- Genome information of the cellulolytic soil actinobacterium Isoptericola dokdonensis DS-3 and comparative genomic analysis of the genus Isoptericola
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Yurim Bae , Sujin Lee , Kitae Kim , Hyun-Kwon Lee , Soon-Kyeong Kwon , Jihyun F. Kim
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J. Microbiol. 2021;59(11):1010-1018. Published online November 1, 2021
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DOI: https://doi.org/10.1007/s12275-021-1452-6
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 Abstract
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The actinobacterial group is regarded as a reservoir of biologically
active natural products and hydrolytic enzymes with
the potential for biomedical and industrial applications. Here,
we present the complete genome sequence of Isoptericola
dokdonensis DS-3 isolated from soil in Dokdo, small islets
in the East Sea of Korea. This actinomycete harbors a large
number of genes encoding carbohydrate-degrading enzymes,
and its activity to degrade carboxymethyl cellulose into glucose
was experimentally evaluated. Since the genus Isoptericola was
proposed after reclassification based on phylogenetic analysis,
strains of Isoptericola have been continuously isolated from
diverse environments and the importance of this genus in the
ecosystem has been suggested by recent culturomic or metagenomic
studies. The phylogenic relationships of the genus
tended to be closer among strains that had been isolated from
similar habitats. By analyzing the properties of published genome
sequences of seven defined species in the genus, a large
number of genes for carbohydrate hydrolysis and utilization,
as well as several biosynthetic gene clusters for secondary
metabolites, were identified. Genomic information of I. dokdonensis
DS-3 together with comparative analysis of the genomes
of Isoptericola provides insights into understanding
this actinobacterial group with a potential for industrial applications.
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Citations
Citations to this article as recorded by  -
Isoptericola maris sp. nov., a novel actinobacterium isolated from the marine sediment in the Bohai Sea, China
Ruixue Jia, Qianqian Huang, Shuxuan Li, Zhaochen Lu, Zeping Xie, Li Tuo, Lelin Han
International Journal of Systematic and Evolutionary Microbiology
.2026;[Epub] CrossRef - Genomic analysis of Isoptericola halotolerans SM2308 reveals its potential involved in fucoidan degradation
Yu-Qi Zhang, Qi Yuan, Ji-Qing Liu, Xiao-Chen Liang, Jing-Ping Wang, Wen-Xin Jiang, Ping-Yi Li
Marine Genomics.2025; 79: 101165. CrossRef - Assessing hydrocarbon degradation capacity of Isoptericola peretonis sp. nov. and related species: a comparative study
Àngela Vidal-Verdú, Adriel Latorre-Pérez, Javier Pascual, Ruth Mañes-Collado, Aitana Nevot-Terraes, Manuel Porcar
Frontiers in Microbiology.2025;[Epub] CrossRef - From lignocellulosic biomass to single cell oil for sustainable biomanufacturing: Current advances and prospects
Yu Duan, Limei Chen, Longxue Ma, Farrukh Raza Amin, Yida Zhai, Guofu Chen, Demao Li
Biotechnology Advances.2024; 77: 108460. CrossRef - A comprehensive review on strategic study of cellulase producing marine actinobacteria for biofuel applications
Ashwini John J, Melvin S. Samuel, Muthusamy Govarthanan, Ethiraj Selvarajan
Environmental Research.2022; 214: 114018. CrossRef
- Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5
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Kiyoung Yoon , Ju Yeon Song , Min-Jung Kwak , Soon-Kyeong Kwon , Jihyun F. Kim
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J. Microbiol. 2017;55(7):561-567. Published online April 22, 2017
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DOI: https://doi.org/10.1007/s12275-017-6427-2
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987
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Abstract
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Flavobacteriaceae, are typically isolated from marine environments.
Polaribacter dokdonensis DSW-5, the type strain
of the species, is a Gram-negative bacterium isolated from the
East Sea of Korea. Whole genome shotgun sequencing was
performed with the HiSeq 2000 platform and paired-end reads
were generated at 188-fold coverage. The sequencing reads
were assembled into two contigs with a total length of 3.08
Mb. The genome sequences of DSW-5 contain 2,776 proteincoding
sequences and 41 RNA genes. Comparison of average
nucleotide identities among six available Polaribacteria genomes
including DSW-5 suggested that the DSW-5 genome
is most similar to that of Polaribacter sp. MED152, which is
a proteorhodopsin-containing marine bacterium. A phylogenomic
analysis of the six Polaribacter strains and 245 Flavobacteriaceae
bacteria confirmed a close relationship of the
genus Polaribacter with Tenacibaculum and Kordia. DSW-5’s
genome has a gene encoding proteorhodopsin and genes encoding
85 enzymes belonging to carbohydrate-active enzyme
families and involved in polysaccharide degradation, which
may play important roles in energy metabolism of the bacterium
in the marine ecosystem. With genes for 238 CAZymes
and 203 peptidases, DSW-5 has a relatively high number of
degrading enzymes for its genome size suggesting its characteristics
as a free-living marine heterotroph.
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Citations
Citations to this article as recorded by - Complete genome of Polaribacter huanghezhanensis KCTC 32516T isolated from glaciomarine fjord sediment of Svalbard
Kyuin Hwang, Hanna Choe, Kyung Mo Kim
Marine Genomics.2023; 72: 101068. CrossRef - Microbial Communities Associated with the White Sea Red Algae as a Source of Xylanolytic Microorganisms
V. D. Salova, A. M. Kholdina, A. D. Mel’nik, K. S. Zayulina, A. G. El’cheninov, A. A. Klyukina, I. V. Kublanov
Микробиология.2023; 92(3): 300. CrossRef - Microbial Communities Associated with the White Sea Red Algae as a Source of Xylanolytic Microorganisms
V. D. Salova, A. M. Kholdina, A. D. Melnik, K. S. Zayulina, A. G. Elcheninov, A. A. Klyukina, I. V. Kublanov
Microbiology.2023; 92(3): 418. CrossRef -
Colwellia maritima sp. nov. and Polaribacter marinus sp. nov., isolated from seawater
Sylvia Kristyanto, Jaejoon Jung, Jeong Min Kim, Keunpil Kim, Mi-hwa Lee, Lujiang Hao, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef - Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish
Su-Won Jeong, Jeong Eun Han, June-Young Lee, Ji-Ho Yoo, Do-Yeon Kim, In Chul Jeong, Jee-Won Choi, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Euon Jung Tak, Hojun Sung, Hyun Sik Kim, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
Journal of Microbiology.2022; 60(6): 576. CrossRef - Repeated evolutionary transitions of flavobacteria from marine to non‐marine habitats
Hao Zhang, Susumu Yoshizawa, Ying Sun, Yongjie Huang, Xiao Chu, José M. González, Jarone Pinhassi, Haiwei Luo
Environmental Microbiology.2019; 21(2): 648. CrossRef - Assessment of bacterial communities in skin ulceration in cultured sea cucumber Apostichopus japonicus (Selenka)
Yi Yang, Yuchun Li, Zhenlin Liang
International Aquatic Research.2018; 10(3): 275. CrossRef
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