The foraging environment is a critical source of microbes for wild birds, yet its role in shaping the gut microbiota of sympatric crane species remains poorly understood. This study investigated this relationship in the Yellow River Delta wetland by analyzing the microbial communities of paired foraging environments and fecal samples from Common Cranes (Grus grus) and White Cranes (Grus leucogeranus) via 16S rRNA gene sequencing. Significant inter-group differences in alpha diversity (ACE, Chao1, Shannon, Simpson) indicated strong environmental filtering effects. Beta diversity (PCoA) revealed pronounced segregation between foraging and fecal samples (PC1 = 25.0%), underscoring a significant microbial turnover between the environment and the gut. Dominant phyla included Proteobacteria (24.6–37.4%), Firmicutes (4.8–29.0%), and Actinobacteriota (12.4–23.3%). LEfSe identified genus-level biomarkers highly specific to sample type and host, including Ligilactobacillus (12.1% in Common Crane feces) and Cryobacterium (9.2% in White Crane feces). SourceTracker analysis indicated that >70% of gut microbial sources remained unknown, suggesting a vast uncharacterized environmental reservoir. Functional prediction highlighted group-specific adaptations, such as elevated amino acid transport metabolism in Common Cranes (9.8% vs. 7.1%; p < 0.05), potentially linked to local dietary resources. Our findings demonstrate that the gut microbiota of cranes is synergistically shaped by host-specific factors and the unique saline–alkaline foraging environment of the wetland.

The avian intestinal microbiota is a vital interface for host/environment interactions, playing a pivotal role in nutrient metabolism, immune regulation, and ecological adaptation. In the Yellow River Delta region, common cranes and white cranes coexist in mixed flocks. During the winter, when food resources are scarce, studying their gut microbiota can effectively reveal the feeding patterns of these two crane species, thereby providing valuable data for crane conservation efforts. This study systematically investigated and compared the intestinal microbiota structures of white cranes (Grus leucogeranus) and common cranes (Grus grus) inhabiting the Yellow River Delta region. The results demonstrated that the predominant phyla of the intestinal microbiota in white and common cranes are Firmicutes and Proteobacteria at the phylum level; Catellicoccus and Lactobacillus were the predominant genera in the crane species. LEfse was used to analyze the differential flora of the intestinal bacterial communities of white cranes and common cranes and to detect the marker species with significant differences between the groups. Based on the COG database, a preliminary functional prediction of the intestinal microbiota was conducted, and 16 metabolic pathways relating to the COG pathway were obtained. In general, although both types of cranes belong to the Grus genus and are distributed in the same area, there are significant differences in the composition and functional characteristics of their intestinal microbiota due to the differences in their feeding composition.