Comparative Analysis of the Composition and Diversity of the Intestinal Microflora of Four Fishes with Different Feeding Habits

Fish are generally classified as herbivorous, carnivorous, omnivorous, or filter-feeders according to feeding habits, including the feeding method and food content. The feeding habits of fish are reflected in their digestive organ, mainly the intestine. The intestine tract is the main site for digestion and nutritional uptake, and it is regarded as a key organ in fish nutrition. Reportedly, fish gut microbiota contributes to digestion and affect gastrointestinal tract development as well as the overall growth of the fish. The disruption of the intestinal microbiota induced by their feeding habit via diet usually affects the digestive functions of the host through disturbance in bacterial digestive enzyme production. Feeding habits determine the feed composition, which shapes the microbial communities in fish. For example, diet has been reported as a dominant cause of variation in the microbiota composition of rainbow trout. In contrast, feeding habit, which is regulated by many factors, including intrinsic and external factors, such as appetite, structure of the digestive tract, and feed palatability, is an important area of research in the intestinal microflora study. The feeding habit of fishes is one of the main factors affecting the differential colonization of fish intestinal flora. For example, the feeding habit increases the colonization of fish intestinal flora in the order omnivorous > herbivorous > carnivorous. It is also known that feeding habits influence intestinal digestion and structure. However, the influence of feeding habit on proximate composition, digestive enzyme secretion, and intestinal histomorphology is currently not well-known in fish. On the contrary, the feeding habit affects the composition and diversity of the intestinal microflora of fish. The composition and diversity of the microbiota in Carassius auratus, Ctenopharyngodon idella, Siniperca chuatsi, and Schizothorax grahami from the same environment have also not previously been studied. The present study aimed to compare and analyze the differences in the composition and diversity of the intestinal microflora of four fish species, investigating the relationship between their feeding habits and intestinal microflora as well. This study collected 12 intestine samples from each of the four fishes with different feeding habits, including omnivorous (C. auratus), herbivorous (C. idella), filter-feeder (S. chuatsi), and carnivorous (S. grahami), from the same pond. The composition and diversity of the microbial communities were determined by using high-throughput sequencing of 16S rRNA. Meanwhile, this study investigated the effects of feeding habits on the composition and diversity of the intestinal microflora of fish and predicted the potential functions of specific microflora with different nutrients. The results showed that the diversity of the intestinal microflora in fish was significantly affected by feeding habit (P < 0.05), such that higher levels occurred in the order omnivorous (C. auratus) > herbivorous (C. idella) > filter-feeder (S. grahami) > carnivorous (S. chuatsi). Proteobacteria and Firmicutes were the common dominant flora among the four fishes, although there were differences at the genera and species levels. For example, Acinetobacter and Bacteroides species were the most dominant flora in S. chuatsi and C. idella, respectively. Function prediction showed that the intestinal tract of S. chuatsi was mainly gram-negative. The disease resistance potential of C. idella was slightly higher than that of the other three fish species. Acinetobacter johnsonii, Acinetobacter lwoffii, and Pseudomonas stutzeri might help the host to digest protein, while Bacteroidetes may help the host to digest cellulose. In conclusion, feeding habit is one of the main factors affecting the differential colonization of fish intestinal flora. Analyzing the correlation between feeding habits and dominant intestinal flora as well as exploring the function of specific flora, could lay a theoretical foundation for studying the microbial effect of fish nutrition metabolism.