Integrated characterization of the gut microbiome and metabolome in female Père David’s deer (Elaphurus davidianus) across a reproductive transition

Although the gut microbiota plays a critical role in energy harvesting in ruminants, the restructuring of the microbiome–metabolome axis during the transition from late pregnancy to the postbreeding season remains poorly understood in the endangered Père David’s deer ( Elaphurus davidianus ). Recovery of this species continues to be influenced by the metabolic and immunological trade-offs associated with reproductive transitions. In a small longitudinal cohort of three adult female E. davidianus , we integrated shotgun metagenomic sequencing with untargeted GC-TOF-MS fecal metabolomics. Each individual was sampled during late pregnancy and again during the postbreeding season, yielding six paired fecal samples. To ensure continuity of individual sampling, GPS tracking was employed. Our exploratory findings suggest a pattern of functional plasticity within a broadly conserved core microbiome. Although microbial richness and diversity remained stable across reproductive stages, nominally significant stage-specific taxonomic and functional differences were observed. During late pregnancy, nominally higher abundances of Bacteroides and Akkermansiaceae, together with starch-degrading enzymes (e.g., GH13_40) and elevated fecal galactose, were observed. In contrast, during the postbreeding season, nominally higher abundances of Clostridiaceae and Sarcina were accompanied by functional patterns suggestive of lipid metabolism and nitrogen recycling (e.g., L-ornithine). Although Procrustes analysis indicated suggestive congruence between microbial and metabolic profiles (M² = 0.33), this congruence is constrained by the small sample size and should therefore be interpreted with caution. None of the differential abundance or metabolomic findings remained significant after false discovery rate correction. These preliminary findings generate hypotheses regarding stage-specific microbiome–metabolome adjustments during the reproductive transition in E. davidianus . To validate these observations, future studies should incorporate larger sample sizes, paired host physiological measurements, and controlled dietary trials. Integrative fecal metagenomic and metabolomic profiling may provide a non-invasive exploratory approach for generating hypotheses in endangered ungulate conservation research.