Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA.
Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
Microbiome. 2023 Jun 1;11(1):125. doi: 10.1186/s40168-023-01545-7.
Several investigations on the microbial diversity and functional properties of the International Space Station (ISS) environment were carried out to understand the influence of spaceflight conditions on the microbial population. However, metagenome-assembled genomes (MAGs) of ISS samples are yet to be generated and subjected to various genomic analyses, including phylogenetic affiliation, predicted functional pathways, antimicrobial resistance, and virulence characteristics.
In total, 46 MAGs were assembled from 21 ISS environmental metagenomes, in which metaSPAdes yielded 20 MAGs and metaWRAP generated 26 MAGs. Among 46 MAGs retrieved, 18 bacterial species were identified, including one novel genus/species combination (Kalamiella piersonii) and one novel bacterial species (Methylobacterium ajmalii). In addition, four bins exhibited fungal genomes; this is the first-time fungal genomes were assembled from ISS metagenomes. Phylogenetic analyses of five bacterial species showed ISS-specific evolution. The genes pertaining to cell membranes, such as transmembrane transport, cell wall organization, and regulation of cell shape, were enriched. Variations in the antimicrobial-resistant (AMR) and virulence genes of the selected 20 MAGs were characterized to predict the ecology and evolution of biosafety level (BSL) 2 microorganisms in space. Since microbial virulence increases in microgravity, AMR gene sequences of MAGs were compared with genomes of respective ISS isolates and corresponding type strains. Among these 20 MAGs characterized, AMR genes were more prevalent in the Enterobacter bugandensis MAG, which has been predominantly isolated from clinical samples. MAGs were further used to analyze if genes involved in AMR and biofilm formation of viable microbes in ISS have variation due to generational evolution in microgravity and radiation pressure.
Comparative analyses of MAGs and whole-genome sequences of related ISS isolates and their type strains were characterized to understand the variation related to the microbial evolution under microgravity. The Pantoea/Kalamiella strains have the maximum single-nucleotide polymorphisms found within the ISS strains examined. This may suggest that Pantoea/Kalamiella strains are much more subjective to microgravity changes. The reconstructed genomes will enable researchers to study the evolution of genomes under microgravity and low-dose irradiation compared to the evolution of microbes here on Earth. Video Abstract.
为了了解空间飞行条件对微生物种群的影响，对国际空间站 (ISS) 环境的微生物多样性和功能特性进行了多项调查。然而，ISS 样本的宏基因组组装基因组 (MAG) 尚未生成，并且尚未对其进行各种基因组分析，包括系统发育归属、预测的功能途径、抗微生物药物耐药性和毒力特征。
总共从 21 个 ISS 环境宏基因组中组装了 46 个 MAG，其中 metaSPAdes 产生了 20 个 MAG，metaWRAP 产生了 26 个 MAG。在所检索的 46 个 MAG 中，鉴定出 18 个细菌物种，包括一个新的属/种组合 (Kalamiella piersonii) 和一个新的细菌物种 (Methylobacterium ajmalii)。此外，四个 bin 显示了真菌基因组；这是首次从 ISS 宏基因组中组装出真菌基因组。五个细菌物种的系统发育分析表明，ISS 具有特异性进化。与细胞膜相关的基因，如跨膜运输、细胞壁组织和细胞形状调节，被富集。对选定的 20 个 MAG 的抗微生物药物耐药性 (AMR) 和毒力基因的变异进行了特征描述，以预测空间中生物安全水平 (BSL) 2 微生物的生态和进化。由于微生物的毒力在微重力下增加，因此将 MAG 的 AMR 基因序列与各自的 ISS 分离株和相应的模式株的基因组进行了比较。在所研究的 20 个 MAG 中，AMR 基因在 Enterobacter bugandensis MAG 中更为普遍，该基因主要从临床样本中分离出来。进一步使用 MAG 分析了在微重力和辐射压力下，ISS 中存活微生物的 AMR 和生物膜形成相关基因是否由于世代进化而发生变异。
对 MAG 和相关 ISS 分离株及其模式株的全基因组序列进行比较分析，以了解在微重力下微生物进化相关的变异。在所检查的 ISS 菌株中，Pantoea/Kalamiella 菌株发现的单核苷酸多态性最多。这可能表明，Pantoea/Kalamiella 菌株更容易受到微重力变化的影响。重建的基因组将使研究人员能够研究与地球上微生物进化相比，微重力和低剂量辐射下基因组的进化。视频摘要。
