Expanding the Bacterial Diversity of the Female Urinary Microbiome: Description of Eight New Corynebacterium Species

Abstract

The genus <i>Corynebacterium</i> is frequently found in the female urinary microbiome (FUM). In-depth characterization of <i>Corynebacterium</i> at the species level has been barely exploited. During ongoing FUM research studies, eight strains (c8Ua_144^T, c8Ua_172^T, c8Ua_174^T, c8Ua_181^T, c9Ua_112^T, c19Ua_109^T, c19Ua_121^T, and c21Ua_68^T) isolated from urine samples of healthy women or diagnosed with overactive bladder could not be allocated to any valid <i>Corynebacterium</i> species. In this work, we aimed to characterize these strains based on a polyphasic approach. The strains were Gram stain positive, rod to coccoid shaped, nonmotile, catalase positive, and oxidase negative. Phylogenetic analysis based on 16S rRNA and <i>rpoB</i> gene sequences indicated that all strains belonged to the genus <i>Corynebacterium</i>. The average nucleotide identity and digital DNA-DNA hybridization values among the genomes of the above eight strains and closely related type strains of the <i>Corynebacterium</i> genus were <95 (74.1%-93.9%) and <70% (22.2%-56.5%), respectively. Mycolic acids were identified in all strains. MK-8(H2) and/or MK-9(H2) were identified as the major menaquinones. The polar lipids' pattern mostly consisted of diphosphatidylglycerol, phosphatidylglycerol, and glycophospholipids. The major fatty acid was C_18:1<i>ω</i>9<i>c</i>. <i>Corynebacterium lehmanniae</i> (c8Ua_144^T = DSM 113405^T = CCP 74^T), <i>Corynebacterium meitnerae</i> (c8Ua_172^T = DSM 113406^T = CCP 75^T), <i>Corynebacterium evansiae</i> (c8Ua_174^T = DSM 113407^T = CCP 76^T), <i>Corynebacterium curieae</i> (c8Ua_181^T = DSM 113408^T = CCP 77^T), <i>Corynebacterium macclintockiae</i> (c9Ua_112^T = DSM 113409^T = CCP 78^T), <i>Corynebacterium hesseae</i> (c19Ua_109^T = DSM 113410^T= CCP 79^T), <i>Corynebacterium marquesiae</i> (c19Ua_121^T = DSM 113411^T = CCP 80^T), and <i>Corynebacterium yonathiae</i> (c21Ua_68^T = DSM 113412^T = CCP 81^T) are proposed. This study evidenced that commonly used methodologies on FUM research presented limited resolution for discriminating <i>Corynebacterium</i> at the species level. Future research studying the biological mechanisms of the new <i>Corynebacterium</i> species here described may shed light on their possible beneficial role for healthy FUM.