Metabarcoding Analyses of Gut Microbiota of Nile Tilapia (Oreochromis niloticus) from Lake Awassa and Lake Chamo, Ethiopia.

Negash Kabtimer Bereded,Konrad J Domig,Manuel Curto,Harald Meimberg,Herwig Waidbacher,Solomon Workneh Fanta,Getachew Beneberu Abebe

doi:10.3390/microorganisms8071040

Negash Kabtimer Bereded, Konrad J Domig + Show 5 more

Open Access

https://doi.org/10.3390/microorganisms8071040

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Abstract

The Nile tilapia (Oreochromis niloticus) gut harbors a diverse microbial community; however, their variation across gut regions, lumen and mucosa is not fully elucidated. In this study, gut microbiota of all samples across gut regions and sample types (luminal content and mucosa) were analyzed and compared from two Ethiopian lakes. Microbiota were characterized using 16S rRNA Illumina MiSeq platform sequencing. A total of 2061 operational taxonomic units (OTUs) were obtained and the results indicated that Nile tilapia from Lake Chamo harbored a much more diversified gut microbiota than Lake Awassa. In addition, the gut microbiota diversity varied significantly across the gut region based on the Chao1, Shannon and Simpson index. The microbiome analyses of all samples in the midgut region showed significantly higher values for alpha diversity (Chao 1, Shannon and Simpson). Beta diversity analysis revealed a clear separation of samples according to sampling areas and gut regions. The most abundant genera were Clostridium_sensu_stricto and Clostridium_XI genera across all samples. Between the two sampling lakes, two phyla, Phylum Fusobacteria and Cyanobacteria, were found to be significantly different. On the other hand, six phyla (Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria and Cyanobacteria) were significantly different across gut regions. In this study, we found that all samples shared a large core microbiota, comprising a relatively large number of OTUs, which was dominated by Proteobacteria, Firmicutes, Cyanobacteria, Fusobacteria and Actinobacteria. This study has established the bases for future large-scale investigations of gut microbiota of fishes in Ethiopian lakes.

Highlights

The microbiota of the gut has a significant effect on the health status of the host
We found that all samples shared a large core microbiota
This study characterizes bacteria associated with the gut of Nile tilapia from Lake Awassa and Lake Chamo using the 16S rDNA metabarcoding technique

Summary

Introduction

The microbiota of the gut has a significant effect on the health status of the host. The microbial community enhances the health of the host by inhibiting the performance of pathogenic microbes [1]and improving the immune response [2]. The microbiota of the gut has a significant effect on the health status of the host. The microbial community enhances the health of the host by inhibiting the performance of pathogenic microbes [1]. Improving the immune response [2]. Gut microbiota facilitates the degradation of non-digestible fibers and synthesizes essential compounds such as vitamins [3]. It was shown to be involved in the development of gut morphology [4]. The microbial structure of the gut changes with the developmental stage of the host and constantly adapts to the current situation [5]. Understanding the related mechanisms is crucial for economical important species, especially in aquaculture activities, where productivity is dependent on the animal health

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