Lotus (Nelumbo nucifera)-based co-culture systems reshape gut microbiota and enhance health and microbial stability in Chinese soft-shelled turtle (Pelodiscus sinensis)

Background The Chinese soft-shelled turtle ( Pelodiscus sinensis ) is a valuable aquaculture species in East/Southeast Asia; however, intensive farming has caused pathogen prevalence and antibiotic overuse, threatening sustainability. The gut microbiome plays a critical role in maintaining host immune barrier functions and overall homeostasis. Modulating gut microbiota would improve the health status of turtles, offering a sustainable disease control and antibiotic reduction strategy. Rice-soft-shell turtle co-cropping has been demonstrated to improve the gut microbiota of turtles; however, the unsuitability of rice cultivation for year-round operation, due to seasonal water level management, and its low turtle yield limit its widespread application. Therefore, we aimed to find an alternative mode. Lotus ( Nelumbo nucifera ) exhibits distinct biological and operational advantages, making it highly suitable for soft-shell turtle ecology. We therefore introduced lotus–turtle (LB) and lotus root–turtle (OB) co-culture systems and compared these modes with the traditional monoculture mode (DZ), assessing survival, production, and microecological interactions among sediment, water, and gut microbiota, to support green turtle farming. Results Over the 3-year observation period, no disease occurred in the LB or OB systems, whereas recurrent bacterial infections were recorded in DZ ponds, accompanied by higher antimicrobial resistance in Aeromonas spp. Although DZ yielded a slightly higher average body weight and production, the LB and OB modes exhibited improved survival rates. Gut microbiota analysis revealed that co-cultured turtles had more stable microbial communities, characterized by dominant Firmicutes (> 95%) and enrichment of potentially beneficial genera such as Romboutsia and Clostridium sensu stricto 1, along with enhanced functional potential for fermentation and chemoheterotrophy. In contrast, the DZ group showed higher abundances of opportunistic pathogens and stress-adaptation functions. Notably, the environmental microbiota significantly affected the gut microbiota in the DZ mode, suggesting increased environmental influence under unstable intestinal conditions. Conclusions Our findings demonstrate that the lotus-based co-culture reshapes the gut and environmental microbiomes, enhances microbial stability, and improves disease resistance, offering an alternative strategy for sustainable turtle farming.