Open Access

Complete genome sequence of Olsenella uli type strain (VPI D76D-27CT)

  • Markus Göker1,
  • Brittany Held3,
  • Susan Lucas2,
  • Matt Nolan2,
  • Montri Yasawong6,
  • Tijana Glavina Del Rio2,
  • Hope Tice2,
  • Jan-Fang Cheng2,
  • David Bruce2, 3,
  • John C. Detter3,
  • Roxanne Tapia3,
  • Cliff Han3,
  • Lynne Goodwin3,
  • Sam Pitluck2,
  • Konstantinos Liolios2,
  • Natalia Ivanova2,
  • Konstantinos Mavromatis2,
  • Natalia Mikhailova2,
  • Amrita Pati2,
  • Amy Chen4,
  • Krishna Palaniappan4,
  • Miriam Land2, 5,
  • Loren Hauser2, 5,
  • Yun-Juan Chang2, 5,
  • Cynthia D. Jeffries2, 5,
  • Manfred Rohde6,
  • Johannes Sikorski1,
  • Rüdiger Pukall1,
  • Tanja Woyke2,
  • James Bristow2,
  • Jonathan A. Eisen2, 7,
  • Victor Markowitz4,
  • Philip Hugenholtz2,
  • Nikos C. Kyrpides2,
  • Hans-Peter Klenk1 and
  • Alla Lapidus2
Standards in Genomic Sciences20103:3010076

DOI: 10.4056/sigs.1082860

Published: 30 August 2010

Abstract

Olsenella uli (Olsen et al. 1991) Dewhirst et al. 2001 is the type species of the genus Olsenella, which belongs to the actinobacterial family Coriobacteriaceae. The species is of interest because it is frequently isolated from dental plaque in periodontitis patients and can cause primary endodontic infection. The species is a Gram-positive, non-motile and non-sporulating bacterium. The strain described in this study was isolated from human gingival crevices. This is the first completed sequence of the genus Olsenella and the fifth sequence from a member of the family Coriobacteriaceae. The 2,051,896 bp long genome with its 1,795 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords

microaerotolerant anaerobe human gingival crevices primary endodontic infections Coriobacteriaceae GEBA

Introduction

Strain VPI D76D-27CT (= DSM 7084 = ATCC 49627 = JCM 12494) is the type strain of the species Olsenella uli, which is the type species of the genus Olsenella [1]. Currently, Olsenella is one out of thirteen genera in the family Coriobacteriaceae [24]. This strain was first described in 1991 by Olsen as ‘Lactobacillus uli’ [1]. Based on 16S rRNA gene sequence divergence and the presence of unique phenotypic characters, the strain was transferred to the new genus Olsenella as O. uli. A second novel species, O. profusa was also described [5]. More recently, a third species, ‘O. umbonata’, was described but is not yet validly published [6].The genus is named in honor of Ingar Olsen, a contemporary Norwegian microbiologist, who first described ‘L. uli’. The species epithet ‘uli’ means ‘of the gum’. Periradicular diseases are arguably among the most common human inflammatory diseases [7], which are often the result of microbial infection of the root canal [8]. Olsenella species, particularly O. uli, are common members of the microbiota associated with primary endodontic infection. O. uli has been found to predominate over other Gram-positive rods, (e.g., Atopobium parvulum) [9] in root canal samples taken after chemomechanical preparation and intracanal medication, suggesting that this species can resist intracanal disinfection measures and thus may be involved in persistent infections [10,11]. Here we present a summary classification and a set of features for O. uli VPI D76D-27CT, together with the description of the complete genomic sequencing and annotation.

Classification and features

Strains from the genus Olsenella are found in human oral cavity and likely in bovine rumen [1]. Strain VPI D76D-27CT was isolated from either human gingival crevices or periodontal pockets [1]. The 16S rRNA gene sequence of VPI D76D-27CT is 97% identical to the cultivable strains N13-17 (AY880046) and S13-10 (AY880047). These strains were isolated from a 63-year old male patient with oral squamous-cell carcinoma [12]. Two other uncultured clone sequences with 100% 16S rRNA gene sequence identity to strain VPI D76D-27CT were reported at the Genbank database (status July 2010) [13]. These were clone OPEN_ROOT_17 (FJ982973), isolated from human root canal, and clone BS34 (AY244985) from cow rumen. The 16S rRNA gene of strain VPI D76D-27CT shares 96.7-96.8% sequence identity with the sequences of the type strains from the other members of the genus Olsenella [14], whereas the other type strains from the family Coriobacteriaceae share 87.3 to 96.7% sequence identity [14]. No phylotypes from environmental screenings or genomic surveys could be linked to the species O. uli or to the genus Olsenella, indicating a rather rare occurrence of these in the habitats screened thus far (as of July 2010).

The cells of strain VPI D76D-27CT are nonmotile (Table 1), Gram-positive rods that occur singly, in pairs, and in short chains (Figure 1) [1]. The central part of the cell may swell; particularly when grown on solid medium. Strain VPI D76D-27CT is microaerotolerant to anaerobic [6] with an optimal growth temperature is 37°C [1]. Colonies on brain heart blood agar are one to two mm in diameter, raised or low convex, entire, and translucent to transparent after five days of anaerobic incubation at 37°C [1]. The cells are unable to grow on media with 6.5% w/v of NaCl. Growth is stimulated by Tween 80 (0.02% v/v). Strain VPI D76D-27CT is able to ferment glycogen, trehalose and starch. Fermentation products from glucose are lactic, acetic, formic and occasionally trace amounts of succinic acid. Lactic acid is a major product of the strain VPI D76D-27CT [1], a feature which was suspected to be important in inflammatory processes of endodontic infections [1,19]. There is little or no gas detected in agar deeps during cell growth. Hydrogen and indole are not produced. Reactions are negative for bile-esculin, DNase and hippurate hydrolysis. This strain does not ferment amygdalin, erythriol, esculin, glycerol, inositol, mannitol, melezitose, melibiose, raffinose, rhamnose, sorbitol and xylose. Acid is produced from fructose, glucose, maltose, mannose, salicin, and sucrose [1]. Strain VPI D76D-27CT does not liquefy gelatin, does not digest meat, does not produce indole, and does not reduce nitrate [1]. It is negative for bile-esculin, DNase, hippurate hydrolysis and catalase activity. However, strain VPI D76D-27CT hydrolyses esculin and produces ammonia from arginine [1].
Figure 1.

Scanning electron micrograph of O. uli VPI D76D-27CT

Table 1.

Classification and general features of O. uli VPI D76D-27CT according to the MIGS recommendations [15].

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [16]

 

Phylum Actinobacteria

TAS [17]

 

Class Actinobacteria

TAS [3,4]

 

Subclass Coriobacteridae

TAS [3,4]

 

Order Coriobacteriales

TAS [3,4]

 

Suborder Coriobacterineae

TAS [3,18]

 

Family Coriobacteriaceae

TAS [3,4]

 

Genus Olsenella

TAS [1,5]

 

Type strain VPI D76D-27C

TAS [1,5]

 

Gram stain

positive

TAS [1]

 

Cell shape

small-elliptical rod that occur singly, in pairs or short chains

TAS [1]

 

Motility

none

TAS [1]

 

Sporulation

none

TAS [1]

 

Temperature range

37°C–45°C

NAS

 

Optimum temperature

37°C

NAS

 

Salinity

< 6.5% NaCl

TAS [1]

MIGS-22

Oxygen requirement

microaerotolerant anaerobic

TAS [6]

 

Carbon source

glucose

TAS [1]

 

Energy source

chemoorganotroph

TAS [1]

MIGS-6

Habitat

human gingival crevices

TAS [1,5]

MIGS-15

Biotic relationship

free-living

NAS

MIGS-14

Pathogenicity

primary endodontic infections

TAS [11,19,20]

 

Biosafety level

2

TAS [21]

 

Isolation

plaque from human gingival crevices

TAS [1]

MIGS-4

Geographic location

not reported

 

MIGS-5

Sample collection time

1987 or before

TAS [1,5]

MIGS-4.1

Latitude

not reported

 

MIGS-4.2

Longitude

not reported

 

MIGS-4.3

Depth

not reported

 

MIGS-4.4

Altitude

not reported

 

Evidence codes - IDA: Inferred from Direct Assay (first time in publication); 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 of the Gene Ontology project [22]. If the evidence code is IDA, then the property was directly observed by one of the authors or an expert mentioned in the acknowledgements.

Chemotaxonomy

Strain VPI D76D-27CT possesses a peptidoglycan type of A4ß based on L-Orn-D-Asp [23]. The major cellular fatty acids of strain VPI D76D-27CT (FAME: fatty acid methyl ester; DMA: dimethylacetyl), when grown in peptone-yeast extract-glucose-Tween 80 broth, are C18:1 cis9 (32.1%, FAME), C18:1 (19.9%, DMA), C10:0 (10.1%, FAME), C17:1 cis8 (6.9%, FAME), C18:1 c11/t9/t6 (5.3%, FAME), C16:1 cis9 (4.8%, FAME), C16:0 (4.0%, DMA), C18:1 cis11 (3.6%, DMA), C14:0 (3.1%, FAME), C16:0 (2.8%, FAME) and C12:0 (2.6%, FAME) [1]. More recent data show a somewhat different fatty acid pattern, which is characterized by a large proportion of unbranched fatty acids (C18:0, 31–50%) and a quite large proportion of polyunsaturated fatty acids (C18:2 cis-9, cis-12; 5.6–8.4%). Presumably, this difference may be attributed to the different growth medium, which is described to be M2 liquid medium containing clarified rumen fluid [6].

Figure 2 shows the phylogenetic neighborhood of O. uli VPI D76D-27CT in a 16S rRNA based tree. The sequence of the unique 16S rRNA gene is identical with the previously published sequence generated from ATCC 49627 (AF292373).
Figure 2.

Phylogenetic tree highlighting the position of O. uli VPI D76D-27CT relative to the type strains within the genus and the type strains of the other genera within the family Coriobacteriaceae. The trees were inferred from 1,408 aligned characters [24,25] of the 16S rRNA gene sequence under the maximum likelihood criterion [26] and as far as possible (note: Olsenella is paraphyletic in this tree) rooted in accordance with the current taxonomy [27]. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 250 bootstrap replicates [28] if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [29] are shown in blue, published genomes in bold [30,31]. Adding the 16S rRNA sequence of the type strain of the not yet validly published species ‘Olsenella umbonata’ (FN178463) to the tree (data not shown) did not change the overall arrangement; ‘O. umbonata’ appeared within the grade between O. uli and O. profusa.

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [32], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [33]. The genome project is deposited in the Genome OnLine Database [29] and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2.
Table 2.

Genome sequencing project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

Finished

MIGS-28

Libraries used

Three genomic libraries: one 454 standard and one 454 10 kb pyrosequence library; one Illumina library

MIGS-29

Sequencing platforms

454 GS Titanium, Illumina GAii

MIGS-31.2

Sequencing coverage

90.5× pyrosequence, 211.8× Illumina

MIGS-30

Assemblers

Newbler version 2.0.1-PreRelease-03-30-2009-gcc-3.4.6-threads, phrap, Velvet

MIGS-32

Gene calling method

Prodigal 1.4, GenePRIMP

 

INSDC ID

CP002106

 

Genbank Date of Release

August 6, 2010

 

GOLD ID

Gc01331

 

NCBI project ID

36641

 

Database: IMG-GEBA

2502422319

MIGS-13

Source material identifier

DSM 7084

 

Project relevance

Tree of Life, GEBA

Growth conditions and DNA isolation

O. uli VPI D76D-27CT, DSM 3776, was grown in medium 104 (PYG modified medium) [34] at 37°C under strictly anaerobic conditions. DNA was isolated from 0.5–1 g of cell paste using MasterPure Gram Positive DNA Purification Kit (Epicentre MGP04100) following the standard protocol as recommended by the manufacturer, with modification st/LALM for cell lysis as described in [33].

Genome sequencing and assembly

The genome of O. uli was sequenced using a combination of Illumina and 454 technologies. An Illumina GAii shotgun library with reads of 434,617,748 bp, a 454 Titanium draft library with average read length of 302 +/− 162.3 bp bases, and a paired end 454 library with average insert size of 9.273 +/− 2.318 kb were generated. All general aspects of library construction and sequencing can be found at http://www.jgi.doe.gov/. Illumina sequencing data was assembled with VELVET, and the consensus sequences were shredded into 1.5 kb overlapped fake reads and assembled together with the 454 data. Draft assemblies were based on 2.0 Mb 454 draft data, and 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20. The initial Newbler assembly contained 149 contigs in 1 scaffold. We converted the initial 454 assembly into a phrap assembly by making fake reads from the consensus, collecting the read pairs in the 454 paired end library. The Phred/Phrap/Consed software package (www.phrap.com) was used for sequence assembly and quality assessment [35] in the following finishing process. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with gapResolution (http://www.jgi.doe.gov/), Dupfinisher [35], or sequencing cloned bridging PCR fragments with subcloning or transposon bombing (Epicentre Biotechnologies, Madison, WI). Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F. Chang, unpublished). A total of 394 additional Sanger reactions were necessary to close gaps and to raise the quality of the finished sequence. Illumina reads were also used to improve the final consensus quality using an in-house developed tool (the Polisher [36],). The error rate of the final genome sequence is less than 1 in 100,000.

Genome annotation

Genes were identified using Prodigal [37] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [38]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes - Expert Review (IMG-ER) platform [39].

Genome properties

The genome consists of a 2,051,896 bp long chromosome with a 64.7% GC content (Table 3 and Figure 3). Of the 1,850 genes predicted, 1,795 were protein-coding genes, and 55 RNAs; fifty six pseudogenes were also identified. The majority of the protein-coding genes (75.9%) were assigned 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.
Figure 3.

Graphical circular map of the genome. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Table 3.

Genome Statistics

Attribute

Value

% of Total

Genome size (bp)

2,051,896

100.00%

DNA coding region (bp)

1,789,074

87.19%

DNA G+C content (bp)

1,327,526

64.70%

Number of replicons

1

 

Extrachromosomal elements

0

 

Total genes

1,850

100.00%

RNA genes

55

2.97%

rRNA operons

1

 

Protein-coding genes

1,795

97.03%

Pseudo genes

56

3.03%

Genes with function prediction

1,404

75.89%

Genes in paralog clusters

160

8.65%

Genes assigned to COGs

1,412

76.32%

Genes assigned Pfam domains

1,429

77.24%

Genes with signal peptides

320

17.30%

Genes with transmembrane helices

423

22.86%

CRISPR repeats

1

 
Table 4.

Number of genes associated with the general COG functional categories

Code

value

%age

Description

J

137

8.9

Translation, ribosomal structure and biogenesis

A

0

0.0

RNA processing and modification

K

140

9.1

Transcription

L

82

5.3

Replication, recombination and repair

B

1

0.1

Chromatin structure and dynamics

D

17

1.1

Cell cycle control, cell division, chromosome partitioning

Y

0

0.0

Nuclear structure

V

44

2.9

Defense mechanisms

T

72

4.7

Signal transduction mechanisms

M

86

5.6

Cell wall/membrane/envelope biogenesis

N

0

0.0

Cell motility

Z

0

0.0

Cytoskeleton

W

0

0.0

Extracellular structures

U

18

1.2

Intracellular trafficking, secretion, and vesicular transport

O

51

3.3

Posttranslational modification, protein turnover, chaperones

C

75

4.9

Energy production and conversion

G

165

10.7

Carbohydrate transport and metabolism

E

150

9.7

Amino acid transport and metabolism

F

56

3.6

Nucleotide transport and metabolism

H

46

3.0

Coenzyme transport and metabolism

I

32

2.1

Lipid transport and metabolism

P

66

4.3

Inorganic ion transport and metabolism

Q

24

1.6

Secondary metabolites biosynthesis, transport and catabolism

R

172

11.1

General function prediction only

S

112

7.2

Function unknown

-

438

23.7

Not in COGs

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Gabriele Gehrich-Schröter to growing O. uli and Susanne Schneider for DNA extraction and quality analysis (both 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, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2 and Thailand Research Fund Royal Golden Jubilee Ph.D. Program No. PHD/0019/2548′ for MY.

Authors’ Affiliations

(1)
DSMZ - German Collection of Microorganisms and Cell Cultures GmbH
(2)
DOE Joint Genome Institute
(3)
Bioscience Division, Los Alamos National Laboratory
(4)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(5)
Oak Ridge National Laboratory
(6)
HZI - Helmholtz Centre for Infection Research
(7)
University of California Davis Genome Center

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