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Complete genome sequence of Meiothermus ruber type strain (21T)

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Standards in Genomic Sciences20103:3010026

  • Published:


Meiothermus ruber (Loginova et al. 1984) Nobre et al. 1996 is the type species of the genus Meiothermus. This thermophilic genus is of special interest, as its members share relatively low degrees of 16S rRNA gene sequence similarity and constitute a separate evolutionary lineage from members of the genus Thermus, from which they can generally be distinguished by their slightly lower temperature optima. The temperature related split is in accordance with the chemotaxonomic feature of the polar lipids. M. ruber is a representative of the low-temperature group. This is the first completed genome sequence of the genus Meiothermus and only the third genome sequence to be published from a member of the family Thermaceae. The 3,097,457 bp long genome with its 3,052 protein-coding and 53 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.


  • thermophilic
  • aerobic
  • non-motile
  • free-living
  • Gram-negative
  • Thermales
  • Deinococci
  • GEBA


Strain 21T (= DSM 1279 = ATCC 35948 = VKM B-1258) is the type strain of the species Meiothermus ruber, which is the type species of the genus Meiothermus [1]. Strain 21T was first described as a member of the genus Thermus by Loginova and Egorova in 1975 [2], but the species name to which it was assigned was not included on the Approved Lists of Bacterial Names [3]. Consequently Thermus ruber was revived, according to Rule 28a of the International Code of Nomenclature of Bacteria [4] in 1984 [5]. It received its current name in 1996 when transferred from the genus Thermus into the then novel genus Meiothermus by Nobre et al. [1]. Currently, there are eight species placed in the genus Meiothermus [6]. The genus name derives from the Greek words ‘meion’ and ‘thermos’ meaning ‘lesser’ and ‘hot’ to indicate an organism in a less hot place [1,6]. The species epithet derives from the Latin word ‘ruber’ meaning red, to indicate the red cell pigmentation [5,6]. Members of the genus Meiothermus were isolated from natural hot springs and artificial thermal environments [1] in Russia [5], Central France [7], both Northern and Central Portugal [8,9], North-Eastern China [10], Northern Taiwan [11] and Iceland [12]. Interestingly, the genus Meiothermus is heterogeneous with respect to pigmentation. The yellow pigmented species also form a distinct group on the basis of the 16S rRNA gene sequence similarity, with the red/orange pigmented strains forming two groups, one comprising M. silvanus and the other the remaining species [9,10]. Like all members of the Deinococci the lipid composition of the cell membrane of members of the genus Meiothermus is based on unusual and characteristic structures. Here we present a summary classification and a set of features for M. ruber 21T, together with the description of the complete genomic sequencing and annotation.

Classification and features

The 16S rRNA genes of the seven other type strains in the genus Meiothermus share between 88.7% (M. silvanus) [13] and 98.8% (M. taiwanensis) [14] sequence identity with strain 21T, whereas the other type strains from the family Thermaceae share 84.5 to 87.6% sequence identity [15]. Thermus sp. R55-10 from the Great Artesian Basin of Australia (AF407749), as well as other reference strains, e.g. 16105 and 17106 [12], and the uncultured bacterial clone 53-ORF05 from an aerobic sequencing batch reactor (DQ376569) show full length 16S rRNA sequences identical to that of strain 21T. A rather large number of isolates with almost identical 16S rRNA gene sequences originates from the Great Artesian Basin of Australia, clone R03 (AF407684), and various hot springs in Hyogo, Japan (strain H328; AB442017), Liaoning Province, China (strain L462; EU418906, and others), Thailand (strain O1DQU (EU376397), a Finnish paper production facility (strain L-s-R2A-3B.2; AM229096) and others), but also the not validly published ‘M. rosaceus’ (99.9%) [16] from Tengchong hot spring in Yunnan (China). Environmental samples and metagenomic surveys do not surpass 81–82% sequence similarity to the 16S rRNA gene sequence of strain 21T, indicating a rather mixed impression about the environmental importance of strains belonging to the species M. ruber, as occurring only in very restricted extreme habitats (status August 2009).

Figure 2 shows the phylogenetic neighborhood of M. ruber 21T in a 16S rRNA based tree. The sequences of the two 16S rRNA gene copies in the genome are identical and differ by only one nucleotide from the previously published sequence generated from ATCC 35948 (Z15059).

A detailed physiological description based on five strains has been given by Loginova et al. [5]. The cells are described as Gram-negative nonmotile rods that are 3 to 6 by 0.5 to 0.8 µm (Table 1), have rounded ends, and are nonsporeforming [5]. In potato-peptone-yeast extract broth incubated at 60°C, filamentous forms (20 to 40 µm in length) are observed along with shorter rods (Figure 1) [5]. No filamentous forms are observed after 16 h of incubation. M. ruber is obligately thermophilic [5]. On potato-peptone-yeast extract medium, the temperature range for growth is approx. 35–70°C, with an optimum temperature at 60°C (the generation time is then 60 min) [5]. A bright red intracellular carotenoid pigment is produced, which resembles retro-dehydro-γ-carotene (neo A, neo B) in its spectral properties [2]. The absorption spectra of acetone, methanol-acetone (l:l), and hexane extracts show three maxima at 455, 483, and 513 nm. The major carotenoid has since been identified as a 1′-β-glucopyranosyl-3,4,3′,4′-tetradehydro-1′,2′-dihydro-β,ψ-caroten-2-one, with the glucose acetylated at position 6 [30]. One strain (strain INMI-a) contains a bright yellow pigment resembling neurosporaxanthine in its spectral properties [5], although it may well have been misidentified, since other species within the genus Meiothermus are yellow pigmented [8,9]. M. ruber is obligately aerobic [5]. It grows in minimal medium supplemented with 0.15% (wt/vol) peptone as an N source, 0.05% (wt/vol) yeast extract, and one of the following carbon sources at a concentration of 0.25% (wt/vol): D-glucose, sucrose, maltose, D-galactose, D-mannose, rhamnose, D-cellobiose, glycerol, D-mannitol, acetate, pyruvate, succinate, fumarate, or DL-malate (sodium salts). No growth occurs if the concentration of D-glucose in the medium is raised to 0.5% (wt/vol) [5]. Only moderate growth occurs when ammonium phosphate (0.1%, wt/vol) is substituted for peptone as the N source. No growth occurs in the control medium without a carbon source. No growth occurs on minimal medium supplemented with 0.25% (wt/vol) D-glucose, 0.05% (wt/vol) yeast extract and one of the following nitrogen sources at a concentration of 0.1% (wt/vol): L-alanine, glycine, L-asparagine, L-tyrosine, L-glutamate, ammonium sulfate, nitrate, or urea. Further lists of carbon source utilization, which differ in part from the above list, are published elsewhere [7,1012]. Nitrates are not reduced and milk is not peptonized [5], but M. ruber strain 21T is positive for catalase and oxidase [10]. The most comprehensive and updated list of physiological properties is probably given by Albuquerque et al [7].
Figure 1.
Figure 1.

Scanning electron micrograph of M. ruber 21T

Figure 2.
Figure 2.

Phylogenetic tree highlighting the position of M. ruber 21T relative to the type strains of the other species within the genus and to the type strains of the other species within the family Thermaceae. The trees were inferred from 1,403 aligned characters [31,32] of the 16S rRNA gene sequence under the maximum likelihood criterion [33] and rooted in accordance with the current taxonomy [34]. 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 [35] if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [36] are shown in blue, published genomes in bold (Thermus thermophilus; AP008226).

Table 1.

Classification and general features of M. ruber 21T according to the MIGS recommendations [17]




Evidence code


Current classification

Domain Bacteria

TAS [18]


Phylum Deinococcus-Thermus

TAS [1,3,1923]


Class Deinococci

TAS [24,25]


Order Thermales

TAS [25,26]


Family Thermaceae

TAS [25,27]


Genus Meiothermus

TAS [1,7]


Species Meiothermus ruber

TAS [1,5]


Type strain 21

TAS [5]


Gram stain


TAS [5]


Cell shape


TAS [5]



non motile

TAS [5]



not reported

TAS [5]


Temperature range


TAS [5]


Optimum temperature


TAS [5]



growth with 1% NaCl

TAS [7]


Oxygen requirement

obligately aerobic

TAS [5]


Carbon source

a diverse set of sugars

TAS [5]


Energy source


TAS [5]



hot springs

TAS [5]


Biotic relationship


TAS [5]



not reported


Biosafety level


TAS [28]



hot spring

TAS [5]


Geographic location

Kamchatka Peninsula, Russia

TAS [5]


Sample collection time

1973 or before

TAS [2]

















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 of the Gene Ontology project [29]. If the evidence code is IDA, then the property was directly observed by one of the authors or an expert mentioned in the acknowledgements


Initial reports on the polar lipids of M. ruber indicated that they consist of two major glycolipids GL1a ( 42%) and GL1b ( 57%) and one major phospholipid PL2 ( 93%), with small amounts of two other phospholipids PL1 and PL3 [37]. Detailed work indicates that in strains of Thermus oshimai, T. thermophilus, M. ruber, and M. taiwanensis the major phospholipid is a 2’-O-(1, 2-diacyl-sn-glycero-3-phospho)-3’-O-(α-N-acetyl-glucosaminyl)-N-glyceroyl alkylamine [38]. This compound is related to the major phosphoglycolipid reported from Deinococcus radiodurans [39] and can be considered to be unambiguous chemical markers for this major evolutionary lineage. The glycolipids are derivatives of a Glcp-> Glcp-> GalNAcyl-> Glcp-> diacyl glycerol [40]. Based on mass spectral data it appears that there may be three distinct derivatives, differing in the fatty acid amide linked to the gatactosamine [40]. These may be divided into one compound containing exclusively 2-hydroxylated fatty acids (mainly 2-OH iso-17:0) and a mixture of two compounds that cannot be fully resolved by thin layer chromatography carrying either 3-hydroxylated fatty acids or unsubstituted fatty acids. The basic glycolipid structure dihexosyl - N-acyl-hexosaminyl - hexosyl - diacylglycerol is a feature common to all members of the genera Thermus and Meiothermus examined to date. There is currently no evidence that members of the family Thermaceae (as currently defined) produce significant amounts of polar lipids containing only two aliphatic side chains. The consequences of having polar lipids containing three aliphatic side chains on membrane structure has yet to be examined. Such peculiarities also indicate the value of membrane composition in helping to unravel evolution at a cellular level. The major fatty acids of the polar lipids are iso-C15:0 (30-40%) and iso-C17:0 (13-17%), followed by anteiso-C15:0, C16:0, iso-C16:0, anteiso-C17:0, iso-C17:0-2OH, and, at least in some studies, iso-C17:1 ω9c (the values range from 3–10%). Other fatty acid values are below 2%, including 3-OH branched chain fatty acids. The values vary slightly between the different studies [7,9,11,12,37]. Detailed structural studies suggest that long chain diols may be present in small amounts, substituting for the 1-acyl-sn-glycerol [38]. Although not routinely reported the presence of alkylamines (amide linked to the glyceric acid of the major phospholipid) can be deduced from detailed structural studies of the major phospholipid [38]. Menaquinone 8 is the major respiratory quinone, although it is not clear which pathway is used for the synthesis of the naphthoquinone ring nucleus [41]. Ornithine is the major diamino acid of the peptidoglycan in the genus Meiothermus [1].

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [42], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [43]. The genome project is deposited in the Genome OnLine Database [36] 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





Finishing quality



Libraries used

Three genomic libraries: one Sanger 8 kb pMCL200 library, one fosmide library and one 454 pyrosequence standard library


Sequencing platforms

ABI3730, 454 Titanium


Sequencing coverage

9.84× Sanger; 27.4× pyrosequence



Newbler version, PGA


Gene calling method

Prodigal 1.4, GenePRIMP





Genbank Date of Release

March 3, 2010





NCBI project ID



Database: IMG-GEBA



Source material identifier

DSM 1279


Project relevance

Tree of Life, GEBA

Growth conditions and DNA isolation

M. ruber 21T, DSM 1279, was grown in DSMZ medium 256 (Nutrient Agar) [44] at 50°C. DNA was isolated from 0.5–1 g of cell paste using Qiagen Genomic 500 DNA Kit (Qiagen, Hilden, Germany) following the standard protocol as recommended by the manufacturer, with modification L for cell lysis as described in Wu et al. [43].

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 can be found at the JGI website ( Pyrosequencing reads were assembled using the Newbler assembler version (Roche). Large Newbler contigs were broken into 3,428 overlap ping 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 adjust inflated q-scores. A hybrid 454/Sanger assembly was made using PGA assembler. Possible misassemblies were corrected and gaps between contgis were closed by primer walks off Sanger clones and bridging PCR fragments and by editing in Consed. A total of 431 Sanger finishing reads were produced to close gaps, to resolve repetitive regions, and to raise the quality of the finished sequence. Illumina reads were used to improve the final consensus quality using an in-house developed tool (the Polisher [45]). The error rate of the completed genome sequence is less than 1 in 100,000. Together, the combination of the Sanger and 454 sequencing platforms provided 37.24× coverage of the genome. The final assembly contains 30,479 Sanger reads and 371,362 pyrosequencing reads.

Genome annotation

Genes were identified using Prodigal [46] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [47]. 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 was performed within the Integrated Microbial Genomes - Expert Review (IMG-ER) platform [48].

Genome properties

The genome consists of a 3,097,457 bp long chromosome with a 63.4% GC content (Table 3 and Figure 3). Of the 3,105 genes predicted, 3,052 were protein-coding genes, and 53 RNAs; thirty eight pseudogenes were also identified. The majority of the protein-coding genes (71.8%) 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



% of Total

Genome size (bp)



DNA Coding region (bp)



DNA G+C content (bp)



Number of replicons



Extrachromosomal elements



Total genes



RNA genes



rRNA operons



Protein-coding genes



Pseudo genes



Genes with function prediction



Genes in paralog clusters



Genes assigned to COGs



Genes assigned Pfam domains



Genes with signal peptides



Genes with transmembrane helices



CRISPR repeats


Table 4.

Number of genes associated with the general COG functional categories








Translation, ribosomal structure and biogenesis




RNA processing and modification








Replication, recombination and repair




Chromatin structure and dynamics




Cell cycle control, cell division, chromosome partitioning




Nuclear structure




Defense mechanisms




Signal transduction mechanisms




Cell wall/membrane/envelope biogenesis




Cell motility








Extracellular structures




Intracellular trafficking and secretion, and vesicular transport




Posttranslational modification, protein turnover, chaperones




Energy production and conversion




Carbohydrate transport and metabolism




Amino acid transport and metabolism




Nucleotide transport and metabolism




Coenzyme transport and metabolism




Lipid transport and metabolism




Inorganic ion transport and metabolism




Secondary metabolites biosynthesis, transport and catabolism




General function prediction only




Function unknown




Not in COGs



We would like to gratefully acknowledge the help of Susanne Schneider (DSMZ) for DNA extraction and quality analysis. 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, UT-Battelle, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2 and SI 1352/1-2.

Authors’ Affiliations

DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
DOE Joint Genome Institute, Walnut Creek, California, USA
Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
University of California Davis Genome Center, Davis, California, USA


  1. Nobre MF, Trüper HG, Da Costa MS. Transfer of Thermus ruber (Loginova et al. 1984), Thermus silvanus (Tenreiro et al. 1995), and Thermus chliarophilus (Tenreiro et al. 1995) to Meiothermus gen. nov. as Meiothermus ruber comb. nov., Meiothermus silvanus comb. nov., and Meiothermus chliarophilus comb. nov., respectively, and emendation of the genus Thermus. Int J Syst Bacteriol 1996; 46:604–606. doi:10.1099/00207713-46-2-604View ArticleGoogle Scholar
  2. Loginova LG, Egorova LA. Obligate thermophilicbacterium Thermus ruber in hot springs of Kamchatka. Mikrobiologiya 1975; 44:661–665.Google Scholar
  3. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225–420. doi:10.1099/00207713-30-1-225View ArticleGoogle Scholar
  4. Lapage SP, Sneath PHA, Lessel EF, Skerman VBD, Seeliger HPR, Clark WA. 1992. International Code of Nomenclature of Bacteria (1990 Revision). Bacteriological Code. American Society for Microbiology, Washington, DC.Google Scholar
  5. Loginova LG, Egorova LA, Golovacheva RS, Seregina LM. Thermus ruber sp. nov., nom. rev. Int J Syst Bacteriol 1984; 34:498–499. doi:10.1099/00207713-34-4-498View ArticleGoogle Scholar
  6. Euzéby JP. List of bacterial names with standing in nomenclature: A folder available on the Internet. Int J Syst Bacteriol 1997; 47:590–592. PubMed doi:10.1099/00207713-47-2-590View ArticlePubMedGoogle Scholar
  7. Albuquerque L, Ferreira C, Tomaz D, Tiago I, Veríssimo A, da Costa MS, Nobre MF. Meiothermus rufus sp. nov., a new slightly thermophilic red-pigmented species and emended description of the genus Meiothermus. Syst Appl Microbiol 2009; 32:306–313. PubMed doi:10.1016/j.syapm.2009.05.002View ArticlePubMedGoogle Scholar
  8. Tenreiro S, Nobre MF, da Costa MS. Thermus silvanus sp. nov. and Thermus chliarophilus sp. nov., two new species related to Thermus ruber but with lower growth temperatures. Int J Syst Bacteriol 1995; 45:633–639. PubMed doi:10.1099/00207713-45-4-633View ArticlePubMedGoogle Scholar
  9. Pires AL, Albuquerque L, Tiago I, Nobre MF, Empadinhas N, Veríssimo A, da Costa MS. Meiothermus timidus sp. nov., a new slightly thermophilic yellow-pigmented species. FEMS Microbiol Lett 2005; 245:39–45. PubMed doi:10.1016/j.femsle.2005.02.011View ArticlePubMedGoogle Scholar
  10. Zhang XQ, Zhang WJ, Wei BP, Xu XW, Zhu XF, Wu M. Meiothermus cateniformans sp. nov., a slightly thermophilic species from north-eastern China. Int J Syst Evol Microbiol 2010; 60:840–844. PubMed doi:10.1099/ijs.0.007914-0View ArticlePubMedGoogle Scholar
  11. Chen MY, Lin GH, Lin YT, Tsay SS. Meiothermus taiwanensis sp. nov., a novel filamentous, thermophilic species isolated in Taiwan. Int J Syst Evol Microbiol 2002; 52:1647–1654. PubMed doi:10.1099/ijs.0.02189-0PubMedGoogle Scholar
  12. Chung AP, Rainey F, Nobre MF, Burghardt J, Costa MSD. Meiothermus cerbereus sp. nov., a new slightly thermophilic species with high levels of 3-hydroxy fatty acids. Int J Syst Bacteriol 1997; 47:1225–1230. PubMed doi:10.1099/00207713-47-4-1225View ArticlePubMedGoogle Scholar
  13. Nobre MF, Trüper HG. Da Costa. Transfer of Thermus ruber (Loginova et al. 1984), Thermus silvanus (Tenreiro et al. 1995), and Thermus chliarophilus (Tenreiro et al. 1995) to Meiothermus gen. nov. as Meiothermus ruber comb. nov., Meiothermus silvanus comb. nov., and Meiothermus chliarophilus comb. nov., respectively, and emendation of the genus Thermus. Int J Syst Bacteriol 1996; 46:604–606. doi:10.1099/00207713-46-2-604View ArticleGoogle Scholar
  14. Chen MY, Lin GH, Lin YT, Tsay SS. Meiothermus taiwanensis sp. nov., a novel filamentous, thermophilic species isolated in Taiwan. Int J Syst Evol Microbiol 2002; 52:1647–1654. PubMed doi:10.1099/ijs.0.02189-0PubMedGoogle Scholar
  15. Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK, Lim YW. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259–2261. PubMed doi:10.1099/ijs.0.64915-0View ArticlePubMedGoogle Scholar
  16. Chen C, Lin L, Peng Q, Ben K, Zhou Z. Meiothermus rosaceus sp. nov. isolated from Tengchong hot spring in Yunnan, China. FEMS Microbiol Lett 2002; 216:263–268. PubMed doi:10.1111/j.1574-6968.2002.tb11445.xView ArticlePubMedGoogle Scholar
  17. 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. PubMed doi:10.1038/nbt1360PubMed CentralView ArticlePubMedGoogle Scholar
  18. 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 doi:10.1073/pnas.87.12.4576PubMed CentralView ArticlePubMedGoogle Scholar
  19. Garrity GM, Lilburn TG, Cole JR, Harrison SH, Euzéby J, Tindall BJ. Taxonomic outline of the Bacteria and Archaea, Release 7.7 March 6, 2007. Part 2 — The Bacteria: Phyla “Aquificae”, “Thermotogae”, “Thermodesulfobacteria”, “Deinococcus-Thermus”, “Chrysiogenetes”, “Chloroflexi”, “Thermomicrobia”, “Nitrospira”, “Deferribacteres”, “Cyanobacteria”, and “Chlorobi”.
  20. Weisburg WG, Giovannoni SJ, Woese CR. The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction. Syst Appl Microbiol 1989; 11:128–134. PubMedView ArticlePubMedGoogle Scholar
  21. Brooks BW, Murray RGE. Nomenclature for Micrococcus radiodurans and other radiation resistant cocci: Deinococcaceae fam. nov. and Deinococcus gen. nov., including five species. Int J Syst Bacteriol 1981; 31:353–360. doi:10.1099/00207713-31-3-353View ArticleGoogle Scholar
  22. Rainey FA, Nobre MF, Schumman P, Stackebrandt E, da Costa MS. Phylogenetic diversity of the deinococci as determined by 16S ribosomal DNA sequence comparison. Int J Syst Bacteriol 1997; 47:510–514. PubMed doi:10.1099/00207713-47-2-510View ArticlePubMedGoogle Scholar
  23. Brock TD, Freeze H. Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophile. J Bacteriol 1969; 98:289–297. PubMedPubMed CentralPubMedGoogle Scholar
  24. Garrity GM, Holt JG. Class I. Deinococci class. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 395.View ArticleGoogle Scholar
  25. List Editor. Validation List no. 85. Validation of publication of new names and new combinations previously effectively published outside the IJ-SEM. Int J Syst Evol Microbiol 2002; 52:685–690. PubMed doi:10.1099/ijs.0.02358-0Google Scholar
  26. Rainey FA, da Costa MS. Order II. Thermales ord. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 403.Google Scholar
  27. da Costa MS, Rainey FA. Family I. Thermaceae fam. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 403–404.Google Scholar
  28. Classification of bacteria and archaea in risk groups. TRBA 466.
  29. 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. Nat Genet 2000; 25:25–29. PubMed doi:10.1038/75556PubMed CentralView ArticlePubMedGoogle Scholar
  30. Burgess ML, Barrow KD, Gao C, Heard GM, Glenn D. Carotenoid glycoside esters from the thermophilic bacterium Meiothermus ruber. J Nat Prod 1999; 62:859–863. PubMed doi:10.1021/np980573dView ArticlePubMedGoogle Scholar
  31. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552. PubMedView ArticlePubMedGoogle Scholar
  32. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452–464. PubMed doi:10.1093/bioinformatics/18.3.452View ArticlePubMedGoogle Scholar
  33. Stamatakis A, Hoover P, Rougemont J. A Rapid Bootstrap Algorithm for the RAxML Web Servers. Syst Biol 2008; 57:758–771. PubMed doi:10.1080/10635150802429642View ArticlePubMedGoogle Scholar
  34. Yarza P, Richter M, Peplies J, Euzeby JP, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rossello-Mora R. The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241–250. PubMed doi:10.1016/j.syapm.2008.07.001View ArticlePubMedGoogle Scholar
  35. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary? Lect Notes Comput Sci 2009; 5541:184–200. doi:10.1007/978-3-642-02008-713View ArticleGoogle Scholar
  36. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346–D354. PubMed doi:10.1093/nar/gkp848PubMed CentralView ArticlePubMedGoogle Scholar
  37. Donato ME, Seleiro EA, da Costa MS. Polar lipid and fatty acid composition of strains of Thermus ruber. Syst Appl Microbiol 1991; 14:234–239.Google Scholar
  38. Yang YL, Yang FL, Jao SC, Chen MY, Tsay SS, Zou W, Wu SH. Structural elucidation of phosphoglycolipids from strains of the bacterial thermophiles Thermus and Meiothermus. J Lipid Res 2006; 47:1823–1832. PubMed doi:10.1194/jlr.M600034-ILR200View ArticlePubMedGoogle Scholar
  39. Anderson R, Hansen K. Structure of a novel phosphoglycolipid from Deinococcus radiodurans. J Biol Chem 1985; 260:12219–12223. PubMedPubMedGoogle Scholar
  40. Ferreira AM, Wait R, Nobre MF, da Costa MS. Characterization of glycolipids from Meiothermus spp. Microbiology 1999; 145:1191–1199. PubMed doi:10.1099/13500872-145-5-1191View ArticlePubMedGoogle Scholar
  41. Hiratsuka T, Furihata K, Ishikawa J, Yamashita H, Itoh N, Seto H, Dairi T. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science 2008; 321:1670–1673. PubMed doi:10.1126/science.1160446View ArticlePubMedGoogle Scholar
  42. Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175–182. PubMed doi:10.1016/j.syapm.2010.03.003View ArticlePubMedGoogle Scholar
  43. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009; 462:1056–1060. PubMed doi:10.1038/nature08656PubMed CentralView ArticlePubMedGoogle Scholar
  44. List of growth media used at DSMZ:
  45. Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for using ultra short reads in microbial genome assembly and finishing. AGBT, Marco Island, FL, 2008.Google Scholar
  46. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal Prokaryotic Dynamic Programming Genefinding Algorithm. BMC Bioinformatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-PubMed CentralView ArticlePubMedGoogle Scholar
  47. Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A gene prediction improvement ipeline for microbial genomes. Nat Methods 2010; 7:455–457. PubMed doi:10.1038/nmeth.1457View ArticlePubMedGoogle Scholar
  48. Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271–2278. PubMed doi:10.1093/bioinformatics/btp393View ArticlePubMedGoogle Scholar


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