Bacterial Diversity of Fresh and Traditional Sun-Dried Bombay Duck (Harpadon nehereus) from Retail Fish Markets of West Bengal, India

Abstract

Bacterial diversity of fresh and traditional sun-dried Bombay duck (Harpadon nehereus), an economically important aquatic species have been analyzed through 16S rRNA gene amplicon sequencing using Illumina’s MiSeq platform. Culture-independent analysis of DNA extracted from the fish flesh showed that fresh (F1) and traditional sun-dried (D2) Bombay duck exhibited little different bacterial diversity (Shannon alpha diversity 9.03 for F1 and 9.62 for D2), although the sample were collected from separate markets. Rhodobacter (136 OTU) and Pseudomonas (125 OTU) were the dominant bacteria. In contrast to fresh Bombay duck, the absence of phylum Chrysiogenetes and Caldithrix in a dry Bombay duck suggests that these gram-negative bacteria are sensitive to sun drying temperature. The co-occurrence of members of the Campylobacterales and Helicobacteraceae, as well as species of Clostridium, Arcobacter, Staphylococcus, and Streptococcus, indicates the possibility of cross-contamination. Our work has led us to conclude that the association of bacteria of public health significance with densely populated urban markets makes people vulnerable to microbial threats. The study recommends an effective quality assurance program for the production of safe dry fish for domestic consumption as well as for export.