Draft genome of Corynebacterium glycinophilum S209 isolated from healthy human skin

TL;DR

This paper presents the draft genome of a Corynebacterium glycinophilum strain isolated from a healthy human's skin.

Contribution

The study provides the first draft genome of C. glycinophilum S209, a strain from the human skin microbiome.

Findings

C. glycinophilum S209 was isolated from the skin of a healthy human female.

The draft genome of this strain is now available for further research.

Abstract

Corynebacterium glycinophilum is an understudied species of this genus, although it has been identified in dairy products as well as the human skin microbiome. Recently, we isolated a strain from the skin of a healthy human female, and here, we present the draft genome of this isolate, C. glycinophilum S209.

Tables

TABLE 1. Genome assembly statistics for C. glycinophilum S209

Genome Attribute	C. glycinophilum S209
Assembly length (bp)	3,609,534
No. of contigs	28
Contigs N50 (bp)	239,860
Coverage (x)	227.95
G + C (%)	64.6
# genes	3,416
# tRNAs	51
Completeness (%)	99.28
Contamination (%)	4.32

Full text

ANNOUNCEMENT

Corynebacterium glycinophilum is a species first proposed in 2015, describing an isolate from a putrefied banana (1). It has subsequently been identified in metagenome-assembled genomes (MAGs) from ripening cheese (C. glyciniphilum isolate 122_S29 and C. glyciniphilum isolate 35_S49 [Accession nos. JAKEBA01000000 and JAKDKC01000000, respectively]) and a human skin sample (C. glyciniphilum isolate oOBflCGst5_bin.2.MAG [Accession no. CALTYC010000000]). Recently, we isolated a strain of C. glycinophilum, taxonomically identified via whole genome sequencing, from a skin swab.

Participants in our institutional review board (IRB)-approved study (IRB no. 3603) were students at Loyola University Chicago and self-identified as female, “healthy,” and had not taken antibiotics within the last 6 months. Each participant was instructed to rub a provided cotton swab (BD BBL CultureSwab) on the middle of their forehead for 60 seconds, after which the swab was inserted into the provided storage solution (Amies media). Within 1 hour of sampling, swabs were swirled and squeezed in the storage media and then spread on mannitol salt (MS) agar plates and incubated for 24 hours at 35°C with 5% CO_2_. Morphologically distinct colonies were selected, placed in MS broth, and incubated under the same conditions. This process was repeated to purify the isolate described here. DNA was extracted using the DNeasy Blood and Tissue kit (Qiagen), following the manufacturer’s protocol for Gram-positive bacteria. Library construction was performed by SeqCoast (Portsmouth, NH, USA) using the Illumina DNA Prep tagmentation kit and unique dual indexes and then sequenced on the Illumina NextSeq2000 platform using a 300-cycle flow cell kit (2 × 150 bp reads). Read demultiplexing, read trimming, and run analytics were performed using DRAGEN v3.10.12 (Illumina) prior to delivery from SeqCoast.

Sequencing produced 9,395,192 raw reads which were then processed and assembled using the BV-BRC v3.51.7 web tool with the “auto” option (2). First, raw reads were trimmed using trim_galore v0.6.5dev (https://github.com/FelixKrueger/TrimGalore), normalized via bbnorm v37.60 (https://sourceforge.net/projects/bbmap/), and assembled using Unicycler (v0.4.8) (3), followed by two rounds of polishing with Pilon v1.24 (4). The publicly available genome sequence was annotated via the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline v6.10 (5). Genome statistics were calculated by BV-BRC. Taxonomic identification was informed by BV-BRC via taxonomic binning of the raw reads and confirmed by the JSpeciesWS (6), calculating the average nucleotide identity (ANI) between the draft genome and the sole representative of the species in the tool’s database, C. glycinophilum AJ 3710 (GCF_000626675.1). Completeness and contamination metrics were computed using CheckM v1.2.3 (7) upon submission to NCBI. Unless otherwise noted, default parameters were used for all software tools.

Table 1 lists the assembly statistics for the genome. Strain S209 shared 98.10% ANI with C. glycinophilum AJ 3710. While several Corynebacterium species are abundantly found on facial skin (8), further investigation is needed to ascertain if C. glycinophilum is a resident or transient member of this environment.