Description of Chloramphenicol Resistant Kineococcus rubinsiae sp. nov. Isolated From a Spacecraft Assembly Facility

A Gram-positive, coccoid, motile, aerobic bacterium, designated strain B12^T was isolated from a Jet Propulsion Laboratory spacecraft assembly cleanroom, Pasadena, CA, United States. Strain B12^T was resistant to chloramphenicol (100 μg/mL), and is a relatively slow grower (3-5 days optimal). Strain B12^T was found to grow optimally at 28 to 32°C, pH 7 to 8, and 0.5% NaCl. Fatty acid methyl ester analysis showed that the major fatty acid of the strain B12^T was anteiso C_{15 : 0} (66.3%), which is also produced by other Kineococcus species. However, arachidonic acid (C_{20 : 4} ω6,9,12,16c) was present in strain B12^T and Kineococcus glutinatus YIM 75677^T but absent in all other Kineococcus species. 16S rRNA analysis revealed that strain B12^T was 97.9% similar to Kineococcus radiotolerans and falls within the Kineococcus clade. Low 16S rRNA gene sequence similarities (<94%) with other genera in the family Kineosporiaceae, including Angustibacter (93%), Kineosporia (94% to 95%), Pseudokineococcus (93%), Quadrisphaera (93%), and Thalassiella (94%) demonstrated that the strain B12^T does not belong to these genera. Phylogenetic analysis of the gyrB gene show that all known Kineococcus species exhibited <86% sequence similarity with B12^T. Multi-locus sequence and whole genome sequence analyses confirmed that B12^T clades with other Kineococcus species. Average nucleotide identity of strain B12^T were 75-78% with other Kineococcus species, while values ranged from 72-75% with species from other genera within family Kineosporiaceae. Average amino-acid identities were 66-72% with other Kineococcus species, while they ranged from 50-58% with species from other genera. The dDDH comparison of strain B12^T genome with members of genera Kineococcus showed 20-22% similarity, again demonstrating that B12^T is distantly related to other members of the genus. Furthermore, analysis of whole proteome deduced from WGS places strain B12^T in order Kineosporiales, confirming that strain B12^T is a novel member of family Kineosporiaceae. Based on these analyses and other genome characteristics, strain B12^T is assigned to a novel species within the genus Kineococcus, and the name Kineococcus rubinsiae sp. nov., is proposed. The type strain is B12^T (=FJII-L1-CM-PAB2^T; NRRL B-65556^T, DSM 110506^T).