acid, pyruvate, and butanoate metabolism pathways, whereas the fecal microbiome in GS was enriched in the genetic potential of starch/sucrose metabolism, glycan degradation, and bile acid biotransformation (adjusted p < 0.05). CAZyme analysis demonstrated that GS was enriched in glycoside hydrolases, polysaccharide lyases, and carbohydrate esterases, while NMG showed higher auxiliary activity family abundance (adjusted p < 0.05). Genome-resolved metagenomics recovered 456 species-level genome bins (SGBs), revealing that GS-enriched SGBs (Rikenellaceae, Oscillospirales CAG-272) contained CAZyme genes associated with pectin degradation, whereas NMG-enriched SGBs contained genes associated with lignin modification and chitin degradation. These findings demonstrate the significant differences in the fecal microbiomes between the two geographically distinct wild red deer populations.