Open Access

High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6T), a diphenol degrader with genes involved in the catechol pathway

  • Spyridon Ntougias
  • , Alla Lapidus
  • , James Han
  • , Konstantinos Mavromatis
  • , Amrita Pati
  • , Amy Chen
  • , Hans-Peter Klenk
  • , Tanja Woyke
  • , Constantinos Fasseas
  • , Nikos C. Kyrpides,
  • and Georgios I. Zervakis
Corresponding author

DOI: 10.4056/sigs.5088950

Received: 20 March 2014

Accepted: 20 March 2014

Published: 15 June 2014

Abstract

Olivibacter sitiensis Ntougias et al. 2007 is a member of the family Sphingobacteriaceae, phylum Bacteroidetes. Members of the genus Olivibacter are phylogenetically diverse and of significant interest. They occur in diverse habitats, such as rhizosphere and contaminated soils, viscous wastes, composts, biofilter clean-up facilities on contaminated sites and cave environments, and they are involved in the degradation of complex and toxic compounds. Here we describe the features of O. sitiensis AW-6T, together with the permanent-draft genome sequence and annotation. The organism was sequenced under the Genomic Encyclopedia for Bacteria and Archaea (GEBA) project at the DOE Joint Genome Institute and is the first genome sequence of a species within the genus Olivibacter. The genome is 5,053,571 bp long and is comprised of 110 scaffolds with an average GC content of 44.61%. Of the 4,565 genes predicted, 4,501 were protein-coding genes and 64 were RNA genes. Most protein-coding genes (68.52%) were assigned to a putative function. The identification of 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase-coding genes indicates involvement of this organism in the catechol catabolic pathway. In addition, genes encoding for β-1,4-xylanases and β-1,4-xylosidases reveal the xylanolytic action of O. sitiensis.

Keywords:

alkaline two-phase olive mill wasteBacteroidetesSphingobacteriaceaehemicellulose degradationβ-1,4-xylanaseβ-1,4-xylosidase

Introduction

The genus Olivibacter currently contains six species with validly published names, all of which are aerobic and heterotrophic, non-motile, rod-shaped Gram-negative bacteria [1-3]. Strain AW-6T (= DSM 17696T = CECT 7133T = CIP 109529T) is the type strain of Olivibacter sitiensis [1], which is the type species of the genus Olivibacter. The strain was isolated from alkaline alperujo, an olive mill sludge-like waste produced by two-phase centrifugal decanters located in the vicinity of Toplou Monastery, Sitia, Greece [1]. The genus name derived from the Latin term oliva and the Neo-Latin bacter, meaning a rod-shaped bacterium living in olives/olive processing by-products [1]. The Neo-Latin species epithet sitiensis pertains to the region Sitia (Crete, Greece) where the olive mill is operating [1]. The other species of the genus are O. soli, O. ginsengisoli, O. terrae, O. oleidegradans and O. jilunii [2-4]. O. soli and O. ginsengisoli were isolated from soil of a ginseng field [2], O. terrae from a compost prepared of cow manure and rice straw [2], O. oleidegradans from a biofilter clean-up facility in a hydrocarbon-contaminated site [3] and O. jilunii from a DDT-contaminated soil [4]. O. sitiensis can be distinguished from O. soli, O. ginsengisoli and O. terrae on the basis of temperature and NaCl concentration ranges for growth, in its ability to assimilate N-acetyl-D-glucosamine, L-histidine, maltose and sorbitol, and for expression of naphthol-AS-BI-phosphohydrolase, in the presence/absence of iso-C15: 1 F, C16: 1 2-OH, anteiso-C17: 1 B and/or iso-C17: 1 I, and in by its DNA G+C content [1,2,4]. Moreover, it differs from O. soli in terms of L-arabinose assimilation and valine arylamidase expression, from O. ginsengisoli in terms of inositol, mannitol and salicin assimilation and in oxidase reaction test, and from O. terrae in terms of L-arabinose and mannitol assimilation, and β-glucuronidase and valine arylamidase expression [1,2,4]. O. sitiensis can be differentiated from O. oleidegradans on the basis of DNA G+C content, pH upper limit for growth, in the ability for assimilation of D-adonitol, L-arabinose, N-acetyl-D-glucosamine, L-histidine, D-lyxose, maltose, melezitoze, salicin and turanose, and for expression of esterase, β-galactosidase, α-mannosidase, urease and valine arylamidase as well as in the presence/absence of some minor fatty acid components of membrane lipids, menaquinone-6 (as minor respiratory quinone) and aminophospholipids (as cellular polar lipids) [1,3,4]. In addition, O. sitiensis can be distinguished from O. jelunii on the basis of DNA G+C content, pH, temperature and NaCl concentration upper limits for growth, lactose fermentation, in the ability for assimilation of acetate, L-arabinose, N-acetyl-D-glucosamine, L-histidine, malonate, maltose, D-mannose, salicin and L-serine, and for expression of α-mannosidase, oxidase and valine arylamidase as well as in the presence/absence of some minor fatty acid components of membrane lipids, menaquinone-8 (as minor respiratory quinone) and aminophospholipids (as cellular polar lipids) [1,4]. Here we present a summary classification and a set of features for O. sitiensis AW-6T, together with the description of the permanent-draft genome sequencing and annotation.

Classification and features

The 16S rRNA gene sequence of O. sitiensis AW-6T was compared using NCBI BLAST under default settings (e.g., considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database [5] and the relative frequencies of taxa and keywords (reduced to their stem [6]) were determined and weighted by BLAST scores. The frequency of genera that belonged to the family Sphingobacteriaceae was 61.8%. The most frequently occurring genera were in order Sphingobacterium (27.7%), Pedobacter (17.1%), Flavobacterium (8.5%), Olivibacter (6.4%), Hymenobacter (6.4%), Mucilaginibacter (4.3%), Cytophaga (4.3%), Flectobacillus (4.3%), Parapedobacter (2.1%), Pseudosphingobacterium (2.1%) and ‘Hevizibacter’ (2.1%) (47 hits in total). The 16S rRNA gene sequence of O. sitiensis AW-6T was the only hit on members of the species in INSDC (=EMBL/NCBI/DDBJ) under the accession number DQ421387 (=NR_043805). Among all other species, the two yielding the highest score were Parapedobacter koreensis Jip14T (DQ680836) [7] and Olivibacter ginsengisoli Gsoil 060T (AB267716) [2], showing similarity in 16S rRNA gene of 90.1% (both of them) and HSP coverages of 99.8% and 99.9% respectively. It is noteworthy that the Greengenes database uses the INSDC (=EMBL/NCBI/DDBJ) annotation, which is not an authoritative source for nomenclature or classification. The highest-scoring environmental sequences was AM114441 ['Interactions U(VI) added natural dependence on various incubation conditions soil uranium mining waste pile clone JG35+U2A-AG9'], which showed identity of 90.3% with HSP coverage of 86.1%. The most frequently occurring keywords within the labels of all environmental samples that yielded hits were 'rumen' (23.1%), 'oil' (10.8%), 'water' (9.7%), 'soil' (9.7%), 'fluid' (9.1%) and 'gut' (9.1%) (186 hits in total). The most frequently occurring keywords within the labels of those environmental samples that yielded hits of a higher score than the highest scoring species were 'waste' (50.0%) and 'soil' (50.0%) (4 hits in total), which are keywords with biological meaning fitting the environment from which O. sitiensis AW-6T was isolated.

Figure 1 shows the phylogenetic neighborhood of O. sitiensis in the 16S rRNA gene sequence-based trees constructed. Independently from the clustering method applied, all Olivibacter species together with Pseudosphingobacterium domesticum and ‘Sphingobacterium’ sp. 21 fell into a distinct cluster, indicating the unique phylogenetic position of genus Olivibacter and the necessity for reconsidering the taxonomic status of the genus Pseudosphingobacterium. In addition, ‘Sphingobacterium’ sp. 21 should be assigned to the genus Olivibacter, and not to the genus Sphingobacterium. In the ML tree, members of the genus Parapedobacter branched together with O. sitiensis, although the unique topology of the genus was established by applying a character-based (parsimony) method. As previously stated by Ntougias et al. [1], S. antarcticum should be reassigned to the genus Pedobacter.

Figure 1

Phylogenetic trees highlighting the position of O. sitiensis relative to the type strains of the species within the family Sphingobacteriaceae. The tree was inferred from 1,288 aligned characters [8,9] of the 16S rRNA gene sequence under A) the maximum likelihood (ML) [10] and B) the maximum-parsimony criterion. In ML tree, the branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 100 ML bootstrap replicates (A) and from 1,000 maximum-parsimony bootstrap replicates (B) [11]. Lineages with strain genome sequencing projects registered in GOLD [12] are labeled with one asterisk, while those listed as 'Complete and Published' with two asterisks (e.g. Pedobacter heparinus [13] and P. saltans [14]).

Cells of O. sitiensis AW-6T are Gram-negative non-motile rods [1] with a length of 1.0-1.3 μm and a width of 0.2-0.3 μm (Table 1 and Figure 2). The temperature range for growth is 5-45°C, with an optimum at 28–32°C [1]. O. sitiensis is neutrophilic, showing no growth at 30 g L-1 NaCl [1]. The pH for growth ranges between 5 and 8, with pH values of 6-7 being the optimum [1]. O. sitiensis is strictly aerobic and chemo-organotrophic; it assimilates mostly D(+)-glucose, protocatechuate and D(+)-xylose, while L-cysteine, D(-)-fructose, D(+)-galactose, L-histidine, lactose, sorbitol and sucrose are also utilized by strain AW-6T [1]. O. sitiensis was found to be sensitive to ampicillin, bacitracin, chloramphenicol, penicillin, rifampicin, tetracycline and trimethoprim, and resistant to kanamycin, polymixin B and streptomycin (antibiotics’ concentration of 50 μg ml-1) [1].

Table 1

Classification and general features of O. sitiensis AW-6T, according to the MIGS recommendations [15].

MIGS ID

    Property

    Term

    Evidence code

    Domain Bacteria

    TAS [16]

    Phylum Bacteroidetes

    TAS [17,18]

    Class Sphingobacteriia

    TAS [18,19]

    Current classification

    Order Sphingobacteriales

    TAS [18,20]

    Family Sphingobacteriaceae

    TAS [21]

    Genus Olivibacter

    TAS [1]

    Species Olivibacter sitiensis

    TAS [1]

    Type-strain AW-6T

    TAS [1]

    Gram stain

    negative

    TAS [1]

    Cell shape

    rod

    TAS [1]

    Motility

    non-motile

    TAS [1]

    Sporulation

    non-sporulating

    TAS [1]

    Temperature range

    mesophile, 5-45°C

    TAS [1]

    Optimum temperature

    28-32°C

    TAS [1]

    Salinity

    neutrophilic and non-halotolerant -    no growth at 30 g l-1 NaCl

    TAS [1]

MIGS-22

    Oxygen requirement

    strictly aerobic

    TAS [1]

    Carbon source

    carbohydrates and amino-acids,    utilization of protocatechuate and sorbitol

    TAS [1]

    Energy metabolism

    chemo-organotroph

    TAS [1]

MIGS-6

    Habitat

    olive mill waste

    TAS [1]

MIGS-15

    Biotic relationship

    free living

    TAS [1]

MIGS-14

    Pathogenicity

    none

    NAS

    Biosafety level

    1

    TAS [22]

MIGS-23.1

    Isolation

    alkaline two-phase olive mill waste (alkaline alperujo)

    TAS [1]

MIGS-4

    Geographic location

    Toplou Monastery, Sitia, Crete, Greece

    TAS [1]

MIGS-5

    Sample collection time

    year 2003

    NAS

MIGS-4.1

    Latitude

    35.220

    TAS [1]

MIGS-4.2

    Longitude

    26.216

    TAS [1]

MIGS-4.3

    Depth

    surface

    NAS

MIGS-4.4

    Altitude

    161 m

    NAS

Evidence codes - 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 code is IDA, then the property was directly observed for a living isolate by one of the authors or an expert mentioned in the acknowledgements.

Figure 2

Electron micrograph of O. sitiensis AW-6T negatively-stained cells. Bar represents 1 μm.

Chemotaxonomy

The major polar lipids of O. sitiensis are phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PME), phosphatidylinositol mannoside (PIM), an unknown phospholipid (PL) and an unknown non-phosphorylated lipid (UL) [4]. Moreover, the main membrane fatty acids of O. sitiensis are C16: 1ω7c and/or iso-C15:0 2-OH, iso-C15:0, iso-C17:0 3-OH and C16:0 [1]. The only respiratory quinone found in O. sitiensis is menaquinone, with seven isoprene subunits (MK-7) [1].

Genome sequencing and annotation

Genome project history

This microorganism was selected for sequencing on the basis of its phylogenetic position [24,25], and is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project [26] which aims in increasing the sequencing coverage of key reference microbial genomes. The genome project is deposited in the Genomes On Line Database [12] and the genome sequence is available from GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI) using state of the art sequencing technology [27]. A summary of the project information is presented in Table 2.

Table 2

Genome sequencing project information.

MIGS ID

    Property

    Term

MIGS-31

    Finishing quality

    High-Quality Draft

MIGS-29

    Sequencing platforms

    Illumina

MIGS-31.2

    Sequencing coverage

    120×

MIGS-30

    Assemblers

    ALLPATHS v. r41043

MIGS-32

    Gene calling method

    Prodigal 2.5

    Genbank ID

    ATZA00000000

    Genbank Date of Release

    September 5, 2013

    GOLD ID

    Gi11724

    NCBI project ID

    165253

    Database: IMG

    2515154027

MIGS-13

    Source material identifier

    DSM 17696T

    Project relevance

    GEBA-KMG, Tree of Life, Biodegradation

Growth conditions and DNA isolation

O. sitiensis strain AW-6T was grown aerobically in DSMZ medium 92 (trypticase soy yeast extract medium) [28] at 28°C. DNA was isolated from 0.5-1 g of cell paste using Jetflex Genomic DNA purification kit (Genomed_600100) following the standard protocol as recommended by the manufacturer but applying a modified cell lysis procedure (1 hour incubation at 58°C with additional 50 µl proteinase K followed by overnight incubation on ice with additional 200 µl PPT-buffer). DNA is available via the DNA Bank Network [29].

Genome sequencing and assembly

The draft genome of Olivibacter sitiensis DSM 17696 was generated at the DOE Joint genome Institute (JGI) using the Illumina technology. An Illumina Standard shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform, which generated 13,155,872 reads totaling 1,973.4 Mbp. All general aspects of library construction and sequencing performed at the JGI can be found at the JGI website [30]. All raw Illumina sequence data were passed through DUK, a filtering program developed at JGI, which removes known Illumina sequencing and library preparation artifacts (Mingkun L, unpublished). The following steps were then performed for assembly: (i) filtered Illumina reads were assembled using Velvet (version 1.1.04) [31], (ii) 1–3 Kbp simulated paired end reads were created from Velvet contigs using wgsim [32] (iii) Illumina reads were assembled with simulated read pairs using Allpaths–LG (version r41043) [33]. The final draft assembly contained 110 contigs in 110 scaffolds. The total size of the genome is 5.1 Mbp and the final assembly is based on 605.8 Mbp of Illumina data, which provides an average 120.0× coverage of the genome.

Genome annotation

Genes were identified using Prodigal [34] as part of the DOE-JGI Annotation pipeline [35]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes (IMG-ER) [36].

Genome properties

The genome is 5,053,571 bp long and comprises 110 scaffolds with an average GC content of 44.61% (Table 3). Of the 4,565 genes predicted, 4,501 were protein-coding genes and 64 RNA genes. Most protein-coding genes (68.52%) were assigned to a putative function, while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.

Table 3

Genome statistics.

Attribute

     Value

     % of Totala

Genome size (bp)

     5,053,571

     100.00%

DNA coding region (bp)

     4,534,282

     89.72%

DNA G+C content (bp)

     2,254,441

     44.61%

DNA scaffolds

     110

Total genes

     4,565

RNA genes

     64

     1.40%

tRNA genes

     47

     1.03%

Protein-coding genes

     4,501

     98.60%

Genes with function prediction (proteins)

     3,128

     68.52%

Genes in paralog clusters

     1,777

     38.93%

Genes assigned to COGs

     3,062

     67.08%

Genes assigned Pfam domains

     3,471

     76.04%

Genes with signal peptides

     501

     10.97%

Genes with transmembrane helices

     1,124

     24.62%

CRISPR repeats

     0

a The 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 4

Number of genes associated with the general COG functional categories.

Code

   Value

    %age

     Description

J

   159

    4.7

     Translation, ribosomal structure and biogenesis

A

   1

    0.0

     RNA processing and modification

K

   283

    8.4

     Transcription

L

   190

    5.7

     Replication, recombination and repair

B

   1

    0.0

     Chromatin structure and dynamics

D

   22

    0.6

     Cell cycle control, cell division, chromosome partitioning

Y

   0

    0.0

     Nuclear structure

V

   99

    2.9

     Defense mechanisms

T

   197

    5.9

     Signal transduction mechanisms

M

   274

    8.1

     Cell wall/membrane biogenesis

N

   7

    0.2

     Cell motility

Z

   0

    0.0

     Cytoskeleton

W

   0

    0.0

     Extracellular structures

U

   63

    1.9

     Intracellular trafficking and secretion, and vesicular transport

O

   120

    3.6

     Posttranslational modification, protein turnover, chaperones

C

   168

    5.0

     Energy production and conversion

G

   259

    7.7

     Carbohydrate transport and metabolism

E

   211

    6.3

     Amino acid transport and metabolism

F

   61

    1.8

     Nucleotide transport and metabolism

H

   148

    4.4

     Coenzyme transport and metabolism

I

   107

    3.2

     Lipid transport and metabolism

P

   238

    7.1

     Inorganic ion transport and metabolism

Q

   52

    1.5

     Secondary metabolites biosynthesis, transport and catabolism

R

   419

    12.5

     General function prediction only

S

   280

    8.3

     Function unknown

-

   1,503

    32.9

     Not in COGs

Based on genomic analysis of the metabolic features, O. sitiensis is an auxotroph for L-alanine, L-arginine, L-histidine, L-isoleucine, L-leucine, L-lysine, L-phenylalanine, L-proline, L-serine, L-tyrosine, L-tryptophan and L-valine, and a prototroph for L-aspartate, L-glutamate and glycine. Selenocysteine and biotin cannot be synthesized by O. sitiensis. Strain AW-6T can utilize L-arabinose and maltose (via orthophosphate activation), whereas no maltose hydrolysis is achieved [1].

Genome analysis revealed the genetic and molecular bases of the degradation of recalcitrant compounds by O. sitiensis. The ability of O. sitiensis to degrade phenolic compounds is verified by the distribution of genes encoding oxidoreductases that act on diphenols and related substances and by the 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase-coding genes that are involved in the catechol pathway. Genes encoding β-1,4-xylanases and β-1,4-xylosidases were also identified in the genome of strain AW-6T, indicating that O. sitiensis is a xylanolytic bacterium involved in the cleavage of β-1,4-xylosic bonds in hemicelluloses. The existence of protocatechuate 3,4-dioxygenase (dioxygenase_C)-coding genes are indicative of the ability of this bacterium to degrade benzoate and 2,4-dichlorobenzoate. Genes encoding carboxymethylenebutenolidase were distributed in the genome of O. sitiensis, indicating its potential for hexachlorocyclohexane and 1,4-dichlorobenzene degradation. Oxidoreductases related to aryl-alcohol dehydrogenases were predicted, showing that O. sitiensis may be also involved in biphenyl and toluene/xylene degradation. This is also strengthened by the identification of an uncharacterized protein, possibly involved in aromatic compounds catabolism. Moreover, putative multicopper oxidases with possible laccase-like activity were identified. Mercuric reductase- and arsenate reductase-coding genes as well as organic solvent tolerance and chromate transport proteins encoded in the genome indicate possible resistance of O. sitiensis to the presence of heavy metals and organic solvents.

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Brian J. Tindall and his team for growing O. sitiensis cultures, and Evelyne-Marie Brambilla for DNA extraction and quality control (all at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, as well as German Research Foundation (DFG) INST 599/1-2.


This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

References

  1. Ntougias S, Fasseas C and Zervakis GI. Olivibacter sitiensis gen. nov., sp. nov., isolated from alkaline olive-oil mill wastes in the region of Sitia, Crete. Int J Syst Evol Microbiol. 2007; 57:398-404 View ArticlePubMed
  2. Wang L, Ten LN, Lee HG, Im WT and Lee ST. Olivibacter soli sp. nov., Olivibacter ginsengisoli sp. nov. and Olivibacter terrae sp. nov., from soil of a ginseng field and compost in South Korea. Int J Syst Evol Microbiol. 2008; 58:1123-1127 View ArticlePubMed
  3. Szabó I, Szoboszlay S, Kriszt B, Háhn J, Harkai P, Baka E, Táncsics A, Kaszab E, Privler Z and Kukolya J. Olivibacter oleidegradans sp. nov., a hydrocarbon degrading bacterium isolated from a biofilter cleanup facility on a hydrocarbon-contaminated site. Int J Syst Evol Microbiol. 2011; 61:2861-2865 View ArticlePubMed
  4. Chen K, Tang SK, Wang GL, Nie GX, Li QF, Zhang JD, Li WJ and Li SP. Olivibacter jilunii sp. nov., isolated from a DDT-contaminated soil. Int J Syst Evol Microbiol. 2013; 63:1083-1088 View ArticlePubMed
  5. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P and Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006; 72:5069-5072 View ArticlePubMed
  6. Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems 1980; 14:130-137.
  7. Kim MK, Na JR, Cho DH, Soung NK and Yang DC. Parapedobacter koreensis gen. nov., sp. nov. Int J Syst Evol Microbiol. 2007; 57:1336-1341 View ArticlePubMed
  8. Lee C, Grasso C and Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics. 2002; 18:452-464 View ArticlePubMed
  9. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000; 17:540-552 View ArticlePubMed
  10. Stamatakis A, Hoover P and Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol. 2008; 57:758-771 View ArticlePubMed
  11. Gouy M, Guindon S and Gascuel O. SeaView Version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol. 2010; 27:221-224 View ArticlePubMed
  12. Pagani I, Liolios K, Jansson J, Chen IMA, Smirnova T, Nosrat B, Markowitz VM and Kyrpides NC. The Genomes OnLine Database (GOLD) v.4: Status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2012; 40:D571-D579 View ArticlePubMed
  13. Han C, Spring S, Lapidus A, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Lucas S, Chen F and Nolan M. Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3T). Stand Genomic Sci. 2009; 1:54-62 View ArticlePubMed
  14. Liolios K, Sikorski J, Lu M, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF and Tapia R. Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113T). Stand Genomic Sci. 2011; 5:30-40 View ArticlePubMed
  15. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ and Angiuoli SV. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008; 26:541-547 View ArticlePubMed
  16. Woese CR, Kandler O and 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 View ArticlePubMed
  17. Krieg NR, Ludwig W, Euzeby J, Whitman WB. Phlum XIV. Bacteroidetes phyl. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 4, Springer-Verlag, New York, 2011, p. 25.
  18. Editor L. Validation List No. 143. Int J Syst Evol Microbiol. 2012; 62:1-4
  19. Kampfer P. Class III. Sphingobacteriia class. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 4, Springer-Verlag, New York, 2011, p. 330.
  20. Kampfer P. Order I. Sphingobacteriales ord. nov. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 4, Springer-Verlag, New York, 2011, p. 330.
  21. Steyn PL, Segers P, Vancanneyt M, Sandra P, Kersters K and Joubert JJ. Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol. 1998; 48:165-177 View ArticlePubMed
  22. Bundesanstalt für Arbeitsschutz und Arbeitsmedizin (BAuA), Classification of prokaryotes (bacteria and archaea) into risk groups. Technical Rule for Biological Agents 466 (TRBA 466), Germany, 2010, p. 157.
  23. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS and Eppig JT. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25:25-29 View ArticlePubMed
  24. Klenk HP and Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol. 2010; 33:175-182 View ArticlePubMed
  25. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M and Tindall BJ. A phylogeny-driven Genomic Encyclopaedia of Bacteria and Archaea. Nature. 2009; 462:1056-1060 View ArticlePubMed
  26. Kyrpides NC, Woyke T, Eisen JA, Garrity G, Lilburn TG, Beck BJ, Whitman WB, Hugenholz P and Klenk HP. Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project. Stand Genomic Sci. 2013; 9:628-634; .View Article
  27. Mavromatis K, Land ML, Brettin TS, Quest DJ, Copeland A, Clum A, Goodwin L, Woyke T, Lapidus A and Klenk HP. The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation. PLoS ONE. 2012; 7:e48837 View ArticlePubMed
  28. List of growth media used at DSMZ. Web Site
  29. Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch A, Berendsohn WG and Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreserv Biobank. 2011; 9:51-55 View ArticlePubMed
  30. . Web Site
  31. Zerbino DR and Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008; 18:821-829 View ArticlePubMed
  32. wgsim. Web Site
  33. Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP and Sykes S. High–quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci USA. 2011; 108:1513-1518 View ArticlePubMed
  34. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW and Hauser LJ. Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010; 11:119 View ArticlePubMed
  35. Mavromatis K, Ivanova NN, Chen IM, Szeto E, Markowitz VM and Kyrpides NC. The DOE-JGI Standard operating procedure for the annotations of microbial genomes. Stand Genomic Sci. 2009; 1:63-67 View ArticlePubMed
  36. Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K and Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009; 25:2271-2278 View ArticlePubMed