الفهرس 
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Abstract
This work aimed to investigate the effect of Aeromonas sobria challenge on the microbial community structure of water and fish gut and histopathological alterations of gills and skin in Nile tilapia reared under biofloc system compared to clear water system. The fish were distributed into four groups: two biofloc groups (A. sobria challenged group and control group) and two clear water system groups (A. sobria challenged group and control group). The fish were challenged by an I/P injection of the A. sobria strain. Genomic DNA was extracted from water and fish gut samples in both systems and subjected for metagenomic 16S rRNA sequencing using Illumina Novaseq 6000 sequencing platform. Severe histopathological alterations were noticed in gills in CWS, while mild histopathological alterations were noticed in gills in BFT. The predominant phyla were Firmicutes, Proteobacteria, Actinobacteria, Verrucomicrobia, Bacteriodetes, and Fusobacteria. Interestingly, Firmicutes was found significantly higher in the gut of fish reared in BFT than in CWS, but after the infection significantly decreased in BFT. The results of this work concluded that BFT could protect the gills of Nile tilapia against the A. sobria challenge. Genera Gemmobacter, Akkermansia, and Cetobacterium increased after infection. So that the use of these genera as probiotic agents competing against the A. sobria challenge needs further studies.