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Background  Members of the species  Kocuria rhizophila , belonging to the family  Micrococcaceae  in the phylum  Actinobacteria , have been isolated from a wide variety of natural sources, such as soil, freshwater, fish gut, and clinical specimens.  K .  rhizophila  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  K .  rhizophila  strain BT304, isolated from the small intestine of adult castrated beef cattle.    Results  The genome of  K .  rhizophila  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  K .  rhizophila  strains, such as DC2201, FDAARGOS 302, and G2. Comparative genomic analysis further revealed that the antibiotic properties of  K .  rhizophila  vary among the strains.    Conclusion  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.    Electronic supplementary material  The online version of this article (10.1186/s13099-018-0270-9) contains supplementary material, which is available to authorized users.

Complete genome sequence of Kocuria rhizophila BT304, isolated from the small intestine of castrated beef cattle