Assessing the impact of broiler genotype on cecal and tracheal microbiome composition using full-length 16S rRNA sequencing

This study examined the tracheal and cecal microbiome composition across three broiler chicken genotypes including a heritage New Hampshire × Columbian cross (NHC) and modern Ross × Ross 308 (R308) and Ross YP × Ross 708 (R708) broilers, using full-length 16S rRNA sequencing. Birds were reared in floor pens, and at 56 d of age, cecal and tracheal samples were collected from 8 birds per genotype and subjected to DNA extraction followed by PCR amplification of full-length 16S rRNA. Obtained amplified PCR product was sequenced using MinION. A total of 1.8 million reads for tracheal samples and 1.2 million reads for ceca samples were obtained from 24 birds. Despite similar alpha diversity matrixes (Shannon, Simpson, Pielou's evenness, and Chao1) across genotypes in both tracheal and cecal samples, beta diversity analysis revealed significant differences in community composition. Tracheal and cecal microbiota varied significantly among genotypes, particularly NHC with the R308 and R708 groups. At the phylum level, Bacillota (Firmicutes) dominated both tracheal and cecal samples across genotypes. In the trachea, NHC and R708 birds exhibited high relative abundance of Enterococcus cecorum, while Jeotgalicoccus meleagridis dominated R308. Differential abundance analysis showed higher abundance of potentially beneficial bacteria such as Limosilactobacillus pontis and Aerococcus viridans in R308 and R708, while NHC birds had higher levels of species like Merdibacter massiliensis and Agathobaculum butyriciproducens. Cecal microbiome analysis revealed genotype-specific enrichment of species, with NHC birds showing higher abundance of potential pathogens like Shigella boydii and Escherichia fergusonii compared to R708. In contrast, R308 birds harboured more potentially beneficial taxa, including Lactobacillus acidophilus and Limosilactobacillus vaginalis, compared to R708. Pairwise comparisons further highlighted Intestinibacter bartlettii and other potentially beneficial microbes being significantly enriched in R308 over R708. Overall, while microbial richness remained consistent, significant genotype-associated differences in bacterial community structure and genotype-specific microbial abundance were observed, emphasizing the influence of host genetics on microbiota composition and potential implications for poultry health and performance.