Commensal microbial communities have immense effects on their vertebrate hosts, contributing to a number of physiological functions as well as host fitness. In particular, host immunity is strongly linked to microbiota composition through poorly understood bi-directional links. Gene expression may be a potential mediator of these links between microbial communities and host function. However few studies have investigated connections between microbiota composition and expression of host immune genes in complex systems. Here we leverage a large study of laboratory-raised fish from the species Gasterosteus aculeatus (three-spined stickleback) to document correlations between gene expression and microbiome composition. First, we examined correlations between microbiome alpha diversity and gene expression. Our results demonstrate robust positive associations between microbial alpha diversity and expression of host immunity. Next, we examined correlations between host gene expression and abundance of microbial taxa. We identified 15 microbial families that were highly correlated to host gene expression. These families were all tightly correlated to host expression of immune genes and processes, falling into one of three categories: those positively correlated, negatively correlated, and neutrally related to immune processes. Furthermore, we highlight several important immune processes that are commonly associated with abundance of these taxons, including both macrophage and B cell functions. Further functional characterization of microbial taxa will help disentangle the mechanisms of the correlations described here. In sum, our study supports prevailing hypotheses of intimate links between host immunity and gut microbiome composition.

中文翻译：

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棘回中免疫基因表达与肠道微生物组组成的协变量

共生微生物群落对其脊椎动物宿主具有巨大影响，有助于许多生理功能以及宿主健康。尤其是，宿主免疫力是通过人们对双向链接了解不足而与微生物群组成密切相关的。基因表达可能是微生物群落与宿主功能之间这些联系的潜在媒介。然而，很少有研究研究微生物群组成与复杂系统中宿主免疫基因表达之间的联系。在这里，我们利用对Gasterosteus aculeatus物种（三刺棘背鱼）的实验室饲养鱼类的大型研究来记录基因表达与微生物组组成之间的相关性。首先，我们研究了微生物组α多样性与基因表达之间的相关性。我们的结果证明了微生物α多样性与宿主免疫表达之间的强正相关。接下来，我们检查了宿主基因表达与微生物类群数量之间的相关性。我们确定了15个与宿主基因表达高度相关的微生物家族。这些家族都与宿主的免疫基因和过程的表达紧密相关，分为三类之一：与免疫过程呈正相关，负相关和中立的那些。此外，我们重点介绍了与这些分类单元丰富相关的几个重要的免疫过程，包括巨噬细胞和B细胞功能。微生物分类群的进一步功能表征将有助于弄清此处描述的相关机制。总共，