Gut microbiota in homologous Chinese soft-shell turtle (Pelodiscus sinensis) under different habitats

Abstract Background Chinese soft-shell turtle (Pelodiscus sinensis) is an important commercial species for its high nutritive and medicinal value, but it has been a vulnerable species due to habitat loss. In this study, homologous juvenile turtles were allocated to lake, pond and paddy field to investigate the habitat effects on turtles. Results The growth, morphology and gut microbial communities were monitored during the 4 months cultural period. It showed higher growth rate of turtles in paddy field and pond. The appearance, visceral coefficients, gut morphology and microbial communities in turtles were distinct among different habitats, which was mainly attributed to food abundance and living space. The diversity of gut microbial community was obviously higher in turtles from paddy field than pond and lake. Significant differences on dominant phyla, genera and species were found among initial samples and subsequent samples from different habitats. Firmicutes was the most abundant phylum in turtle gut sampled from greenhouse at initial and Proteobacteria was the most abundant phylum after cultivated in different habitats. The functional predictions indicated that both habitat type and sampling time had significant effects on metabolic pathways, especially amino acid and carbohydrate metabolism. Conclusion The microbial abundance was different among the habitats and varied within cultural periods. Gut microbes in turtles from paddy field presented high diversity and richness. Rice-turtle coculture was a potential ecological and economic farming mode for its high production and quality of both turtles and rice, which would play important roles in wild turtle protection, food security and paddy field environment improvement.