Description of the genome sequence of Corynebacterium species (Marseille-Q4381)

TL;DR

This paper presents the genome sequence of a Corynebacterium strain isolated from healthy skin.

Contribution

The study provides a new genome sequence and annotation for a Corynebacterium species.

Findings

A Corynebacterium strain, Marseille-Q4381, was isolated from healthy skin in 2020.

The genome sequence and its annotation characteristics are described in detail.

Abstract

In 2020, we isolated a Corynebacterium strain, Marseille-Q4381, from healthy skin. We describe herein its genome sequence and annotation characteristics.

Figures

Circular genome map for Corynebacterium sp. strain Marseille-Q4381.

Tables

TABLE 1. Comparison between Corynebacterium sp. strain Marseille-Q4381 and other relative speciesa

Species name	No. Base pairs	Percent G + C	No. proteins	dDDH (d4, in %) compared with Corynebacterium sp. strain Marseille-Q4381 genome	C.I. (d4, in %)	G + C content difference (in %) with Corynebacterium sp. strain Marseille-Q4381 genome	Bioproject accession reference
Corynebacterium afermentans DSM 44280	2,326,687	64.85	2,171	20.7	[18.5–23.1]	0.38	PRJEB18848
Corynebacterium bouchesdurhonense SN14	2,255,535	68.02	2,147	21.4	[19.1–23.8]	2.78	PRJEB13138
Corynebacterium sp strain Marseille-Q4381	2,197,730	65.24	2,120	-	-	-	PRJNA1077295
Corynebacterium coyleae DSM 44184	2,568,936	61.32	2,419	20.7	[18.5–23.1]	3.92	PRJNA303722
Corynebacterium fournieri Marseille-P2948	2,357,034	65.04	2,305	21.3	[19.1–23.7]	0.2	PRJEB20393
Corynebacterium godavarianum LMG 29598	2,521,298	65.65	2,235	20.9	[18.7–23.3]	0.41	PRJNA555895
Corynebacterium hadale NBT06-6	2,679,199	65.18	2,362	20.7	[18.5–23.1]	0.06	PRJNA396693
Corynebacterium haemomassiliense Marseille-Q3615	2,578,128	65.28	2,331	21.2	[18.9–23.6]	0.04	PRJNA646616
Corynebacterium jeddahense JCB	2,472,125	67.22	2,341	21.7	[19.4–24.1]	1.98	PRJEB4941
Corynebacterium mucifaciens ATCC 700355	2,180,241	65.49	2,028	20.5	[18.3–22.9]	0.25	PRJNA622446
Corynebacterium riegelii DSM 44326	2,519,232	60.43	2,283	20.2	[18.0–22.6]	4.81	PRJNA231221
Corynebacterium senegalense Marseille-P4329	2,310,902	68.65	2,173	20.5	[18.3–22.9]	3.42	PRJEB24601
Corynebacterium timonense 5401744	2,633,085	66.62	2,470	19.7	[17.5–22.1]	1.62	PRJNA303719
Corynebacterium timonense DSM 45434	2,551,022	66.86	2,376	19.8	[17.6–22.2]	1.38	PRJEB67
Corynebacterium tuscaniense CCUG 51321	2,232,117	59.42	2,073	21.5	[19.3–24.0]	5.82	PRJNA224116
Corynebacterium ureicelerivorans DSM 45051	2,328,188	65.01	1,922	21	[18.8–23.4]	0.23	PRJNA257688

Full text

ANNOUNCEMENT

In 2020, a novel bacterial strain named Marseille-Q4381 was isolated from the forehead skin swab of a healthy 60-year-old woman. Despite efforts, matrix-assisted desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) failed to identify the isolate. Subsequent analysis of the 16S rRNA and genome-to-genome comparison revealed that the taxon belonged to a bacterium within the family Corynebacteriaceae, in the phylum Actinobacteria.

Sampling adhered to the protocol approved by the ethics committee Sud-Est IV (ID-RCB: 2019-A01508-49). Routine subcultures were done on Columbia Agar with 5% sheep blood at 31°C. MALDI-TOF MS protein analysis was conducted using a Microflex spectrometer.

Genomic DNA (gDNA) extraction involved mechanical and chemical pretreatment with 0.5 mm Silica glass beads, acid washed, and a FastPrep-24 5G Grinder, followed by lysozyme incubation and extraction using the EZ1 biorobot with the EZ1 DNA tissues kit (Qiagen). Sequencing and barcoding were performed using MiSeq Technology with the Nextera XT DNA sample prep kit, and read length and paired-end reads were generated from MiSeq. The quality control was conducted using Trimmomatic software v0.36 (1), yielding 959,380 reads before sorting and 922,736 after sorting.

Genome assembly with Spades v 3.10 (2) produced 20 contigs with a coverage value of 26.4× and a N50 = 187,76 Kb, Annotation via the PGAP v6,4 pipeline (3) identified 2,112 protein-coding sequences (CDS), the genome contains 60 RNA genes, including 4 rRNAs (1 complete 5S, 1 complete 16S, and 1 complete 23S), with 3 partial 5S rRNAs, 51 tRNAs, and 3 ncRNAs. The circular map of the genome was generated using the CG View server online tool (4). The genome, spanning 2,197,730 base pairs, had a GC content of 65.24% (Fig. 1). All the software tools were used with their default parameters.

Circular genome map for Corynebacterium sp. strain Marseille-Q4381.

To confirm taxonomic position, the 16S rRNA sequence was blasted (BLASTN v2.13.0) against the nr database, and genome sequence data were uploaded to the Type (Strain) Genome Server (TYGS) (5) for taxonomic analysis. Closely related type strains were determined using the MASH algorithm and 16S rRNA gene sequences, with phylogenomic inference conducted through pairwise comparisons and digital DNA-DNA hybridization (dDDH) values calculated. Detailed comparison information is summarized in Table 1.