Community Structure and Functional Annotations of the Skin Microbiome in Healthy and Diseased Catfish, Heteropneustes fossilis

Effects of Citrobacter freundii on sturgeon: Insights from skin mucosal immunology and microbiota

Skin mucus analysis has recently been used as a non-invasive method to evaluate for fish welfare. The present research study was conducted to examine the skin mucosal immunity and skin microbiota profiles of sturgeons infected with Citrobacter freundii. Our histology results showed that the thickness of the epidermal layer of skin remained thinner, and the number of mucous cells was significantly decreased in sturgeons after infection (p < 0.05). Total protein, alanine aminotransferase, aspartate aminotransferase, superoxide dismutase, and creatine kinase levels in the mucus showed biphasic pattern (decrease and then increase). Lactate dehydrogenase, lysozyme, and acid phosphatase activities in the mucus showed an increasing trend after infection. Furthermore, 16S rRNA sequencing also revealed that C. freundii infection also affected the diversity and community structure of the skin mucus microbiota. An increase in microbial diversity (p > 0.05) and a decrease in microbial abundance (p < 0.05) after infection were noted. The predominant bacterial phyla in the skin mucus were Proteobacteria, Fusobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Specifically, the relative abundance of Fusobacteria increased after infection. The predominant bacterial genera in the skin mucus were Cetobacterium, Pelomonas, Bradyrhizobium, Flavobacterium, and Pseudomonas. The relative abundance of Cetobacterium, Pseudomonas, and Flavobacterium increased after infection. Our current research findings will provide new insights into the theoretical basis for future research studies exploring the mechanism of sturgeon infection with C. freundii.

Skin Microbial Community Associated to Strawberry Disease in Farmed Rainbow Trout (Oncorhynchus mykiss Walbaum, 1792)

Aquaculture plays a crucial role in addressing the growing global demand for food. However, diseases associated with intensive aquaculture practices, especially those affecting the skin, can present significant challenges to both fish health and the industry as a whole. Strawberry disease (SD), also known as red-mark syndrome, is a persistent and non-lethal skin condition observed in Rainbow Trout (Oncorhynchus mykiss) in the United States and various European countries. SD is a nonlethal skin condition of an unclear etiology that affects rainbow trout reared in freshwater close to the harvest period. We used a RNA-based approach to examine active microbiota in the SD skin lesions and compared to non-injured skin. Our results, based on using 16S rRNA gene next-generation sequencing, showed that the skin microbiota was dominated by the phyla Firmicutes, Proteobacteria, and Actinobacteria. The comparisons of the skin microbiota between injured and non-injured samples showed differences in the alpha diversity (Fisher index) and beta diversity metrics (ANOSIM). At the genus level, both Pseudomonas and Candidatus Midichloria were highlighted as the most abundant taxa detected in samples obtained from fish affected with strawberry diseases. In contrast, the most abundant taxa in non-injured skin were Escherichia-Shigella, Streptococcus, and Pseudoalteromonas. In conclusion, our study on SD revealed distinct differences in the microbiota composition between skin lesions and non-injured skin. This is the first description of microbiota associated with SD-injured skin samples using an RNA approach.