Shrimp disease progression increases the gut bacterial network complexity and abundances of keystone taxa

Abstract

Gut keystone taxa disproportionally affect the function and stability of their resident community and thus are candidate targets for improving host health. However, how disease progression alters the assembly of gut bacterial community remains unclear. To fill this knowledge gap, we conducted Illumina sequencing of the bacterial 16S rRNA gene to explore the co-occurrence network and dynamic in the predicted functions of Pacific white shrimp (Litopenaeus vannamei) gut microbiota on disease progression. Results showed that temporal changes in the gut bacterial communities are positively parallel with shrimp disease severity. The diseased shrimp harboured a more complex bacterial network, higher connectivity and more diverse keystone taxa compared with the healthy cohorts. Gut keystone taxa were affiliated with Verrucomicrobiales and Alteromonadales in healthy shrimp, which shifted to Rhodobacterales, Vibrionales and Flavobacteriales in diseased cohorts. Removal of keystone taxa from co-occurrence networks led to network fragmentation in diseased shrimp, suggesting their fundamental role in sustaining the stability of gut microbiota. The relative abundances of the predicted functional pathways facilitating immune system and metabolism significantly (P < .05) decreased in the diseased shrimp. Intriguingly, the potentials of immunity and infectious diseases were significantly and positively associated with the relative abundances of keystone taxa. This work aids our understanding of the compositional, functional and ecological dynamics of gut microbiota over a shrimp disease progression. Additionally, the identified keystone taxa might facilitate the development of diagnostic and therapeutic targets for shrimp disease.