The Kocurious case of Noodlococcus: genomic insights into Kocuria rhizophila from characterisation of a laboratory contaminant

Abstract

The laboratory contaminant Noodlococcus was named for its coccoid cells and unusual colony morphology, which resembled a pile of noodles. Along with laboratory characterisation and electron microscopy, we generated a complete Noodlococcus genome sequence using Illumina and Oxford Nanopore data. The genome consisted of a single, circular, 2732108 bp chromosome that shared 97.5% Average Nucleotide Identity (ANI) with the Kocuria rhizophila type strain TA68. We identified genomic features involved in replication (oriC), carotenoid synthesis (crt), and genome defence (CRISPR-Cas), and discovered four novel mobile elements (ISKrh4-7). Despite its environmental ubiquity and relevance to food production, bioremediation, and human medicine, there have been few genomic studies of the Kocuria genus. We conducted a comparative, phylogenetic, and pangenomic examination of all 257 publicly available Kocuria genomes, with a particular focus on the 56 that were identified as K. rhizophila. We found that there are two phylogenetically distinct clades of K. rhizophila, with within-clade ANI values of 96.7-100.0% and between-clade values of 89.5-90.4%. The second clade, which we refer to as K. pseudorhizophila, exhibited ANI values of <95% relative to TA68 and constitutes a separate species. Delineation of the two clades would be consistent with the rest of the genus, where all other species satisfy the 95% ANI threshold criteria. Differences in the K. rhizophila and K. pseudorhizophila pangenomes likely reflect phenotypic as well as evolutionary divergence. This distinction is relevant to clinical and industrial settings, as strains and genomes from both clades are currently used interchangeably, which may lead to reproducibility issues and phenotype-genotype discordance. Investigating an innocuous laboratory contaminant has therefore provided useful insights into the understudied species K. rhizophila, prompting an unexpected reassessment of its taxonomy. Impact statementBacterial genome sequence databases are dominated by a relatively small number of medically relevant genera, while most of the global bacterial populations diversity is largely uncharacterised. Kocuria is a widespread bacterial genus with industrial and medical relevance. Despite its ubiquity, only 22 complete and 235 draft Kocuria genomes were publicly available at the outset of this study. Our phylogenetic and pangenomic examination of all available Kocuria genomes was the first for this genus, providing insights into its diversity and taxonomy. Most notably, we found that Kocuria rhizophila is comprised of two clades that are sufficiently divergent to constitute different species, but are frequently used interchangeably in experimental and genomic research. The complete, high-quality Noodlococcus genome generated and characterised here can serve as a reference for true K. rhizophila, particularly while there is only a draft genome sequence available for type strain TA68. Data summarySequencing reads and the assembled Noodlococcus genome are available from NBCI BioProject accession PRJNA835814 and BioSample accession SAMN28111796. The complete sequence of the Noodlococcus chromosome can be found in the GenBank nucleotide database under accession number CP097204.1. Entries for the novel insertion sequences ISKrh4 to ISKrh7 can be found in the ISFinder database (https://isfinder.biotoul.fr).