Gut microbial composition of the cyprinids Cyprinella lutrensis (Red shiner) and Notropis stramineus (Sand shiner): insights from wild fish populations
The gut microbiome represents a highly intricate ecosystem that exerts a pivotal influence on the host's physiology and health through various interactions and its ability to impact a wide range of physiological processes. In this study, we investigated the bacterial communities of two small-bodied fish species, Cyprinella lutrensis (Red shiner) and Notropis stramineus (Sand shiner) and surrounding waters, collected from Nebraska rivers. Our study focused on evaluating microbial diversity in small-bodied fish in Nebraska rivers and identifying autochthonous microbes present within these species irrespective of location to better understand bacterial community assembly and possible roles of such bacterial species. Our results revealed that both Red shiner and Sand shiner exhibited gut bacterial communities dominated by typical bacterial phyla found in freshwater fish. We discovered that the phylum Bacteroidota was minimally abundant in both species and significantly lower in relative abundance compared to the surrounding water microbial community. Furthermore, we found that the gut microbiomes of Red shiner and Sand shiner differed from the microbial community in the surrounding water, suggesting that these fish species contain host associated bacterial species that may provide benefits to the host. The fish gut bacterial communities were sensitive to environmental conditions such as turbidity, dissolved oxygen, temperature, and total nitrogen. Our findings also show bacterial community differences between fish species, although they shared notable similarities in bacterial phyla composition. The predicted metabolic-related pathways analysis revealed dominance of pathways related to membrane transport activity. These findings contribute to a better understanding of the gut bacterial composition of wild, freshwater, small-bodied fish and highlight the influence of environmental and host factors on bacterial composition and assembly.