Study of microbial diversity and potential human pathogens in freshwater aquaculture environment

Aquaculture is major source of food and employment. However, aquaculture worldwide has become increasingly susceptible to new diseases mainly due to movement of live animals, the increased use of high density farming systems, and increasing anthropogenic pressures on aquatic ecosystems. In villages, entry of human wastes in private or community owned aquaculture is quite common. Microbial contamination in fish occurs from the environment in which it is growing and during post-harvest handling including freezing, processing, packing etc. Enhanced focus on integrated fish farming, in which livestock wastes from cattle, pig and poultry (cow/pig dung, poultry manure etc.) are used as inputs, may sometimes lead to bacterial zoonotic infections. Intensive fish farming cannot be supported by naturally available food alone and has to be supplemented with formulated feeds. Any bacterial pathogen present in livestock wastes and suppliemental feeds may eventually get transmitted to human through aquatic intermediates. Cooking generally destroys most harmful bacteria, but undercooked foods, processed ready-to-eat foods, and under processed foods can contain harmful bacteria posing serious health threats. Fishery products are important reservoirs for many of the bacterial pathogens, including Salmonella spp., Listeria spp., Vibrio parahaemolyticus, V. vulnificus, V. cholerae, Clostridium botulinum, Escherichia coli and Mycobacterium marinum.There have been some studies for detection of fish-borne human pathogens. However, almost no information is available about overall composition of various microbial communities associated with aquaculture environment. There is urgent need to study the inter-relationship between microbial communities and human pathogens in freshwater aquaculture environment followed by development of molecular methods for detection and quantification of these pathogens for routine quality assurance of raw and processed products. This study intends to use Next Generation Sequencing (NGS) based metagenomic approach by sequencing of 16S ribosomal RNA hypervariable regions. After understanding the microbial communities, molecular assays will be developed for detection and quantification of human pathogens belonging to these communities.