Geographical Differences and Temporal Dynamics of Intestinal Microbiota in Endangered Great Bustard Otis tarda Based on Environmental DNA Metabarcoding.

Intestinal microbiota plays a crucial role in host physiological adaptation, though research on the characteristics of intestinal microbiota in the endangered great bustard Otis tarda has been initiated, with prior studies focusing on gut microbial composition, diversity dynamics, and the impacts of captivity and overwintering periods. Comprehensive insights into geographical differences and short-term temporal dynamics across diverse habitats remain limited. Here, we used fecal environmental (eDNA) metabarcoding to investigate the geographical differences and temporal dynamics of the intestinal microbiota in great bustards from Hebei (HB), Inner Mongolia Autonomous Region (NMG), and Shaanxi (SX) provinces of China, with temporal sampling in two sites (the confluence area of the Yellow River and the Weihe and the Luohe rivers) of SX during December 2024-March 2025. Results revealed that the great bustard intestinal microbiota was dominated by Firmicutes, Proteobacteria, and Bacteroidota at the phylum level, with core genera including Lachnoclostridium, Subdoligranulum, and Blautia. Significant geographical divergence was observed in the NMG population (grassland habitat), which exhibited a unique enrichment of Verrucomicrobiota (especially Akkermansia), while SX (farmland) and HB populations were dominated by Firmicutes. Temporal dynamics in SX showed fluctuations in microbial diversity and composition, which may be linked to temporal dietary shifts in winter (inferred from habitat vegetation characteristics, as direct diet measurement was not conducted). Functional predictions indicated conserved metabolic functions across populations, with variations in genetic information processing and environmental adaptation-related functions. These findings highlight that the great bustard's intestinal microbiota may be shaped by habitat-specific factors (i.e., diet and environment, inferred from habitat type) and temporal changes, providing insights into putative microbial mechanisms underlying the ecological adaptation of the endangered great bustard O. tarda. This study contributes to understanding host-microbiota interactions in endangered avians and supports evidence-based conservation strategies.