Institute of Microbiology, University of Greifswaldgrid.5603.0, Greifswald, Germany.
Institute of Biochemistry, University of Greifswaldgrid.5603.0, Greifswald, Germany.
Microbiol Spectr. 2021 Oct 31;9(2):e0018221. doi: 10.1128/Spectrum.00182-21. Epub 2021 Oct 6.
Seasonal influenza outbreaks represent a large burden for the health care system as well as the economy. While the role of the microbiome has been elucidated in the context of various diseases, the impact of respiratory viral infections on the human microbiome is largely unknown. In this study, swine was used as an animal model to characterize the temporal dynamics of the respiratory and gastrointestinal microbiome in response to an influenza A virus (IAV) infection. A multi-omics approach was applied on fecal samples to identify alterations in microbiome composition and function during IAV infection. We observed significantly altered microbial richness and diversity in the gastrointestinal microbiome after IAV infection. In particular, increased abundances of were detected, while and decreased. Moreover, our metaproteomics data indicated that the functional composition of the microbiome was heavily affected by the influenza infection. For instance, we identified decreased amounts of flagellin, correlating with reduced abundances of and , possibly indicating involvement of a direct immune response toward flagellated during IAV infection. Furthermore, enzymes involved in short-chain fatty acid (SCFA) synthesis were identified in higher abundances, while metabolome analyses revealed rather stable concentrations of SCFAs. In addition, 16S rRNA gene sequencing was used to characterize effects on the composition and natural development of the upper respiratory tract microbiome. Our results showed that IAV infection resulted in significant changes in the abundance of and in the upper respiratory tract. Surprisingly, temporal development of the respiratory microbiome structure was not affected. Here, we used swine as a biomedical model to elucidate the impact of influenza A H1N1 infection on structure and function of the respiratory and gastrointestinal tract microbiome by employing a multi-omics analytical approach. To our knowledge, this is the first study to investigate the temporal development of the porcine microbiome and to provide insights into the functional capacity of the gastrointestinal microbiome during influenza A virus infection.
季节性流感爆发对医疗保健系统和经济造成了巨大负担。虽然微生物组在各种疾病中的作用已经阐明，但呼吸道病毒感染对人类微生物组的影响在很大程度上尚不清楚。在这项研究中，猪被用作动物模型，以描述呼吸道和胃肠道微生物组对甲型流感病毒（IAV）感染的时间动态。应用多组学方法对粪便样本进行分析，以确定 IAV 感染过程中微生物组组成和功能的变化。我们观察到 IAV 感染后胃肠道微生物组的微生物丰富度和多样性明显改变。特别是，检测到 的丰度增加，而 和 的丰度减少。此外，我们的宏蛋白质组学数据表明，流感感染严重影响了微生物组的功能组成。例如，我们发现鞭毛蛋白的含量减少，与 和 的丰度降低相关，这可能表明在 IAV 感染期间，针对鞭毛 的直接免疫反应参与其中。此外，还鉴定出参与短链脂肪酸（SCFA）合成的酶的丰度增加，而代谢组学分析显示 SCFA 的浓度相对稳定。此外，还使用 16S rRNA 基因测序来描述对上呼吸道微生物组组成和自然发育的影响。我们的结果表明，IAV 感染导致上呼吸道中 和 的丰度发生显著变化。令人惊讶的是，呼吸道微生物组结构的时间发展没有受到影响。在这里，我们使用猪作为生物医学模型，通过采用多组学分析方法，阐明甲型流感 H1N1 感染对呼吸道和胃肠道微生物组结构和功能的影响。据我们所知，这是第一项研究猪微生物组的时间发展并深入了解甲型流感病毒感染期间胃肠道微生物组的功能能力的研究。
