Email this article 
Post a Comment 1 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
2 DOE Joint Genome Institute, Walnut Creek, California, USA
3 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
4 Lawrence Livermore National Laboratory, Livermore, California, USA
5 University of California Davis Genome Center, Davis, California, USA
6 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
Print publication date: July 20, 2009.
Abstract
Kytococcus sedentarius (ZoBell and Upham 1944) Stackebrandt et al. 1995 is the type strain of the species, and is of phylogenetic interest because of its location in the Dermacoccaceae, a poorly studied family within the actinobacterial suborder Micrococcineae. K. sedentarius is known for the production of oligoketide antibiotics as well as for its role as an opportunistic pathogen causing valve endocarditis, hemorrhagic pneumonia, and pitted keratolysis. It is strictly aerobic and can only grow when several amino acids are provided in the medium. The strain described in this report is a free-living, nonmotile, Gram-positive bacterium, originally isolated from a marine environment. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Dermacoccaceae and the 2,785,024 bp long single replicon genome with its 2639 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
Keywords: mesophile, free-living, marine, aerobic, opportunistic pathogenic, Dermacoccaceae.
This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Strain 541T (DSM 20547 = ATCC 14392 = JCM 11482 = CCM 314 and other culture collections) is the type strain of the species Kytococcus sedentarius, which is the type species of the genus Kytococcus [1]. Strain 541T was first described as Micrococcus sedentarius (ZoBell and Upham 1944) [2] and later emended as K. sedentarius in a taxonomic dissection of the genus Micrococcus [1]. The organism is of interest for its biotechnological potential as source of natural antibiotics (oligoketides), for its role as an opportunistic pathogen, and for its position in the tree of life, where it represents the scarcely populated genus Kytococcus (2 species) within in the actinobacterial family Dermacoccaceae [1] (Figure 1). K. sedentarius 541T was first isolated around 1944 from a marine environment [2], but strains of the species were also frequently isolated from human skin [7]. More recently, closely related strains were also isolated from culture-dependant environmental screenings of a non-saline alkaline groundwater environment in Cabeco de Vide in southern Portugal [8], screening for pelagic bacteria in South Korea [9], tropical marine sediments from the intertidal zone off the coast of the Republic Palau [10], from the ciliate Collinia sp.), an endoparasite of euphausiids from the Gulf of California (unpublished literature, GenBank record EU090136), and in a culture-independent analysis of the microbial burden and diversity in commercial airline cabins [11]. Screening of environmental genomic samples and surveys reported at the NCBI BLAST server indicated no closely related phylotypes that can be linked to the species or genus. Here we present a summary classification and a set of features for K. sedentarius strain 541T (Table 1), together with the description of the complete genomic sequencing and annotation.
Figure 1 Phylogenetic tree of K. sedentarius strain 541T with all type strains of the family Dermacoccaceae, inferred from 1,456 aligned 16S rRNA characters [3] under the maximum likelihood criterion [4,5]. The tree was rooted with four members of the neighboring family Intrasporangiaceae. 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. Strains with a genome-sequencing project registered in GOLD [6] are printed in blue; published genomes in bold. |
| MIGS ID | Property | Term | Evidence code |
|---|---|---|---|
| Current classification | Domain Bacteria | ||
| Phylum Actinobacteria | |||
| Class Actinobacteria | TAS [13] | ||
| Order Actinomycetales | TAS [14] | ||
| Suborder Micrococcineae | TAS [13] | ||
| Family Dermacoccaceae | TAS [15] | ||
| Genus Kytococcus | TAS [1] | ||
| Species Kytococcus sedentarius | TAS [1] | ||
| Type strain 541 | |||
| Gram stain | positive | TAS [1] | |
| Cell shape | spherical, predominantly in tetrads | TAS [1] | |
| Motility | nonmotile | TAS [1] | |
| Sporulation | non-sporulating | TAS [1] | |
| Temperature range | mesophilic | TAS [1] | |
| Optimum temperature | 28-36°C | TAS [1] | |
| Salinity | nonhalophilic, but growth in media up to 10% (w/v) NaCl |
TAS [1] | |
| MIGS-22 | Oxygen requirement | mandatory aerobe | TAS [1] |
| Carbon source | not reported | ||
| Energy source | unknown, not starch | NAS | |
| MIGS-6 | Habitat | marine | TAS [2] |
| MIGS-15 | Biotic relationship | free-living | NAS |
| MIGS-14 | Pathogenicity | in rare cases | TAS [16,17] |
| Biosafety level | 1 | TAS [18] | |
| Isolation | slide submerged in sea water | TAS [2] | |
| MIGS-4 | Geographic location | probably San Diego | TAS [2] |
| MIGS-5 | Sample collection time | about or before 1944 | TAS [2] |
| MIGS-4.1 MIGS-4.2 | Latitude – 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 the Gene Ontology project [19]. If the evidence code is IDA, then the property was directly observed, for a live isolate by one of the authors, or another expert mentioned in the acknowledgements.
K. sedentarius cells are spherical/coccoid and occur predominantly in tetrads which can be arranged in cubical packets [1] (Figure 2). Cells are described as Gram-positive, nonmotile, non-encapsulated, and not endospore-forming [1]. K. sedentarius 541T is strictly aerobic and chemoorganotrophic, requires methionine and other amino acids for growth, and grows well in NaCl at concentrations up to 10% (w/v) [1].
Figure 2 Scanning electron micrograph of K. sedentarius strain 541T (Manfred Rohde, Helmholtz Centre for Infection Biology, Braunschweig) |
K. sedentarius (strain NK0508) is capable of degrading diphenylarsenic acid [20], but not starch [1], and does not produce acids from most carbohydrates and alcohols [1]. Its optimal growth temperature is 28-36°C. Nitrate is reduced to nitrite by some K. sedentarius strains [1]. K. sedentarius is not only described as the source of the oligoketide antibiotics monensin A and B [21], but has also been associated with pitted keratolysis [16], opportunistic infections, and fatal hemorrhagic pneumonia [17].
Figure 1 shows the phylogenetic neighborhood of K. sedentarius strain 541T in a 16S rRNA based tree. Analysis of the 16S rRNA gene copies in the genome of strain 541T differed by one nucleotide from each other, and by up to two nucleotides from the previously published 16S rRNA sequence generated from DSM 20547 (X87755).
The murein of K. sedentarius strain 541T contains L-Lys-Glu2, a variation of cell wall type A4α [1]. Mycolic acids and teichonic acids were not reported [1]. Strain 541T contains only completely unsaturated menaquinones with 8-11 isoprene subunits (MK8 to MK11), with MK8 dominating [1]. The major cellular fatty acids are methyl-branched chain iso-C17:1 and anteiso-C17:0, as well as the straight chain saturated C15:0 and C17:0 [1]. Phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylinositol were identified as dominating polar lipids [1]. Reported cytochromes include aa3, c626, c550, b557, b561, and b564 [1].
This organism was selected for sequencing on the basis of its phylogenetic position, and is part of the GenomicEncyclopedia ofBacteria andArchaea project. The genome project is deposited in the Genome OnLine Database [6] and 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.
| MIGS ID | Property | Term |
|---|---|---|
| MIGS-31 | Finishing quality | Finished |
| MIGS-28 | Libraries used | Two genomic Sanger libraries: 8kb pMCL200 and fosmid pcc1Fos libraries. |
| MIGS-29 | Sequencing platforms | ABI3730 |
| MIGS-31.2 | Sequencing coverage | 17.3x Sanger |
| MIGS-30 | Assemblers | phrap |
| MIGS-32 | Gene calling method | Genemark 4.6b, tRNAScan-SE-1.23, infernal 0.81 |
| Genbank ID | ABUD00000000 | |
| Genbank Date of Release | N/A | |
| NCBI project ID | 21067 | |
| GOLD ID | Gc01042 | |
| Database: IMG-GEBA | 2500901761 | |
| MIGS-13 | Source material identifier | DSM 20547 |
| Project relevance | Tree of Life, GEBA |
K. sedentarius strain 541T, DSM20547, was grown in DSMZ medium 92 (3% trypticase soy broth, 0.3% yeast extract) at 30°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 for cell lysis in first freezing for 20 min. (-70°C), then heating 5 min. (98°C), and cooling 15 min to 37°C; adding 1.5 ml lysozyme (standard: 0.3 ml, only), 1.0 ml achromopeptidase, 0.12 ml lysostaphine, 0.12 ml mutanolysine, 1.5 ml proteinase K (standard: 0.5 ml, only), followed by overnight incubation at 35°C.
The genome was sequenced using a combination of 8 kb and fosmid DNA libraries. All general aspects of library construction and sequencing performed at the JGI website. Draft assemblies were based on 60,742 total reads. The Phred/Phrap-/Consed software package was used for sequence assembly and quality assessment [22-24]. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with Dupfinisher [25] or transposon bombing of bridging clones (Epicentre Biotechnologies, Madison, WI). Gaps between contigs were closed by editing in Consed, custom priming, or PCR amplification (Roche Applied Science, Indianapolis, IN). A total of 1,255 additional reactions were necessary to close gaps and to raise the quality of the finished sequence. The completed genome sequence of K. sedentarius 541T contains 61,582 reads. The error rate of the completed genome sequence is less than 1 in 100,000. Together all libraries provided > 17x coverage of the genome.
Genes were identified using GeneMark [26] as part of the genome annotation pipeline in the Integrated Microbial Genomes Expert Review (IMG-ER) system [27], followed by a round of manual curation using JGI’s GenePRIMP pipeline. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. The tRNAScanSE tool [28] was used to find tRNA genes, whereas ribosomal RNAs were found by using the tool RNAmmer [29]. Other non-coding RNAs were identified by searching the genome for the Rfam profiles using INFERNAL (v0.81) [30]. Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes (IMG) platform [31].
The metabolic Pathway/Genome Database (PGDB) was computationally generated using Pathway Tools software version 12.5 [32] and MetaCyc version 12.5 [33], based on annotated EC numbers and a customized enzyme name mapping file. It has undergone no subsequent manual curation and may contain errors, similar to a Tier 3 BioCyc PGDB [34].
The genome is 2,785,024 bp long and comprises one main circular chromosome with a 71.6% GC content (Table 3 and Figure 3). Of the 2,703 genes predicted, 2,639 were protein-coding genes, 64 encoded RNAs. Eighty-four pseudogenes were also identified. In addition, 72.1% of the genes were assigned with a putative function while the remaining ones were annotated as hypothetical proteins.
| Attribute | Value | % of Total |
|---|---|---|
| Genome size (bp) | 2,785,024 | |
| DNA Coding region (bp) | 2,558,989 | 91.88% |
| DNA G+C content (bp) | 1,994,844 | 71.63% |
| Number of replicons | 1 | |
| Extrachromosomal elements | 0 | |
| Total genes | 2703 | 100.00% |
| RNA genes | 64 | 2.37% |
| rRNA operons | 2 | |
| Protein-coding genes | 2639 | 97.63% |
| Pseudo genes | 84 | 3.11% |
| Genes with function prediction | 1948 | 72.07% |
| Genes in paralog clusters | 288 | 10.65% |
| Genes assigned to COGs | 1851 | 68.48% |
| Genes assigned Pfam domains | 1908 | 70.59% |
| Genes with signal peptides | 539 | 19.94% |
| Genes with transmembrane helices | 595 | 22.01% |
| CRISPR repeats | 0 | 0 |
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. |
The distribution of genes into COGs functional categories is presented in Table 4, and a cellular overview diagram is presented in Figure 4, followed by a summary of metabolic network statistics shown in Table 5.
| Code | Value | % | Description | |
|---|---|---|---|---|
| J | 151 | 5.7 | Translation | |
| A | 1 | 0.0 | RNA processing and modification | |
| K | 143 | 5.4 | Transcription | |
| L | 160 | 6.1 | Replication, recombination and repair | |
| B | 2 | 0.1 | Chromatin structure and dynamics | |
| D | 22 | 0.8 | Cell cycle control, mitosis and meiosis | |
| Y | 0 | 0.0 | Nuclear structure | |
| V | 56 | 2.1 | Defense mechanisms | |
| T | 73 | 2.8 | Signal transduction mechanisms | |
| M | 111 | 4.2 | Cell wall/membrane biogenesis | |
| N | 2 | 0.1 | Cell motility | |
| Z | 1 | 0.0 | Cytoskeleton | |
| W | 0 | 0.0 | Extracellular structures | |
| U | 27 | 1.0 | Intracellular trafficking and secretion | |
| O | 64 | 2.4 | Posttranslational modification, protein turnover, chaperones | |
| C | 99 | 3.8 | Energy production and conversion | |
| G | 116 | 4.4 | Carbohydrate transport and metabolism | |
| E | 185 | 7.0 | Amino acid transport and metabolism | |
| F | 75 | 2.8 | Nucleotide transport and metabolism | |
| H | 101 | 3.8 | Coenzyme transport and metabolism | |
| I | 86 | 3.3 | Lipid transport and metabolism | |
| P | 117 | 4.4 | Inorganic ion transport and metabolism | |
| Q | 46 | 1.7 | Secondary metabolites biosynthesis, transport and catabolism | |
| R | 229 | 8.7 | General function prediction only | |
| S | 160 | 6.1 | Function unknown | |
| - | 788 | 29.9 | Not in COGs | |
Figure 4 Schematic cellular overview of all pathways of the K. sedentarius strain 541T metabolism. Nodes represent metabolites, with shape indicating class of metabolite. Lines represent reactions. |
| Attribute | Value |
|---|---|
| Total genes | 2703 |
| Enzymes | 531 |
| Enzymatic reactions | 922 |
| Metabolic pathways | 185 |
| Metabolites | 662 |
We would like to gratefully acknowledge the help of Katja Steenblock (DSMZ) for growing K. sedentarius 541T cultures. 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.
| 1. | Stackebrandt E, Koch C, Gvozdiak O, Schumann P. Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend. Int J Syst Bacteriol 1995; 45: 682-692. [pmid:7547287] |
| 2. | ZoBell CE. Upham HC. A list of marine bacteria including descriptions of sixty new species. Bull Scripps Inst Oceanogr Calif 1944; 5: 239-292. |
| 3. | 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] [pmid:11934745] |
| 4. | Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17: 368-376. [doi:10.1007/BF01734359] [pmid:7288891] |
| 5. | 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] [pmid:18853362] |
| 6. | 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] [pmid:17981842] |
| 7. | Kloss WE, Tornabebe TG, Schleifer KH. Isolation and characterization of Micrococci from human skin, including two species: Micrococcus lylae and Micrococcus kristinae. Int J Syst Bacteriol 1974; 24: 79-101; doi:10.1099/00207713-24-1-79. |
| 8. | Tiago I, Chung AP, Verissimo A. Bacterial diversity in a nonsaline alkaline environment: heterotrophic aerobic populations. Appl Environ Microbiol 2004; 70:7378-7387 [doi:10.1128/AEM.70.12.7378-7387.2004] [pmid:15574939] |
| 9. | .Bhattarai HD, Lee YK, Cho KH, Lee HK, Shin HE. The study of antagonistic interactions among pelagic bacteria: a promising way to coin environmental friendly antifouling compounds. Hydrobiologica 2006; 568: 417-423. [doi:10.1007/s10750-006-0220-2] |
| 10. | Gontang EA, Fenical W, Jensen PR. Phylogenetic diversity of gram-positive bacteria cultured from marine sediments. Appl Environ Microbiol 2007; 73: 3272-3282. [doi:10.1128/AEM.02811-06] [pmid:17400789] |
| 11. | Osman S, La Duc MT, Dekas A, Newcombe D, Venkateswaran K. Microbial burden and diversity of commercial airline cabin air during short and long durations of travel. ISME J 2008; 2: 482-497. [doi:10.1038/ismej.2008.11] [pmid:18256704] |
| 12. | 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] [pmid:18464787] |
| 13. | Stackebrandt E, Rainey F, Ward-Rainey N. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 1997; 47: 479-491. |
| 14. | Buchanan RE. Studies in the Nomenclature and Classification of the Bacteria: VIII. The Subgroups and Genera of the Actinomycetales. J Bacteriol 1918; 3: 403-406. [pmid:16558803] |
| 15. | Stackebrandt E, Schumann P. Description of Bogoriellaceae fam. nov., Dermacoccaceae fam. nov., Rarobacteraceae fam. nov. and Sanguibacteraceae fam. nov. and emendation of some families of the suborder Micrococcineae. Int J Syst Evol Microbiol 2000; 50: 1279-1285. [pmid:10843073] |
| 16. | Longshaw CM, Wright JD, Farrell AM, Holland KT. Kytococcus sedentarius, the organism associated with pitted keratolysis, produces two keratin-degrading enzymes. J Appl Microbiol 2002; 93: 810-816. [doi:10.1046/j.1365-2672.2002.01742.x] [pmid:12392527] |
| 17. | Levenga H, Donnelly P, Blijlevens N, Verweij P, Shirango H, de Pauw B. Fatal hemorrhagic pneumonia caused by infection due to Kytococcus sedentarius--a pathogen or passenger? Ann Hematol 2004; 83: 447-449. [doi:10.1007/s00277-003-0831-x] [pmid:14689234] |
| 18. | Anonymous. Biological Agents: Technical rules for biological agents. www.baua.de. |
| 19. | 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] [pmid:10802651] |
| 20. | Nakamiya K, Nakayama T, Ito H, Edmonds JS, Shibata Y, Morita M. Degradation of arylarsenic compounds by microorganisms. FEMS Microbiol Lett 2007; 274: 184-188. [doi:10.1111/j.1574-6968.2007.00835.x] [pmid:17697081] |
| 21. | Pospísil S, Benada O, Kofronova O, Petricek M, Janda L, Havlicek V. Kytococcus sedentarius (formerly Micrococcus sedentarius) and Dermacoccus nishinomiyaensis (formerly Micrococcus nishinomiyaensis) produce monensins, typical Streptomyces cinnamonensis metabolites. Can J Microbiol 1998; 44: 1007-1011. [doi:10.1139/cjm-44-10-1007] [pmid:9933918] |
| 22. | Ewing B, Green P. Base-calling of automated sequencer traces using phred II. Error probabilities. Genome Res 1998; 8: 186-194. [pmid:9521922] |
| 23. | Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998; 8: 175-185. [pmid:9521921] |
| 24. | Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Res 1998; 8: 195-202. [pmid:9521923] |
| 25. | Han CS, Chain P. Finishing repeat regions automatically with Dupfinisher. 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. |
| 26. | Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29: 2607-2618. [doi:10.1093/nar/29.12.2607] [pmid:11410670] |
| 27. | Markowitz V, Mavromatis K, Ivanova N, Chen I-M, Chu K, Palaniappan K, Szeto E, Anderson I, Lykidis A, Kyrpides N. Expert Review of Functional Annotations for Microbial Genomes. (Submited 2009). |
| 28. | Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25: 955-964. [doi:10.1093/nar/25.5.955] [pmid:9023104] |
| 29. | Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35: 3100-3108. [doi:10.1093/nar/gkm160] [pmid:17452365] |
| 30. | Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 2005; 33: D121-D124. [doi:10.1093/nar/gki081] [pmid:15608160] |
| 31. | Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis A, Mavromatis K, et al. The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res 2008; 36: D528-D533. [doi:10.1093/nar/gkm846] [pmid:17933782] |
| 32. | Karp PD, Paley S, Romero P. The pathway tools software. [PMID: 12169551]. Bioinformatics 2002; 18(Suppl1): S225-S232. [pmid:12169551] |
| 33. | Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, et al. The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 2008; 36: D623-D631. [doi:10.1093/nar/gkm900] [pmid:17965431] |
| 34. | Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahren D, Tsoka S, Darzentas N, Kunin V, Lopez-Bigas N. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 2005; 33: 6083-6089. [doi:10.1093/nar/gki892] [pmid:16246909] |
This work is licensed under a Creative Commons Attribution 3.0 License.
 |
This article doi:10.4056/sigs.761 has been cited by 74 other articles: |
Complete genome sequence of Thermobispora bispora type strain (R51T)
Liolios et al.
Stand. Genomic Sci. 2(3) 318.
10.4056/sigs.962171
Complete genome sequence of Leptotrichia buccalis type strain (C-1013-bT)
Ivanova et al.
Stand. Genomic Sci. 1(2) 126.
10.4056/sigs.1854
Complete genome sequence of Desulfomicrobium baculatum type strain (XT)
Copeland et al.
Stand. Genomic Sci. 1(1) 29.
10.4056/sigs.13134
Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3T)
Pitluck et al.
Stand. Genomic Sci. 3(3) 285.
10.4056/sigs.1253298
Complete genome sequence of Methanothermus fervidus type strain (V24ST)
Anderson et al.
Stand. Genomic Sci. 3(3) 315.
10.4056/sigs.1283367
Complete genome sequence of Oceanithermus profundus type strain (506T)
Pati et al.
Stand. Genomic Sci. 4(2) 210.
10.4056/sigs.1734292
Complete genome sequence of Saccharomonospora viridis type strain (P101T)
Pati et al.
Stand. Genomic Sci. 1(2) 141.
10.4056/sigs.20263
Complete genome sequence of Atopobium parvulum type strain (IPP 1246T)
Copeland et al.
Stand. Genomic Sci. 1(2) 166.
10.4056/sigs.29547
Complete genome sequence of Halorhabdus utahensis type strain (AX-2T)
Anderson et al.
Stand. Genomic Sci. 1(3) 218.
10.4056/sigs.31864
Complete genome sequence of Odoribacter splanchnicus type strain (1651/6T)
Göker et al.
Stand. Genomic Sci. 4(2) 200.
10.4056/sigs.1714269
Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139T)
Land et al.
Stand. Genomic Sci. 4(2) 233.
10.4056/sigs.1784330
Complete genome sequence of Sulfurospirillum deleyianum type strain (5175T)
Sikorski et al.
Stand. Genomic Sci. 2(2) 149.
10.4056/sigs.671209
Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134T)
Pukall et al.
Stand. Genomic Sci. 1(3) 262.
10.4056/sigs.41646
Complete genome sequence of Rhodothermus marinus type strain (R-10T)
Nolan et al.
Stand. Genomic Sci. 1(3) 283.
10.4056/sigs.46736
Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255T)
Saunders et al.
Stand. Genomic Sci. 1((2)) 174.
10.4056/sigs.33592
Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575T)
Spring et al.
Stand. Genomic Sci. 1(3) 242-253.
10.4056/sigs.39508
Complete genome sequence of Catenulispora acidiphila type strain (ID 139908T)
Copeland et al.
Stand. Genomic Sci. 1(2) 119.
10.4056/sigs.17259
Complete genome sequence of Kangiella koreensis type strain (SW-125T)
Han et al.
Stand. Genomic Sci. 1(3) 226.
10.4056/sigs.36635
Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1T)
Pukall et al.
Stand. Genomic Sci. 1(3) 234.
10.4056/sigs.37633
Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883T)
Chovatia et al.
Stand. Genomic Sci. 1(3) 254.
10.4056/sigs.40645
Complete genome sequence of Geodermatophilus obscurus type strain (G-20T)
Ivanova et al.
Stand. Genomic Sci. 2(2) 158.
10.4056/sigs.711311
Complete genome sequence of Stackebrandtia
nassauensis type strain (LLR-40K-21T)
Munk et al.
Stand. Genomic Sci. 1(3) 1.
10.4056/sigs.47643
Complete genome sequence of Streptobacillus moniliformis type strain (9901T)
Nolan et al.
Stand. Genomic Sci. 1(3) 1.
10.4056/sigs.48727
Complete genome sequence of Streptosporangium roseum type strain (NI 9100T)
Nolan et al.
Stand. Genomic Sci. 2(1) 29.
10.4056/sigs.631049
Complete genome sequence of Desulfohalobium retbaense type strain (HR100T)
Spring et al.
Stand. Genomic Sci. 2(1) 38.
10.4056/sigs.581048
Complete genome sequence of Veillonella parvula type strain (Te3T)
Gronow et al.
Stand. Genomic Sci. 2(1) 57.
10.4056/sigs.521107
Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IAT)
Mavromatis et al.
Stand. Genomic Sci. 2(1) 9.
10.4056/sigs.591104
Complete genome sequence of Gordonia bronchialis type strain (3410T)
Ivanova et al.
Stand. Genomic Sci. 2(1) 19.
10.4056/sigs.611106
Complete genome sequence of Segniliparus rotundus type strain (CDC 1076T)
Sikorski et al.
Stand. Genomic Sci. 2(2) 203.
10.4056/sigs.791633
Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034T)
Glavina Del Rio et al.
Stand. Genomic Sci. 2(1) 87.
10.4056/sigs.661199
Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyRT)
Han et al.
Stand. Genomic Sci. 4(3) 371.
10.4056/sigs.2004648
Complete genome sequence of Tsukamurella paurometabola type strain (no. 33T)
Munk et al.
Stand. Genomic Sci. 4(3) 342.
10.4056/sigs.1894556
Complete genome sequence of Rhodospirillum rubrum type strain (S1T)
Munk et al.
Stand. Genomic Sci. 4(3) 293.
10.4056/sigs.1804360
Complete genome sequence of Nakamurella multipartita type strain (Y-104T)
Tice et al.
Stand. Genomic Sci. 2(2) 168.
10.4056/sigs.721316
Complete genome sequence of Kribbella flavida type strain (IFO 14399T)
Pukall et al.
Stand. Genomic Sci. 2(2) 185.
10.4056/sigs.731321
Complete genome sequence of Thermocrinis albus type strain (HI 11/12T)
Wirth et al.
Stand. Genomic Sci. 2(2) 194.
10.4056/sigs.761490
Complete genome sequence of Spirosoma linguale type strain (1T)
Lail et al.
Stand. Genomic Sci. 2(2) 176.
10.4056/sigs.741334
Complete genome sequence of Conexibacter woesei type strain (ID131577T)
Pukall et al.
Stand. Genomic Sci. 2(2) 212.
10.4056/sigs.751339
Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300T)
Harmon-Smith et al.
Stand. Genomic Sci. 2(2) 220.
10.4056/sigs.811799
Complete genome sequence of Marivirga tractuosa type strain (H-43T)
Pagani et al.
Stand. Genomic Sci. 4(2) 154.
10.4056/sigs.1623941
Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21T)
Chang et al.
Stand. Genomic Sci. 5(1) 97.
10.4056/sigs.2114901
Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2T) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010.
Klenk et al.
Stand. Genomic Sci. 5(1) 121.
10.4056/sigs.2144922
Complete genome sequence of Tolumonas auensis type strain (TA 4T)
Chertkov et al.
Stand. Genomic Sci. 5(1) 112.
10.4056/sigs.2184986
Complete genome sequence of Desulfarculus baarsii type strain (2st14T)
Sun et al.
Stand. Genomic Sci. 3(3) 276.
10.4056/sigs.1243258
Complete genome sequence of Thermaerobacter marianensis type strain (7p75aT)
Han et al.
Stand. Genomic Sci. 3(3) 337.
10.4056/sigs.1373474
Complete genome sequence of Aminobacterium colombiense type strain (ALA-1T)
Chertkov et al.
Stand. Genomic Sci. 2(3) 280.
10.4056/sigs.902116
Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24T)
Mavromatis et al.
Stand. Genomic Sci. 2(3) 290.
10.4056/sigs.952166
Complete genome sequence of Brachyspira murdochii type strain (56-150T)
Pati et al.
Stand. Genomic Sci. 2(3) 260.
10.4056/sigs.831993
Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460T)
Kiss et al.
Stand. Genomic Sci. 2(3) 270.
10.4056/sigs.892105
Complete genome sequence of Archaeoglobus profundus type strain (AV18T)
von Jan et al.
Stand. Genomic Sci. 2(3) 327.
10.4056/sigs.942153
Complete genome sequence of Thermosphaera aggregans type strain (M11TLT)
Spring et al.
Stand. Genomic Sci. 2(3) 245.
10.4056/sigs.821804
Complete genome sequence of Arcobacter nitrofigilis type strain (CIT)
Pati et al.
Stand. Genomic Sci. 2(3) 300.
10.4056/sigs.912121
Complete genome sequence of Haliangium ochraceum type strain (SMP-2T)
Ivanova et al.
Stand. Genomic Sci. 2(1) 96.
10.4056/sigs.69.1277
Complete genome sequence of Haloterrigena turkmenica type strain (4kT)
Saunders et al.
Stand. Genomic Sci. 2(1) 107.
10.4056/sigs.681272
Complete genome sequence of Intrasporangium calvum type strain (7 KIPT)
Glavina Del Rio et al.
Stand. Genomic Sci. 3(3) 294.
10.4056/sigs.1263355
Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6T)
Zeytun et al.
Stand. Genomic Sci. 4(2) 131.
10.4056/sigs.1463589
Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1T)
Sikorski et al.
Stand. Genomic Sci. 3(3) 304.
10.4056/sigs.1273360
Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers.
Reeve et al.
Stand. Genomic Sci. 2(3) 347.
10.4056/sigs.852027
Complete genome sequence of Actinosynnema mirum type strain (101T)
Land et al.
Stand. Genomic Sci. 1(1) 46.
10.4056/sigs.21137
Complete genome sequence of Acidaminococcus fermentans type strain (VR4T)
Chang et al.
Stand. Genomic Sci. 3(1) 1.
10.4056/sigs.1002553
Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228T)
Mavromatis et al.
Stand. Genomic Sci. 3(2) 1.
10.4056/sigs.1143106
Complete genome sequence of Olsenella uli type strain (VPI D76D-27CT)
Göker et al.
Stand. Genomic Sci. 3(1) 76.
10.4056/sigs.1082860
Complete genome sequence of ‘Thermobaculum terrenum’ type strain (YNP1T)
Kiss et al.
Stand. Genomic Sci. 3(2) 153.
10.4056/sigs.1153107
Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288T)
Sikorski et al.
Stand. Genomic Sci. 3(1) 57.
10.4056/sigs.1062906
Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1T)
Göker et al.
Stand. Genomic Sci. 3(1) 66.
10.4056/sigs.1072907
Complete genome sequence of Halomicrobium mukohataei type strain (arg-2T)
Tindall et al.
Stand. Genomic Sci. 1(3) 270.
10.4056/sigs.42644
Complete genome sequence of Vulcanisaeta distributa type strain (IC-017T)
Mavromatis et al.
Stand. Genomic Sci. 3(2) 117.
10.4056/sigs.1113067
Complete genome sequence of Arcanobacterium haemolyticum type strain (11018T)
Yasawong et al.
Stand. Genomic Sci. 3(2) 126.
10.4056/sigs.1123072
Complete genome sequence of Ferrimonas balearica type strain (PATT)
Nolan et al.
Stand. Genomic Sci. 3(2) 174.
10.4056/sigs.1161239
Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1T)
Djao et al.
Stand. Genomic Sci. 3(3) 268.
10.4056/sigs.1233249
Complete genome sequence of Truepera radiovictrix type strain (RQ-24T)
Ivanova et al.
Stand. Genomic Sci. 4(1) 91.
10.4056/sigs.1563919
The State of Standards in Genomic Sciences
Garrity
Stand. Genomic Sci. 5(3) 262.
10.4056/sigs.2515706
Complete genome sequence of the halophilic and highly halotolerant Chromohalobacter salexigens type strain (1H11T)
Copeland et al.
Stand. Genomic Sci. 5(3) 379.
10.4056/sigs.2285059
Culturable bacteria isolated from snow cores along the 1300 km traverse from Zhongshan Station to Dome A, East Antarctica
Yan et al.
Extremophiles () .
10.1007/s00792-012-0434-3
Acknowledgements
We would like to gratefully acknowledge the support of many members of the Genomic Standards Consortium, the broader genomic science community, and those who have indicated their willingness to serve as editors, reviewers and contributors.
Funding for SIGS is provided by a grant from the Office of the Vice President for Research and Graduate Studies at Michigan State University, the Michigan State University Foundation, and the US Department of Energy Biological and Environmental Research DE-FG02-08ER64707.
Standards in Genomic Sciences is indexed in:
 |  |  |
 |  |
Sponsors of the Genomic Standards Consortium:
 |