Determination of Spoilage Microbiota of Pacific White Shrimp During Ambient and Cold Storage Using Next-Generation Sequencing and Culture-Dependent Method

Abstract

This study was conducted to determine the initial and spoilage microbiota of Pacific white shrimp during ambient and cold storage using next-generation sequencing (NGS) and a culture-dependent method. The quality changes were also evaluated by sensory analysis and total volatile basic nitrogen (TVB-N) values. After 1 d of storage, the psychrotrophic bacteria were only 5.97 log CFU/g, accounting for 1.1% of the mesophilic bacteria counts (7.94 log CFU/g). The psychrotrophic bacteria counts exceeded the counts of mesophilic bacteria for shrimp stored at 4 °C after 6 d of storage, indicating that psychrotrophic bacteria became predominant. The NGS was used to identify the bacterial species in samples stored at 25 and 4 °C. The results showed that the dominant microorganisms were Vibrio at 25 °C, and Acinetobacter, Psychrobacter, and Shewanella at 4 °C. By the culture-dependent method based on 16S rRNA gene and VITEK®2 CompactA system, it showed that the dominant microorganisms were Proteus spp. at 25 °C, and Shewanella putrefaciens, Acinetobacter johnsonii, and Aeromonas sobria at 4 °C. In conclusion, differences in results of microbiota analyzed by culture dependent and independent approaches were observed. The combination of both methodologies may provide more comprehensive information about the dominant spoilage microbiota in Pacific white shrimp during ambient and cold storage.

Keywords: 16S rRNA; Litopenaeus vannamei; next-generation sequencing; psychrotrophic bacteria; spoilage microbiota.