The diversity of Oreochromis niloticus gut microbiome domains, eukaryotes, bacteria and archaea, was studied to understand the contribution of microbiota to the health of the fish. Fishes were collected from four different Khors, Kalabsha, Wadi Abyad, Tushka and Korosko, of Lake Nasser, Egypt. The approach of this study depends on culture-independent PCR/DGGE and sequence of small subunit of rRNA genes, 18S rRNA gene and 16S rRNA gene. The DGGE patterns displayed 5, 12 and 5 band groups, phylotypes, for eukaryotic 18S rRNA gene, bacterial and archaeal 16S rRNA genes, respectively, in gut contents from the studied khors. DGGE showed bands, which were common and specific for each site and could be used as a bar code to certify the origin of the fish. Statistical analyses, using binary matrix, showed 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. Bacterial phylotypes in all studied khors were located in the branch of cyanobacteria, alpha proteobacteria, but most of them constituted unique phylogenetic lineages within the branch of uncultured environmental bacteria. All archaeal phylotypes were located in the branch of methanogenic uncultured euryarchaeota. Some helminthes, of the genera Neoechinorhynchus and Catenula, -like rRNA gene phylotypes were recorded in guts from Kalabsha, Tushka and Korosko, suggesting common gut parasitic worms. The DGGE patterns and sequence analyses showed high similarities of eukaryote, bacteria and archaea rRNA gene phylotype compositions in fish guts from distant khors, implicating core gut microbiome. This is the first survey of all microbiome domains in tilapia guts at Lake Nasser based on molecular approaches.

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Amin, O. M., N. V. Ha and D. N. Ha (2011). First report of Neoechinorhynchus (Acanthocephala: Neoechinorhynchidae) from marine fish of the eastern seaboard of Vietnam, with the description of six new species. Parasite, 18: 21-34.

Austin, B. (2002). The Bacterial Microflora of Fish. Science World Journal, 2: 558-572.

Baldo, L., J. L. Riera, A. Tooming-Klunderud, M. M. Albà and W. Salzburger (2015). Gut Microbiota Dynamics during Dietary Shift in Eastern African Cichlid Fishes. PLoS ONE 10: doi: 10.1371/journal.pone.0127462.

Balirwa, J. S. (1998). Lake Victoria wetlands and the ecology of the Nile tilapia, Oreochromis niloticus (L.). PhD Thesis, Agricultural Univ., Wageningen, Balkema, Rotterdam, the Netherlands.

Bolnick, D. I., L. K. Snowberg, P. E. Hirsch, C. L. Lauber, R. Knight, J. G. Caporaso and R. Svanbäck (2014). Individuals' diet diversity influences gut microbial diversity in two freshwater fish (three spine stickleback and Eurasian perch). Ecology Letters, 17: 979-987.

Casamayor, E. O., H. Schäfer, L. Bañeras, C. Pedrós-Alió and G. Muyzer (2000). Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: comparison by microscopy and denaturing gradient gel electrophoresis. Applied Environmental Microbiology, 66: 499-508.

Elsaied, H., H. Kimura and T. Naganuma (2002). Molecular characterization and endosymbiotic localization of the gene encoding D-ribulose 1, 5-bisphosphate carboxylase-oxygenase (RuBisCO) form II in the deepsea vestimentiferan trophosome. Microbiology, 148: 1947-1957.

El-Shabrawy, G. M. and H. J. Dumont (2003). Spatial and seasonal variation of the zooplankton in the coastal zone and main khors of Lake Nasser (Egypt). Hydro-biologia, 491: 119-132.

Gharib, S. M. and A. M. Abdel-Halim (2006). Spatial variation of phyto-plankton and some physico-chemical variables during the highest flood season in Lake Nasser (Egypt). Egyptian Journal of Aquatic Research, 32: 246-263.

Giatsis, C., D. Sipkema, H. Smidt, H. Heilig, G. Benvenuti, J. Verreth and M. Verdegem (2015). The impact of rearing environment on the development of gut microbiota in tilapia larvae. Scientific Reports, 5: 18206. doi: 10.1038/ srep18206.

Handelsman, J. (2004). Metagenomics: Application of Genomics to Uncultured Microorganisms. Microbiology and Molecular Biology Reviews, 68: 669-685.

Heyndrickx, M., L. Vauterin, P. Vandamme, K. Kerster and P. De Vos (1996). Applicability of combined amplified ribosomal DNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy. Journal of Microbiological Methods, 26: 247-259.

Jaccard, P. (1908). Nouvelles recherché sur la distribution fllorale. ulletin de la Soci t Vaudoise des Sciences Naturelles, 44: 223-270.

Larsson, K. and U. Jondelius (2008). Phylogeny of catenulida and support for platyhelminthes. Organisms, Diversity and Evolution, 8: 378-387.

Latif, A. F. A. (1984). Lake Nasser. The new manmade lake in Egypt (with reference to Lake Nubia). In El-Serveir, F. B. T. (ed.), Ecosystems of the World, Lakes and Reservoirs, 32: 385-416.

Maiwore, J., N. L. Tatsadjieu, D. Montet, G. Loiseau and C. M. F. Mbofung (2009). Comparison of bacterial communities of tilapia fish from Cameroon and Vietnam using PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis). African Journal of Biotechnology, 8: 7156-7163.

Melo, F. T., P. A. Costa, E. G. Giese, S. L. Gardner and J. N. Santos (2013). A description of Neoechinorhynchus (Neoechinorhynchus) veropesoi n. sp. (Acanthocephala: Neoechinor-hynchidae) from the intestine of the silver croaker fish Plagioscion squamosissimus (Heckel, 1840) (Osteichthyes: Sciaenidae) off the east coast of Brazil. Journal of Helminthology, 89: 34-41.

Muschick, M., A. Indermaur and W. Salzburger (2012). Convergent evolution within an adaptive radiation of Cichlid fishes. Current Biology, 22: 2362-2368.

Muschick, M., P. Nosil, M. Roesti, M. T. Dittmann, L. Harmon and W. Salzburger (2014). Testing the stages model in the adaptive radiation of cichlid fishes in East African Lake Tanganyika. Proceedings Biological Sciences/ The Royal Society, 281, DOI: 10. 1098/rspb.2014.0605

Muyzer, G., E. C. De Waal and A. G. Uitterlinden (1993). Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes encoding for 16S rRNA. Applied Environmental Microbiology, 59: 695-700.

Navarrete, P., R. T. Espejo and J. Romero (2009). Molecular analysis of microbiota along the digestive tract of juvenile Atlantic salmon (Salmo salar L.). Microbial Ecology, 57: 550-561.

Navarrete, P., F. Magne, C. Araneda, P. Fuentes, L. Barros, R. Opazo, R. Espejo and J. Romero (2012). PCR-TTGE analysis of 16S rRNA from rainbow trout (Oncorhyn-chusmykiss) gut microbiota reveals host-specific communities of active bacteria. PloS one 7: doi:10. 1371/journal.pone.0031335.

Njiru, M., J. B. Okeyo-Owuor, M. Muchiri and I. G. Cowx (2004). Shifts in the food of Nile tilapia, Oreochromis niloticus (L.) in Lake Victoria, Kenya. African Journal of Ecology, 42: 163-170.

Nubel, U., B. Engelen, A. Felske, J. Snaidr, A. Wieshuber, R. I. Amann, W. Ludwig and H. Backhaus (1996). Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. Bacteriology, 178: 5636-5643.

Ramdani, M., N. Elkhiati, R. J. Flower, H. H. Birks, M. M. Kraïem, A. A. Fathi and S. T. Patrick (2001). Open water zooplankton communities in North African wetland lakes: the CASSARINA Project. Aquatic Ecology, 35: 319-333.

Roeselers, G., E. K. Mittge, W. Z. Stephens, D. M. Parichy, C. M. Cavanaugh, K. Guillemin and J. F. Rawls (2011). Evidence for a core gut microbiota in the zebra fish. International Society for Microbial Ecology, 5: 1595-1608.

Salzburger, W. (2009). The interaction of sexually and naturally selected traits in the adaptive radiations of Cichlid fishes. Molecular ecology, 18: 169-85.

Star, B., T. H. Haverkamp, S. Jentoft and K. S. Jakobsen (2013). Next generation sequencing shows high variation of the intestinal microbial species composition in Atlantic cod caught at a single location. BioMed Central Microbiology, 13: 248.

Sullam, K. E., B. E. Rubin, C. M. Dalton, S. S. Kilham, A. S. Flecker and J. A. Russel (2015). Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies. International Society for Microbial Ecology, 9: 1508-1522.

Suzuki, M. T. and S. J. Giovannoni (1996). Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Applied Environmental Microbiology, 62: 625-630.

Tatsadjieu, N. L., J. Maïworé, M. B. Hadjia, G. Loiseau, D. Montet and C. M. F. Mbofung (2010). Study of the microbial diversity of Oreochromis niloticus of three lakes of Cameroon by PCR-DGGE: Application to the determination of the geographical origin. Food Control, 21: 673-678.

Trewavas, E. (1983). Tilapiine Species of the Genera Sarotherodon, Oreochromis and Danakila. London British Museum (Natural History) Publication No. 583.

Van der Maarel, M., W. Sprenger, R. Haanstra and L. J. Forney (1999). Detection of methanogenic archaea in seawater particles and the digestive tract of a marine fish species. FEMS Microbiology Letters, 173: 189-194.

Van Hannen, E. J., M. P. van Agterveld, H. J. Gons and H. J. Landbroek (1998). Revealing genetic diversity of eukaryotic organisms in aquatic environments by denaturing gel electrophoresis. Journal of Phycology, 34: 206-213.

Van Kessel, M. A., B. E. Dutilh, K. Neveling, M. P. Kwint, J. A. Veltman, G. Flik, M. S. M. Jetten, P. H. M. Klaren and H. J. M. Op den Camp (2011). Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpio L.). AMB Express, 1: 41. doi: 10.1186/2191 -0855-1-41

Van Zwieten, P. A. M., C. Béné, J. Kolding, R. Brummett and J. Valbo-Jørgensen (2011). Review of tropical reservoirs and their fisheries. The cases of Lake Nasser, Lake Volta and Indo-Gangetic Basin reservoirs. FAO Fisheries and Aquaculture Technical Paper. No. 557. Rome, FAO. 2011. pp 148.

Welcomme, R. L. (1967). Observations on the biology of introduced species of Tiliapia in Lake Victoria. Revue de Zoologie et Botanique Africaines, 76: 249-279.

Xing, M., Z. Hou, J. Yuan, Y. Liu, Y. Qu and B. Liu (2013). Taxonomic and functional metagenomic profiling of gastrointestinal tract microbiome of the farmed adult turbot (Scophthalmus maximus). FEMS Microbiology Ecology, 86: 432-43.

Ye, L., J. Amberg, D. Chapman, M. Gaikowski and W. Liu (2014). Fish gut microbiota analysis differentiates physiology and behavior of invasive Asian carp and indigenous American fish. International Society for Microbial Ecology, 8: 541-551.


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