Non-contiguous finished genome sequence and description of the gliding bacterium Flavobacterium seoulense sp. nov.
© Shin et al.; licensee BioMed Central. 2014
Received: 8 July 2014
Accepted: 24 November 2014
Published: 29 December 2014
Flavobacterium seoulense strain EM1321T is the type strain of Flavobacterium seoulense sp. nov., a proposed novel species within the genus Flavobacterium. This strain is a Gram-reaction-negative, aerobic, rod-shaped bacterium isolated from stream water in Bukhansan National Park, Seoul. This organism is motile by gliding. Here, we describe the features of Flavobacterium seoulense EM1321T, together with its genome sequence and annotation. The genome comprised 3,792,640 bp, with 3,230 protein-coding genes and 52 RNA genes.
KeywordsFlavobacterium Gliding motility Aerobic Flavobacteriaceae
Flavobacterium is the type genus of the family Flavobacteriaceae in the phylum Bacteroidetes. Flavobacterium was proposed by Bergey et al. [1, 2] and the description was emended by Bernardet et al. . Flavobacterium species have been isolated from various environments, including seawater, freshwater, river sediments, and soil [4–8]. Members of the genus Flavobacterium are Gram-negative, rod-shaped, yellow-pigmented, aerobic bacteria. At the time of writing, about 118 Flavobacterium species with validly published names have been described ; however, the genomes of only 14 type strains in this genus have been sequenced.
Flavobacterium seoulense sp. nov. strain EM1321T (= KACC 18114T = JCM 30145T) was isolated from stream water in Bukhansan National Park, Seoul, Korea. Here, we present a summary classification and the features of Flavobacterium seoulense EM1321T as well as its genome sequence and annotation.
Classification and features
Classification and general features of Flavobacterium seoulense EM1321 T according to the MICG recommendations 
Species F. seoulense
Seoul, South Korea
Sample collection time
Phenotypic characteristics of Flavobacterium seoulense EM1321 T and phylogenetically related Flavobacterium species
F. seoulense EM1321 T
F. soli KACC 17417 T
F. nitratireducens JCM 17678 T
Cell length (μm)
G + C content (mol%)
Genome sequencing information
Genome project history
Genome sequencing project information
One paired-end Illumina library
CLCbio CLC Genomics Workbench, version 6.5.1
Gene calling method
Genbank Date of Release
Source Material Identifier
KACC 18114, JCM 30145
Growth conditions and DNA isolation
Flavobacterium seoulense EM1321T was cultured aerobically on R2A agar medium at 30°C. Genomic DNA was extracted using the QIAamp DNA mini kit (Qiagen).
Genome sequencing and assembly
The genome of strain EM1321T was sequenced at ChunLab, Inc. by using an Illumina Miseq_PE_300 system with 2 × 300 paired-end reads. The Illumina platform provided 166× coverage (for a total of 3,792,640 sequencing reads) of the genome. CLC Genomics Workbench (ver. 6.5.1) was used for sequence assembly and quality assessment. The final draft assembly contained 56 contigs.
The genes in the assembled genome were predicted with Rapid Annotation using Subsystem Technology (RAST) server databases  and the gene-caller GLIMMER 3.02 . The predicted ORFs were annotated by searching clusters of orthologous groups (COGs)  using the SEED database . RNAmmer 1.2  and tRNAscan-SE 1.23  were used to identify rRNA genes and tRNA genes, respectively. CRISPR repeats were examined using CRISPR recognition tool (CRT) . CLgenomics™ 1.06 (ChunLab) was used to visualize the genomic features.
% of total a
Genome size (bp)
DNA coding region (bp)
G + C content (bp)
Genes with function prediction
Genes assigned to COGs
Genes assigned Pfam domains
Genes with signal peptides
Genes with transmembrane helices
Number of genes associated with the 25 general COG functional categories
RNA processing and modification
Replication, recombination, and repair
Chromatin structure and dynamics
Cell cycle control, mitosis, and meiosis
Signal transduction mechanisms
Cell wall/membrane biogenesis
Intracellular trafficking and secretion
Posttranslational modification, protein turnover, and chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport, and catabolism
General function prediction only
Not in COGs
Based on the results from phylogenetic and phenotypic analyses, we formally propose the creation of the new species Flavobacterium seoulense sp. nov. for strain EM1321T. The non-contiguous genome sequence of the type strain was determined and described here.
Description of Flavobacterium seoulense sp. nov
Flavobacterium seoulense (seo.ul.en’se. N.L. neut. adj., named after Seoul, Korea, the geographical origin of the type strain).
Aerobic, Gram-reaction negative. Cells are rod shaped and motile by gliding. Does not have a flagellum. The colonies are yellow in color and translucent on R2A agar medium. Grows at 4–35°C, with optimum growth at 30°C and in 0–4% (w/v) NaCl. Catalase- and oxidase-positive. Positive for alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, acid phosphatase, naphthol-AS-BI-phosphohydrolase, β-galactosidase, and valine arylamidase. Positive for nitrate reduction, but negative for indole production, glucose fermentation, arginine dihydrolase, urease activity, and aesculin and gelatin hydrolysis. Negative for lipase, trypsin, α-chymotrypsin, α-galactosidase, β-glucuronidase, α-glucosidase, β-glucosidase, N-acetyl-β-glucosaminidase, or cystine arylamidase activity. This strain assimilated d-glucose and l-arabinose, but not d-mannitol, d-mannose, d-maltose, N-acetylglucosamine, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, or phenylacetic acid. Produces acid from l-arabinose, d-xylose, d-galactose, d-glucose, d-fructose, d-mannose, and d-lactose.
The G + C content of the genome is 33.25%. The 16S rRNA and genome sequences are deposited in GenBank under accession numbers KJ461685 and JNCA00000000.1, respectively. The type strain EM1321T (= KACC 18114T = JCM 30145T) was isolated from stream water in Bukhansan National Park, Seoul, Korea.
This work was supported by the Basic Science Research Programs through the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT, and Future Planning (NRF-2013R1A1A3010041) and supported by a Korea University Grant.
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