Genomic characterization of Microbacterium meiriae sp. nov., a novel bacterium isolated from the International Space Station

During the microbial surveillance of the International Space Station (ISS) in April 2018, four Gram-stain positive bacterial strains, designated as F6_8S_P_2B^T, F6_8S_P_3A, F6_8S_P_3B and F6_8S_P_3C, belonging to the genus Microbacterium were isolated from the walls of crew quarters. All four strains exhibited high 16S rRNA gene sequence similarity (> 99%), low average nucleotide identity (93%), and < 49.7% digital DNA: DNA hybridization values with the closest recognized Microbacterium paraoxydans DSM 15019^T, delineating new phylogenetic branches within the genus. Further whole-genome sequencing (WGS) and phylogenomic analysis revealed a close genetic relationship (> 98% ANI; > 83% dDDH) between the ISS strains and Microbacterium sp. LTR1 strain isolated from the larva skin of Lissotriton vulgaris from Tula region, Russia, which was misidentified as M. paraoxydans. The pangenomic analysis also shows high correlation between the ISS strains and their proximity to the type strain M. paraoxydans DSM 15019^T. These analyses suggest that strain LTR1, previously characterized as M. paraoxydans, should be included in this new Microbacterium clade alongside the four novel ISS strains. Functional genome analysis revealed unique proteins associated with transcription, defense, and metabolism. The genome harbored toxin-antitoxin modules (e.g., VapBC, Phd/YuzE), stress response regulators (FrmR, YhcF), and genes involved in formaldehyde resistance and glycoside hydrolase activity. Secondary metabolite gene clusters included beta-lactone, terpene, and T3PKS. Notably, tetracycline resistance gene tet(42) was present, indicating potential clinical relevance. The ISS strains grew at 4-40 °C, 0.5-8% NaCl, and pH 6.0-9.0. Chemotaxonomic features included anteiso-C15:0 and anteiso-C17:0 as major fatty acids, MK-12 as the predominant menaquinone, and ornithine as the diagnostic diamino acid in B2β-type peptidoglycan. The genomic DNA G+C content was 70.03 mol%. The polyphasic taxonomy showed that the ISS isolates along with LTR1 represent distinct strains of a new Microbacterium species, herein named Microbacterium meiriae. The type strain is F6_8S_P_2B^T (DSM 115935^T = NRRL B-65668^T).