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Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845T)
Standards in Genomic Sciencesvolume 1, pages101–109 (2009)
Capnocytophaga ochracea (Prévot et al. 1956) Leadbetter et al. 1982 is the type species of the genus Capnocytophaga. It is of interest because of its location in the Flavobacteriaceae, a genomically not yet charted family within the order Flavobacteriales. The species grows as fusiform to rod shaped cells which tend to form clumps and are able to move by gliding. C. ochracea is known as a capnophilic (CO2-requiring) organism with the ability to grow under anaerobic as well as aerobic conditions (oxygen concentration larger than 15%), here only in the presence of 5% CO2. Strain VPI 2845T, the type strain of the species, is portrayed in this report as a gliding, Gram-negative bacterium, originally isolated from a human oral cavity. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the flavobacterial genus Capnocytophaga, and the 2,612,925 bp long single replicon genome with its 2193 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
Strain VPI 2845T (= DSM 7271 = ATCC 27872 = JCM 1296) is the type strain of Capnocytophaga ochracea, and the type species of the genus Capnocytophaga. C. ochracea was first described by Prévot et al.  as ‘Fusiformis nucleatus var. ochraceus’ and later renamed by Leadbetter et al . Other synonyms for C. ochracea are ‘Bacteroides oralis var. elongatus’ , ‘Bacteroides ochraceus’ (basonym)  and “Ristella ochraceus” (sic) . The organism is of significant interest for its position in the tree of life where the genus Capnocytophaga (8 species) is located within the large family of the Flavobacteriaceae. First, Leadbetter et al. placed the genus Capnocytophaga in the family of the Cytophagaceae within the order Cytophagales  which was emended in 2002 by the Subcommittee on the Taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes . C. ochracea is most often found in association with animal and human hosts. In general, it is a normal inhabitant of the human mouth and other non-oral sites. C. ochracea is associated with juvenile and adult periodontitis [8,9] and may cause severe infections in immunocompromised as well as in immunocompetent patients [10–12]. Among these are endocarditis, endometritis, osteomyelitis, abscesses, peritonitis, and keratitis. Here we present a summary classification and a set of features for C. ochracea VPI 2845T together with the description of the complete genomic sequence and annotation.
Classification and features
Genbank lists 16S rRNA sequences for only a few small number of cultivated strains belonging to C. ochraceae, all of them isolated from human oral cavity (e.g. U41351, U41353, DQ012332). Phylotypes (sequences from uncultivated bacteria) closely linked to C. ochracea also originate in almost exclusively from human oral samples collected from European, American, Asian and African samples (AF543292, AF543298, AY278613, AM420149, AY429469, FJ470418). Only two bacterial clones are reported from non-human sources. One was isolated from Strongylocentrotus intermedius (sea urchin) in the Sea of Japan (EU432412, EU432438), and the second from Oncorhynchus mykiss (rainbow trout) caught in Scotland (AM179907). Screening of environmental genomic samples and surveys reported at the NCBI BLAST server indicated no closely related phylotypes (>91% sequence identity) that can be linked to the species or genus.
Figure 1 shows the phylogenetic neighborhood of C. ocharcea VPI 2845T in a 16S rRNA based tree. All four 16S rRNA gene copies in the genome of strain VPI 2845T are identical, but differ by two nucleotides from the previously published 16S rRNA sequence (U41350) generated from ATCC 27872.
C. ochracea is Gram-negative, has no flagellae and is motile by gliding (Table 1, Figure 2). Cells are pigmented and the name ‘ochracea’ is derived from the yellow color exhibited by harvested cell mass . It is a catalase- and oxidase-negative species. C. ochracea is usually susceptible to a number of antibiotics, however, resistance is increasing in this species [23,24]. Furthermore, C. ochracea is known to possess an immunosuppressive factor . All strains of C. ochracea are capable of fermenting glucose, sucrose, maltose and mannose, whereas most strains ferment amygdalin, fructose, galactose, lactose and raffinose . The optimal growth temperature is 37°C. Nitrate is reduced to nitrite, and dextran, glycogen, starch and aesculin are hydrolysed by most strains. Indole is not produced. Acetic and succinic acid are the main metabolic end products of fermentation .
Analysis of amino acids and amino sugars of the peptidoglycan revealed that glucosamine, muramic acid, D-glutamic acid, alanine, and diaminopimelic acid were the principal components and the peptidoglycan belongs to the Alγ-type. Serine and glycine were not found . As in other Capnocytophaga strains, the fatty acid pattern of strain C. ochracea VPI 2845T is dominated by iso-branched chain saturated fatty acids i-C15:0 (63.5%), C18:2 (8.1%) and i-3OH C17:0 (13.8%) [23,27,28]. Phosphatidylethanolamine and an ornithine-amino lipid were identified as dominating polar lipids, as well as lesser amounts of lysophosphatidyl-ethanolamine . In addition, the unusual sulfonolipid capnine (2-amino-3-hydroxy-15-methylhexadecane-1-sulfonic acid) was identified as major cell wall component .
Genome sequencing and annotation
Genome project history
This organism was selected for sequencing on the basis of its phylogenetic position, and is part of the Genomic Encyclopedia of Bacteria and Archaea project. The genome project is deposited in the Genomes OnLine Database  and the complete genome sequence in GenBank (CP001632). Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2.
Growth conditions and DNA isolation
C. ochracea VPI 2845T, DSM 7271, was grown under anaerobic conditions in DSMZ medium 340 (Capnocytophaga Medium, ) plus 0.1% NaHCO3 at 37°C. DNA was isolated from 1–1.5 g of cell paste using Qiagen Genomic 500 DNA Kit (Qiagen, Hilden, Germany) with a modified protocol, L, for cell lysis, as described in Wu et al. .
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 at the JGI website. 454 Pyrosequencing reads were assembled using the Newbler assembler version 1.1.02.15 (Roche). Large Newbler contigs were broken into 2,919 overlapping fragments of 1,000 bp 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 or transposon bombing of bridging clones . Gaps between contigs were closed by editing in Consed, custom primer walk or PCR amplification. A total of 226 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 35.1× coverage of the genome.
Genes were identified using Prodigal  as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline . 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 .
The genome is 2,612,925 bp long and comprises one circular chromosome with a 39.6% GC content (Table 3). Of the 2,252 genes predicted, 2,193 were protein coding genes, and 59 RNAs; 22 pseudogenes were also identified. Genes assigned with putative functions comprised 61.7% of the genome, while the remaining genes were annotated as hypothetical proteins. The properties and the statistics of the genome are summarized in Table 3. The distribution of genes into COG functional categories is presented in Figure 3 and Table 4.
de Cadore F, Prévot AR, Tardieux P, Joubert L. Recherches sur Fusiformis nucleatus (Knorr) et son pouvoir pathogène pour l’homme et les animaux. Ann Inst Pasteur (Paris) 1956; 91:787–798. PubMed
Leadbetter ER. Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB: List No. 8. Int J Syst Bacteriol 1982; 32:266–268.
Loesche WJ, Socransky SS, Gibbons RJ. Bacteroides oralis, Proposed New Species Isolated from the Oral Cavity of Man. J Bacteriol 1964; 88:1329–1337. PubMed
Holdeman LV, Moore WEC. Bacteroides. Anaerobe Laboratory Manual, Virginia Polytechnic Institute Anaerobe. Blacksburg, VA 1972.
Sebald M. Etudes sur les bactéries anaérobies gram-négatives asporulée. Lavel, France: Imprimerie Barnéoud S. A.; 1962.
Leadbetter ER, Holt SC, Socransky SS. Capnocytophaga: new genus of gram-negative gliding bacteria. I. General characteristics, taxonomic considerations and significance. Arch Microbiol 1979; 122:9–16. doi:10.1007/BF00408040 PubMed
Bernardet JF, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070. doi:10.1099/ijs.0.02136-0 PubMed
Holt SC, Simpson JL, Leadbetter ER. Some characteristics of “gliding” bacteria isolated from human dental plaque. J Dent Res 1975; 54:ABS L208.
Newman MG, Weiner MS, Angel I, Grinenko V.H.J.K. Predominant cultivable microbiota of the gingival crevice in “supernormal” patients. J Dent Res 1977; 56:B121.
Desai SS, Harrison RA, Murphy MD. Capnocytophaga ochracea causing severe sepsis and purpura fulminans in an immunocompetent patient. J Infect 2007; 54:e107–e109; doi:10.1016/j.jinf.2006.06.014 PubMed
Bonatti H, Rossboth DW, Nachbaur D, Fille M, Aspock C, Hend I, Hourmont K, White L, Malnick H, Allerberger FJ. A series of infections due to Capnocytophaga spp in immunosuppressed and immunocompetent patients. Clin Microbiol Infect 2003; 9:380–387. doi:10.1046/j.1469-0691.2003.00538.x PubMed
Duong M, Besancenot JF, Neuwirth C, Buisson M, Chavanet P, Portier H. Vertebral osteomyelitis due to Capnocytophaga species in immunocompetent patients: report of two cases and review. Clin Infect Dis 1996; 22:1099–1101. PubMed
Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452–464. doi:10.1093/bioinformatics/18.3.452 PubMed
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552. PubMed
Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 2008; 57:758–771. doi:10.1080/10635150802429642 PubMed
Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2008; 36:D475–D479. doi:10.1093/nar/gkm884 PubMed
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541–547. doi:10.1038/nbt1360 PubMed
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87: 4576–4579. PubMed
Garrity GM, Holt J. Taxonomic Outline of the Archaea and Bacteria. Bergey’s Manual of Systematic Bacteriology, 2nd Ed. In: G. Garrity GM, Boone DR, Castenholz RW Eds. Vol 1 The Archaea, Deeply Branching and Phototrophic Bacteria. 2001 pp. 155–166
Socransky SS, Holt SC, Leadbetter ER, Tanner AC, Savitt E, Hammond BF. Capnocytophaga: new genus of gram-negative gliding bacteria. III. Physiological characterization. Arch Microbiol 1979; 122:29–33. doi:10.1007/BF00408042 PubMed
Anonymous. Biological Agents: Technical rules for biological agents www.baua.de TRBA 466.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25–29. doi:10.1038/75556 PubMed
Wang HK, Chen YC, Teng LJ, Hung CC, Chen ML, Du SH, Pan HJ, Hsueh PR, Chang SC. Brain abscess associated with multidrug-resistant Capnocytophaga ochracea infection. J Clin Microbiol 2007; 45:645–647.doi:10.1128/ICM.01815-06 PubMed
Rosenau A, Cattier B, Gousset N, Harriau P, Philippon A, Quentin R. Capnocytophaga ochracea: characterization of a plasmid-encoded extended-spectrum TEM-17 beta-lactamase in the phylum Flavobacter-bacteroides. Antimicrob Agents Chemother 2000; 44:760–762. doi:10.1128/AAC.44.3.760-762.2000 PubMed
Ochiai K, Senpuku H, Kurita-Ochiai T. Purification of immunosuppressive factor from Capnocytophaga ochracea. J Med Microbiol 1998; 47:1087–1095. doi:10.1099/00222615-47-12-1087 PubMed
Hanagata T. Chemical structure and immunobiological activities of peptidoglycan isolated from Capnocytophaga species. Kanagawa Shigaku 1990; 25:316–326. PubMed
Dees SB, Karr DE, Hollis D, Moss CW. Cellular fatty acids of Capnocytophaga species. J Clin Microbiol 1982; 16:779–783. PubMed
Vandamme P, Vancanneyt M, van Belkum A, Segers P, Quint WG, Kersters K, Paster BJ, Dewhirst FE. Polyphasic analysis of strains of the genus Capnocytophaga and Centers for Disease Control group DF-3. Int J Syst Bacteriol 1996; 46:782–791. PubMed
Holt SC, Doundowlakis J, Takacs BJ. Phospholipid composition of gliding bacteria: oral isolates of Capnocytophaga compared with Sporocytophaga. Infect Immun 1979; 26:305–310. PubMed
Godchaux W, III, Leadbetter ER. Capnocytophaga spp. contain sulfonolipids that are novel in procaryotes. J Bacteriol 1980; 144:592–602. PubMed
List of media used at DSMZ for cell growth: http://www.dsmz.de/microorganisms/media_list.php
Wu M, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova N, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopedia of Bacteria and Archaea. Nature (In press).
Han CS, Chain P. Finishing repeat regions automatically with Dupfinisher CSREA Press. In: Arabnia AR, Valafar H, editors. Proceedings of the 2006 international conference on bioinformatics & computational biology; 2006 June 26–29. CSREA Press. p 141–146.
Anonymous. Prodigal Prokaryotic Dynamic Programming Genefinding Algorithm. Oak Ridge National Laboratory and University of Tennessee 2009 http://compbio.ornl.gov/prodigal
Pati A, Ivanova N, Mikhailova, N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes (Submitted).
Markowitz V, Mavromatis K, Ivanova N, Chen IM, Chu K, Kyrpides N. Expert Review of Functional Annotations for Microbial Genomes. Bioinformatics 2009; 25: 2271–2278.
We would like to gratefully acknowledge the help of Sabine Welnitz for growing C. ochracea 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, well as German Research Foundation (DFG) INST 599/1-1.