Project description:The soil actinomycete Kocuria rhizophila belongs to the suborder Micrococcineae, a divergent bacterial group for which only a limited amount of genomic information is currently available. K. rhizophila is also important in industrial applications; e.g., it is commonly used as a standard quality control strain for antimicrobial susceptibility testing. Sequencing and annotation of the genome of K. rhizophila DC2201 (NBRC 103217) revealed a single circular chromosome (2,697,540 bp; G+C content of 71.16%) containing 2,357 predicted protein-coding genes. Most of the predicted proteins (87.7%) were orthologous to actinobacterial proteins, and the genome showed fairly good conservation of synteny with taxonomically related actinobacterial genomes. On the other hand, the genome seems to encode much smaller numbers of proteins necessary for secondary metabolism (one each of nonribosomal peptide synthetase and type III polyketide synthase), transcriptional regulation, and lateral gene transfer, reflecting the small genome size. The presence of probable metabolic pathways for the transformation of phenolic compounds generated from the decomposition of plant materials, and the presence of a large number of genes associated with membrane transport, particularly amino acid transporters and drug efflux pumps, may contribute to the organism's utilization of root exudates, as well as the tolerance to various organic compounds.
Project description:A case of persistent bloodstream infection with Kocuria rhizophila related to a damaged central venous catheter in a 3-year-old girl with Hirschsprung's disease is reported. The strain was identified as K. rhizophila by 16S rRNA gene sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry. Arbitrarily primed PCR analysis showed a clonal strain. The repeated septic episodes were resolved with the catheter repair.
Project description:<h4>Background</h4>Members of the species <i>Kocuria rhizophila</i>, belonging to the family <i>Micrococcaceae</i> in the phylum <i>Actinobacteria</i>, have been isolated from a wide variety of natural sources, such as soil, freshwater, fish gut, and clinical specimens. <i>K</i>. <i>rhizophila</i> is important from an industrial viewpoint, because the bacterium grows rapidly with high cell density and exhibits robustness at various growth conditions. However, the bacterium is an opportunistic pathogen involved in human infections. Here, we sequenced and analyzed the genome of the <i>K</i>. <i>rhizophila</i> strain BT304, isolated from the small intestine of adult castrated beef cattle.<h4>Results</h4>The genome of <i>K</i>. <i>rhizophila</i> BT304 consisted of a single circular chromosome of 2,763,150 bp with a GC content of 71.2%. The genome contained 2359 coding sequences, 51 tRNA genes, and 9 rRNA genes. Sequence annotations with the RAST server revealed many genes related to amino acid, carbohydrate, and protein metabolism. Moreover, the genome contained genes related to branched chain amino acid biosynthesis and degradation. Analysis of the OrthoANI values revealed that the genome has high similarity (>?97.8%) with other <i>K</i>. <i>rhizophila</i> strains, such as DC2201, FDAARGOS 302, and G2. Comparative genomic analysis further revealed that the antibiotic properties of <i>K</i>. <i>rhizophila</i> vary among the strains.<h4>Conclusion</h4>The relatively small number of virulence-related genes and the great potential in production of host available nutrients suggest potential application of the BT304 strain as a probiotic in breeding beef cattle.
Project description:We describe the first case of a Kocuria rhizophila infection in a boy with methylmalonic aciduria. A single clone was isolated from blood samples drawn through a port system and from peripheral veins during septic episodes within a 2-year period. K. rhizophila expands the emerging number of "micrococci" considered to be etiologically relevant.