Metagenomes associated with the publication Ensemble Binning Approach to Identify Functional Diversity in Cleanroom Environments

Abstract for data:
This study involved the generation of 26 medium and high-quality metagenome-assembled genomes (MAGs) from published metagenomic datasets. These MAGs originated from NASA cleanrooms, specifically the Jet Propulsion Laboratory (JPL) and Kennedy Space Center's Payload Hazardous Servicing Facility (KSC-PHSF).

The original sequence data for these MAGs were derived from NCBI Genbank BioProjects PRJNA668809 PRJNA681008 and PRJNA327691. The respective original publications contributing these datasets include Wood et al., 2021, Highlander et al., 2023, and Bashir et al., 2016. All MAGs generated and described in this study are submitted under BioProject PRJEB90846.

The MAGs were assembled using Megahit and binned via an ensemble approach integrating MaxBin2, MetaBAT2, and CONCOCT, followed by refinement with DasTool and dRep. Quality assessment was performed using CheckM, with completeness scores ranging from 65.62% to 99.64% and contamination scores from 0.00% to 6.75%. Each MAG is derived from specific cleanroom metagenome samples, identified by their SRA accession (e.g., SRR13152093 for JPL 2018 samples, SRR393690 for KSC 2007 samples). Geographic coordinates for the sampling locations are 34.2013° N, 118.1714° W for JPL and 28.5744° N, 80.6520° W for KSC. The assemblies are characterized as "Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs", reflecting their high or medium quality according to MIMAG standards.

Abstract for the paper:
Cleanroom environments, crucial for spacecraft assembly, are subject to stringent sterilisation protocols to minimise microbial contamination. However, tolerant microbes can persist and pose a potential risk for planetary protection. This study employs an ensemble binning approach, integrating multiple metagenome binning programs, to analyse published metagenomic datasets generated from NASA cleanrooms to investigate functional diversity within cleanrooms. Twenty-six medium and high quality, non-redundant metagenome-assembled genomes (MAGs) spanning six bacterial phyla were generated. Functional analysis of these MAGs identified potential metabolic pathways for the degradation of commonly used cleaning agents, suggesting that these compounds could serve as carbon sources. Furthermore, genomic analyses identified diverse physiological tolerances, with many MAGs possessing polyextremophilic traits, including resistance to high salinity , temperature, and alkalinity. Growth Rate Index analysis also suggested some MAGs were actively replicating within the cleanroom environments. This study demonstrates the power of ensemble binning in revealing the functional diversity and adaptive strategies of cleanroom microbiomes and provides critical insights for refining planetary protection protocols.