Analysis of the Gut Microbiome of Nile Tilapia Oreochromis Niloticus L. Fed Diets Supplemented with Previda® and Saponin

Candis Ray,Allen Davis D,Andrea Tarnecki,Arias Cr,Noemi Bujan,Browdy C

doi:10.21767/1307-234x.1000116

Abstract

The use of prebiotics in aquaculture aims at increasing the numbers of beneficial microbes in the gastrointestinal tract of fishes. However, the true effect of prebiotics exert on the fish microbiome is for the most part unknown. This study aimed at investigating the effects of the commercial prebiotic Previda® and the feed supplement saponin on Nile tilapia (Oreochromis niloticus L.). We used 454 pyrosequencing to characterize the gut microbiome of fish fed diets containing Previda®, saponin, a combination of both, and a control diet. After data normalization, 98,300 sequence reads were analyzed resulting in 331 unique operational taxonomic units (OTUs). Three phyla were present in all samples: Fusobacteria, Bacteroidetes, and Proteobacteria. Fusobacteria was the predominant phylum in all samples accounting for more than 80% of the OTUs. Within the Fusobacteria, the predominant genus was Cetobacterium with more than 76% of the sequences being ascribed to that species. Barnesiella was the second most common genus with more than 6% of the total sequences. Overall, there was not a significant difference in the composition of the gut microbiomes regardless of the diet. The overwhelming numbers of Cetobacterium sp. present in the gut of Nile tilapia could overshadow the effect of the treatments on other genera.

Highlights

The use of probiotics and prebiotics in aquaculture has increased tremendously in recent years as a sustainable alternative to the use of antibiotics
Several studies have looked at what factors shape and modulate the development of the tilapia gut microbiome (Giatsis et al, 2015, Giatsis et al, 2014)
While the gut is not fully developed, the effects of environmental factors such as water physicochemical parameters are stronger. Those studies concluded that water in the rearing tanks is the primary source for bacteria found in the tilapia gut

Summary

Introduction

The use of probiotics and prebiotics in aquaculture has increased tremendously in recent years as a sustainable alternative to the use of antibiotics. The main goal for administering probiotics (live microorganisms) or prebiotics (fermentation byproducts that promote the growth of beneficial microbes) is to manipulate the gut microbial community or gut microbiome to improve host fitness, mainly through the exclusion of opportunistic pathogens (Balcazar et al, 2006). The characterization of gut microbial communities in fish was biased due to the use of culture-dependent methods that vastly underestimated the species richness of the gut microbiome. The development of cost-effective generation sequencing methods promoted the use of culture-independent methods resulting in detailed descriptions of these complex microbial communities. Several studies have analyzed the effects of different feed additives in the intestinal bacterial community of tilapia; those studies employed a fingerprint-based method (DGGE) suitable for identifying changes in the communities but without describing species composition (Pedrotti et al, 2015, He et al, 2011, Zhou et al, 2009, Liu et al, 2014)

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