Complete genome of single locus sequence typing D1 strain Cutibacterium acnes CN6 isolated from healthy facial skin

Abstract

Objectives

Cutibacterium acnes is a Gram-positive bacterium commonly found on human skin, particularly in sebaceous areas. While it is typically considered a commensal, specific strain types based on single locus sequence typing (SLST) have been associated with pathogenic conditions or healthy skin. Recently, SLST D1 strains, part of phylotype IA1, have received attention for their potential benefits related to skin health. However, their genetic characteristics remain underexplored. Therefore, the whole genome of C. acnes CN6, an SLST D1 strain isolated from the facial skin of a healthy individual, was sequenced to expand the understanding of SLST D1 strains and identify genomic features that may support skin health.

Data description

The whole genome sequencing of C. acnes CN6 was conducted using MinION reads based on de novo assembly, revealing a single circular complete chromosome. With the length of 2,550,458 bp and G + C content of 60.04%, the genome contains 2,492 genes, including 2,433 CDSs, 9 rRNAs, 46 tRNAs, 4 ncRNAs, and 134 pseudo genes. Previously predicted virulence proteins of C. ances were detected in the genome. Genome comparation with 200 C. acnes strains isolated from healthy facial skin revealed SLST D1 strain-specific genes and a unique variant of the znuC gene in D1 strains.

Objective

Cutibacterium acnes is a Gram-positive bacterium that is prevalent across human skin, especially in sebaceous areas [1]. While C. acnes is a commensal microbe in skin microenvironment, it can act as an opportunistic pathogen, contributing to various pathological states. It has been associated with acne vulgaris, osteoarticular prosthesis infections, and other clinical conditions when the skin microbiome balanced is disrupted [2,3,4,5,6]. In contrast, certain strains of C. acnes play a crucial role in maintaining skin homeostasis and promoting skin barrier function, potentially contributing to overall skin health and resilience [7, 8].

Previous studies have suggested a potential association between specific C. acnes strains and particular pathogenic conditions based on molecular typing systems such as single-locus sequence typing (SLST) [9,10,11]. C. acnes is classified into phylotypes (IA1, IA2, IB, IC, II, and III), each containing specific SLST classes [12]. Notably, SLST classes H (phylotype IB) and K (phylotype II) have been linked to healthy skin [13]. Recently, C. acnes SLST D1 strains, belonging to phylotype IA1, have garnered attention for its potential benefits to skin health [14,15,16]. However, the current understanding of C. acnes SLST D1 strains remains incomplete, necessitating further research.

To address this, we performed whole genome sequencing of a C. acnes SLST D1 strain, named CN6, which was isolated from the facial skin of a healthy individuals without any skin disease. With only a single SLST class D genome classified as “complete” in NCBI GenBank—strain CBS-BPNBT19153, which was isolated from contaminated platelet blood concentrates [17]—we aimed to expand the genetic background of SLST D1 strains through this study. Additionally, we identified unique genomic characteristics of the C. acnes SLST D1 strain CN6 by comparing its genomic differences with other C. acnes strains isolated from the healthy facial skin, providing insights into facial skin health.

Data description

C. acnes CN6 was isolated from a facial skin swab sample collected from a healthy individual without any skin conditions. The pure isolate of C. acnes CN6 was cultivated in Brain Heart Infusion agar for 5 days at 37 °C under anaerobic condition using a GasPak EZ anaerobe pouch system (BD, USA). Genomic DNA was extracted using the Wizard genomic DNA purification kit (Promega, USA), following the manufacturer’s instructions. The quality and quantity of the extracted DNA was assessed through Nanodrop One Spectrophotometer (Thermo Fisher Scientific, USA) and Qubit 3.0 fluorometer (Thermo Fisher Scientific, USA).

The whole genome sequencing library was constructed using SQK-LSK109 ligation sequencing kit (Oxford Nanopore Technologies [ONT], UK), along with the NEBNext companion module (New England Biolabs, USA). Sequencing was performed on the ONT MinION platform by loading the library into FLOWMIN111 R10.3 flow cell at the KNU NGS Core Facility (Kyungpook National University, Republic of Korea). To generate FASTQ files of the sequencing data, base calling was performed using Guppy v 6.5.7 [18] in high- accuracy mode, followed by using NanoStat v 1.6.0 [19] to calculate sequence statics. A total of 203,933 reads with mean read quality score of 12.5 and N₅₀ of 4,114 bp was obtained (Data file 1). After removing low-quality reads with Filtlong v 0.2.1 (https://github.com/rrwick/Filtlong), de novo assembly was performed using Flye v 2.9.1 [20] with the modification for the genome size option (–genome-size 2.5 m). The SLST strain type was classified using the online typing tool available at http://medbac.dk/slst_server_script.html [11], and gene annotation was performed using NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v 6.8 [21] and Prokka v 1.14.6 [22] which facilitated the identification of coding sequences (CDSs), rRNAs, tRNAs, and other genomic features.

The complete genome of C. acnes CN6 has a total length of 2,550,458 bp with G + C content of 60.04% and coverage of 183x. It encodes a total of 2,492 genes, including 2,433 CDSs, 9 rRNAs, 46 tRNAs, 4 ncRNAs, and 134 pseudo genes (Data file 2).

Predicted virulence proteins were detected using BLASTX based on previously predicted virulence factors in C. acnes KPA171202 [23, 24], except for hyaluronate lyase (HYL). Since KPA171202 (phylotype IB) possesses the HylB variant, we identified HYL using the HylA variant from C. acnes HL043PA1 (phylotype IA1) [25, 26] (Data file 3). Additionally, a comparative genome analysis was conducted using Roary [27] with 200 C. acnes strains isolated from healthy facial skin, including two SLST D1 strains, available on NCBI GenBank database as of August 2024 (Data file 4). A total of 9 genes, excluding unknown genes, were identified as unique to D1 strains among the 4,952 genes in the pan-genome of 201 C. acnes strains (Data file 5). Furthermore, a unique variant of the znuC gene, which is associated with bacterial survival and virulence under zinc-limited conditions [28, 29], was found to be conserved among the D1 strains. This variant is 822 bp in length, compared to the 804 bp length observed in other SLST types (Data file 6).

Table 1 Overview of data files/data sets

Limitations

To fully capture the genetic diversity and potential functional variations within SLST D1 strains of C. acnes, further studies involving a larger and more diverse collection of SLST D1 strains, as well as strains from other SLST types, are recommended to validate and broaden these findings.