The structural and functional characteristics of the gut microbiota of Marsupenaeus japonicus as revealed by 16S rRNA gene amplicon sequencing

Abstract:

[Background] Gut microbiota plays a pivotal role in the physiological activities of prawns. The Kuruma prawn (Marsupenaeus japonicus) is one of the most important seawater prawn species for aquaculture in China. However, until now, little is known about the structure and function of gut microbiota in M. japonicus. [Objective] To explore the bacterial structure and function in the intestines of M. japonicus and to investigate the impact of external (water and feed) microbes on the structure of M. japonicus gut microbiota by using high-throughput sequencing technology. [Methods] After 60 days of culture period, the M. japonicus intestines (n=3), pond water (n=3), and prawn feed (n=3) samples were collected respectively, and then total genome DNA was extracted from each sample for 16S rRNA gene amplicon sequencing. The comparative analysis of bacterial composition of all samples was based on bioinformatics methods, and PICRUSt software was performed to predict the functional profiles of M. japonicus gut microbiota. [Results] A total of 822 713 valid reads were obtained from the sequencing data, resulting in 3 416 OTUs after data rarefying, and there were 28.49%, 59.30% of OTUs observed in prawn gut samples could also be found in water and diet samples, respectively. The predominant phyla observed in prawn gut samples were Proteobacteria, Bacteroidetes, Firmicutes, and Fusobacteria, which were different from those present in water and diet samples, expect for Proteobacteria and Bacteroidetes. The major genera identified in prawn gut samples were Vibrio, Aliivibrio, Pseudoalteromonas, Pseudofulvibacter, Colwellia, Fusibacter, Photobacterium, Desulfovibrio, Psychrobacter, and Arcobacter. Moreover, culture-associated environmental microbes were distinct from those present in prawn intestines, and included Marivita (the most abundant genus in water samples) and Pseudomonas (the most abundant genus in diet samples). PICRUSt analysis revealed that the core functional profile of gut bacterial community in M. japonicus was metabolism, including amino acid metabolism, carbohydrate metabolism, energy metabolism, and etc. [Conclusion] There existed some similarities in gut microbiota structure between M. japonicus and other pawn species. The structure of M. japonicus gut microbiota, which played a certain role in daily metabolic activities of the host, was partly influenced by the external microbes.