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Complete genome sequence of Paenibacillus sp. YPD9-1 isolated from the gut microbiome of Hexagrammos agrammus
Korean J. Microbiol. 2023;59(1):45-48
Published online March 31, 2023
© 2023 The Microbiological Society of Korea.

Dong-Gyun Kim, Hyun-Kyoung Jung, Jungwook Park, Young-Ok Kim, Hee Jeong Kong, and Young-Sam Kim*

Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
Correspondence to: *E-mail:; Tel.: +82-51-720-2453; Fax: +82-51-720-2456
Received February 27, 2023; Revised March 20, 2023; Accepted March 21, 2023.
Paenibacillus sp. YPD9-1, a novel bacterium showing antifungal activity was isolated from a gut content of a spotty belly greenling Hexagrammos agrammus. The genome sequence of strain YPD9-1 which is 6,569,197 bp with 47.6% G + C content was obtained by using Nanopore platform. The complete genome contains total 6,165 genes including 5,998 CDSs, 42 RNAs, 121 tRNAs, and 524 pseudogenes. Additionally, gene clusters encoding secondary metabolites such as antimicrobial and beneficial substances, macrobrevin, paeninodin, and ectoine were identified from the genome. The findings might provide insight into the characteristics of Paenibacillus species and the industrial application of their property.
Keywords : Paenibacillus sp., complete genome, spotty belly greenling

Paenibacillus species are prevalent in various environments, including soil, water, humans, plants, and animals. Paenibacillus species are known for their characteristics to produce a wide range of antimicrobial substances, enzymes, and metabolites that contribute to their adaptation and survival in different ecological niches (Grady et al., 2016). Paenibacillus species have been studied extensively for their potential applications in agriculture, bioremediation, and industrial processes. In soil, Paenibacillus species have been shown to promote plant growth and are involved in nitrogen fixation, degradation of organic matter, and suppression of plant pathogens (Basu et al., 2021). They are also known to play roles in the bioremediation of toxic heavy metals in polluted environments (Govarthanan et al., 2016) and their enzymes such as amylases, cellulases, chitinase, lipase, and pectinases may be applicable to various industrial fields (Grady et al., 2016).

Strain YPD9-1 was isolated from the gut content of a spotty belly greenling Hexagrammos agrammus collected near Dokdo island, South Korea (37°14'19.6"N 131°51'51.2"E). The gut content was serially diluted and inoculated on yeast peptone dextrose agar (YPD, Difco), then incubated at 25°C for three days. 16S rDNA sequence of the strain YPD9-1 exhibited low similarity compared to the close species Paenibacillus pocheonensis Gsoil 1138 T (similarity of 97.2%), P. aestuarii CJ25 T (97.1%), and P. aceris KUDC4121 T (96.4%) which all belong to the genus Paenibacillus.

For genome sequencing, genomic DNA of the strain was purified by using MiniBEST Bacteria Genomic DNA Extraction Kit (TaKaRa) according to the manufacturer’s instructions and analyzed using the Nanopore platform (Flongle, Oxford). The sequence reads were assembled using CANU assembler (version 2.0; [Koren et al., 2017]). Through the assembly of subreads, a complete genome which is 3,892,138 bp with 66.1 mol% was generated (Fig. 1). The genome was subjected to annotation analysis using NCBI Prokaryotic Genome Annotation Pipeline (PGAP; [Tatusova et al., 2016]) and a total of 6,165 genes including 5,998 CDSs, 42 ribosomal RNAs (5S, 16S, 23S), 121 tRNAs, and 524 pseudogenes were annotated from the genome (Table 1). PHAge Search Tool Enhanced Release (PHASTER; [Arndt et al., 2016]) was used to detect inserted phage sequences and one incomplete prophage sequence (15 kb, 49.18 G + C mol%) encoding one portal protein, two phage-like proteins, and 16 hypothetical proteins was detected.

Genomic features of <italic>Paenibacillus</italic> sp. YPD9-1
Feature Value
Genome length (bp) 6,569,197
G + C content (%) 47.6
Total genes 6,165
Total CDS 5,998
rRNAs (5S, 16S, 23S) 14, 14, 14
tRNAs 121
ncRNAs 4
Pseudogenes 524

Fig. 1. Complete genome of Paenibacillus sp. YPD9-1. From the center to the outside: G + C content (black), GC skew (green and purple), CDSs on the reverse strand and forward strand (blue).

AntiSMASH 6.0 (Blin et al., 2021) was used to identify gene clusters related to secondary metabolite, and 12 gene clusters involved in the biosynthesis of paeninodin (similarity of 80%), macrobrevin (80%), paenilipoheptin (7%), ectoine (75%), and polysaccharide B (6%), and other metabolites were detected. Those metabolites which may be synthesized by the strain YPD9-1 are well known beneficial substances. Paeninodin and macrobrevin produced by Paenibacillus species are known to have effective antibacterial activity (Zhu et al., 2016; Eltokhy et al., 2021), and ectoine produced by bacteria is used as a protective agent in cosmetics (Bownik and Stępniewska, 2016). Metabolites related to antifungal activity shown by the strain were not detected by AntiSMASH. However, endoglucanase (UniProtKB: P19424) which is known to have antifungal activity (Grady et al., 2016; Philip et al., 2020) was confirmed by PGAP annotation. The results of this study showed potential valuable properties of Paenibacillus sp. YPD9-1 and may provide a basis for understanding the ecology of Paenibacillus species. Additional molecular biological analyses are in progress to investigate the substances produced by the strain YPD9-1.

Nucleotide sequence accession number

The strain YPD9-1 has been deposited in the Korean Collection for Type Cultures (KCTC) with the preservation number KCTC 43424 and its genome sequence has been deposited in GenBank under the accession number of CP090978.

적 요

Paenibacillus sp. YPD9-1은 Paenibacillus 속에 속하는 신종 균주로 대한민국 독도 근해에서 채집한 노래미 Hexagrammos agrammus의 장 내용물로부터 분리되었다. 항진균 활성을 나타내는 균주 YPD9-1의 전장유전체는 6,569,197 bp (G + C 함량 47.6%) 길이의 환형으로 총 5,998 개 CDS 서열, 42개 rRNA (5S, 16S, 23S) 서열, 121개 tRNA 서열, 그리고 총 524개의 pseudogene 서열을 포함하며, 이차대사산물 합성과 관련된 유전자 클러스터 탐색결과 paeninodin, macrobrevin, ectoine 등 항균, 유용 대사산물 관련 클러스터가 확인되었다. 본 연구는 Paenibacillus 속 신종 균주 YPD9-1의 유전체 분석을 통해 Paenibacillus 속 미생물의 잠재적 활용과 생태학적 특성 연구에 유익한 정보를 제공할 것으로 사료된다.


This research was supported by National Institute of Fisheries Science (R2023050) grant funded by the Ministry of Oceans and Fisheries.

Conflict of Interest

The authors have no conflict of interest to report.

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