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Abstract：
Our understanding of the gut microbiota of animals is largely based on studies of mammals. To better understand the evolutionary basis of symbiotic relationships between animal hosts and indigenous microbes, it is necessary to investigate the gut microbiota of non-mammalian vertebrate species. In particular, fish have the highest species diversity among groups of vertebrates, with approximately 33,000 species. In this study, we comprehensively characterized gut bacterial communities in fish.
We analyzed 227 individual fish representing 14 orders, 42 families, 79 genera, and 85 species. The fish gut microbiota was dominated by Proteobacteria (51.7%) and Firmicutes (13.5%), different from the dominant taxa reported in terrestrial vertebrates (Firmicutes and Bacteroidetes). The gut microbial community in fish was more strongly shaped by host habitat than by host taxonomy or trophic level. Using a machine learning approach trained on the microbial community composition or predicted functional profiles, we found that the host habitat exhibited the highest classification accuracy. Principal coordinate analysis revealed that the gut bacterial community of fish differs significantly from those of other vertebrate classes (reptiles, birds, and mammals).
Collectively, these data provide a reference for future studies of the gut microbiome of aquatic animals as well as insights into the relationship between fish and their gut bacteria, including the key role of host habitat and the distinct compositions in comparison with those of mammals, reptiles, and birds. Video Abstract.
We analyzed 227 individual fish representing 14 orders, 42 families, 79 genera, and 85 species. The fish gut microbiota was dominated by Proteobacteria (51.7%) and Firmicutes (13.5%), different from the dominant taxa reported in terrestrial vertebrates (Firmicutes and Bacteroidetes). The gut microbial community in fish was more strongly shaped by host habitat than by host taxonomy or trophic level. Using a machine learning approach trained on the microbial community composition or predicted functional profiles, we found that the host habitat exhibited the highest classification accuracy. Principal coordinate analysis revealed that the gut bacterial community of fish differs significantly from those of other vertebrate classes (reptiles, birds, and mammals).
Collectively, these data provide a reference for future studies of the gut microbiome of aquatic animals as well as insights into the relationship between fish and their gut bacteria, including the key role of host habitat and the distinct compositions in comparison with those of mammals, reptiles, and birds. Video Abstract.
摘要：
我们对动物肠道微生物群的理解很大程度上是基于对哺乳动物的研究。为了更好地理解动物宿主和本土微生物之间共生关系的进化基础，有必要研究非哺乳动物脊椎动物物种的肠道菌群。特别是,鱼类在脊椎动物群中具有最高的物种多样性，大约有33,000种。在这项研究中,我们全面地表征了鱼类的肠道细菌群落。
我们分析了227条个体鱼，代表14条订单，42个家庭,79属，85种。鱼肠菌群以变形杆菌（51.7%）和厚壁菌（13.5%）为主，与陆生脊椎动物（Firmicutes和拟杆菌）中报道的优势类群不同。鱼类的肠道微生物群落受宿主栖息地的影响比受宿主分类学或营养水平的影响更大。使用对微生物群落组成或预测功能概况进行训练的机器学习方法，我们发现寄主栖息地表现出最高的分类精度。主坐标分析显示，鱼类的肠道细菌群落与其他脊椎动物种类（爬行动物，鸟,和哺乳动物）。
集体，这些数据为未来对水生动物肠道微生物组的研究以及对鱼类与其肠道细菌之间关系的见解提供了参考，包括宿主栖息地的关键作用以及与哺乳动物相比的独特组成，爬行动物,和鸟。视频摘要。
我们分析了227条个体鱼，代表14条订单，42个家庭,79属，85种。鱼肠菌群以变形杆菌（51.7%）和厚壁菌（13.5%）为主，与陆生脊椎动物（Firmicutes和拟杆菌）中报道的优势类群不同。鱼类的肠道微生物群落受宿主栖息地的影响比受宿主分类学或营养水平的影响更大。使用对微生物群落组成或预测功能概况进行训练的机器学习方法，我们发现寄主栖息地表现出最高的分类精度。主坐标分析显示，鱼类的肠道细菌群落与其他脊椎动物种类（爬行动物，鸟,和哺乳动物）。
集体，这些数据为未来对水生动物肠道微生物组的研究以及对鱼类与其肠道细菌之间关系的见解提供了参考，包括宿主栖息地的关键作用以及与哺乳动物相比的独特组成，爬行动物,和鸟。视频摘要。
