Aims The aim of this study was to determine the intestinal microflora of Anguilla marmorata at different growth rates and to identify potential probiotic/pernicious bacteria. Methods and Results Bacterial communities from eight different eels' intestinal sites (including the intestinal contents and the intestinal mucosa) from three fish groups (three fast‐, two medium‐, and three stunted‐growth samples), two water samples, and one diet sample were characterized by Illumina next‐generation sequencing. The data revealed that the predominant genera (relative abundance of bacteria genera >1%) in the intestine of fast‐ and medium‐growth groups were Cetobacterium, Edwardsiella, Clostridium, Lactococcus, Bacteroides, Plesiomonas and Akkermansia. The dominant genus in the stunted‐growth group was Spiroplasma. Moreover, culture‐associated (water and feed) environmental microbes were distinct from those present in fish intestines, and included Flavobacterium (the dominant bacteria in water) and Corynebacterium (the dominant bacteria in feed). Conclusions Only minor differences in gut microbial communities were observed between the fast‐growth group and the medium‐growth group; however, significant differences were observed between the normal‐growth group (including the fast‐growth group and medium‐growth group, which showed uninhibited growth during the rearing stage) and the stunted‐growth group. Together, these data suggested that intestinal microbes were significantly associated with marbled eels’ growth rate. Significance and Impact of the Study In this study, we demonstrated for the first time, the intestinal bacterial communities of A. marmorata at different growth rates. Moreover, we found that the genus Spiroplasma was abundant in the guts of stunted‐growth eels, which had never been noticed. Such a finding indicates that the genus Spiroplasma plays a key role associated with retardation in growth and should be controlled to recover the growth of stunted eels, which is meaningful to farmers.

The Siamese crocodile (Crocodylus siamensis) is a freshwater, endangered crocodile with high economic value in the farming industry. Gut microflora plays an essential role in host physiological activity, and it contributes significantly to both the health and diseased states of animals. However, thus far, no study has focused on the correlation between diseases and intestinal bacterial communities in crocodilians. Here, we first compared the composition and function of gut microbial communities in captive juvenile C. siamensis suffering from anorexia and healthy crocodile controls using deep amplicon sequencing. The gut microbial diversity of anorexic crocodiles was much lower than the healthy individuals. Obvious changes in gut microbial composition were observed between sick and healthy crocodiles, except for Cetobacterium somerae of phylum Fusobacteria. In particular, the abundance of Bacteroides luti, Clostridium disporicum, Plesiomonas shigelloides, and Odoribacter sp. in the gut flora of healthy crocodiles was distinctly higher than the diseased group. Conversely, the species Edwardsiella tarda was overrepresented in the gut of anorexic crocodiles compared to the healthy group. Furthermore, in anorexic crocodiles, the predicted microbial functions that were related to amino acid metabolism, biosynthesis of other secondary metabolites, nucleotide metabolism, replication and repair, and translation were significantly reduced, while signal transduction was significantly enriched. These findings of the present study provide a reference to enrich the field of gut microorganism studies in crocodilians and suggest that alterations in the composition and function of gut bacteria in C. siamensis juveniles may be associated with anorexia in crocodiles.