Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL, USA.
Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA.
Microbiome. 2019 Aug 9;7(1):113. doi: 10.1186/s40168-019-0724-4.
Space environment imposes a range of challenges to mammalian physiology and the gut microbiota, and interactions between the two are thought to be important in mammalian health in space. While previous findings have demonstrated a change in the gut microbial community structure during spaceflight, specific environmental factors that alter the gut microbiome and the functional relevance of the microbiome changes during spaceflight remain elusive.
We profiled the microbiome using 16S rRNA gene amplicon sequencing in fecal samples collected from mice after a 37-day spaceflight onboard the International Space Station. We developed an analytical tool, named STARMAPs (Similarity Test for Accordant and Reproducible Microbiome Abundance Patterns), to compare microbiome changes reported here to other relevant datasets. We also integrated the gut microbiome data with the publically available transcriptomic data in the liver of the same animals for a systems-level analysis.
We report an elevated microbiome alpha diversity and an altered microbial community structure that were associated with spaceflight environment. Using STARMAPs, we found the observed microbiome changes shared similarity with data reported in mice flown in a previous space shuttle mission, suggesting reproducibility of the effects of spaceflight on the gut microbiome. However, such changes were not comparable with those induced by space-type radiation in Earth-based studies. We found spaceflight led to significantly altered taxon abundance in one order, one family, five genera, and six species of microbes. This was accompanied by a change in the inferred microbial gene abundance that suggests an altered capacity in energy metabolism. Finally, we identified host genes whose expression in the liver were concordantly altered with the inferred gut microbial gene content, particularly highlighting a relationship between host genes involved in protein metabolism and microbial genes involved in putrescine degradation.
These observations shed light on the specific environmental factors that contributed to a robust effect on the gut microbiome during spaceflight with important implications for mammalian metabolism. Our findings represent a key step toward a better understanding the role of the gut microbiome in mammalian health during spaceflight and provide a basis for future efforts to develop microbiota-based countermeasures that mitigate risks to crew health during long-term human space expeditions.
太空环境对哺乳动物的生理机能和肠道微生物群构成了一系列挑战，人们认为两者之间的相互作用对哺乳动物在太空中的健康很重要。虽然之前的研究结果表明，在太空飞行过程中，肠道微生物群落结构发生了变化，但改变肠道微生物组的具体环境因素以及太空飞行过程中微生物组变化的功能相关性仍不清楚。
我们使用 16S rRNA 基因扩增子测序技术，对国际空间站上为期 37 天的太空飞行后小鼠的粪便样本进行了微生物组分析。我们开发了一种名为 STARMAPs（相似性测试用于一致和可重复的微生物丰度模式）的分析工具，用于将这里报告的微生物组变化与其他相关数据集进行比较。我们还将肠道微生物组数据与同一动物肝脏中公开的转录组数据进行了整合，以进行系统水平的分析。
我们报告了微生物组 alpha 多样性的升高和微生物群落结构的改变，这些改变与太空环境有关。使用 STARMAPs，我们发现观察到的微生物组变化与之前在航天飞机任务中飞行的小鼠报告的数据具有相似性，这表明太空飞行对肠道微生物组的影响具有可重复性。然而，这种变化与地面上基于太空辐射的研究中诱导的变化并不相同。我们发现太空飞行导致一个门、一个科、五个属和六个种的微生物的丰度发生了显著变化。这伴随着推断的微生物基因丰度的变化，表明能量代谢能力发生了改变。最后，我们确定了肝脏中表达与推断的肠道微生物基因含量一致改变的宿主基因，特别是强调了参与蛋白质代谢的宿主基因与参与腐胺降解的微生物基因之间的关系。
这些观察结果揭示了导致太空飞行过程中肠道微生物组发生强烈变化的特定环境因素，这对哺乳动物代谢具有重要意义。我们的研究结果为更好地理解肠道微生物组在哺乳动物太空飞行健康中的作用奠定了基础，并为未来开发基于微生物组的对策提供了基础，以减轻长期人类太空任务中机组人员健康面临的风险。
