Integrated analysis of the structure and function of bacterial community in water and shrimp intestine microbes reveals their interaction

Abstract

Shrimp is closely associated with different microbial populations of the gut and the environment, particularly of the water. Despite significant microbiome research in shrimp, a direct relationship between the shrimp's gut microbiota and the habitat environment remains unclear. The bacterial profiles of the shrimp intestine and its aqueous environment were compared by compiling data from earlier research to characterize the dynamic interaction between shrimp and habitat. According to the integrated analysis, shrimp, water, and sediment all had significant operational taxonomic units (OTUs), with shrimp intestine having less OTUs and sediment having more. Furthermore, 66 biological activities were shown to be common in shrimp and water bacteria, including nitrate reduction, methylotrophy, methanol oxidation, intracellular parasites, human infectious diarrhoea, fermentation, and others. These mechanisms might represent the primary bacterial processes related with intestine function, revealing new information on shrimp and water ecology. Although the relative abundances in the bacterial composition were different in shrimp intestine, water and sediment, the bacterial communities were almost similar, indicating the close interaction between host and the environment in microbiome. Notably, the significant distribution of disease-related pathogens including Vibrio and Flavobacterium in shrimp intestine and habitat water provided valuable information for disease prediction and shrimp health management in the aquaculture industry. In summary, many common microbes and bacterial processes that occur in the shrimp intestine and surrounding environment were revealed, and further functional analysis might help to modulate these processes to promote shrimp development and health.

Keywords

• microbiome
• bacterial community
• intestine
• public data
• shrimp