Journal of Fisheries and Life Sciences

Author(s): Anuj Tyagi and Balwinder Singh

Abstract: Next-Generation Sequencing (NGS) based 16S rRNA gene metagenomics studies are significantly contributing to understand microbial diversities in relatively unexplored agricultural sub-disciplines. However, experimental variations such as primer selection and polymerase chain reaction (PCR) bias can have great impact on outcomes of these studies. Here, we compared two 16S rRNA variable (V3 and V4) region specific primer pairs for study of microbial diversity in sediment and fish (Labeo rohita) gut samples. Clear bias in terms of diversity and community representation was observed in NGS dataset generated from V3 primers, whereas V4 primer showed much better results. Overall diversity in sediment sample was found to be much higher than gut sample. Proteobacteria followed by Verrucomicrobia were most dominant phyla in sediment and fish gut samples. Presence of known cellulose degraders (Clostridium spp., Ruminococcus spp., Eubacterium spp. and Bacteroides spp.) and Short Chain Fatty Acid (SCFA) producers (Faecalibacterium prausnitzii, Veillonella spp. and Megasphaera spp.) suggested that gut microbiota played an important role in digestion, physiology, metabolism and health of L. rohita. Gut microbiota also harbored potentially fish and human pathogenic bacteria. Very few sequences belonging to known probiotic bacteria (Bacillus spp., Streptococcus spp. and Bifidobacterium spp.) were observed. This study serves as preliminary investigation of microbial diversity in aquaculture environment and impact of primer specific variations on estimated diversity.