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Abstract Mai Abdel Monem Mohamed Wassel: Molecular Identification of Planktonic Meals for Tilapia Species based on rRNA Gene Analyses. Unpublished M.Sc. Thesis, Department of Genetics, Faculty of Agriculture, Ain Shams University, 2016. The diversity of Oreochromis niloticus gut microbiome domains, eukaryotes, bacteria and archaea, was studied in order to understand the contribution of these microbiotas to the health of the fish in four different Khors, Kalabsha, Wadi Abyad, Tushka and Korosko, Lake Nasser, Egypt. The approach of this study based on culture-independent PCR/DGGE and sequence of small subunit of rRNA genes, eukaryotic 18S rRNA gene and prokaryotic, bacterial and archaeal, 16S rRNA genes. The DGGE patterns displayed 5, 12 and 5 band groups, phylotypes, for eukaryotic 18S rRNA gene, bacterial and archaeal 16S rRNA genes, respectively, in fish gut contents from all studied khors. DGGE showed rRNA gene bands, which were common and specific for each site and could be used as barcodes to certify the origin of the fish. Statistical analyses, using binary matrix, showed that numbers of DGGE bands, 1, 2 and 2, for eukaryotes, bacteria and archaea, respectively, were commonly occurred in all studied khors. The DGGE phylotype, 3.Euk.Kr characterized eukaryotes in Khor Korosko. Phylogenetic analyses showed that two of eukaryotic phylotypes, 1.Euk.Kl.Kr and 2.Euk.Common, were belonged to crustacean, Ostracoda, of the genera Darwinula and Vestalenula. Some helminths, of the genera Neoechinorhynchus and Catenula, -like rRNA gene phylotypes were recorded in guts from Kalabsha, Tushka and Korosko, suggesting common gut parasitic worms. Cyanobacteria-like phylotypes were recorded in gut contents from all studied khors. Most bacteria-like phylotypes constituted unique phylogenetic lineages within the branch of uncultured environmental bacteria. All archaeal phylotypes were located in the branch of methanogenic uncultured Euryarchaeota. The similarity index analysis of the DGGE gel patterns indicated that the eukaryotic composition in Kalabsha and Tushka had similarity, 75% with Jaccard and 86% with Dice. Also, the eukaryotic phylotype compositions of guts from Korosko and Tushka showed similarity, 20% with Jaccard and 33.3% with Dice. The bacterial phylotype compositions of Wadi Abyad and Tushka were the most similar to each other among studied khors with similarity percentage of 90% with Jaccard and 94% with Dice, while Wadi Abyad and Korosko showed low similarity 27.3% with Jaccard and 42.9% with Dice. Archaeal phylotype compositions were similar in all studied khors. The DGGE patterns and sequence analyses showed some similarities of eukaryote, bacteria and archaea rRNA gene phylotype compositions in fish guts from distant khors, implicating existence of core gut microbiome. This is the first phylogenetic survey of all microbiome domains in tilapia guts at Lake Nasser. Keywords: Lake Nasser; Oreochromis niloticus; DGGE; rRNA; Phylogenetic analyses |