Longitudinal analysis of broiler cecal microbiome: unraveling the species level dynamics across age and sex

This study investigated the longitudinal dynamics of the cecal microbiome in male and female broiler chickens from hatch (d 0) to market age (d 42) using full-length 16S rRNA gene sequencing via Oxford Nanopore Technology. Microbial composition, diversity, and differential abundance were assessed across four time points (d 0, 14, 28, and 42). Alpha diversity analyses showed no significant differences between male and female within the same age group. The longitudinal comparisons revealed significantly lower diversity on d 0 compared to later timepoints in both male and female. Beta diversity analyses using Bray-Curtis and Jaccard metrics demonstrated distinct microbial community clustering at d 0 and a major compositional shift by d 14. PERMANOVA confirmed age as a significant factor influencing microbial composition. However, both sex and age influenced the dominant bacterial species. On d 0, Enterococcus faecalis was the most abundant in both males (58.57%) and females (61.35%). Whereas on d 42, Romboutsia ilealis (14.12%) became the predominant species in female and Negativibacillus massiliensis (9.7%) in males. In addition to the variation in the dominant species, differential abundance analysis revealed that bacterial species such as Clostridium celatum, C. disporicum, C. jeddahitimonense, and C. saudiense, had significantly higher abundance at d 0 compared to later time points in both males and females. Whereas bacterial species such as Bittarella massiliensis, Turicibacter bilis,and Turicibacter sanguinis had significantly higher abundance at d 28 and 42. Furthermore, core microbiome analysis showed microbial richness plateaued at approximately 330-350 species from d 14 onward. Our results indicate that early microbial communities are more sex-specific and they gradually converge over time probably due to extrinsic environmental factors.