Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition

Supplemental tables and figures for manuscript titled: "Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition" <strong>Abstract</strong> NASA has been monitoring the microbial burden of spacecraft since the 1970’s Viking missions. Originally based upon culture-based and then focused 16S sequencing techniques, we have now applied whole metagenomic sequencing of cleanroom samples at the Jet Propulsion Lab (JPL), including the Spacecraft Assembly Facility (SAF) with the goals of taxonomic identification and for functional assignment. Our samples included facility pre-filters, cleanroom vacuum debris, and surface wipes. The taxonomic composition was carried out by three different analysis tools. Hierarchical clustering analysis separated vacuum particles from SAF DNA samples. Vacuum particle samples were the most diverse while DNA samples from the ISO facilities and the SAF were the least diverse; all three were dominated by Proteobacteria. Wipe samples had higher diversity and were predominated by Actinobacteria, including human commensals <em>Cutibacterium acnes</em> and <em>Corynebacterium</em>. Taxa identified by the three methods were not identical, supporting the use of multiple methods for metagenome characterization. Likewise, functional annotation was performed using multiple methods. Vacuum particle and SAF tricarboxylic acid cycle and amino acid biosynthesis suggested that many of the identified microorganisms have the ability to grow in nutrient-limited environments. In total, 18 high quality metagenome assembled genomes were generated and were dominated by <em>Moraxella osloensis</em> or <em>Malassezia restricta</em>. A <em>M. osloensis </em>MAG was assembled into a single circular scaffold and gene annotated. This includes a rigorous quantitative determination of microbial loads, and a qualitative dissection of microbial composition. Genomic assembly led to greater confidence of species identification and their functional roles.本数据集为以下手稿的补充表格与附图：《航天器关联表面的多维度宏基因组分析揭示与行星保护相关的微生物群落组成》。 **摘要** 自20世纪70年代维京号（Viking）任务以来，美国国家航空航天局（NASA）便持续监测航天器的微生物载荷。本研究早期基于培养组学及靶向16S测序技术，如今我们已在喷气推进实验室（Jet Propulsion Lab, JPL）的航天器装配设施（Spacecraft Assembly Facility, SAF）中对洁净室样本开展全宏基因组测序，旨在实现物种分类鉴定与功能注释。本次研究的样本涵盖洁净室预过滤器、真空吸尘碎屑以及表面擦拭拭子。 我们借助三种不同的分析工具完成物种分类组成分析。层级聚类分析可将真空颗粒样本与SAF的DNA样本有效区分。真空颗粒样本的物种多样性最高，而ISO设施与SAF的DNA样本多样性最低；三类样本均以变形菌门（Proteobacteria）为优势类群。擦拭拭子样本的多样性更高，优势类群为放线菌门（Actinobacteria），包含人体共生菌痤疮丙酸杆菌（*Cutibacterium acnes*）和棒状杆菌属（*Corynebacterium*）。三种分析方法鉴定得到的类群并不完全一致，这证实了采用多方法开展宏基因组特征分析的必要性。 同样，本研究采用多种方法开展功能注释。真空颗粒样本与SAF样本的三羧酸循环及氨基酸生物合成通路分析结果显示，多数鉴定出的微生物具备在营养受限环境中生长的能力。最终共获得18条高质量宏基因组组装基因组（metagenome assembled genomes, MAGs），优势类群为奥斯陆莫拉菌（*Moraxella osloensis*）和限制性马拉色菌（*Malassezia restricta*）。其中一株奥斯陆莫拉菌的MAG被组装为单个环状骨架，并完成了基因注释。本研究包含对微生物载荷的精准定量测定，以及对微生物群落组成的定性解析。基因组组装提升了物种鉴定及其功能解析的可信度。