Draft Genome Sequences of Three Capnocytophaga cynodegmi Strains Isolated from the Oral Cavity of Healthy Dogs

Abstract

Here, we present the draft genome sequences of three strains of Capnocytophaga cynodegmi. In contrast to the very close relationship among them, C. cynodegmi and Capnocytophaga canimorsus differ dramatically in terms of virulence in humans. Comparative genomics provided some understanding on how Capnocytophaga species may switch from being dog commensals to human pathogens.

GENOME ANNOUNCEMENT

Capnocytophaga cynodegmi (formerly CDC dysgonic fermenter-2-like) is a common oral commensal of dogs and cats, with prevalence rates as high as 86% and 84%, respectively (1). It belongs to the Bacteroidetes phylum, where it is very closely related to Capnocytophaga canimorsus, another commensal of the dog mouth (2, 3). Together, the two species display a significant number of features that differentiate them from other members of the Capnocytophaga genus (4). Beside subtle differences in their 16S rRNA gene sequences (4), C. cynodegmi strains can be differentiated from C. canimorsus strains by the light-yellow color displayed by colonies grown on sheep blood agar and by the capacity to ferment sucrose, raffinose, inulin, and melibiose (4). Contrary to C. canimorsus, C. cynodegmi is not a severe and sepsis-causing human pathogen, although some cases of human infections have been reported to consist mostly of wound or corneal infections (4, 5–8).

Three strains of C. cynodegmi, Ccy74, Ccyn2B, and Ccyn_ATCC 49044, were isolated from canine oral swabs and identified by 16S RNA sequencing (4, 9). The strains were selected as dispersed representatives of the species C. cynodegmi, according to 16S rRNA phylogenetics and limited phenotyping (9). Genomic DNA was extracted using the Genomic-tip 500/G DNA extraction kit (catalog no. 10262; Qiagen), according to the manufacturer’s instructions, followed by an additional phenol-chloroform purification step. Sequencing was performed at LGC Genomics, Berlin, Germany, on one Illumina HiSeq 2000 channel and generated approximatively 10.8 ± 1.0 million 100-bp single reads per strain. De novo assembly was performed with Velvet, with optimized parameters (10). On average, draft assemblies accounted for 2.69 ± 0.01 Mb for 90 (Ccy74), 67 (Ccyn2B), and 111 (Ccyn_ATCC 49044) contigs. Genome metrics and automated annotation were conducted at the LABGeM, France Génomique (11). The G+C content (34.40% ± 0.01%) is lower than that of the closely related C. canimorsus (36.16% ± 0.08%). Each genome contains a fairly similar number of coding sequences (2,484 ± 18). Ccyn2B exhibits significantly more strain-specific coding sequences (CDSs) (350) than those in Ccy74 (75) and Ccyn_ATCC 49044 (72). The C. cynodegmi core genome is composed of 1,910 families of orthologs, of which 341 are specific to C. cynodegmi compared to seven genomes of C. canimorsus (2, 3, 12). While 253 clusters of orthologs were of unknown function, genes involved in aromatic amino acid synthesis (the complete l-tryptophan synthesis pathway from chorismate, 5 genes), glycan chain foraging (a complete polysaccharide utilization locus, 8 genes) (13), oxidative respiration and oxidative stress resistance (5 genes), and lipopolysaccharide (LPS) and polysaccharide biosynthesis (5 genes) formed the major functional clusters of the species-exclusive core genome. With respect to iron acquisition, a homolog to the heme-binding HmuY protein (14) was found in each of the three C. cynodegmi genomes, in addition to a locus encoding the iron capture system of Bacteroidetes (15).

Nucleotide sequence accession numbers.

These whole-genome shotgun projects have been deposited in ENA under the accession numbers CDOD00000000 (Ccyn2B), CDOG00000000 (Ccy74), and CDOF00000000 (Ccyn_ATCC 49044). The versions described in this paper are the initial versions.