The Impact of Sampling Season and Catching Site (Wild and Aquaculture) on Gut Microbiota Composition and Diversity of Nile Tilapia (Oreochromis niloticus)

Abstract

The gut microbiota of fishes is known to play an essential role in diverse aspects of host biology. The gut microbiota of fish is affected by various environmental parameters, including temperature changes, salinity and diet. Studies of effect of environment on gut microbiota enables to have a further understanding of what comprises a healthy microbiota under different environmental conditions. However, there is insufficient understanding regarding the effects of sampling season and catching site (wild and aquaculture) on the gut microbiota of Nile tilapia. This study characterised gut microbial composition and diversity from samples collected from Lake Tana and the Bahir Dar aquaculture facility centre using 16S rDNA Illumina MiSeq platform sequencing. Firmicutes and Fusobacteria were the most dominant phyla in the Lake Tana samples, while Proteobacteria was the most dominant in the aquaculture samples. The results of differential abundance testing clearly indicated significant differences for Firmicutes, Fusobacteria, Bacteroidetes and Cyanobacteria across sampling months. However, Proteobacteria, Chloroflexi, Fusobacteria and Cyanobacteria were significantly enriched in the comparison of samples from the Lake Tana and aquaculture centre. Significant differences were observed in microbial diversity across sampling months and between wild and captive Nile tilapia. The alpha diversity clearly showed that samples from the aquaculture centre (captive) had a higher diversity than the wild Nile tilapia samples from Lake Tana. The core gut microbiota of all samples of Nile tilapia used in our study comprised Firmicutes, Proteobacteria and Fusobacteria. This study clearly showed the impact of sampling season and catching site (wild and aquaculture) on the diversity and composition of bacterial communities associated with the gut of Nile tilapia. Overall, this is the first study on the effects of sampling season and catching site on the gut microbiota of Nile tilapia in Ethiopia. Future work is recommended to precisely explain the causes of these changes using large representative samples of Nile tilapia from different lakes and aquaculture farms.

Investigating the Effect of an Oxytetracycline Treatment on the Gut Microbiome and Antimicrobial Resistance Gene Dynamics in Nile Tilapia (Oreochromis niloticus)

“…These findings would therefore demonstrate a certain degree of resistance in the gut microbiome community of Nile tilapia in response to a single OTC exposure, and agree with a similar study in this fish species [17]. The microbiomes of both baseline and post-OTC treated fish in this study were dominated by Fusobacteria, supporting previous findings that members of this phylum are conserved in fish species, where they play a role in vitamin production for the fish host [19,25,[42][43][44]. Resilience and enrichment in Fusobacteria following antibiotic treatment has been reported in zebrafish (Danio rerio) when exposed to OTC at similar or lower levels, respectively [45,46].…”

“…The gastrointestinal tract of Nile tilapia is colonised by a community of microorganisms or "microbiome", comprised predominantly of Fusobacteria, Firmicutes, and Proteobacteria [19,20]. In this fish species, gut microbiome members play a pivotal role in supporting host physiology and health, through microbial-mediated functions involved in disease resistance, growth, and metabolism [21,22].…”

The gut bacterial microbiome of Nile tilapia (Oreochromis niloticus) from lakes across an altitudinal gradient

“…In our study, Firmicutes was the most abundant phylum in the Lake Awassa and Lake Chamo samples, whereas Fusobacteriota was the dominant phylum in the samples of Lake Hashengie and Lake Tana. Previous studies on the intestinal microbial communities of Nile tilapia from Ethiopian lakes showed dominance by the phylum Firmicutes followed by Fusobacteriota [15,39]. Fusobacteriota was also reported as a dominant phylum from the intestine of Nile tilapia of Lake Nasser in Egypt [40] and captive Nile tilapia [41].…”

“…The functions of gut microbial communities depend on their structure, which is in uenced by several host-associated elements, such as genetic makeup, season, stress, and geographical location [15][16][17].…”

Substrate preferences, phylogenetic and biochemical properties of proteolytic bacteria present in the digestive tract of Nile tilapia (<i>Oreochromis niloticus</i>)

“…Moreover, seasonal fluctuation of water temperature was also found to change the composition of gut microbiota in Nile tilapia. Bereded et al in a recent study demonstrated modifications of both the diversity and composition of gut bacteria with seasonal and spatial variation [69] .…”