Draft Genome Sequence of Turicella otitidis ATCC 51513, Isolated from Middle Ear Fluid from a Child with Otitis Media

Abstract

Turicella otitidis is an unusual corynebacterium with a controversial role in otitis media in children. Metabolic capabilities deduced from the draft genome indicate its adaptation to habitats on the human skin and in the intestine. The lack of candidate virulence factors implies that T. otitidis has a low pathogenic potential.

GENOME ANNOUNCEMENT

Turicella otitidis was initially isolated from middle ear fluids from children with otitis media in Switzerland (2). It differs from most corynebacteria in lacking mycolic acids and producing the major menaquinones MK-10 and MK-11. T. otitidis clusters within the boundaries of the genus Corynebacterium, along with the amycolate species Corynebacterium amycolatum (2, 7). Besides otitis media, it has been associated with mastoiditis (1), otorrhea (8), and posterior auricular abscess in children (9). However, the significance of T. otitidis in acute or chronic otitis media has been discussed controversially (3). Holzmann and coworkers suggested that T. otitidis is part of the normal bacterial flora of the external auditory canal in some children and not the causative agent of otitis media (4). Addressing its unusual taxonomic position and its controversial role in pathogenesis, we sequenced the type strain to deduce its pathogenic potential and lifestyle from the genome sequence.

T. otitidis ATCC 51513 (DSM 8821) was obtained from DSMZ (Braunschweig, Germany) and grown in M216 medium (37 g/liter brain heart infusion, 2 g/liter yeast extract) at 37°C. Genomic DNA was extracted by using Genomic-tips 500/G and the Genomic DNA Buffer Set according to the manufacturer's instructions (Qiagen). We obtained 14,028,862 whole-genome shotgun reads by using Genome Analyzer IIx (Illumina) and 238,974 3k paired-end reads using the Genome Sequencer FLX system (Roche/454), representing a total of 1.2 Gb and 580-fold genome coverage.

Illumina reads were assembled into 4,765 contigs with Velvet (13) 1.1.05. These contigs were further assembled along with the paired-end data by using GS Assembler 2.6, finally yielding 223 contigs in 5 scaffolds and 27 nonscaffolded contigs. Manual inspection of the assembly led to a circular chromosome, as the scaffold representing the rRNA genes provided the linkages among the four unique scaffolds. The deduced draft genome sequence of T. otitidis ATCC 51513 has a size of 2,077,086 bp with an average G+C content of 71.35%. Subsequent bioinformatic analysis of the genome sequence followed established protocols for corynebacterial genomes (11), predicting 1,452 protein-coding regions and 51 tRNAs.

Reconstruction of the metabolic pathways of T. otitidis revealed distinct features of its amino acid metabolism that are potentially associated with its natural habitats. The genome encodes a four-step histidine utilization pathway that catalyzes the conversion of l-histidine to l-glutamate. This is remarkable, as histidine is found in only low concentrations in the middle ear and is known as a limiting factor in the growth of pathogenic bacteria associated with otitis media (5). However, l-histidine is present in various concentrations on human skin. Moreover, the T. otitidis genome contains genes for the synthesis of selenocysteine and its incorporation into selenoproteins, thereby enhancing its adaptability to changing environmental conditions (12). T. otitidis is also able to catabolize the cysteine derivative taurine, a major constituent of bile, also found in the human intestine (10). This gene repertoire is consistent with the detection of T. otitidis in the microbial community of the human ileum (6).

Nucleotide sequence accession numbers.

The draft genome sequence of T. otitidis ATCC 51513 is available at the European Nucleotide Archive under accession numbers CAJZ01000001 to CAJZ01000250.