Microbiome analysis of Litopenaeus vannamei reveals Vibrio as main risk factor of white faeces syndrome

The diversity of the gut microbiota substantially influences the health of the host, including shrimps. White faeces syndrome (WFS) is a multifactorial shrimp disease that can cause severe financial losses in Litopenaeus vannamei aquaculture industry. WFS in shrimps is caused not only by the microsporidian Enterocytozoon hep-atopenaei infection but also by gut microbial dysbiosis, specifically the Vibrio species. The objectives of this study are to explore the gut microbiota composition in L. vannamei shrimps and to gain insights into the genetic factors associated with the development of WFS. For this, PacBio Sequel II platform was utilized to obtain full-length sequencing of the 16S rRNA gene (V1-V9). Significant variations in the intestinal bacterial abundance were observed between healthy and WFS-affected shrimps. At the genus level, Candidatus Bacilloplasma, Photo-bacterium, Pirellula, Rhodobacter and Lactococcus are abundantly present in the healthy shrimps, whereas, Cya-nobium PCC-6307, Staphylococcus, and Vibrio are overrepresented in WFS shrimp. V. parahaemolyticus was identified as the predominant species in WFS samples. Function prediction analysis revealed that shrimp samples affected by WFS exhibited decreased lipid metabolism pathways, while showing elevated nucleotide metabolism and glycan biosynthesis pathways. Additionally, exosome and bacterial toxin pathways are more commonly found in diseased samples than in healthy ones, suggesting the potential involvement of unfavourable gut flora colonization. Our study provides clear understanding of the gut microbial community, specifically at the species level, distinguishing between WFS and healthy shrimps. Additionally, it emphasizes the role of Vibrio in the development of WFS and underscores the significance of analysing the core genes related to pathogens in studying the etiology of the disease.

Automated summary

The diversity of the gut microbiota has a significant impact on the health of hosts, including shrimps. White faeces syndrome (WFS) is a shrimp disease caused by Enterocytozoon hepatopenaei infection and gut microbial dysbiosis, specifically Vibrio species. This study aims to explore the gut microbiota composition in Litopenaeus vannamei shrimps and investigate the genetic factors associated with WFS development. The results show significant variations in intestinal bacterial abundance between healthy and WFS-affected shrimps, with different genera present in each group. Vibrio parahaemolyticus was identified as the predominant species in WFS samples. Function prediction analysis revealed metabolic pathway differences between healthy and diseased shrimps. This study provides valuable insights into the gut microbial community and highlights the importance of Vibrio in WFS development.