Open Access

Non-contiguous finished genome sequence and description of the gliding bacterium Flavobacterium seoulense sp. nov.

  • Su-Kyoung Shin1,
  • Heemoon Goo2,
  • Yong-Joon Cho3,
  • Soonsung Kwon4,
  • Dongeun Yong4 and
  • Hana Yi1, 2, 5Email author
Standards in Genomic Sciences20149:34

DOI: 10.1186/1944-3277-9-34

Received: 8 July 2014

Accepted: 24 November 2014

Published: 29 December 2014

Abstract

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.

Keywords

Flavobacterium Gliding motility Aerobic Flavobacteriaceae

Introduction

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. [3]. Flavobacterium species have been isolated from various environments, including seawater, freshwater, river sediments, and soil [48]. 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 [9]; 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

Based on its 16S rRNA gene phylogeny and phenotypic characteristics, strain EM1321T was classified as a member of the genus Flavobacterium (Table 1). Preliminary sequence-based identification using the 16S RNA gene sequences in the EzTaxon database [10] indicated that strain EM1321T was most closely related to F. granuli Kw05T (GenBank accession no. AB180738) with a sequence similarity of 96.54%. This value was lower than the 98.7% 16S rRNA gene sequence similarity as a threshold recommended by Stackebrandtia and Ebers [11] to delineate a new species without carrying out DNA-DNA hybridization. Subsequent phylogenetic analysis was performed using the 16S rRNA gene sequences of strain EM1321T and related species. Sequences were aligned according to the bacterial rRNA secondary structure model using the jPHYDIT [12]. Phylogenic trees were constructed using neighbor-joining (NJ) and maximum-likelihood (ML) methods implemented in MEGA version 5 [13]. The resultant tree topologies were evaluated by bootstrap analyses with 1,000 random samplings. Strain EM1321T formed a monophyletic clade together with Flavobacterium soli [5] in both the NJ and ML trees; however, the clustering was not supported by the bootstrap analysis (Figure 1). Flavobacterium nitratireducens [8] was further recovered as a sister group of the monophyletic clade in the ML tree only. Based on these phylogenetic trees, F. soli KACC 17417T and F. nitratireducens JCM 17678T were selected as reference strains and were obtained from the corresponding culture collections for comparative study.
Table 1

Classification and general features of Flavobacterium seoulense EM1321 T according to the MICG recommendations [14]

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [15]

  

Phylum Bacteroidetes

TAS [16, 17]

  

Order Flavobacteriales

TAS [17, 18]

  

Family Flavobacteriaceae

TAS [3, 1921]

  

Genus Flavobacterium

TAS [13, 22]

  

Species F. seoulense

IDA

  

Strain EM1321T

IDA

 

Gram stain

Negative

IDA

 

Cell shape

Rod-shaped

IDA

 

Motility

Gliding

IDA

 

Sporulation

Non-sporulating

IDA

 

Temperature range

4–35°C

IDA

 

Optimum temperature

30°C

IDA

MIGS-6

Habitat

Freshwater

IDA

MIGS-6.3

Salinity

0–4%

IDA

MIGS-22

Oxygen requirement

Aerobic

IDA

 

Carbon source

d-glucose, l-arabinose

IDA

MIGS-15

Biotic relationship

Free-living

IDA

MIGS-14

Pathogenicity

Non-pathogenic

NAS

MIGS-4

Geographic location

Seoul, South Korea

IDA

MIGS-5

Sample collection time

September 2013

IDA

MIGS-4.1

Latitude

37°36′52′′N

IDA

MIGS-4.2

Longitude

126°59′19′′E

IDA

 

Isolation

Stream water

IDA

Evidence codes - IDA: Inferred from Direct Assay; TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [23]. If the evidence is IDA, the property was directly observed by one of the authors.

Figure 1

Phylogenetic tree highlighting the position of Flavobacterium seoulense EM 1321 T relative to the type strains of other species within the genus Flavobacterium . The strains and their corresponding GenBank accession numbers of 16S rRNA genes are indicated in parentheses. The sequences were aligned using jPHYDIT and the phylogenetic inferences were obtained using neighbour-joining method with MEGA version 5 [13]. The numbers at nodes are the percentage of bootstrap values obtained by 1,000 replicates. Solid circles indicate that the corresponding nodes were also recovered in maximum-likelihood tree. Bar, 0.01 substitutions per nucleotide position.

Strain EM1321T was Gram-reaction negative. Cells of strain EM1321T were rod shaped with rounded ends and motile by gliding. The cells were 1.0–1.5 μm × 0.3–0.5 μm in size (Figure 2). No flagellum was observed. The colonies were yellow in color and translucent on R2A agar medium. Growth occurred aerobically at 4–35°C, and optimal growth was observed at 30°C. The cells grew in 0–4% (w/v) NaCl. Strain EM1321T exhibited catalase and oxidase activities. Physiological and biochemical properties were tested by using the API 20NE, API 50CH, and API ZYM systems (BioMérieux). In the API ZYM system, enzyme activity was detected for alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, acid phosphatase, naphthol-AS-BI-phosphohydrolase, β-galactosidase, and valine arylamidase (Table 2). No activity was detected for lipase, trypsin, α-chymotrypsin, α-galactosidase, β-glucuronidase, α-glucosidase, N-acetyl-β-glucosaminidase, cystine arylamidase, α-mannosidase, and α-fucosidase. In the API 20NE system, positive reactions were observed for nitrate reduction and negative reactions were observed for indole production, glucose fermentation, arginine dihydrolase, urease activity, and aesculin and gelatin hydrolysis. The strain assimilated d-glucose and l-arabinose, but not d-mannitol, d-mannose, d-maltose, potassium gluconate, N-acetylglucosamine, capric acid, adipic acid, malic acid, trisodium citrate, or phenylacetic acid. Acid was produced from l-arabinose, d-xylose, d-galactose, d-glucose, d-fructose, d-mannose, and d-lactose (API 50CH).
Figure 2

Transmission electron micrograph of Flavobacterium seoulense EM1321 T . Scale bar, 200 nm.

Table 2

Phenotypic characteristics of Flavobacterium seoulense EM1321 T and phylogenetically related Flavobacterium species

Characteristic

F. seoulense EM1321 T

F. soli KACC 17417 T

F. nitratireducens JCM 17678 T

Cell length (μm)

1.0–1.5

1.0–3.0a

1.0–1.5b

Oxygen requirement

Aerobic

Aerobica

Aerobicb

Gram stain

-

-a

-b

Salt requirement

0–4%

0–2%a

0–1%b

Motility

+

+a

-b

Spore formation

-

-

-

Production of

   

Alkaline phosphatase

+

+

+

Acid phosphatase

+

+

+

Catalase

+

+

+

Oxidase

+

+

+

Nitrate reductase

+

-

+

Urease

-

-

+

α-Galactosidase

-

-

+

β-Galactosidase

+

-

-

β-Glucuronidase

-

-

-

α-Glucosidase

-

-

+

β-Glucosidase

-

+*

-

N-Acetyl-β-glucosaminidase

-

-

+

Indole

-

-

-

Esterase

+

+

+

Esterase lipase

+

+

+

Naphthol-AS-BI-phosphohydrolase

+

+

+

Leucine arylamidase

+

+

+

Cystine arylamidase

-

-

+

Valine arylamidase

+

+*

+

Utilization of

   

d-glucose

+

-*

+

l-arabinose

+

-*

-

d-mannose

-

-*

+

d-mannitol

-

-

-

d-maltose

-

-*

+

G + C content (mol%)

33.25

36.9a

36.3b

Habitat

Freshwater

Soila

Seawaterb

+: positive result, -: negative result.

aData from Yoon et al. [5].

bData from Nupur et al. [8].

*Data incongruent with a previous study [5].

Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) MS protein analysis was carried out as previously described [24]. Deposits were done from 12 isolated colonies for each strain (strain EM1321T and reference strains). Measurements were made with a Microflex spectrometer (Bruker Daltonics, Leipzig, Germany). Spectra were recorded in the positive linear mode for the mass range of 2,000 to 20,000 Da (parameter settings: ion source 1 (IS1), 20 kV; IS2, 18.5 kV; lens, 7 kV). The time of acquisition was between 30 seconds and 1 minute per spot. The twelve EM1321T spectra were imported into the MALDI BioTyper software (version 2.0; Bruker) and analyzed by standard pattern matching (with default parameter settings) against 4,613 bacterial spectra including eight Flavobacterium species, used as reference data, in the BioTyper database. For strain EM1321T spectrum (Figure 3), no significant score was obtained, suggesting that our isolate was not a member of the eight known species in the database. Spectrum differences with the two closely related Flavobacterium species are shown in Figure 4.
Figure 3

Reference mass spectrum from Flavobacterium seoulense EM1321 T . Spectra from 12 individual colonies were compared and a reference spectrum was generated.

Figure 4

Gel view comparing the Flavobacterium seoulense EM1321 T spectrum with those of other members in the genus Flavobacterium . The gel view displays the raw spectra of all loaded spectrum files arranged in a pseudo-gel-like look. The x-axis records the m/z value. Peak intensity is shown as a gray-scale scheme code. The color bar and the right y-axis indicate the relation between the color of a peak and peak intensity in arbitrary units.

Genome sequencing information

Genome project history

Flavobacterium seoulense EM1321T was selected for genome sequencing based on its phylogenetic position and its 16S rRNA similarity to other members of the genus Flavobacterium. The genome sequence was deposited in GenBank under accession number JNCA00000000.1. A summary of the project and the Minimum Information about a Genome Sequence (MIGS) [14] are shown in Table 3.
Table 3

Genome sequencing project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

High-quality draft

MIGS-28

Libraries used

One paired-end Illumina library

MIGS-29

Sequencing platforms

Illumina MiSeq

MIGS-31.2

Fold coverage

166×

MIGS-30

Assemblers

CLCbio CLC Genomics Workbench, version 6.5.1

MIGS-32

Gene calling method

Glimmer 3.0

 

Genbank ID

JNCA00000000.1

 

Genbank Date of Release

2014/05/27

 

BIOPROJECT

PRJNA248341

 

Project relevance

Environmental, Biotechnological

MIGS-13

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.

Genome annotation

The genes in the assembled genome were predicted with Rapid Annotation using Subsystem Technology (RAST) server databases [25] and the gene-caller GLIMMER 3.02 [26]. The predicted ORFs were annotated by searching clusters of orthologous groups (COGs) [11] using the SEED database [27]. RNAmmer 1.2 [28] and tRNAscan-SE 1.23 [29] were used to identify rRNA genes and tRNA genes, respectively. CRISPR repeats were examined using CRISPR recognition tool (CRT) [30]. CLgenomics™ 1.06 (ChunLab) was used to visualize the genomic features.

Genome properties

The genome comprised a circular chromosome with a length of 3,792,640 bp and 33.25% G + C content (Figure 5 and Table 4). It is composed of 56 contigs. Of the 3,282 predicted genes, 3,230 were protein-coding genes and 52 were RNA genes (2 rRNA genes and 50 tRNA genes). The sequencing coverage of rRNA operon (673×) indicated that 4 copies of rRNA operons are exist in this genome. The majority of the protein-coding genes (2,054 genes, 62.58%) were assigned putative functions, while the remaining genes were annotated as hypothetical proteins (1,176 genes, 35.83%). The properties of and statistics for the genome are summarized in Table 4. The distribution of genes into COG functional categories is presented in Table 5 and Figure 5.
Figure 5

Graphical circular map of the genome. Starting from the outmost circle and moving inwards, each ring of the circle contains information on a genome: rRNA/tRNA, genes on the reverse strand (colored according to the COG categories), genes on the forward strand (colored according to the COG categories), GC skew, and GC ratio.

Table 4

Genome statistics

Attribute

Value

% of total a

Genome size (bp)

3,792,640

100

DNA coding region (bp)

3,386,688

89.30

G + C content (bp)

1,261,070

33.25

Total genes

3,282

100

RNA genes

52

1.58

rRNA operons

4

-

Protein-coding genes

3,230

98.42

Pseudo genes

45

1.37

Genes with function prediction

2,054

62.58

Genes assigned to COGs

2,281

69.50

Genes assigned Pfam domains

1,997

60.85

Genes with signal peptides

119

3.63

Genes with transmembrane helices

682

20.78

CRISPR repeats

0

-

aThe total is based on either the size of the genome in base pairs or the total number of protein-coding genes in the annotated genome.

Table 5

Number of genes associated with the 25 general COG functional categories

Code

Value

% a

Description

J

157

4.86

Translation

A

1

0.03

RNA processing and modification

K

148

4.58

Transcription

L

123

3.81

Replication, recombination, and repair

B

0

0.00

Chromatin structure and dynamics

D

23

0.71

Cell cycle control, mitosis, and meiosis

Y

0

0.00

Nuclear structure

V

40

1.24

Defense mechanisms

T

121

3.75

Signal transduction mechanisms

M

220

6.81

Cell wall/membrane biogenesis

N

18

0.56

Cell motility

Z

0

0.00

Cytoskeleton

W

0

0.00

Extracellular structures

U

45

1.39

Intracellular trafficking and secretion

O

81

2.51

Posttranslational modification, protein turnover, and chaperones

C

122

3.78

Energy production and conversion

G

207

6.41

Carbohydrate transport and metabolism

E

170

5.26

Amino acid transport and metabolism

F

62

1.92

Nucleotide transport and metabolism

H

127

3.93

Coenzyme transport and metabolism

I

93

2.88

Lipid transport and metabolism

P

170

5.26

Inorganic ion transport and metabolism

Q

42

1.30

Secondary metabolites biosynthesis, transport, and catabolism

R

318

9.85

General function prediction only

S

196

6.07

Function unknown

-

949

29.38

Not in COGs

aThe total is based on the total number of protein coding genes in the annotated genome.

Conclusions

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.

Declarations

Acknowledgements

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.

Authors’ Affiliations

(1)
Department of Public Health Sciences, BK21PLUS Program in Embodiment: Health-Society Interaction, Graduate School, Korea University
(2)
School of Biosystem and Biomedical Science, Korea University
(3)
Chunlab, Inc
(4)
Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine
(5)
Korea University Guro Hospital, Korea University

References

  1. Bergey DH, Harrison FC, Breed RS WHB, Huntoon FM: Bergey’s Manual of Determinative Bacteriology, Volume 4. 1st edition. Baltimore: The Williams and Wilkins Co; 1923:1–442.Google Scholar
  2. Skerman VBD, Mcgowan V, Sneath PHA: Approved lists of bacterial names. Int J Syst Bacteriol 1980, 30: 225–420. 10.1099/00207713-30-1-225View ArticleGoogle Scholar
  3. Bernardet JF, Segers P, Vancanneyt M, Berthe F, Kersters K, Vandamme P: Cutting a gordian knot: Emended classification and description of the genus Flavobacterium , emended description of the family Flavobacteriaceae , and proposal of Flavobacterium hydatis nom nov (basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 1996, 46: 128–148. 10.1099/00207713-46-1-128View ArticleGoogle Scholar
  4. Kim BY, Weon HY, Cousin S, Yoo SH, Kwon SW, Go SJ, Stackebrandt E: Flavobacterium daejeonense sp. nov. and Flavobacterium suncheonense sp. nov., isolated from greenhouse soils in Korea. Int J Syst Evol Microbiol 2006, 56: 1645–1649. 10.1099/ijs.0.64243-0View ArticlePubMedGoogle Scholar
  5. Yoon JH, Kang SJ, Oh TK: Flavobacterium soli sp nov., isolated from soil. Int J Syst Evol Microbiol 2006, 56: 997–1000. 10.1099/ijs.0.64119-0View ArticlePubMedGoogle Scholar
  6. Tamaki H, Hanada S, Kamagata Y, Nakamura K, Nomura N, Nakano K, Matsumura M: Flavobacterium limicola sp. nov., a psychrophilic, organic-polymer-degrading bacterium isolated from freshwater sediments. Int J Syst Evol Microbiol 2003, 53: 519–526. 10.1099/ijs.0.02369-0View ArticlePubMedGoogle Scholar
  7. Kim JH, Kim KY, Cha CJ: Flavobacterium chungangense sp. nov., isolated from a freshwater lake. Int J Syst Evol Microbiol 2009, 59: 1754–1758. 10.1099/ijs.0.007955-0View ArticlePubMedGoogle Scholar
  8. Nupur Bhumika V, Srinivas TN, Kumar PA: Flavobacterium nitratireducen s sp. nov., an amylolytic bacterium of the family Flavobacteriaceae isolated from coastal surface seawater. Int J Syst Evol Microbiol 2013, 63: 2490–2496.View ArticlePubMedGoogle Scholar
  9. NamesforLife, LLC: http://doi.namesforlife.com/10.1601/tx.8071
  10. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J: Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012, 62: 716–721. 10.1099/ijs.0.038075-0View ArticlePubMedGoogle Scholar
  11. Stackebrandt E, Ebers J: Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006, 33: 152–155.Google Scholar
  12. Jeon YS, Chung H, Park S, Hur I, Lee JH, Chun J: jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences. Bioinformatics 2005, 21: 3171–3713. 10.1093/bioinformatics/bti463View ArticlePubMedGoogle Scholar
  13. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28: 2731–2739. 10.1093/molbev/msr121PubMed CentralView ArticlePubMedGoogle Scholar
  14. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, dePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glockner FO, Goldstein P, Guralnick R, Haft D, Hancock D, et al.: The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008, 26: 541–547. 10.1038/nbt1360PubMed CentralView ArticlePubMedGoogle Scholar
  15. Woese CR, Kandler O, Wheelis ML: Towards a natural system of organisms: proposal for the domains Archaea , Bacteria , and Eucarya . Proc Natl Acad Sci USA 1990, 87: 4576–4579. 10.1073/pnas.87.12.4576PubMed CentralView ArticlePubMedGoogle Scholar
  16. Krieg NR, Ludwig W, Euzéby J, Whitman WB, Phylum XIV: Bacteroidetes phyl. nov. In Bergey’s Manual of Systematic Bacteriology, Volume 4. 2nd edition. Edited by: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB. New York: Springer; 2011:25.Google Scholar
  17. Euzéby JP: Validation List No. 143. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2012, 62: 1–4.View ArticleGoogle Scholar
  18. Bernardet JF, Order I: Flavobacteriales ord. nov. In Bergey’s Manual of Systematic Bacteriology, Volume 4. 2nd edition. Edited by: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paste RBJ, Ward NL, Ludwig W, Whitman WB. New York: Springer; 2011:105.Google Scholar
  19. Bernardet JF, Family I: Flavobacteriaceae . In Bergey’s Manual of Systematic Bacteriology, Volume 4. 2nd edition. Edited by: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paste RBJ, Ward NL, Ludwig W, Whitman WB. New York: Springer; 2011:106–111.Google Scholar
  20. Bernardet JF, Nakagawa Y, Holmes B: Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002, 52: 1049–1070. 10.1099/ijs.0.02136-0PubMedGoogle Scholar
  21. List Editor: Validation List No. 41. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Bacteriol 1992, 42: 327–328.View ArticleGoogle Scholar
  22. Holmes B, Owen RJ: Proposal that Flavobacterium breve be substituted as the type species of the genus in place of Flavobacterium aquatile and emended description of the genus Flavobacterium : status of the named species of Flavobacterium. Request for an Opinion. Int J Syst Bacteriol 1979, 29: 416–426. 10.1099/00207713-29-4-416View ArticleGoogle Scholar
  23. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25: 25–29. 10.1038/75556PubMed CentralView ArticlePubMedGoogle Scholar
  24. Seng P, Drancourt M, Gouriet F, La Scola B, Fournier PE, Rolain JM, Raoult D: Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 2009, 49: 543–551. 10.1086/600885View ArticlePubMedGoogle Scholar
  25. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O: The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008, 9: 75. 10.1186/1471-2164-9-75PubMed CentralView ArticlePubMedGoogle Scholar
  26. Delcher AL, Bratke KA, Powers EC, Salzberg SL: Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007, 23: 673–679. 10.1093/bioinformatics/btm009PubMed CentralView ArticlePubMedGoogle Scholar
  27. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, et al.: The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 2005, 33: 5691–5702. 10.1093/nar/gki866PubMed CentralView ArticlePubMedGoogle Scholar
  28. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW: RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007, 35: 3100–3108. 10.1093/nar/gkm160PubMed CentralView ArticlePubMedGoogle Scholar
  29. Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25: 955–964. 10.1093/nar/25.5.0955PubMed CentralView ArticlePubMedGoogle Scholar
  30. Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P: CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 2007, 8: 209. 10.1186/1471-2105-8-209PubMed CentralView ArticlePubMedGoogle Scholar

Copyright

© Shin et al.; licensee BioMed Central. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.