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Bacterial populations within hypersaline lakes often exhibit uncultured unique species. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), followed by sequencing of 16S rRNA gene approach was applied in order to explore, for the first time, the bacterial communities within the hypersaline Lakes, Aghormy, Zeiton and Maraqi, Siwa Oasis, Egypt. The DGGE profile displayed 12 phylotypes of 16S rRNA gene, representing the total species richness within the three studied lakes. The phylotypes were varied among lakes, but were restricted to two phylogenetic groups, Bacteroidetes, which occurred in all lakes, and Alphaproteobacetria, which showed abundance in only Lakes Zeiton and Maraqi. Single spirochete-like phylotype characterized the Lake Aghormy. A phylotype, which was recorded in both of Aghormy and Zeiton, represented a first recorded of Lewinella agarilytica in hypersaline inland lakes. Sequence homology results suggested novel indigenous bacterial phylotypes. Key words: Siwa lakes, halophilic bacteria, 16S rRNA gene, molecular diversity.

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.

To understand the contribution of gut microflora to the feeding and health of Mugil cephalus in a Mediterranean estuary, we have explored and evaluated the diversity of rRNA genes in gut contents of both of adults and fingerlings. Bulk DNAs were extracted from the fish guts, followed by PCR, cloning and sequencing of eukaryote 18S rRNA gene; bacterial and archaeal 16S rRNA genes. Rarefaction analyses recorded 11, 18 and 13 phylotype groups of rRNA genes for eukaryotes, bacteria and archaea, respectively, in the adult guts. The fingerling guts contained 6 and 11 phylotype groups of rRNA genes for eukartyotes and bacteria, respectively, while lacked archaea. Adult and fingerling guts were dominated by zooplankton-like 18S rRNA gene phylotypes, belonging to those of rotifers, genus Brachionus and copepods, genus Apocyclops. Both of diatoms, genus Cyclotella- and fish-like rRNA gene phylotypes were recorded only in adult guts. Phylotypes, which belonged to uncultured proteobacteria and cyanobacteria, covered most of the bacterial 16S rRNA gene composition of adult guts. Bacteroidetes-like phylotypes characterized the fingerling guts. The study showed the first record of uncultured thaumarchaeote-like 16S rRNA genes in the fish guts, opening a window for exploring thaumarchaeote biological significances in fish metabolism. The fish guts represented a reservoir for geographic distant species and reflected the plankton ecosystem variability at the studied estuary. The pollution in the estuary could shape a fraction of the fish gut microbiota. To our knowledge, this work presented the first complete profile of rRNA gene diversities for all known microbiome domains in fish guts.