Phylogenetic characterization of eukaryotic and prokaryotic gut flora of Nile tilapia, Oreochromis niloticus, along niches of Lake Nasser, Egypt, based on rRNA gene high-throughput sequences

Abstract

Abstract Studies of phylogenetic diversity of fish gut flora often focus on bacteria, leaving a gap in characterization of flora from other domains. This study focused on first exploring of phylogenetic composition of the gut flora, belonging to all domains, eukaryotes, bacteria and archaea, of the tilapia fish, Oreochromis niloticus, inhabiting Lake Nasser, Egypt, based on rRNA gene high-throughput sequencing. Specimens were collected from four distant lake natural fish feeding niches, Khor Kalabsha, Khor Wadi Abyad, Khor Korosko and Khor Toshka. Metagenomic DNA was extracted from fish gut contents, followed by PCR and next generation sequencing of both of eukaryotic 18S- and prokaryotic 16S rRNA genes. A total of 2491, 19005 and 9032 rRNA gene OTUs, were recorded, for eukaryotes, bacteria and archaea, respectively, in the guts from the four niches. Fish guts from Khor Toshka, harbored the highest diversity of bacterial and archaeal 16S rRNA gene sequences. Some 18S rRNA gene OTUs, belonging to members of class Ostracoda, molluscs, and phylum Bacillariophyta, diatoms, beside of 16S rRNA gene OTUs assigned to genus Synechococcus, phylum Cyanobacteria, were recorded in guts from all studied niches, suggesting favorite foods for the fish throughout the lake. Other rRNA gene OTUs, affiliated with the diatom genus Fragilaria, cyanobacterial family Pseudanabaenaceae and genus Oscillatoria, characterized guts from Khor Toshka and Khor Kalabsha, respectively. OTUs, belonging to genus Cetobacterium, phylum Fusobacteria; genera, Methanobacterium and Methanosaeta, phylum Euryarchaeota, constituted the core gut microbiome. Neoechinorhynchus-like OTUs were recorded in guts from all niches, implicating common tilapia gut parasites at Lake Nasser. Guts from all niches harbored several unique archaeal 16S rRNA gene OTUs, but did not match known archaeal phyla. Hence, a large number of phylogenetic shared taxa persist across guts from distant niches, with respect to some OTUs, characterizing gut contents of specific niches.