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An early microbial landscape: inspiring endeavor from the China Space Station Habitation Area Microbiome Program (CHAMP)

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Abstract

China’s progressing space program, as evidenced by the formal operation of the China Space Station (CSS), has provided great opportunities for various space missions. Since microbes can present potential risks to human health and the normal operation of spacecraft, the study on space-microorganisms in the CSS is always a matter of urgency. In addition, the knowledge on the interactions between microorganisms, astronauts, and spacecraft equipment will shed light on our understanding of life activities in space and a closed environment. Here, we present the first comprehensive report on the microbial communities aboard the CSS based on the results of the first two survey missions of the CSS Habitation Area Microbiome Program (CHAMP). By combining metagenomic and cultivation methods, we have discovered that, in the early stage of the CSS, microbial communities are dominated by human-associated microbes, with strikingly large differences in both composition and functional diversity compared to those found on the International Space Station (ISS). While the samples from two missions of CHAMP possessed substantial differences in microbial composition, no significant difference in functional diversity was found, although signs of accumulating antibiotic resistance were evident. Meanwhile, strong bacteria co-occurrence was noted within the station’s microbiota. At the strain level, environmental isolates from the CSS exhibited numerous genomic mutations compared to those from the Assembly, Integration, and Test (AIT) center, potentially linked to the adaptation to the unique conditions of space. Besides, the intraspecies variation within four high-abundance species suggests possible propagation and residency effects between sampling sites. In summary, this study offers critical insights that not only advance our understanding of space microbiology but also lay the groundwork for effective microbial management in future long-term human space missions.

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Availability of data and materials

The genomic sequences of 19 genomes in the present study have been deposited in the National Microbiology Data Center with accession numbers NMDCN0006IF5–NMDCN0006IFM. The metagenomic sequencing data of all 18 environmental samples has been deposited in the National Genomics Data Center under accession number PRJCA033252 and National Microbiology Data Center under accession number NMDC10019486.

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Acknowledgement

This work was supported by the China Space Station Engineering Aerospace Technology Experiment Program (2019HJS002), the general program of the National Natural Science Foundation of China (32170659) and China Agricultural University Young Talent Program in Life Science (006). We would like to extend our deepest gratitude to the China Manned Space Engineering Office for their invaluable support. We also appreciate the support of High-performance Computing Platform of China Agricultural University and Beijing Computing Center for providing computational resources.

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  1. Shenzhou Space Biotechnology Group, Beijing, 100086, China

    Junxia Yuan, Ziwei He, Wende Zhang, Lei Dang & Hong Yin

  2. Beijing Institute of Spacecraft System Engineering, Beijing, 100094, China

    Jinlu Yang, Yan Song, Kanyan Xu & Pei Guo

  3. College of Biological Sciences, China Agricultural University, Beijing, 100193, China

    Yue Sun, Yaqi Meng, Ziding Zhang & Wenyu Shi

  4. Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China

    Na Lv

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  1. Junxia Yuan
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Yuan, J., Yang, J., Sun, Y. et al. An early microbial landscape: inspiring endeavor from the China Space Station Habitation Area Microbiome Program (CHAMP). Sci. China Life Sci. (2025). https://doi.org/10.1007/s11427-024-2894-2

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