Open Access

Complete genome sequence of Arcanobacterium haemolyticum type strain (11018T)

  • Montri Yasawong1,
  • Hazuki Teshima2, 3,
  • Alla Lapidus2,
  • Matt Nolan2,
  • Susan Lucas2,
  • Tijana Glavina Del Rio2,
  • Hope Tice2,
  • Jan-Fang Cheng2,
  • David Bruce2, 3,
  • Chris Detter2, 3,
  • Roxanne Tapia2, 3,
  • Cliff Han2, 3,
  • Lynne Goodwin2, 3,
  • 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 Rohde1,
  • Johannes Sikorski6,
  • Rüdiger Pukall6,
  • Markus Göker6,
  • Tanja Woyke2,
  • James Bristow2,
  • Jonathan A. Eisen2, 7,
  • Victor Markowitz4,
  • Philip Hugenholtz2,
  • Nikos C. Kyrpides2 and
  • Hans-Peter Klenk6
Standards in Genomic Sciences20103:3020126

DOI: 10.4056/sigs.1123072

Published: 31 October 2010

Abstract

Arcanobacterium haemolyticum (ex MacLean et al. 1946) Collins et al. 1983 is the type species of the genus Arcanobacterium, which belongs to the family Actinomycetaceae. The strain is of interest because it is an obligate parasite of the pharynx of humans and farm animal; occasionally, it causes pharyngeal or skin lesions. It is a Gram-positive, nonmotile and non-sporulating bacterium. The strain described in this study was isolated from infections amongst American soldiers of certain islands of the North and West Pacific. This is the first completed sequence of a member of the genus Arcanobacterium and the ninth type strain genome from the family Actinomycetaceae. The 1,986,154 bp long genome with its 1,821 protein-coding and 64 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords

obligate parasite human pathogen pharyngeal lesions skin lesions facultative anaerobe Actinomycetaceae Actinobacteria GEBA

Introduction

Strain 11018T (= DSM 20595 = CCM 5947 = ATCC 9345 = NBRC 15585) is the type strain of the species A. haemolyticum, which is the type species of its genus Arcanobacterium [1]. Arcanobacterium is one of six genera in the family Actinomycetaceae [24]. The genus currently consists of nine validly described species. The strain was first described in 1946 by MacLean as ‘Corynebacterium haemolyticum’ [5]. Based on chemical features and the presence of unique phenotypic characteristics, the strain was subsequently transferred to the new genus Arcanobacterium as A. haemolyticum [1] and emended by Lehnen et al. in 2006 [6]. The generic name drives from the Latin word ‘arcanus’, meaning ‘secretive’ and the Latin word ‘bacterium’, a small rod, meaning ‘secretive bacterium’ [1]. The species epithet is derived from the Latin word ‘haema’ meaning ‘blood’ and the Neo-Latin word ‘lyticus’ meaning ‘able to loose or able to dissolve’ referring to blood-dissolving or hemolytic when the cells grow on blood agar [1]. There are many medical case reports that A. haemolyticum is occasionally isolated in patients with brain abscess [79], cellulitis [10,11], endocarditis [12], meningitis [13], peritonitis [14], post-traumatic ankle joint infection [15], septic arthritis [16], septicemia [17], sinusitis [11], soft tissue infections [18], venous ulcer infection [19], vertebral osteomyelitis [20] and wound infection [21,22]. Only rarely are cases reported in animals, where pathogenicity of A. haemolyticum has not been well documented [2325]. Here we present a summary classification and a set of features for A. haemolyticum strain 11018T, together with the description of the complete genomic sequencing and annotation.

Classification and features

Strain 11018T is an obligate parasite of the pharynx of human and farm animals; occasionally it causes pharyngeal or skin lesions [26]. The strain was isolated from infections in American soldiers [5]. The 16S rRNA gene sequence of strain 11018T (AJ234059) is 99% identical to six culturable strains that were reported in GenBank (status July 2010). Five strains were isolated from infected horses [23]. Another culturable strain, Tr2-2X-1 (FJ477385), was isolated from gasoline contaminated soil. The 16S rRNA gene of strain 11018T shares 93.3-97.9% sequence identity with the sequences of the type strains from the other members of the genus Arcanobacterium [27]. The next closest relative outside of the genus Arcanobacterium is Dermacoccus barathri MT2.1T (92.3% sequence similarity) [27]. No phylotypes from environmental screening or metagenomic surveys could be linked to A. haemolyticum or even the genus Arcanobacterium, indicating a rare occurrence of these species in the habitats screened thus far (as of July 2010). A representative genomic 16S rRNA sequence of A. haemolyticum 11018T was compared using BLAST with the most resent release of the Greengenes database [28] and the relative frequencies of taxa and keywords, weighted by BLAST scores, were determined. The five most frequent genera were Arcanobacterium (42.4%), Dermacoccus (12.6%), Actinomyces (10.8%), Terrabacter (9.9%) and Sanguibacter (5.7%). The five most frequent keywords within the labels of environmental samples were ‘skin’ (6.6%), ‘human’ (5.0%), ‘feedlot’ (4.6%), ‘elbow’ (3.4%) and ‘microbiota’ (3.3%). The BLAST keywords analysis supports the biological insights into A. haemolyticum strain 11018T as described above.

Figure 1 shows the phylogenetic neighborhood of A. haemolyticum strain 11018T in a 16S rRNA based tree. The sequences of the four 16S rRNA gene copies in the genome differ from each other by up to two nucleotides, and differ by up to five nucleotides from the previously published sequence generated from CIP 103370 (AJ234059) which contains one ambiguous base call.
Figure 1.

Phylogenetic tree highlighting the position of A. haemolyticum strain 11018T relative to the type strains of the other species within the genus Arcanobacterium and to the type strains of the other genera within the family Actinomycetaceae. The trees were inferred from 1,388 aligned characters [29,30] of the 16S rRNA gene sequence under the maximum likelihood criterion [31] and rooted in accordance with the current taxonomy. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates [32] if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [33] are shown in blue, published genomes in bold.

The cells of strain 11018T are slender or irregular rods (0.3–0.8 × 1.0–5.0 µm) [Table 1 and Figure 2]. The cells are Gram-positive, nonmotile, not acid-fast and without endospores [1]. In young cultures, cells may show clubbed ends sometimes arranged in V formation, but there are no filaments. In older cultures, cells segment into short, irregular rods and cocci [1]. Strain 11018T is facultatively anaerobic. The cells grow slowly on nutrient agar, but grow better on horse blood agar, giving small, convex, translucent colonies surrounded by a zone of complete hemolysis after two days at 37°C [1]. The selective medium for this strain was developed by Coman [39] and contains 5% sheep blood and 3.5% of NaCl. Cell growth is enhanced by the addition of CO2 [1]. The optimum growth temperature is 37°C [1,26]. Cells do not withstand heating at 60°C for 15 min [1,5]. Strain 11018T is chemoorganotrophic and requires nutritionally rich media for growth [1,26]. The fermentative metabolism of this strain produces acid but does not produce gas from glucose and several other carbohydrates on which growth occurs [1,26]. Acid production is mainly acetic, lactic and succinic acids [1,26]. Catalase, nitrate reduction and gelatine hydrolysis reactions are negative [6]. Strain 11018T produces N-acetyl-β-galactosidase, alkaline phosphatase, extracellular DNase, β-galactosidase, α-glucosidase and pyrazinamidase. It does not produce acid phosphatase, α-chymotrypsin, cystine arylamidase, esterase (C4), esterase lipase (C8), α-fucosidase, α-galactosidase, β-glucosidase, β-glucuronidase, leucine arylamidase, lipase (C14), α-mannosidase, naphthol-AS-BI-phosphohydrolase, trypsin, valine arylamidase and urease [1,6]. Strain 11018T is not able to ferment adonitol, L-arabitol, erythritol, D-fructose, glycerol, glycogen, D-mannitol and D-xylose. It is resistant to oxytetracycline (30µg per disc) but susceptible to nalidixic acid (30µg per disc), sulfamethoxazole trimethoprim (25µg per disc), amikacin (10µg per disc) or cefoxitin (30µg per disc) [1,42].
Figure 2.

Scanning electron micrograph of A. haemolyticum strain 11018T

Table 1.

Classification and general features of A. haemolyticum strain 11018T according to the MIGS recommendations [34].

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [35]

 

Phylum Actinobacteria

TAS [36]

 

Class Actinobacteria

TAS [3]

 

Subclass Actinobacteridae

TAS [3,4]

 

Order Actinomycetales

TAS [25,37]

 

Suborder Actinomycineae

TAS [3,4]

 

Family Actinomycetaceae

TAS [25,37]

 

Genus Arcanobacterium

TAS [1,6,38]

 

Species Arcanobacterium haemolyticum

TAS [1,5,38]

 

Type strain 11018

TAS [1]

 

Gram stain

positive

TAS [1]

 

Cell shape

slender, irregular rods (0.3–0.8 × 1.0–5.0 µm)

TAS [1]

 

Motility

none

TAS [1]

 

Sporulation

none

TAS [1]

 

Temperature range

not reported

 
 

Optimum temperature

37°C

TAS [1]

 

Salinity

3.5%

TAS [39]

MIGS-22

Oxygen requirement

facultatively anaerobic

TAS [1]

 

Carbon source

carbohydrates

TAS [1,5,6]

 

Energy source

chemoorganotroph

TAS [26]

MIGS-6

Habitat

pharynx of humans and farm animals

TAS [26]

MIGS-15

Biotic relationship

obligate parasite

TAS [26]

MIGS-14

Pathogenicity

pharyngeal or skin lesions

TAS [26]

 

Biosafety level

2

TAS [40]

 

Isolation

infections amongst American soldiers

TAS [5]

MIGS-4

Geographic location

North and West Pacific

TAS [5]

MIGS-5

Sample collection time

1946 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 [41]. 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 11018T possesses peptidoglycan type A5α based on L-Lys-L-Lys-D-Glu (unpublished, Norbert Weiss [43]). The predominant menaquinone is MK-9(H4) (85%) complemented by 15% MK-8(H4) [6]. The major cellular fatty acids when grown on blood agar at 35°C are straight-chain unsaturated acids C18:1 ω9c (37.0%), and saturated acids C18:0 (24.7%), C16:0 (22.5%) [6], which is similar to the cellular fatty acids spectrum reported from cells grown on sheep blood agar [31]: C18:1 cis9 (29%), C16:0 (23%), C18:2 (18%), C18:0 (17%), C10:0 (3%) and C14:0 (2%).

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [44], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [45]. The genome project is deposited in the Genome OnLine Database [33] 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: 454 pyrosequence standard, PE (12.5 kb insert size) libraries and one Illumina standard library

MIGS-29

Sequencing platforms

454 GS FLX Titanium, Illumina GAii

MIGS-31.2

Sequencing coverage

83.8 × pyrosequence, 36.8 × Illumina

MIGS-30

Assemblers

Newbler version 2.0.0-PostRelease-11/04/2008, phrap, Velvet

MIGS-32

Gene calling method

Prodigal 1.4, GenePRIMP

 

INSDC ID

CP002045

 

Genbank Date of Release

June 4, 2010

 

GOLD ID

Gc01291

 

NCBI project ID

37925

 

Database: IMG-GEBA

646564505

MIGS-13

Source material identifier

DSM 20595

 

Project relevance

Tree of Life, GEBA

Growth conditions and DNA isolation

A. haemolyticum strain 11018T, DSM 20595, was grown anaerobically in DSMZ medium 104 (PYG modified medium) [46] at 37°C. DNA was isolated from 1–1.5 g of cell paste using MasterPure Gram Positive DNA Purification Kit (Epicentre MGP04100), with a modified protocol for cell lysis, st/LALM, as described in Wu et al. [45].

Genome sequencing and assembly

The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website. Pyrosequencing reads were assembled using the Newbler assembler version 2.0.0-PostRelease-11/04/2008 (Roche). The initial Newbler assembly consisted of 116 contigs in 28 scaffolds and was converted into a phrap assembly by making fake reads from the consensus, collecting the read pairs in the 454 paired end library. Illumina GAii sequencing data was assembled with Velvet [47] 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 166.4 Mb 454 draft and all of the 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20.

The Phred/Phrap/Consed software package was used for sequence assembly and quality assessment 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, Dupfinisher [48], or sequencing cloned bridging PCR fragments with subcloning or transposon bombing (Epicentre Biotechnologies, Madison, WI) [49]. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F. Chang, unpublished). A total of 140 additional 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 [50]. The error rate of the completed genome sequence is less than 1 in 100,000. Together, the combination of the Illumina and 454 sequencing platforms provided 120.6 ×coverage of the genome. The final assembly contains 2.03 million Illumina reads and 0.52 million pyrosequencing reads.

Genome annotation

Genes were identified using Prodigal [51] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [52]. 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 [53].

Genome properties

The genome consists of a 1,986,154 bp long chromosome with a 53.1% GC content (Table 3 and Figure 3). Of the 1,885 genes predicted, 1,821 were protein-coding genes, and 64 RNAs; 90 pseudogenes were also identified. The majority of the protein-coding genes (68.5%) were assigned with 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)

1,986,154

100.00%

DNA coding region (bp)

1,744,192

87.82%

DNA G+C content (bp)

1,055,308

53.13%

Number of replicons

1

 

Extrachromosomal elements

0

 

Total genes

1,885

100.00%

RNA genes

64

3.40%

rRNA operons

4

 

Protein-coding genes

1,821

96.60%

Pseudo genes

90

4.77%

Genes with function prediction

1,292

68.54%

Genes in paralog clusters

154

8.17%

Genes assigned to COGs

1,308

69.39%

Genes assigned Pfam domains

1,402

74.38%

Genes with signal peptides

391

20.74%

Genes with transmembrane helices

492

26.10%

CRISPR repeats

1

 
Table 4.

Number of genes associated with the general COG functional categories

Code

Value

%age

Description

J

136

9.7

Translation, ribosomal structure and biogenesis

A

1

0.1

RNA processing and modification

K

99

7.1

Transcription

L

119

8.5

Replication, recombination and repair

B

0

0.0

Chromatin structure and dynamics

D

21

1.5

Cell cycle control, cell division, chromosome partitioning

Y

0

0.0

Nuclear structure

V

36

2.6

Defense mechanisms

T

51

3.6

Signal transduction mechanisms

M

75

5.4

Cell wall/membrane/envelope biogenesis

N

0

0.0

Cell motility

Z

0

0.0

Cytoskeleton

W

0

0.0

Extracellular structures

U

27

1.9

Intracellular trafficking and secretion, and vesicular transport

O

56

4.0

Posttranslational modification, protein turnover, chaperones

C

86

6.1

Energy production and conversion

G

125

8.9

Carbohydrate transport and metabolism

E

77

5.5

Amino acid transport and metabolism

F

58

4.1

Nucleotide transport and metabolism

H

56

4.0

Coenzyme transport and metabolism

I

34

2.4

Lipid transport and metabolism

P

93

6.6

Inorganic ion transport and metabolism

Q

12

0.9

Secondary metabolites biosynthesis, transport and catabolism

R

152

10.9

General function prediction only

S

87

6.2

Function unknown

-

577

30.6

Not in COGs

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Gabriele Gehrich-Schröter for growing A. haemolyticum cultures 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 599/1-1 and SI 1352/1-2 and Thailand Research Fund Royal Golden Jubilee Ph.D. Program No. PHD/0019/2548 for MY.

Authors’ Affiliations

(1)
HZI - Helmholtz Centre for Infection Research
(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)
DSMZ - German Collection of Microorganisms and Cell Cultures GmbH
(7)
University of California Davis Genome Center

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