Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada.
Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, Michigan, USA.
Mol Ecol. 2023 Aug;32(15):4427-4446. doi: 10.1111/mec.17039. Epub 2023 Jun 7.
Differences in gut microbiome composition are linked with health, disease and ultimately host fitness; however, the molecular mechanisms underlying that relationship are not well characterized. Here, we modified the fish gut microbiota using antibiotic and probiotic feed treatments to address the effect of host microbiome on gene expression patterns. Chinook salmon (Oncorhynchus tshawytscha) gut gene expression was evaluated using whole transcriptome sequencing (RNA-Seq) on hindgut mucosa samples from individuals treated with antibiotic, probiotic and control diets to determine differentially expressed (DE) host genes. Fifty DE host genes were selected for further characterization using nanofluidic qPCR chips. We used 16S rRNA gene metabarcoding to characterize the rearing water and host gut microbiome (bacterial) communities. Daily administration of antibiotics and probiotics resulted in significant changes in fish gut and aquatic microbiota as well as more than 100 DE genes in the antibiotic and probiotic treatment fish, relative to healthy controls. Normal microbiota depletion by antibiotics mostly led to downregulation of different aspects of immunity and upregulation of apoptotic process. In the probiotic treatment, genes related to post-translation modification and inflammatory responses were up-regulated relative to controls. Our qPCR results revealed significant effects of treatment (antibiotic and probiotic) on rabep2, aifm3, manf, prmt3 gene transcription. Moreover, we found significant associations between members of Lactobacillaceae and Bifidobacteriaceae with host gene expression patterns. Overall, our analysis showed that the microbiota had significant impacts on many host signalling pathways, specifically targeting immune, developmental and metabolic processes. Our characterization of some of the molecular mechanisms involved in microbiome-host interactions will help develop new strategies for preventing/ treating microbiome disruption-related diseases.
肠道微生物组的组成差异与健康、疾病，最终与宿主适应性有关；然而，这种关系的分子机制尚不清楚。在这里，我们使用抗生素和益生菌饲料处理来改变鱼类的肠道微生物组，以研究宿主微生物组对基因表达模式的影响。我们用抗生素、益生菌和对照饮食处理的个体的后肠黏膜样本进行全转录组测序（RNA-Seq），评估了奇努克鲑鱼（Oncorhynchus tshawytscha）肠道的基因表达情况，以确定差异表达（DE）的宿主基因。我们使用纳米流 qPCR 芯片进一步对 50 个宿主基因进行了特征分析。我们用 16S rRNA 基因 metabarcoding 来描述养殖水和宿主肠道微生物组（细菌）群落。与健康对照组相比，抗生素和益生菌的日常给药导致了鱼类肠道和水生微生物组的显著变化，以及抗生素和益生菌处理鱼类中超过 100 个 DE 基因的变化。抗生素对正常微生物群的消耗主要导致了免疫的不同方面下调和凋亡过程上调。在益生菌处理中，与对照组相比，与翻译后修饰和炎症反应相关的基因上调。我们的 qPCR 结果显示，处理（抗生素和益生菌）对 rabep2、aifm3、manf、prmt3 基因转录有显著影响。此外，我们发现乳杆菌科和双歧杆菌科的成员与宿主基因表达模式之间存在显著关联。总的来说，我们的分析表明，微生物组对许多宿主信号通路有显著影响，特别是针对免疫、发育和代谢过程。我们对微生物组-宿主相互作用中涉及的一些分子机制的特征分析，将有助于开发预防/治疗与微生物组破坏相关疾病的新策略。
