<italic>Bacillus safensis</italic> FO-36b and <italic>Bacillus pumilus</italic> SAFR-032: a whole genome comparison of two spacecraft assembly facility isolates.

Background: <italic>Bacillus</italic> strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of <italic>Bacillus safensis</italic> strain FO-36b, which produces spores resistant to peroxide and radiation was determined. The genome was compared to the complete genome of <italic>B. pumilus S</italic>AFR-032, and the draft genomes of <italic>B. safensis</italic> JPL-MERTA-8-2 and the type strain <italic>B. pumilus</italic> ATCC7061^T. Additional comparisons were made to 61 draft genomes that have been mostly identified as strains of <italic>B. pumilus</italic> or <italic>B. safensis.</italic> Results: The FO-36b gene order is essentially the same as that in SAFR-032 and other <italic>B. pumilus</italic> strains. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by MERTA and ATCC7061^T. The FO-36b genome has ten unique open reading frames and two phage-like regions, homologous to the <italic>Bacillus</italic> bacteriophage SPP1 and <italic>Brevibacillus</italic> phage Jimmer1. Differing remnants of the Jimmer1 phage are found in essentially all <italic>B</italic>. <italic>safensis / B. pumilus</italic> strains. Seven unique genes are part of these phage elements. Whole Genome Phylogenetic Analysis of the <italic>B. pumilus, B. safensis</italic> and other <italic>Firmicutes</italic> genomes, separate them into three distinct clusters. Two clusters are subgroups of <italic>B. pumilus</italic> while one houses all the <italic>B. safensis</italic> strains. The Genome-genome distance analysis and a phylogenetic analysis of <italic>gyrA</italic> sequences corroborated these results. Conclusions: It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can alter the expression levels of key proteins thereby changing the organism's resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. Multiple genome comparison indicates that many strains named as <italic>B. pumilus</italic> likely belong to the <italic>B. safensis</italic> group. [ABSTRACT FROM AUTHOR]