Microsporidian infection disrupts gut microbiome and drives metabolic dysregulation in Macrobrachium nipponense.

The gut microbiome plays a crucial role in maintaining host health, yet its functions in aquatic animals remain incompletely understood. Given its economic significance in Asian aquaculture, the oriental river prawn (Macrobrachium nipponense) was chosen to assess microbiome dynamics during infection with Potaspora macrobrachium, an emerging microsporidian pathogen. Histopathological analysis confirmed severe microsporidian infections in diseased prawns. Using 16S rRNA gene sequencing (Illumina MiSeq), we characterized infection-induced shifts in the gut microbiome's composition and structure. Bacterial communities showed significant divergence between health states, with infection status being the primary clustering determinant. The microbiome was dominated by Proteobacteria (86.4 %), Bacteroidota (6.89 %), Firmicutes (3.41 %), and Actinobacteriota (1.69 %), displaying distinct abundance patterns. Disease-state indicators included Rikenellaceae, Pseudomonas oryzihabitans, and Bacteroides fragilis among others. Critically, functional prediction revealed that metabolic pathways, particularly carbohydrate metabolism, amino acid metabolism, and cofactor/vitamin metabolism, were significantly altered in infected prawns, suggesting that P. macrobrachium infection reprograms the metabolic activity of the gut microbiome.