Complete genome sequence of Olsenella uli type strain (VPI D76D-27C) - PubMed (original) (raw)

. 2010 Aug 20;3(1):76-84.

doi: 10.4056/sigs.1082860.

Brittany Held, Susan Lucas, Matt Nolan, Montri Yasawong, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, David Bruce, John C Detter, Roxanne Tapia, Cliff Han, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D Jeffries, Manfred Rohde, Johannes Sikorski, Rüdiger Pukall, Tanja Woyke, James Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C Kyrpides, Hans-Peter Klenk, Alla Lapidus

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

Markus Göker et al. Stand Genomic Sci. 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: Coriobacteriaceae; GEBA; human gingival crevices; microaerotolerant anaerobe; primary endodontic infections.

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Figures

Figure 1

Figure 1

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

Figure 2

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.

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.

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