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Complete genome of Chryseobacterium pectinilyticum G2-70 isolated from effluent of a livestock manure treatment plant
Korean J. Microbiol. 2020;56(4):401-403
Published online December 31, 2020
© 2020 The Microbiological Society of Korea.

Swati Tyagi1,2†, Haeseong Lee1†, Hyeonbin Kim1, Kui-Jae Lee1, and Jong-Chan Chae1*

1Division of Biotechnology, Jeonbuk National University, Iksan 54596, Republic of Korea
2Rice Breeding Platform, International Rice Research Institute-South Asia Regional Centre (ISARC), Varanasi 221106, India
Correspondence to: E-mail: chae@jbnu.ac.kr;
Tel.: +82-63-850-0840; Fax: +82-63-850-0834
These authors contributed equally to this work.
Received September 10, 2020; Revised October 26, 2020; Accepted November 2, 2020.
Abstract
A Gram-reaction-negative, rod-shaped, and non-motile bacterium designated as Chryseobacterium pectinilyticum G2-70 was isolated from the effluent of a livestock manure treatment plant. The complete genome of the strain consisted of a chromosome with 2,823,139 bp and one circular plasmid with 16,106 bp. The genome with a G + C content of 31.21% contained 2,621 predicted coding sequences, 51 tRNA genes, and 15 rRNA genes. Strain G2-70 showed resistance against amoxicillin as well as ciprofloxacin and the chromosomal DNA contained the corresponding genes, blaOXA (class D beta-lactamase) and adeL (fluoroquinolone antibiotic efflux pump).
Keywords : Chryseobacterium, effluent water, genome
Body

The genus Chryseobacterium, first proposed by Vandamme et al. (1994), is a member of the Flavobacteriaceae family. Members of the genus Chryseobacterium have been isolated from various environments including freshwater (Kirk et al., 2013), clinical samples (Holmes et al., 2013), fish (Loch and Faisal, 2014), and meat (de Beer et al., 2005). Several Chrysebacterium species were reported as new sources of biocontrol agents against pepper and bean (Kim et al., 2012). The members of this genus are chemotaxonomically characterized with menaquinone 6 (MK-6) as a predominant respiratory quinone, branched-chain fatty acids, and a DNA G + C content in the range of 30~40% (Dahal et al., 2020).

Chryseobacterium pectinilyticum G2-70 was isolated from the effluent of a livestock manure treatment plant in Gongju, Republic of Korea by inoculation on Mueller-Hinton (MH) agar plate and incubation at 30°C for 48 h. The cells were Gram-reaction negative, non-motile, non-spore forming, and rod-shaped with approximately 1.8~2.0 μm in length and 0.7~0.9 μm in width. Cells grew on tryptone soy agar (TSA), nutrient agar, brain heart infusion agar, and Luria-Bertani agar. The colonies of strain G2-70 were convex, translucent, smooth, and circular after 48 h cultivation at 30°C on TSA medium. Strain G2-70 was able to grow at temperature range of 20~37°C (optimum 30°C) and pH range of pH 4.0 and 10.5 (optimum 7.0) and also tolerate up to NaCl concentration of 1% (w/v). The major fatty acids of the strain were C13:0 (4.68%), iso-C15:0 (47.64%), iso-C15:0 3-OH (5.12%), iso-C17:0 3-OH (14.21%), and summed features 3 (C16:1ω7c and C16:1ω6c) (22.03%). And the predominant respiratory quinone was MK-6. The strain was deposited in KCTC and NBRC under deposition numbers 62509 and 113273.

The DNA was extracted from the cells using a genomic DNA extraction kit (ExgeneTM Cell SV mini, GeneAll). Genome sequencing was performed for long-read sequences on an MK1B MinION device using R9.4 flow cells and for the short-read sequences on Illumina iSeq 100 platform. Both platforms generated 2.5 Gb and 854.6 Mb sequencing reads corresponding 925× and 316× in coverage, respectively. The obtained long and short-read sequences were qualified with Guppy (v.3.6.1 Oxford Nanopore) and FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), respectively. Contigs were generated with both long and short-read sequences using Unicycler (v0.4.8, Wick et al., 2017), hybrid assembler. Annotation was performed with Prokka (Seemann, 2014). Total 2,621 coding sequences (CDSs), 51 tRNA genes, and 15 rRNA genes (5 of 5S, 5 of 16S, 5 of 23S) were found as described in Table 1. Complete genome of strain G2-70 contained a circular chromosome of 2,823,139 bp with one plasmid of 16,106 bp. Genome maps were generated with genome circular viewer using PATRIC server (Davis et al., 2020) as shown in Fig. 1.

Genome features of Chryseobacterium pectinilyticum G2-70

Contig Size CDS rRNA tRNA ncRNA GC%
Chromosome 2,823,139 bp 2,604 15 51 3 36.71
Plasmid 16,106 bp 17 0 0 0 30.83


Fig. 1. Circular maps of Chryseobacterium pectinilyticum G2-70 genome. Circular genome was generated using PATRIC server. Each colored track represented CDS, AMR genes, and GC contents. From outside of the center, the colored track represented as followed: blue, chromosome; green and purple, forward coding sequence and reverse coding sequence; cyan, non-coding sequence; red, antimicrobial resistance genes; light purple, GC content.

The closest strain of G2-70 was Amniculibacterium aquaticum KYPW7 showing 99.86% sequence similarity of 16S rRNA gene and 99.09% of ANI value. While strain KYPW7 was only resistant to beta-lactam class antibiotics (penicillin G and ampicillin), strain G2-70 was resistant to beta-lactam as well as fluoroquinolone class antibiotics (amoxicillin and ciprofloxacin) but sensitive to gentamicin, sulfamethoxazole, trimethoprim, streptomycin cephalexin, tetracycline, erythromycin, rifampicin, tylosin, clindamycin, meropenem, and chloramphenicol. The chromosome of G2-70 harbored the corresponding antibiotic resistant genes for amoxicillin and ciprofloxacin, which were blaOXA (class D beta-lactamase) and adeL (fluoroquinolone antibiotic efflux pump) genes, respectively.

Nucleotide sequence accession number

The genome sequence of Chryseobacterium pectinilyticum G2-70 has been deposited in NCBI GenBank under accession nos. CP080898 and CP080899.

적 요

그람 음성이며 비운동성 간균인 Chryseobacterium pectinilyticum G2-70을 가축 분뇨 처리장 방류수로부터 분리하였다. 완전 해독된 G2-70 균주의 유전체는 2,823,138 bp의 염색체와 16,106 bp 크기의 플라스미드로 구성되어 있었다. 31.21%의 GC함량으로 구성된 유전체에는 2,621개의 암호화된 염기서열들과 51개의 tRNA 유전자, 15개의 rRNA 유전자가 존재하였다. G2-70 균주는 아목사실린과 시프로플록사신 항생제에 내성을 보였으며 염색체 DNA에서 관련 내성 유전자들인 blaOXA(클래스 D 베타락타메이즈 유전자)와 adeL (플로로퀴놀론 항생제 배출 펌프 유전자)이 검출되었다.

Acknowledgments

This study was supported by the Korea Ministry of Environment (MOE) as The Environmental Health Action Program under Project No. 2016001350005.

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