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Genome Sequences
bacteriologyBacteriologyComplete genome sequence of Pigmentibacter ruber isolated from a human patient in Japan
https://orcid.org/0000-0001-6317-9077
Hayashi Masahiro 1 2 3 Data curation Funding acquisition Investigation Methodology Validation Writing – original draft hayashi.masahiro.w8@f.gifu-u.ac.jp

Niwa Ayumi 4 Formal analysis Investigation Resources Validation
Yonetamari Jun 4 5 Formal analysis Investigation Methodology Resources
Muto Yoshinori 2 Data curation Formal analysis Software Visualization Writing – review and editing
Yokoyama Sodai 2 4 Investigation Methodology Validation
Nakamura Motohiro 4 Investigation Methodology Validation
Yokobori Yuta 4 Investigation Methodology Validation
Ogawa Mizuki 4 Investigation Methodology Validation
Ichioka Rina 4 Investigation Methodology Validation
Kikuchi Ryosuke 4 Supervision Writing – review and editing
Okura Hiroyuki 6 Supervision Writing – review and editing
Ogura Shinji 7 Supervision Writing – review and editing
Tetsuka Nobuyuki 8 Writing – review and editing
Baba Hisashi 9 Project administration Supervision Writing – review and editing
Tanaka Kaori 1 2 3 Project administration Supervision Writing – review and editing
1 Institute for Glyco-core Research iGCORE, Gifu University , Gifu City, Gifu, Japan
2 Division of Anaerobe Research, Life Science Research Center, Gifu University , Gifu, Japan
3 Gifu University Center for Conservation of Microbial Genetic Resource , Gifu, Japan
4 Division of Clinical Laboratory, Gifu University Hospital , Gifu, Japan
5 United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University , Gifu City, Gifu, Japan
6 Department of Cardiology, Gifu University Graduate School of Medicine , Gifu, Japan
7 Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine , Gifu, Japan
8 Department of Infection Control, Gifu University Graduate School of Medicine , Gifu, Japan
9 Center for Nutrition Support and Infection Control, Gifu University Hospital , Gifu, Japan
Editor Bruno Vincent Michael University of Maryland School of Medicine , Baltimore, Maryland, USA

Address correspondence to Masahiro Hayashi, hayashi.masahiro.w8@f.gifu-u.ac.jp
The authors declare no conflict of interest.

9 2024
20 8 2024
20 8 2024
13 9 e00133-2412 2 2024
17 7 2024
Copyright © 2024 Hayashi et al.
2024
Hayashi et al.
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

ABSTRACT

Pigmentibacter ruber is a newly described bacterium belonging to the Silvanigrellaceae family that was isolated from human blood in 2021. We report the complete genome sequence of a clinical isolate of P. ruber (GTC16762) obtained from a human patient in Japan. Its genome contains a 3.6-Mb chromosome and three circular plasmids.

KEYWORDS

Pigmentibacter ruber
clinical isolate
cover-dateSeptember 2024
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pmcANNOUNCEMENT

Pigmentibacter ruber (Silvanigrellaceae family) is a Gram-negative, rod-shaped, aerobic, non-motile, pleomorphic bacterium with red pigmented colonies (1, 2). P. ruber GTC16762 was isolated from a 78-year-old male Japanese patient with necrotizing fasciitis and septicemia in 2021 (3). He was receiving corticosteroid treatment for erythroderma and presented to his previous physician with symptoms of fever, redness, and left lower extremity swelling. A pares of blood culture collected on admission tested positive after 3 days. The blood culture medium was centrifuged at 1,200 × g for 10 minutes, and the sediment was used for subculture with trypticase soy agar with 5% sheep blood (Nippon Becton Dickinson Co., Ltd.) and Chocolate II agar (Nippon Becton Dickinson Co., Ltd.) at 35°C under aerobic conditions and at 35°C under 5% CO2, respectively. Pink, smooth-shaped colonies were observed after 72 hours. 16S rRNA gene sequencing determined by Sanger sequencing prior to genome sequencing confirmed the presence of the Silvanigrellaceae family.

Bacteria were grown in trypticase soy agar with 5% sheep blood (Nippon Becton Dickinson Co., Ltd.) at 35°C under aerobic conditions for 72 hours. The colonies were scraped, suspended in TE buffer, and pelleted by centrifugation. Genomic DNA was extracted from the pellet using NucleoBond HMW DNA (TAKARA, Japan).

The entire genome of the isolate was sequenced using long-read sequencing by Oxford Nanopore Technologies (Tokyo, Japan) and short-read sequencing by DNBSEQ (MGITech Co., Ltd., Shenzhen, China) (4, 5). For long-read sequencing, a library was constructed using a ligation sequencing kit (SQK-LSK-109; Oxford Nanopore Technologies [ONT]) without shearing. Small DNA fragments were removed using a Short Read Eliminator (Pacific Bioscience of California, Inc, USA), and sequencing was performed using GridION X5 (ONT) on a FLO-MIN106 flow cell. Long-read sequence data were base-called with Guppy v.5.0.11. The raw reads were trimmed and quality-filtered using NanoFilt v.2.7.1 (https://github.com/wdecoster/nanofilt). For short-read sequencing, the MGIEasy FS PCR Free DNA library prep set (MGI Tech) was used for library construction. Subsequently, 150-bp paired-end sequencing was performed using DNBSEQ-G400 (MGI Tech). Raw sequencing reads were processed using fastp v.0.20.1 (6) with “-q 30 n 20 t 1 T 1” parameters. Short-read quality was checked using fastp v.0.20.1 (6), and the mean long-read quality was scored using NanoPlot 1.32.1 (7). High-quality short-read (over 89% of bases > Q30 averaged) and long-read (mean read quality of 14.4) sequences were assembled using Unicycler v.0.4.8 (8) with default settings. The assembly was rotated to start with the dnaA gene on the forward strand. The assembled contig graph was visualized using Bandage v.0.8.1 (9), and blobtools v.1.1 (10) confirmed the assembled genomic data integrity.

Quality assessment and genome statistics were computed using QUAST (v5.2.0) (7) and CheckM (v1.2.2), respectively (11). According to CheckM, the genome assembled in this study was 94.78% complete and 0.0% contaminated. The DDBJ Fast Annotation and Submission Tool (12) with default settings predicted 3,396 coding sequences, 15 ribosomal RNAs, and 43 transfer RNAs (Table 1). The closest relative of P. ruber GTC 16762 was P. ruber HNSRY-1 (GCF_009792895.1, average nucleotide identity value: 99.1) according to the Genome Taxonomy Database (GTDB, https://gtdb.ecogenomic.org).

TABLE 1 Information of the complete genome sequence of a Pigmentibacter ruber strain isolated from a Japanese patient

	Strain name	
Parameter	P. ruber GTC16762	
DNBSEQ sequencinga	 	
 No. of reads	7,563,914	
 Size (kb)	1,134,587	
 Avg coverage (x)	293	
 DRA accession no.	DRR523861	
ONT seqencinga	 	
 No. of reads	100,547	
 Size (kb)	834,587	
 Avg read length (bp)	8,301	
 Avg coverage (x)	216	
 N50	13,113	
 DRA accession no.	DRR523860	
Assembly	 	
 Genome structure	One chromosome and three plasmids	
 DDBJ/GenBank accession no.	AP029159 (GTC16762)	
 (Chromosome/plasmid name)	AP029160 (pGTC16762-1)	
	AP029161 (pGTC16762-2)	
	AP029162 (pGTC16762-3)	
	 	
Genome size (bp)	3614887 (GTC16762)	
 (Chromosome/ plasmid name)	140423 (pGTC16762-1)	
	67953 (pGTC16762-2)	
	44767 (pGTC16762-3)	
GC content (%)	 	
 (Chromosome/ plasmid name)	29.76 (GTC16762)	
	29.89 (pGTC16762-1)	
	27.75 (pGTC16762-2)	
	31 (pGTC16762-3)	
No. of coding sequencesb	3,396	
Number of rRNAsb	15	
Number of tRNAsb	43	
Number of CRISPRsb	2	
a DRA, DDBJ Sequence Read Archive.

b DFAST, DDBJ Fast Annotation and Submission Tool. CRISPR: clustered regularly interspaced short palindromic repeats.

ACKNOWLEDGMENTS

We thank Kyoko Hatazaki, Akiko Katano, and Ayako Nagasawa for technical support.

DATA AVAILABILITY

The 16S rRNA sequence and genome sequences of the P. ruber (GTC16762) strain from human patient were deposited in DDBJ (https://www.ddbj.nig.ac.jp/index.html) with accession numbers LC795719 and AP029159-AP029162, respectively. Raw sequence data were deposited in the DDBJ/Sequence Read Archive under accession numbers DRR523860 and DRR523861 for GTC16762.

ETHICS APPROVAL

The study was approved by the Ethics Committees of Gifu University (Gifu, Japan; Approval Number 2022-145).
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