Marine Rhodotorula NH-1 enhances the growth of red claw crayfish (Cherax quadricarinatus) by optimizing the intestinal microbiota: Evidence from genome, transcriptome, and metabolome analyses

We identified a fast-growing Rhodotorula strain NH-1 with high astaxanthin biosynthetic capacity in this study. Genomic analysis revealed key genes involved in microbial astaxanthin synthesis, and metabolite profiling identified antibacterial compounds such as 2-ethylhexanol, highlighting its probiotic potential. Dietary supplementation of NH-1 at varying concentrations in red claw crayfish (Cherax quadricarinatus) modulated the gut microbiome, significantly reducing Flavobacterium, Enterobacter, and Chitinophagaceae, while increasing Bacilloplasma, Wallemia, Pichia, Clavispora, Aspergillus, and Alternaria decreased, whereas Rhodotorula abundance rose. These microbial shifts were linked to transcriptomic and metabolomic changes, including enhanced digestive and immune enzyme activities, upregulation of immune-related genes, and modulation of hepatopancreatic pathways (e.g., mitochondrial complex IV assembly and cell death regulation). Levels of phosphatidylcholine and other metabolites related to nutrient absorption also increased, which improves growth performance and elevates astaxanthin accumulation in C. quadricarinatus. This project contains the raw ITS gut mycobiome data.