Characterization and Dynamics of the Gut Microbiota in Rice Fishes at Different Developmental Stages in Rice-Fish Coculture Systems

Abstract

The rice-fish system (RFS), a traditional coculture farming model, was selected as a “globally important agricultural heritage system.” Host-associated microbiota play important roles in development, metabolism, physiology, and immune function. However, studies on the gut microbiota of aquatic animals in the RFS are scarce, especially the lack of baseline knowledge of the dynamics of gut microbial communities in rice fish during different developmental stages. In this study, we characterized the microbial composition, community structure, and functions of several sympatric aquatic animals (common carp (Cyprinus carpio), crucian carp (Carassius carassius), and black-spotted frogs (Pelophylax nigromaculatus)), and the environment (water) in the RFS using 16S rRNA gene sequencing. Moreover, we investigated stage-specific signatures in the gut microbiota of common carp throughout the three developmental stages (juvenile, sub-adult, and adult). Our results indicated that the Fusobacteriota, Proteobacteria, and Firmicutes were dominant gut microbial phyla in rice fish. The differences in gut microbial compositions and community structure between the three aquatic species were observed. Although no significant differences in alpha diversity were observed across the three developmental stages, the microbial composition and community structure varied with development in common carp in the RFS, with an increase in the relative abundance of Firmicutes in sub-adults and a shift in the functional features of the community. This study sheds light on the gut microbiota of aquatic animals in the RFS. It deepens our understanding of the dynamics of gut microflora during common carp development, which may help improve aquaculture strategies in the RFS.

Variation in the gut microbiota during the early developmental stages of common carp (Cyprinus carpio L.) and its correlation with feed and pond water

“…4C) that CCE and CCY are similar to WE in terms of OTU level and genus classi cation, and can cluster together rst, which also indicates that in the very early stage of carp development, especially before feeding. The water environment has a great in uence on its ora, which is also consistent with the reports of many kinds of sh [41] [29] [42].…”

The impact of host development and density stress on the diversity of microbial communities in the gut and its surrounding environment of the Chinese alligator

“…The findings of this study reveal that Chinese alligators maintain a consistent core microbiota throughout their growth stages. The diversity of the gut microbiome, as measured by the α diversity index, shows minimal variation, and no significant differences, which aligns with research conducted on carp and zebrafish (Stephens et al., 2016; Tao et al., 2022). It is worth noting that the α diversity index reaches its highest point at 8Y and reaches its lowest point at 4Y.…”

A Comparative Study on Effects of Three Butyric Acid-Producing Additives on the Growth Performance, Non-specific Immunity, and Intestinal Microbiota of the Sea Cucumber Apostichopus japonicus

“…Furthermore, the Pearson correlation analysis revealed that the abundance of Verrucomicrobiota and unclassified_ f_Rhodobacteraceae had a positive correlation with WGR, and the abundance of Firmicutes and Verrucomicrobiota had a positive correlation with SGR. Previous studies have shown that Firmicutes break down carbohydrates and degrade plant cell wall components to produce short-chain fatty acids, which provide nutrients for the host [36]. Furthermore, some Firmicutes have the ability to boost host immunity by upregulating immune genes expression [37].…”