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The composition of the gut microbiome plays important roles in digestion, nutrient absorption, and health. Here, we analyzed the microbial composition in the duodenum and ileum of yellow broilers. Chickens were grouped based on feed efficiency (high feed efficiency [HFE] and low feed efficiency [LFE] groups;  n  = 22 each). Microbial samples from the duodenum and ileum were collected, and  16S  rRNA sequencing of the V3–V4 region was performed. The dominant bacteria in the duodenum were from the phyla Firmicutes and Cyanobacteria and the genera  Lactobacillus ,  Faecalibacterium , and  Ruminococcus . In the ileum, the phyla Firmicutes and Proteobacteria and the genera  Lactobacillus ,  SMB53  and  Enterococcus  were predominant. Alpha diversity analysis showed that the microbiota diversity was significantly higher in the duodenum than in the ileum. The structure of the ileal microbiota was similar between groups, and the species richness of the microbiota in the HFE group was significantly higher than that in the LFE group. In the HFE and LFE groups, Firmicutes and Cyanobacteria were negatively correlated, and  Lactobacillus  had medium to high negative correlations with most other genera. Functional prediction analysis showed that the gluconeogenesis I pathway was the most abundant differential metabolic pathway and was significantly altered in the LFE group. Moreover, although the microbial community structures were similar in the duodenum and ileum, the diversity of the microbial community was significantly higher in the duodenum than in the ileum. Pearson correlation analysis revealed that the phylum Chloroflexi and genera  Acinetobacter ,  Pseudomonas ,  Bacillus  and  Neisseria  were with coefficients <−0.3 or >0.3. In the ileum,  Ruminococcus  may be associated with HFE whereas  Faecalibacterium  may be associated with LFE. These findings may provide valuable foundations for future research on composition and diversity of intestinal microbes and provide insights into the roles of intestinal microbes in improving feed efficiency and the industrial economic benefits of yellow broilers.

Microbial Composition in the Duodenum and Ileum of Yellow Broilers With High and Low Feed Efficiency