Determination of the cecal microbiota profile of Anadolu-T broiler breeder chickens using 16S metagenomic sequencing

The gut microbiota has significant effects on the performance, health status, and immune systems of chickens. The complex microbial community structure begins to form after chicks hatch with the intake of feed, water, and air into the digestive system. Disrupting the balance of this system can lead to the proliferation of pathogenic microorganisms. Until recently, studies on microbiota relied on traditional microbiological techniques that cultured only a small fraction of the microbial diversity. However, significant advancements in DNA sequencing and bioinformatics have enabled the identification of diverse bacterial populations in environmental samples. In this study, a total of 2000 broiler chickens from 5 pure lines bred since 2015 at the Eskisehir Gecit Kusagı Agricultural Research Institute’s Broiler Chicken Breeding and Improvement Department were used. A total of 100 cecal fecal samples were randomly collected, with 20 samples from each pure line at 3, 8, 15, 25, and 32 weeks of age. DNA was isolated from these samples and the diversity of the bacterial flora in the cecum was investigated using 16S rDNA gene sequencing. Across all samples, the most abundant genus identified was Bacteroides, with an average relative abundance of 9.125%, while Ruminococcus was the least abundant genus, with an average relative abundance of 0.005%. A total of 306 different species were identified. The most abundant species detected was Akkermansia muciniphila, with an average relative abundance of 1.4 ± 8.31%. This study is the first to examine the cecum microbiota of Anadolu-T pure lines, a local genotype bred in Türkiye, on a line-by-line and temporal basis.