Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight

Jiang et al. Microbiome (2019) 7:113 https://doi.org/10.1186/s40168-019-0724-4 RESEARCH Open Access Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight Peng Jiang1, Stefan J. Green2, George E. Chlipala2, Fred W. Turek1 and Martha Hotz Vitaterna1* Abstract Background: 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. Methods: 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. Results: 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 spacetype 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. Conclusions: 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. Keywords: Space environment, Microgravity, Cosmic radiation, 16S rRNA amplicon sequencing, RNA-seq * Correspondence: 1 Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL, USA Full list of author information is available at the end of the article © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Jiang et al. Microbiome (2019) 7:113 Background The gastrointestinal microbiota plays an important role in mammalian health by interacting with host immune, metabolic, and neuropsychiatric functions [1, 2]. The space environment imposes many challenges to mammalian physiology, including functions known to interact with the gut microbiota in a bidirectional fashion. Specific space environmental factors, such as microgravity and radiation, are thought to alter the gut microbiota, representing a risk to astronaut health, especially during long-term spaceflight missions [3]. We previously studied the gut microbiome of a twin astronaut and found alterations during his 1-year mission onboard the International Space Station (ISS), which were not observed in his twin brother on Earth during the same period of time [4]. Similarly, spaceflight-associated microbiome changes were observed in mice flown on a space shuttle mission (STS-135) for 13 days [5]. However, the specific space environmental Page 2 of 18 factors that influence the gut microbiome and the impact of these changes on host functions remain unknown. In 2014, NASA carried out the first ISS-based rodent research mission (RR-1), with the primary goal of validating hardware and operations for future rodent research missions [6]. RR-1 involved four groups of mice (Fig. 1a), and fecal samples from a subset of these animals were available, providing an opportunity to study the effects of spaceflight on the murine gut microbiome. Using 16S rRNA gene amplicon sequencing, we profiled the microbiome in these RR-1 samples and report spaceflight-associated changes in the gut microbial diversity and composition. We developed an analytical tool, Similarity Test for Accordant and Reproducible Microbiome Abundance Patterns (STARMAPs), to test the similarity of microbiome variations between two datasets. Using this method, we found the spaceflight-associated microbiome changes during RR-1 were similar to those during STS- A B C Fig. 1 Microbial diversity of RR-1 fecal samples. a Animal groups involved in RR-1, highlighting group differences in the environmental conditions and durations (for details see the “Methods” section). The ISSES simulates the temperature, humidity, and CO2 partial pressure of the ISS environment based on data recorded onboard with a 3-day delay. b The number of microbial species observed in each sample (left) and the Shannon index (right) of microbial alpha diversity (i.e., within-sample diversity) varied among experimental groups of RR-1. c Analysis of beta diversity (i.e., between-sample diversity) using PCA on ILR-transformed relative abundance data found significant differences in the microbial composition among RR-1 experimental groups and specifically between Flight and Ground samples. Diversity analyses shown were performed using species-level data, and similar results were found at higher taxonomic levels as well (Additional file 1). Sample sizes in b and c: Basal, n = 10; Vivarium, n = 8; Ground, n = 7; Flight, n = 6 Jiang et al. Microbiome (2019) 7:113 135, suggesting a robust effect of spaceflight. However, when comparing the microbiome changes during RR-1 to those induced by space-type (...truncated)