Reintroduction is an effective strategy in the conservation of endangered species under scientific monitoring. Intestinal flora plays an important role in the envir onmental adaptation of endangered Père David’s deer (Elaphurus davidianus). In this study, 34 fecal samples from E. davidianus were collected from different habitats in Tianjin city of China to investigate differences in the intestinal flora under captive and semi-free-ranging conditions. Based on 16S rRNA high-throughput sequencing technology, a total of 23 phyla and 518 genera were obtained. Firmicutes was dominant in all individuals. At the genus level, UCG-005 (13.05%) and Rikenellaceae_RC9_gut_group (8.94%) were dominant in captive individuals, while Psychrobacillus (26.53%) and Pseudomonas (11.33%) were dominant in semi-free-ranging individuals. Alpha diversity results showed that the intestinal flora richness and diversity were significantly (P < 0.001) higher in captive individuals than in semi-free-ranging individuals. Beta diversity analysis also showed a significant difference (P = 0.001) between the two groups. In addition, some age- and sex-related genera such as Monoglobus were identified. In summary, the structure and diversity of intestinal flora showed significant habitat variation. This is the first time an analysis has been undertaken of the structural differences of the intestinal flora in Père David’s deer, under different habitats in the warm temperate zone, providing a reference basis for the conservation of endangered species.

Understanding how wetland habitat micromodification impacts the health of birds through dietary and microbial adjustments is critical for their conservation. Tianjin Qilihai Wetland serves as a critical migration stopover site for the oriental stork ( Ciconia boyciana ), while having undergone a habitat micromodification. In this study, the fecal samples of oriental storks across pre-change group (collected in 2022), under-change group (collected in 2023), and post-change group (collected in 2024) from Tianjin Qilihai Wetland were analyzed by integrating fecal microhistology with 16S rRNA sequencing. The results showed that, at the phylum level, the dominant bacterial phyla of oriental storks in the three years all contained Firmicutes and Actinobacteria, and at the genus level, the dominant bacterial genera of gut microbiota were Paeniclostridium and Lactobacillus . The abundances of Paeniclostridium and Lactobacillus were highest in under-change group. Ten species of plants belonging to 10 genera and 8 families were identified based on microscopic examination, of which Abutilon theophrasti was unique in pre-change group, Suaeda glauca and Nelumbo nucifera were unique in under-change group. During the environmental micromodifications, the quality of the wetland environment declined, and the types and quantity of food resources available changed, which in turn affected the diet choice and gut microbiota structure of oriental storks. The research provides a reference for wetland micromodifications and wildlife conservation.

Understanding diet–health linkages in endangered oriental storks (Ciconia boyciana) occupying non-traditional overwintering habitats is imperative for conservation prioritization. Integrated high-throughput sequencing and microscopic analyses revealed their food composition, gut microbiome profile, and critical associations between diet selection and health status. Dominant gut microbial phyla included Firmicutes (64.62%), Fusobacteriota (24.08%), and Bacteroidota (4.10%), with Clostridium_sensu_stricto_1 (21.93%), Paeniclostridium (14.21%), and Fusobacterium (12.58%) at genus level. Microscopic examination of fecal samples identified six plant species (three families, six genera), while sequencing detected five plant-derived and two animal-derived food families. Both methods confirmed Poaceae, Cannabaceae, and Apocynaceae; sequencing uniquely revealed Malvaceae and Leguminosae. There was a significant negative correlation between Cyprinidae and Bacteroidota (0.01 < p ≤ 0.05). Both diet composition and gut microbial structure of the Ciconia boyciana in this study reflect flexible adaptation in response to winter thermoregulation and local food availability, providing a scientific basis for evidence-based conservation of this endangered species as well as other ecologically similar species. This work offers practical guidance for habitat restoration and dietary supplementation in non-traditional wintering sites while informing conservation strategies for ecologically similar species. Due to the limited sample size, future efforts will expand sampling to more accurately characterize population-level dietary patterns and gut microbiota profiles, thereby strengthening conservation decision-making.