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

Elsaied, Hosam; Soliman, Taha; Abu-Taleb, Hany T.; Goto, Hironobu; Jenke-Kodam, Holger

doi:10.1016/j.egg.2019.100037

Cited by 23 publications

(18 citation statements)

References 52 publications

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“…The results of this study showed that the gut microbiota of Nile tilapia from Lake Tana were dominated by the phyla Firmicutes and Fusobacteria. These results were in agreement with the findings of a gut microbiota study performed on Nile tilapia of Lake Nasser in Egypt, where they reported that Fusobacteria was the dominant phylum [ 52 ]. Ray et al [ 53 ]; however, in their study, Firmicutes were less abundant, contradicting our results where they were the dominant phylum along with Fusobacteria.…”

Section: Discussionsupporting

confidence: 92%

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

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Beneberu

Fanta

et al. 2021

Biology

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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.

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Section: Discussionsupporting

confidence: 92%

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

Bereded

Beneberu

Fanta

et al. 2021

Biology

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“…Similarly, Candis et al [ 51 ] identified Fusobacterium at significantly higher levels in the gut of Nile tilapia. Moreover, Fusobacteria-like OTUs were reported from fish gut as a core microflora [ 62 ]. On the other hand, Cyanobacteria was reported as a major component of gut microbiome from the gut of Nile tilapia in Egypt [ 62 ].…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, Fusobacteria-like OTUs were reported from fish gut as a core microflora [ 62 ]. On the other hand, Cyanobacteria was reported as a major component of gut microbiome from the gut of Nile tilapia in Egypt [ 62 ].…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2020

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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.

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“…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]. Clostridiaceae and Peptostreptococcaceae were the predominant families from samples of Lake Awassa and Chamo, while Fusobacteriaceae was the most dominant in Lake Hashengie and Lake Tana.…”

Section: Discussionmentioning

confidence: 82%

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

Bereded

Beneberu

Fanta

et al. 2022

Preprint

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BackgroundMicroorganisms inhabiting the gut play a significant role in supporting fundamental physiological processes of the host, which contributes to their survival in varied environments. Several studies have shown that altitude affects the composition and diversity of intestinal microbial communities in terrestrial animals. However, little is known about the impact of altitude on the gut microbiota of aquatic animals. The current study examined the variations in the gut microbiota of Nile tilapia (Oreochromis niloticus) from four lakes along an altitudinal gradient in Ethiopia by using 16S rDNA Illumina MiSeq high-throughput sequencing. ResultsThe results indicated that low-altitude samples typically displayed greater alpha diversity. The results of principal coordinate analysis (PCoA) showed significant differences across samples from different lakes. Firmicutes was the most abundant phylum in the Lake Awassa and Lake Chamo samples whereas Fusobacteriota was the dominant phylum in samples from Lake Hashengie and Lake Tana. The ratio of Firmicutes to Bacteroidota in the high-altitude sample (Lake Hashengie, altitude 2440 m) was much higher than the ratio of Firmicutes to Bacteroidota in the low altitude population (Lake Chamo, altitude 1235 m). We found that the relative abundances of Actinobacteriota, Chloroflexi, Cyanobacteria, and Firmicutes were negatively correlated with altitude, while Fusobacteriota showed a positive association with altitude. Despite variability in the abundance of the gut microbiota across the lakes, some shared microbial communities were detected. ConclusionsIn summary, this study showed the indirect influence of altitude on gut microbiota. Altitude has the potential to modulate the gut microbiota composition and diversity of Nile tilapia. Future work will be needed to elucidate the functional significance of gut microbiota variations based on the geographical environment. Significance and Impact of the Study: Our study determined the composition and diversity of the gut microbiota in Nile tilapia collected from lakes across an altitude gradient. Our findings greatly extend the baseline knowledge of fish gut microbiota in Ethiopian lakes that plays an important role in this species sustainable aquaculture activities and conservation.

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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

Cited by 23 publications

References 52 publications

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

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

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

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

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