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Background: Phytase supplementation in broiler diets is a common strategy to improve phosphorus (P) digestibility and to reduce its loss by excretion. An enhanced P availability, and its concomitant supplementation with calcium (Ca), can affect the composition of the microbial community in the digestive tract of broilers. Here, we aim to distinguish the effects of mineral P, Ca and phytase on the composition of microbial communities in the gastrointestinal tract (GIT) of broiler chickens.Results: Statistical differences were observed between digesta and mucosa samples for each GIT section. However? The analyses of 56 individual birds showed a high microbial composition variability within the replicates of the same diet. The average similarity within replicates of digesta and mucosa samples across all diets ranged from 29-81% in crop, 18-48% in ileum and 16-38% in caeca. Broilers fed a diet only supplemented with Ca had the lowest body weight gain and feed conversation values and the lowest microbial diversity, while all? diets supplemented with P showed the best performance results. An effect of each diet on crop mucosa was observed, however, similar results were not obtained from digesta samples. Microbial communities colonizing the ileum mucosa samples showed an effect of P supplementation. Caeca-derived samples showed the highest microbial diversity when compared to the other sections. Prominent OTUs were related to genus Faecalibacterium and Pseudoflavonifractor, known by its influence on gut health and as butyrate producers. Conclusions: Each diet affected microbial communities within individual sections, however, no diet showed a comprehensive effect across the entire GI tract, which can primarily be attributed to the great variability among replicates. Lower microbial diversity together with Ca supplementation have a negative influence in the growth performance of broilers. The sunbstantial community differences between digesta and mucosa derived samples indicate that both habitats have to be considered when the influence of diet on the gut microbiota, broiler growth performance and animal health is investigated. |