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

Manon Boxberger, Stéphanie Rivoire, Lorlane Le Targa, Valérie Cenizo,

Bernard La Scola

► To cite this version:

Manon Boxberger, Stéphanie Rivoire, Lorlane Le Targa, Valérie Cenizo, Bernard La Scola. Description of the genome sequence of Corynebacterium species (Marseille-Q4381). Microbiology Resource Announcements, 2025, 14 (3), pp.e0070724. 10.1128/mra.00707-24. hal-05005729

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Submitted on 17 Nov 2025

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<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
# Description of the genome sequence of *Corynebacterium* species (Marseille-Q4381)

Manon Boxberger,¹ Stéphanie Rivoire,² Lorlane Le Targa,¹,³ Valérie Cenizo,² Bernard La Scola¹

**AUTHOR AFFILIATIONS** See affiliation list on p. 3.

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

**KEYWORDS** *Corynebacterium*, skin microbiota

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.

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.

## ACKNOWLEDGMENTS

The PhD grant for M.B. was supported by a collaboration between M&L Laboratories and Aix Marseille University (PVM 2018-200). L.L.T. is a PhD student at Aix-Marseille University

Editor Jason E. Stajich, University of California
Riverside, Riverside, California, USA

Address correspondence to Bernard La Scola,
bernard.la-scola@univ-amu.fr.

The PhD grant for M.B. was supported by a collaboration between M&L Laboratories and Aix Marseille University (PVM 2018-200). L.L.T. is a PhD student at Aix-Marseille University in the MEPHI research unit and is supported by the company Bioshell.

See the funding table on p. 3.

Received 26 June 2024

Accepted 9 December 2024

Published 27 January 2025

Copyright © 2025 Boxberger et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
<table><caption>TABLE 1 Comparison between *Corynebacterium* sp. strain Marseille-Q4381 and other relative speciesª</caption><thead><tr><th>Species name</th><th>No. Base pairs</th><th>Percent G + C</th><th>No. proteins</th><th>dDDH (d4, in %) compared with Corynebacterium sp. strain Marseille-Q4381 genome</th><th>C.I. (d4, in %)</th><th>G + C content difference (in %) with Corynebacterium sp. strain Marseille-Q4381 genome</th><th>Bioproject accession reference</th></tr></thead><tbody><tr><td>Corynebacterium afermentans DSM 44280</td><td>2,326,687</td><td>64.85</td><td>2,171</td><td>20.7</td><td>[18.5-23.1]</td><td>0.38</td><td>PRJEB18848</td></tr><tr><td>Corynebacterium bouchesdurhonense SN14</td><td>2,255,535</td><td>68.02</td><td>2,147</td><td>21.4</td><td>[19.1-23.8]</td><td>2.78</td><td>PRJEB13138</td></tr><tr><td><strong>Corynebacterium sp. strain Marseille-Q4381</strong></td><td><strong>2,197,730</strong></td><td><strong>65.24</strong></td><td><strong>2,120</strong></td><td>-</td><td>-</td><td>-</td><td>PRJNA1077295</td></tr><tr><td>Corynebacterium coyleae DSM 44184</td><td>2,568,936</td><td>61.32</td><td>2,419</td><td>20.7</td><td>[18.5-23.1]</td><td>3.92</td><td>PRJNA303722</td></tr><tr><td>Corynebacterium fournieri 2,357,034 Marseille-P2948</td><td>65.04</td><td>2,305</td><td>21.3</td><td>21.3</td><td>[19.1-23.7]</td><td>0.2</td><td>PRJEB20393</td></tr><tr><td>Corynebacterium godavarianum LMG 29598</td><td>2,521,298</td><td>65.65</td><td>2,235</td><td>20.9</td><td>[18.7-23.3]</td><td>0.41</td><td>PRJNA555895</td></tr><tr><td>Corynebacterium hadale NBT06-6</td><td>2,679,199</td><td>65.18</td><td>2,362</td><td>20.7</td><td>[18.5-23.1]</td><td>0.06</td><td>PRJNA396693</td></tr><tr><td>Corynebacterium haemomassiliense Marseille-Q3615</td><td>2,578,128</td><td>65.28</td><td>2,331</td><td>21.2</td><td>[18.9-23.6]</td><td>0.04</td><td>PRJNA646616</td></tr><tr><td>Corynebacterium jeddahense JCB</td><td>2,472,125</td><td>67.22</td><td>2,341</td><td>21.7</td><td>[19.4-24.1]</td><td>1.98</td><td>PRJEB4941</td></tr><tr><td>Corynebacterium mucifaciens ATCC 700355</td><td>2,180,241</td><td>65.49</td><td>2,028</td><td>20.5</td><td>[18.3-22.9]</td><td>0.25</td><td>PRJNA622446</td></tr><tr><td>Corynebacterium riegelii DSM 44326</td><td>2,519,232</td><td>60.43</td><td>2,283</td><td>20.2</td><td>[18.0-22.6]</td><td>4.81</td><td>PRJNA231221</td></tr><tr><td>Corynebacterium senegalense Marseille-P4329</td><td>2,310,902</td><td>68.65</td><td>2,173</td><td>20.5</td><td>[18.3-22.9]</td><td>3.42</td><td>PRJEB24601</td></tr><tr><td>Corynebacterium timonense 5401744</td><td>2,633,085</td><td>66.62</td><td>2,470</td><td>19.7</td><td>[17.5-22.1]</td><td>1.62</td><td>PRJNA303719</td></tr><tr><td>Corynebacterium timonense DSM 45434</td><td>2,551,022</td><td>66.86</td><td>2,376</td><td>19.8</td><td>[17.6-22.2]</td><td>1.38</td><td>PRJEB67</td></tr><tr><td>Corynebacterium tuscanense CCUG 51321</td><td>2,232,117</td><td>59.42</td><td>2,073</td><td>21.5</td><td>[19.3-24.0]</td><td>5.82</td><td>PRJNA224116</td></tr><tr><td>Corynebacterium ureicelerivorans DSM 45051</td><td>2,328,188</td><td>65.01</td><td>1,922</td><td>21</td><td>[18.8-23.4]</td><td>0.23</td><td>PRJNA257688</td></tr></tbody></table>

in the MEPHI research unit and is supported by the company Biosellall. This work was also supported by the National Research Agency under reference ANR-10-IAHU-03.

<footnote>ªComparing the bacteria to itself is not relevant; the dash ("-") represents with 100%. Bold represents the data of the bacterium.</footnote>
<figure><img src="image_2.png" /><figcaption>FIG 1 Circular genome map for Corynebacterium sp. strain Marseille-Q4381.</figcaption></figure>

## AUTHOR AFFILIATIONS

## AUTHOR ORCIDs

Bernard La Scola http://orcid.org/0000-0001-8006-7704

## FUNDING

<table><thead><tr><td>Funder</td><td>Grant(s)</td><td>Author(s)</td></tr></thead><tbody><tr><td>Agence Nationale de la Recherche (ANR)</td><td>ANR-10-IAHU-03</td><td>Stephanie Rivoire</td></tr></tbody></table>

## AUTHOR CONTRIBUTIONS

Manon Boxberger, Conceptualization, Formal analysis, Investigation, Writing – original draft | Stéphanie Rivoire, Investigation, Writing – review and editing | Lorlane Le Targa, Formal analysis | Valérie Cenizo, Validation, Writing – review and editing | Bernard La Scola, Conceptualization, Funding acquisition, Project administration, Supervision, Validation, Writing – review and editing

<footnote n="1">¹UR MEPHI, Aix Marseille University, AP-HM, IHU-Méditerranée Infection, Marseille, France</footnote>

<footnote n="2">²Groupe L'Occitane, R&D Department, Zone Industrielle Saint Maurice, Manosque, Alpes-de Haute-Provence, France</footnote>

<footnote n="3">³Biosellal, Dardilly, France</footnote>
DATA AVAILABILITY

The raw sequencing reads have been deposited in the Sequence Read Archive (SRA) under the accession number SRR28047222, and the corresponding BioProject ID is PRJNA1077295. This Whole-Genome Shotgun project has been deposited at DDBJ/ENA/ GenBank under the accession number JBAJNR000000000. The version described in this paper is version JBAJNR010000000.

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