A metagenomic analysis of gut microbiome phylogeny among four economically important carp species from wild and aquaculture farms
Shrihari Ashok Pingle, Abhay John Khandagle.
Abstract
The present study was carried out to compare the gut microbiome of Indian Major Carp and Common carp from wild and aquaculture setting through 16S rDNA sequencing. The library of 16S rDNA V3-V4 hypervariable regions of gut microbiota was amplified, followed by sequencing using Illumina MiSeq. The analysis of sequencing data carried out through the Quantitative Insights into Microbial Ecology pipeline suggests that Proteobacteria, Firmicutes, Cyanobacteria and Actinobacteria are the most dominant phyla. Some microbial phyla were found to be species-specific. Genera such as Bacillus, Sphingomonas, and Clostridium were highly abundant in cultured forms indicating their role in the survival of cultured forms under considerable ecological stress. The α-diversity and β- diversity indicators suggest that the gut microbiome of cultured forms shows more diversity and also resembles a great extent. Absence of Bacillus spp. in wild form, and low abundance of Lactococcus spp. indicates the need of finding alternatives for probiotics. The insights from the present study can be used for further exploring the role of the gut microbiome in aspects such as growth, immunity and other physiological functions of the fish.
Key words: Aquaculture, Fish gut, Gut Microbiome, Major Carps, Metagenomics
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