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Complete genome sequence of Atopobium parvulum type strain (IPP 1246T)

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Standards in Genomic Sciences20091:1020166

https://doi.org/10.4056/sigs.29547

©  The Author(s) 2009

  • Published:

The Erratum to this article has been published in Standards in Genomic Sciences 2010 2:2030361

Abstract

Atopobium parvulum (Weinberg et al. 1937) Collins and Wallbanks 1993 comb. nov. is the type strain of the species and belongs to the genomically yet unstudied Atopobium/Olsenella branch of the family Coriobacteriaceae. The species A. parvulum is of interest because its members are frequently isolated from the human oral cavity and are found to be associated with halitosis (oral malodor) but not with periodontitis. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Atopobium, and the 1,543,805 bp long single replicon genome with its 1369 protein-coding and 49 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords

  • halitosis
  • obligately anaerobic
  • human respiratory tract
  • risk group 2
  • malodor
  • Coriobacteriaceae

Introduction

Strain IPP 1246T (= DSM 20469 = ATCC 33793 = JCM 10300) is the type strain of the species Atopobium parvulum and was first described by Weinberg et al. 1937 as ‘Streptococcus parvulus’ (basonym) [1]. In 1992 it was reclassified as A. parvulum [2]. A. parvulum is of high interest because it has frequently been isolated from the human oral cavity, especially from the tongue dorsum, where it has been associated with patients suffering from halitosis (oral malodor) [3,4]. In general, the malodorous compounds are volatile sulfur compounds, with the most frequent ones being hydrogen sulfide, methyl mercaptan, and dimethyl sulfide, which are produced by bacterial metabolism of the sulfur containing amino acids cysteine and methionine [3,4]. However, for A. parvulum itself, the production of these substances has not yet been studied. A. parvulum has not been found to be significantly associated with chronic periodontitis, though a participation in periodontitis can not be fully excluded [5]. Nevertheless, A. parvulum has been associated with odontogenic infections, e.g. dental implants, but also with the saliva of healthy subjects [6]. Here we present a summary classification and a set of features for A. parvulum IPP 1246T together with the description of the complete genomic sequencing and annotation.

Classification and features

Phylotypes with significant 16S sequence similarity to strain IPP 1246T were observed from intubated patients (EF510777) and from metagenomic human skin surveys (GQ081350) [7]. No significant similarities were found in human gut metagenomes (highest similarity is 92%, BABE01011651) [8], or in marine metagenomes (87%, AACY020304192) [9] (status June 2009).

Figure 1 shows the phylogenetic neighborhood of A. parvulum strain IPP P1246T in a 16S rRNA based tree. The sequence of the sole copy of the 16S rRNA gene in the genome is identical with the previously published sequence generated from ATCC 22793 (AF292372), but differs by four nucleotides from the sequence used for the last taxonomic emendation (X67150) [2].
Figure 1.
Figure 1.

Phylogenetic tree of A. parvulum strain IPP 1246T, all other type strains of the genus Atopobium and the type strains of all other genera within the Coriobacteriaceae, inferred from 1345 aligned characters [10,11] of the 16S rRNA gene sequence under the maximum likelihood criterion [12]. The tree was rooted with the type strains of the genera within the subclass Rubrobacteridae. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1000 bootstrap replicates if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [13] are shown in blue, published genomes in bold, including two of which are reported in this issue of SIGS [14,15]

The cells are cocci (approximately 0.3 to 0.6 µm in diameter) that occur singly, in pairs, in clumps, and in short chains, occasionally with central swelling [16,17] (Table 1 and Figure 2). The strains are non-motile and obligate anaerobic. Interestingly, growth is substantially stimulated by 0.02% (vol/vol) Tween 80 and by 10% (vol/vol) rabbit serum added to culture media [16]. Strain IPP 1246T is susceptible to chloramphenicol (12 µg/ml), clindamycin (1.6 µg/ml), erythromycin (3 µg/ml), penicillin G (2 U/ml), and tetracycline (6 µg/ml) [17].
Figure 2.
Figure 2.

Scanning electron micrograph of A. parvulum IPP 1246T

Table 1.

Classification and general features of A. parvulum IPP 1146T according to the MIGS recommendations [18].

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [19]

 

Phylum Actinobacteria

TAS [20]

 

Class Actinobacteria

TAS [20]

 

Subclass Coriobacteridae

TAS [21]

 

Order Coriobacteriales

TAS [21]

 

Suborder “Coriobacterineae”

TAS [21]

 

Family Coriobacteriaceae

TAS [21]

 

Genus Atopobium

TAS [2]

 

Species Atopobium parvulum

TAS [2]

 

Type strain IPP 1246

 
 

Gram stain

positive

TAS [16]

 

Cell shape

small cocci that occasionally appear to be elliptical

TAS [16]

 

Motility

nonmotile

TAS [17]

 

Sporulation

nonsporulating

TAS [16]

 

Temperature range

25°C–45°C

TAS [17]

 

Optimum temperature

37°C–45°C

TAS [17]

 

Salinity

less than 6.5% NaCl

TAS [17]

MIGS-22

Oxygen requirement

obligate anaerobic

TAS [17]

 

Carbon source

acid production from cellobiose, esculin, fructose, galactose, glucose, inulin, lactose, maltose, mannose, salicin, sucrose, and trehalose

TAS [17]

 

Energy source

carbohydrates

TAS [17]

MIGS-6

Habitat

human respiratory tract.

TAS [1,17]

MIGS-15

Biotic relationship

free living

NAS

MIGS-14

Pathogenicity

associated with halitosis and human oral infections

TAS [3,4,6]

 

Biosafety level

2

TAS [22]

 

Isolation

unknown for this specific strain, but Weinberg et al reported that the principal habitat was the respiratory tract.

TAS [1,17]

MIGS-4

Geographic location

unknown, probably France

TAS [1,17]

MIGS-5

Sample collection time

before 1937

TAS [1,17]

MIGS-4.1

Latitude - Longitude

unknown

 

MIGS-4.2

 

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 the Gene Ontology project [23]. If the evidence code is IDA the property was directly observed for a living isolate by one of the authors or another expert mentioned in the acknowledgements.

Strain IPP 1126T produces acid (final pH < 4.7) from cellobiose, esculin, fructose, galactose, glucose, inulin, lactose, maltose, mannose, salicin, sucrose, and trehalose; erythritol and xylose were weakly fermented; no acid was produced from amygdalin, arabinose, glycerol, glycogen, inositol, mannitol, melezitose, melibiose, pectin, raffinose, rhamnose, ribose, sorbitol, or starch. Esculin was hydrolyzed; neither starch nor hippurate was hydrolyzed. Nitrate was not reduced. Indole was not formed. A solid acid curd formed in milk; neither milk, gelatin, nor meat was digested. Neither catalase, urease, deoxyribonuclease, lecithinase, nor lipase was detected [17]. Other enzyme activities are positive for acid phosphatase, alanine arylamidase, arginine arylamidase, β-galactosidase, leucine arylamidase, pyroglutamic acid arylamidase, glycine arylamidase, tyrosine arylamidase, but negative for arginine dihydrolase, histidine arylamidase, proline arylamidase, serine arylamidase, as determined using the API system [24].

Chemotaxonomy

The chemotaxonomy of A. parvulum IPP 1246T is unfortunately hardly studied. There are no data known on the polar lipids. The strain possesses cell-wall peptidoglycan of type A4α, L-Lys-D-Asp (type A11.31 according to the DSMZ catalogue of strains; http://www.dsmz.de/microorganisms/main.php?content_id=35) [25]. The major cellular fatty acids (FAME: fatty acid methyl ester; DMA: dimethylacetyl) are C18:1 cis-9 (38.2%, FAME), C18:1 cis-9 (24.1%, DMA), C16:1 cis-9 (5.0%, FAME), C17:1 cis-8 (5.0%, FAME), C18:1 c11/t9/t6 (5.0%, FAME), C18:1 cis-11 (3.9%, DMA), C14:0 (3.4%, FAME), C10:0 (3.0%, FAME) [16].

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of each phylogenetic position, and is part of the Genomic Encyclopedia of Bacteria and Archaea project. The genome project is deposited in the Genome OnLine Database [13] 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

Two Sanger libraries: 8kb pMCL200 and fosmid pcc1Fos One 454 pyrosequence standard library

MIGS-29

Sequencing platforms

ABI3730, 454 GS FLX

MIGS-31.2

Sequencing coverage

7.8× Sanger; 43.4× pyrosequence

MIGS-30

Assemblers

Newbler, phrap

MIGS-32

Gene calling method

Prodigal, GenePRIMP

 

Genbank ID

CP001721

 

Genbank Date of Release

September 9, 2009

 

GOLD ID

Gc01099

 

NCBI project ID

29401

 

Database: IMG-GEBA

2501533209

MIGS-13

Source material identifier

DSM 20469

 

Project relevance

Tree of Life, GEBA

Growth conditions and DNA isolation

A. parvulum strain IPP 1246T, DSM 20469, was grown anaerobically in DSMZ medium 104 (modified PYG; Medium [26]) at 37°C. DNA was isolated from 0.5–1 g of cell paste using the JGI CTAP procedure with a modified protocol for cell lysis as described in Wu et al. [27].

Genome sequencing and assembly

The genome was sequenced using a combination of Sanger and 454 sequencing platforms. All general aspects of library construction and sequencing performed at the JGI can be found on the JGI website. 454 Pyrosequencing reads were assembled using the Newbler assembler version 1.1.02.15 (Roche). Large Newbler contigs were broken into 1,716 overlapping fragments of 1000bp and entered into assembly as pseudo-reads. The sequences were assigned quality scores based on Newbler consensus q-scores with modifications to account for overlap redundancy and to adjust inflated q-scores. A hybrid 454/Sanger assembly was made using the parallel phrap assembler (High Performance Software, LLC). Possible mis-assemblies were corrected with Dupfinisher [28] or transposon bombing of bridging clones (Epicentre Biotechnologies, Madison, WI). Gaps between contigs were closed by editing in Consed, custom primer walk or PCR amplification. A total of 125 Sanger finishing reads were produced to close gaps, to resolve repetitive regions, and to raise the quality of the finished sequence. The error rate of the completed genome sequence is less than 1 in 100,000. Together all sequence types provided 51.2 x coverage of the genome. The final assembly contains 12,842 Sanger and 359,479 pyrosequence reads.

Genome annotation

Genes were identified using Prodigal [29] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [30]. 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 were performed within the Integrated Microbial Genomes Expert Review (IMG-ER) platform [31].

Genome properties

The genome is 1,543,805 bp long and comprises one main circular chromosome with a 45.7% GC content (Table 3 and Figure 3). Of the 1419 genes predicted, 1369 were protein coding genes, and 50 RNAs. Sixteen pseudogenes were also identified. The majority of the genes (74.5%) 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.
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)

1,543,805

100.00%

DNA Coding region (bp)

1,396,223

90.44%

DNA G+C content (bp)

705,312

45.69%

Number of replicons

1

 

Extrachromosomal elements

0

 

Total genes

1419

100.00%

RNA genes

49

3.52%

rRNA operons

1

 

Protein-coding genes

1369

96.48%

Pseudo genes

16

1.13%

Genes with function prediction

1059

74.63%

Genes in paralog clusters

69

4.86%

Genes assigned to COGs

1096

77.24%

Genes assigned Pfam domains

1084

76.39%

Genes with signal peptides

240

16.91%

Genes with transmembrane helices

339

23.89%

CRISPR repeats

0

 
Table 4.

Number of genes associated with the general COG functional categories

Code

Value

% age

Description

J

128

9.3

Translation, ribosomal structure and biogenesis

A

0

0.0

RNA processing and modification

K

85

6.2

Transcription

L

72

5.3

Replication, recombination and repair

B

1

0.1

Chromatin structure and dynamics

D

18

1.3

Cell cycle control, mitosis and meiosis

Y

0

0.0

Nuclear structure

V

42

3.1

Defense mechanisms

T

46

3.4

Signal transduction mechanisms

M

70

5.1

Cell wall/membrane biogenesis

N

1

0.1

Cell motility

Z

0

0.0

Cytoskeleton

W

0

0.0

Extracellular structures

U

20

1.5

Intracellular trafficking and secretion

O

44

3.2

Posttranslational modification, protein turnover, chaperones

C

44

3.2

Energy production and conversion

G

115

8.4

Carbohydrate transport and metabolism

E

105

7.7

Amino acid transport and metabolism

F

53

3.9

Nucleotide transport and metabolism

H

37

2.7

Coenzyme transport and metabolism

I

23

1.7

Lipid transport and metabolism

P

59

4.3

Inorganic ion transport and metabolism

Q

11

0.8

Secondary metabolites biosynthesis, transport and catabolism

R

125

9.1

General function prediction only

S

90

6.6

Function unknown

-

273

19.9

Not in COGs

Notes

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Katja Steenblock for growing A. parvulum 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, as well as German Research Foundation (DFG) INST 599/1-1.

Authors’ Affiliations

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

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