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.

肠道微生物组（gut microbiome）是一类高度复杂的生态系统，可通过多种相互作用及调控诸多生理过程的能力，对宿主的生理状态与健康产生关键影响。本研究针对从美国内布拉斯加州河流中采集的两种小型鱼类——红闪鱼（Cyprinella lutrensis, Red shiner）与沙闪鱼（Notropis stramineus, Sand shiner）及其周边水体的细菌群落展开调查。本研究旨在评估内布拉斯加州河流中小型鱼类的微生物多样性，并识别两种鱼类体内不受采样地点影响的固有微生物，以更好地解析细菌群落构建机制及此类细菌的潜在功能。研究结果显示，红闪鱼与沙闪鱼的肠道细菌群落均以淡水鱼类中常见的细菌菌门为优势类群。我们发现，拟杆菌门（Bacteroidota）在两种鱼类中的丰度均较低，且其相对丰度显著低于周边水体的微生物群落。此外，红闪鱼与沙闪鱼的肠道微生物组与周边水体的微生物群落存在显著差异，这表明这两种鱼类拥有与宿主共生的细菌类群，此类类群可能对宿主有益。鱼类肠道细菌群落对浊度、溶解氧、温度及总氮等环境条件具有敏感性。尽管两种鱼类在细菌菌门组成上存在显著相似性，但本研究同样发现不同鱼类间的细菌群落存在差异。预测代谢通路分析结果显示，膜转运相关通路占据主导地位。本研究结果有助于进一步加深对野生淡水小型鱼类肠道细菌组成的理解，并揭示了环境与宿主因素对细菌群落组成及构建过程的影响。