Standards in Genomic Sciences (2009) 1: 166-173 DOI:10.4056/sigs.29547 The Genomic Standards Consortium Complete genome sequence of Atopobium parvulum type strain (IPP 1246T) Alex Copeland1, Johannes Sikorski2, Alla Lapidus1, Matt Nolan1, Tijana Glavina Del Rio1, Su- san Lucas1, Feng Chen1, Hope Tice1, Sam Pitluck1, Jan-Fang Cheng1, R��diger Pukall2, Olga Chertkov1,3, Thomas Brettin1,3, Cliff Han1,3, John C. Detter1,3, Cheryl Kuske1,3, David Bruce1,3, Lynne Goodwin1,3, Natalia Ivanova1, Konstantinos Mavromatis1, Natalia Mikhailova1, Amy Chen4, Krishna Palaniappan4, Patrick Chain1,5, Manfred Rohde6, Markus G��ker2, Jim Bris- tow1, Jonathan A. Eisen1,7, Victor Markowitz4, Philip Hugenholtz1, Nikos C. Kyrpides1, Hans- Peter Klenk2*, and John C. Detter1,3 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Labora- tory, 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 *Corresponding author: Hans-Peter Klenk Keywords: halitosis, obligately anaerobic, human respiratory tract, risk group 2, malodor, Co- riobacteriaceae 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 repli- con genome with its 1369 protein-coding and 49 RNA genes is part of the Genomic Encyclo- pedia of Bacteria and Archaea project. Introduction Strain IPP 1246T (= DSM 20469 = ATCC 33793 = JCM 10300) is the type strain of the species Atopo- bium parvulum and was first described by Wein- berg et al. 1937 as ���Streptococcus parvulus��� (ba- sonym) [1]. In 1992 it was reclassified as A. parvu- lum [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 malo- dorous compounds are volatile sulfur compounds, with the most frequent ones being hydrogen sul- fide, 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 periodon- titis, though a participation in periodontitis can not be fully excluded [5]. Nevertheless, A. parvu- lum has been associated with odontogenic infec- tions, e.g. dental implants, but also with the saliva of healthy subjects [6]. Here we present a sum- mary classification and a set of features for A. par- vulum IPP 1246T together with the description of the complete genomic sequencing and annotation.

Copeland, et al. http://standardsingenomics.org 167 Classification and features Phylotypes with significant 16S sequence similari- ty to strain IPP 1246T were observed from intu- bated patients (EF510777) and from metagenom- ic human skin surveys (GQ081350) [7]. No signifi- cant similarities were found in human gut meta- genomes (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 nuc- leotides from the sequence used for the last tax- onomic emendation (X67150) [2]. Figure 1. Phylogenetic tree of A. parvulum strain IPP 1246T, all other type strains of the genus Ato- pobium 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 ��m 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. Interes- tingly, 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 ��g/ml), clindamycin (1.6 ��g/ml), erythromycin (3 ��g/ml), penicillin G (2 U/ml), and tetracycline (6 ��g/ml) [17]. Strain IPP 1126T produces acid (final pH 4.7) from cellobiose, esculin, fructose, galactose, glu- cose, 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 hy- drolyzed. Nitrate was not reduced. Indole was not formed. A solid acid curd formed in milk neither milk, gelatin, nor meat was digested. Neither cata- lase, urease, deoxyribonuclease, lecithinase, nor lipase was detected [17]. Other enzyme activities are positive for acid phosphatase, alanine aryla- midase, arginine arylamidase, ��-galactosidase, leucine arylamidase, pyroglutamic acid arylami- dase, glycine arylamidase, tyrosine arylamidase,