Genome sequence and description of Corynebacterium ihumii sp. nov

Abstract

Corynebacterium ihumii strain GD7(T) sp. nov. is proposed as the type strain of a new species, which belongs to the family Corynebacteriaceae of the class Actinobacteria. This strain was isolated from the fecal flora of a 62 year-old male patient, as a part of the culturomics study. Corynebacterium ihumii is a Gram positive, facultativly anaerobic, nonsporulating bacillus. Here, we describe the features of this organism, together with the high quality draft genome sequence, annotation and the comparison with other member of the genus Corynebacteria. C. ihumii genome is 2,232,265 bp long (one chromosome but no plasmid) containing 2,125 protein-coding and 53 RNA genes, including 4 rRNA genes. The whole-genome shotgun sequence of Corynebacterium ihumii strain GD7(T) sp. nov has been deposited in EMBL under accession number GCA_000403725.

Keywords: Corynebacterium ihumii; culturomics; genome; taxono-genomics.

Figure 1

Phylogenetic tree highlighting the position of Corynebacterium ihumii strain GD7^T relative to other type strains within the Corynebacterium genus. GenBank accession numbers are indicated for each strain. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained using the neighbor-joining method within the MEGA software. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 1,000 times to generate a majority consensus tree. Mycobacterium tuberculosis was used as an outgroup. The scale bar represents a 2% nucleotide sequence divergence.

Figure 2

Gram staining of C. ihumii strain GD7^T

Figure 3

Transmission electron microscopy of C. ihumii strain GD7^T, using a Morgani 268D (Philips) at an operating voltage of 60kV. The scale bar represents 1 μm.

Figure 4

Reference mass spectrum from C. ihumii strain GD7^T. Spectra from 12 individual colonies were compared and a reference spectrum was generated.

Figure 5

Gel view comparing C. ihumii sp. nov. strain GD7^T (= CSUR P902 = DSM 45751) to other members of the Corynebacterium genus. The gel view displays the raw spectra of all loaded spectrum files arranged in a pseudo-gel like look. The x-axis records the m/z value. The left y-axis displays the running spectrum number originating from subsequent spectra loading. The peak intensity is expressed by a Gray scale scheme code. The color bar and the right y-axis indicate the relation between the color a peak is displayed with and the peak intensity in arbitrary units.

Figure 6

Graphical circular map of the chromosome. From the outside in, the outer two circles show open reading frames oriented in the forward and reverse directions (colored by COG categories), respectively. The third circle marks the rRNA gene operon (red) and tRNA genes (green). The fourth circle shows the G+C% content plot. The inner-most circle shows the GC skew, purple and olive indicating negative and positive values, respectively.

Figure 7

Distribution of functional classes of predicted genes of Corynebacterium ihumii strain GD7^T (colored in thick red line) along with other Corynebacterium genomes according to the clusters of orthologous groups of proteins.