Open Access

Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyRT)

  • Cliff Han,
  • , Romano Mwirichia
  • , Olga Chertkov,
  • , Brittany Held,
  • , Alla Lapidus
  • , Matt Nolan
  • , Susan Lucas
  • , Nancy Hammon
  • , Shweta Deshpande
  • , Jan-Fang Cheng
  • , Roxanne Tapia,
  • , Lynne Goodwin,
  • , Sam Pitluck
  • , Marcel Huntemann
  • , Konstantinos Liolios
  • , Natalia Ivanova
  • , Ioanna Pagani
  • , Konstantinos Mavromatis
  • , Galina Ovchinikova
  • , Amrita Pati
  • , Amy Chen
  • , Krishna Palaniappan
  • , Miriam Land,
  • , Loren Hauser,
  • , Evelyne-Marie Brambilla
  • , Manfred Rohde
  • , Stefan Spring
  • , Johannes Sikorski
  • , Markus Göker
  • , Tanja Woyke
  • , James Bristow
  • , Jonathan A. Eisen,
  • , Victor Markowitz
  • , Philip Hugenholtz,
  • , Nikos C. Kyrpides
  • , Hans-Peter Klenk
  • and John C. Detter,
Corresponding author

DOI: 10.4056/sigs.2004684

Received: 01 July 2011

Published: 01 July 2011

Abstract

Syntrophobotulus glycolicus Friedrich et al. 1996 is currently the only member of the genus Syntrophobotulus within the family Peptococcaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of tree of life. When grown in pure culture with glyoxylate as carbon source the organism utilizes glyoxylate through fermentative oxidation, whereas, when grown in syntrophic co-culture with homoacetogenic or methanogenic bacteria, it is able to oxidize glycolate to carbon dioxide and hydrogen. No other organic or inorganic carbon source is utilized by S. glycolicus. The subdivision of the family Peptococcaceae into genera does not reflect the natural relationships, particularly regarding the genera most closely related to Syntrophobotulus. Both Desulfotomaculum and Pelotomaculum are paraphyletic assemblages, and the taxonomic classification is in significant conflict with the 16S rRNA data. S. glycolicus is already the ninth member of the family Peptococcaceae with a completely sequenced and publicly available genome. The 3,406,739 bp long genome with its 3,370 protein-coding and 69 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords:

glycolate-oxidizingGram-negative staining with Gram-positive cell wall structurestrictly anaerobicchemotrophicmesophilicnon-motilerod-shapedspore-formingPeptococcaceaeClostridialesGEBA

Introduction

Strain FlGlyRT (= DSM 8271) is the type strain of Syntrophobotulus glycolicus within the monotypic genus Syntrophobotulus [1], which is affiliated to the family Peptococcaceae within the order Clostridiales [2]. The genus name is derived from the latinized Greek syntrophos meaning having grown up with one, and the Latin botulus, sausage, a syntrophic sausage-like item [3]. The species epithet is derived from the Neo-Latin acidum glycolicum meaning 'glycolic acid', 'referring to the key substrate of this species, glycolic acid [3]. The major characteristic that differentiates this genus from other bacteria is the ability to oxidize glyoxylate under anaerobic conditions [3]. The major source of glycolate in nature is excretion by algae and other photoautotrophs and chemoautotrophs [4-7]. Strain FlGlyRT was isolated from anoxic sewage sludge in Konstanz, Germany [3], but was also mentioned in earlier reports [8]. No further isolates have been reported until now. Here we present a summary classification and a set of features for S. glycolicus FlGlyRT, together with the description of the complete genomic sequencing and annotation.

Classification and features

A representative genomic 16S rRNA sequence of strain FlGlyRT was compared using NCBI BLAST [9] under default settings (e.g., considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database [10] and the relative frequencies of taxa and keywords (reduced to their stem [11]) were determined, weighted by BLAST scores. The most frequently occurring genera were Desulfitobacterium (45.4%), Desulfosporosinus (19.3%), Dehalobacter (18.0%), Heliobacterium (13.8%) and Syntrophobotulus (2.6%) (85 hits in total). Regarding the single hit to sequences from members of the species, the average identity within HSPs was 99.7%, whereas the average coverage by HSPs was 99.7%. Among all other species, the one yielding the highest score was Dehalobacter restrictus (Y10164), which corresponded to an identity of 95.0% and an HSP coverage of 85.2%. (Note that the Greengenes database uses the INSDC (= EMBL/NCBI/DDBJ) annotation, which is not an authoritative source for nomenclature or classification.) The highest-scoring environmental sequence was AJ278164 (‘Dehalobacter sp. clone SHD-11' [12]), which showed an identity of 95.3% and an HSP coverage of 86.8%. The most frequently occurring keywords within the labels of environmental samples which yielded hits were 'soil' (6.5%), 'microbi' (6.4%), 'respons' (4.8%), 'paddi, rice' (4.6%) and 'condit' (4.5%) (165 hits in total). The most frequently occurring keyword within the labels of environmental samples which yielded hits of a higher score than the highest scoring species was 'dehalobact' (100.0%) (1 hit in total). The BLAST analysis results concur with earlier reports on the ecology and the physiology of the isolate whereby it was isolated from a co-culture with other sulfate-reducing bacteria [3,8].

Figure 1 shows the phylogenetic neighborhood of S. glycolicus in a 16S rRNA based tree. The sequences of the four 16S rRNA gene copies in the genome differ from each other by up to eight nucleotides, and differ by up to 14 nucleotides from the previously published 16S rRNA sequence X99706, which contains two ambiguous base calls.

Figure 1

Phylogenetic tree highlighting the position of S. glycolicus relative to the type strains of the most closely related genera within the family Peptococcaceae. The tree was inferred from 1,306 aligned characters [13,14] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [15] and rooted with the type species of the family. The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 700 ML bootstrap replicates [16] (left) and from 1,000 maximum parsimony bootstrap replicates [17] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [18] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks [19-21].

As two of the genera selected for Figure 1, Desulfotomaculum and Pelotomaculum, appeared as paraphyletic in the tree, we conducted both unconstrained heuristic searches for the best tree under the maximum likelihood (ML) [15] and maximum parsimony (MP) criterion [17] as well as searches constrained for the monophyly of all genera (for details of the data matrix see the figure caption). The best-known ML tree had a log likelihood of -12,054.61, whereas the best trees found under the constraint had a log likelihood of -12,209.39 and were significantly worse in the SH test as implemented in RAxML [15] (p < 0.01). The best-known MP trees had a score of 2,018 whereas the best trees found under the constraint had a score of 2,076 and were significantly worse in the KH test as implemented in PAUP* [17] (p < 0.0001). Accordingly, the current classification of the group is in significant conflict with the 16S rRNA data and apparently does not reflect its natural relationships. The classification could be improved if combinations of phenotypic character states were found which characterize a set of appropriately rearranged, then monophyletic genera. However, it might also be that the goal to 'define' each genus in terms of unique combinations of few, potentially arbitrarily selected character states is over-ambitious, if not misleading in this group of organisms. Apparently a taxonomic revision of the family appears to be necessary which focuses more strongly on the genealogy of the organisms than previous treatments.

Cells of strain FlGlyRT are Gram-positive, spore forming and slightly curved rods of 2.5-3.5 by 0.5 µm in size [3] (Figure 2). Though the organism is reported to be non-motile, numerous genes associated with flagellar motility are present in the genome (see below). Growth occurs between 15°C and 37°C with an optimum at 28°C, and in a pH range of 6.7 to 8.3, with an optimum at pH 7.3 [3] (Table 1). The reported habitat for this strain is sewage sludge and anoxic freshwater sediments [3]. Initial isolation condition was from defined co-cultures of fermenting bacteria with homoacetogenic or methanogenic bacteria which converted glycolate completely to CO2 and H2, with concomitant reduction of CO2 to either acetate or methane [3,8]. Later strain FlGlyRT was identified as the primary fermenting partner in these co-cultures and glyoxylate was the substrate [3]. Strain FlGlyRT grows optimally in freshwater medium although growth also occurred in brackish-water medium with 110 mM NaC1 and 5 mM MgCl [3]. Strain FlGlyRT is strictly anaerobic, growing chemotrophically in pure culture by fermentative oxidation of glyoxylate [3]. In pure culture, glyoxylic acid is fermented to carbon dioxide, hydrogen, and glycolic acid [3]. However, in syntrophic co-culture with, e.g., Methanospirillum hungatei or Acetobacterium woodii as a partner, glycolic acid is converted to carbon dioxide and hydrogen [3]. Glycolate oxidation to glyoxylate and vice versa is coupled to a membrane-bound electron transport system that catalyzes either a proton potential-driven reversed electron transport from glycolate to hydrogen or a hydrogen-dependent glyoxylate reduction coupled to ATP synthesis by electron transport phosphorylation [34,35]. Due to the oxygenase activity of the D-ribulose-1,5-bisphosphate carboxylase at low CO2 and high O2 concentrations, the phosphoglycolate formed in these organisms is subsequently dephosphorylated to glycolate [8]. It is reported that no other organic or inorganic substrates are used [3], even though a total of 78 carbohydrate transport and metabolism genes are found the genome of this organism (COGS table). Neither sulfate, sulfite, thiosulfate, elemental sulfur, nor nitrate are reduced [3].

Figure 2

Scanning electron micrograph of S. glycolicus FlGlyRT

Table 1

Classification and general features of S. glycolicus FlGlyRT according to the MIGS recommendations [22] and the NamesforLife database [23].

MIGS ID

    Property

    Term

    Evidence code

    Current classification

    Domain Bacteria

    TAS [24]

    Phylum Firmicutes

    TAS [25,26]

    Class Clostridia

    TAS [27,28]

    Order Clostridiales

    TAS [29,30]

    Family Peptococcaceae

    TAS [29,31]

    Genus Syntrophobotulus

    TAS [3]

    Species Syntrophobotulus glycolicus

    TAS [3]

    Type strain FlGlyR

    TAS [3]

    Gram stain

    negative

    TAS [3]

    Cell shape

    rod shaped, slightly curved

    TAS [3]

    Motility

    non-motile

    TAS [3]

    Sporulation

    sporulating

    TAS [3]

    Temperature range

    15°C-37°C

    TAS [3]

    Optimum temperature

    28°C

    TAS [3]

    Salinity

    tolerates ~6% NaCl

    TAS [3]

MIGS-22

    Oxygen requirement

    strictly anaerobic

    TAS [3]

    Carbon source

    glyoxylate

    TAS [3]

    Energy metabolism

    chemotrophic

    TAS [3]

MIGS-6

    Habitat

    marine, sludge, fresh water

    TAS [3]

MIGS-15

    Biotic relationship

    free-living

    TAS [3]

MIGS-14

    Pathogenicity

    not reported

    Biosafety level

    1

    TAS [32]

    Isolation

    anoxic sludge from municipal sewage treatment plant

    TAS [3,8]

MIGS-4

    Geographic location

    Konstanz, Germany

    TAS [3,8]

MIGS-5

    Sample collection time

    1991 or before

    TAS [3,8]

MIGS-4.1

    Latitude

    47.67

    NAS

MIGS-4.2

    Longitude

    9.16

    NAS

MIGS-4.3

    Depth

    unknown

MIGS-4.4

    Altitude

    about 420 m

    NAS

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

Chemotaxonomy

Strain FlGlyRT has no cytochromes and the cells contain menaquinone-7-10, with MK-9 as major fraction [3]. Although the cells stain Gram-negative, the ultrastructural analysis shows a Gram-positive cell wall architecture [3].

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [36], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [37]. The genome project is deposited in the Genome On Line Database [18] 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

MIGS ID

     Property

     Term

MIGS-31

     Finishing quality

     Finished

MIGS-28

     Libraries used

     Three genomic libraries: one 454 pyrosequence standard library,     one 454 PE library (13 kb insert size), one Illumina library

MIGS-29

     Sequencing platforms

     Illumina GAii, 454 GS FLX Titanium

MIGS-31.2

     Sequencing coverage

     167.0 × Illumina; 48.0 × pyrosequence

MIGS-30

     Assemblers

     Newbler version 2.3 (Roche), Velvet 0.7.63, phrap SPS - 4.24

MIGS-32

     Gene calling method

     Prodigal 1.4, GenePRIMP

     INSDC ID

     CP002547

     Genbank Date of Release

     March 4, 2011

     GOLD ID

     Gc01670

     NCBI project ID

     38111

     Database: IMG-GEBA

     2503707006

MIGS-13

     Source material identifier

     DSM 8271

     Project relevance

     Tree of Life, GEBA

Growth conditions and DNA isolation

S. glycolicus FlGlyRT, DSM 8271, was grown anaerobically in DSMZ medium 298b (FlGlyM-medium) [38] at 28°C. DNA was isolated from 0.5-1 g of cell paste using Jetflex Genomic DNA Purification kit (GENOMED 600100) following the standard protocol as recommended by the manufacturer, adding 10 µL proteinase K to the standard lysis solution for 50 minutes at 58°C. DNA is available through the DNA Bank Network [39].

Genome sequencing and assembly

The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website [40]. Pyrosequencing reads were assembled using the Newbler assembler. The initial Newbler assembly consisting of 38 contigs in two scaffolds was converted into a phrap [41] assembly by making fake reads from the consensus, to collect the read pairs in the 454 paired end library. Illumina sequencing data (602.6 Mb) was assembled with Velvet [42] and the consensus sequences were shredded into 1.5 kb overlapped fake reads and assembled together with the 454 data. 454 draft assembly was based on 163.5 Mb 454 draft data and all of the 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20. The Phred/Phrap/Consed software package [41] was used for sequence assembly and quality assessment in the subsequent finishing process. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with gapResolution [40], Dupfinisher, or sequencing cloned bridging PCR fragments with subcloning or transposon bombing (Epicentre Biotechnologies, Madison, WI) [43]. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F. Chang, unpublished). A total of 331 additional reactions were necessary to close gaps and to raise the quality of the finished sequence. Illumina reads were also used to correct potential base errors and increase consensus quality using a software Polisher developed at JGI [44]. The error rate of the completed genome sequence is less than 1 in 100,000. Together, the combination of the Illumina and 454 sequencing platforms provided 215.0 × coverage of the genome. The final assembly contained 327,738 pyrosequence and 15,336,223 Illumina reads.

Genome annotation

Genes were identified using Prodigal [45] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [46]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGR-Fam, 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 [47].

Genome properties

The genome consists of a 3,406,739bp long chromosome with a GC content of 46.4% (Table 3 and Figure 3). Of the 3,439 genes predicted, 3,370 were protein-coding genes, and 69 RNAs; 119 pseudogenes were also identified. The majority of the protein-coding genes (68.7%) were assigned 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.

Table 3

Genome Statistics

Attribute

    Value

   % of Total

Genome size (bp)

    3,406,739

   100.00%

DNA coding region (bp)

    2,989,609

   87.76%

DNA G+C content (bp)

    1,579,030

   46.35%

Number of replicons

    1

Extrachromosomal elements

    0

Total genes

    3,439

   100.00%

RNA genes

    69

   2.01%

rRNA operons

    4

Protein-coding genes

    3,370

   97.99%

Pseudo genes

    119

   3.46%

Genes with function prediction

    2364

   68.74%

Genes in paralog clusters

    710

   20.65%

Genes assigned to COGs

    2,399

   69.76%

Genes assigned Pfam domains

    2,561

   74.47%

Genes with signal peptides

    463

   13.46%

Genes with transmembrane helices

    848

   24.66%

CRISPR repeats

    2

Figure 3

Graphical circular map of chromosome. 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 4

Number of genes associated with the general COG functional categories

Code

    value

    %age

    Description

J

    152

    5.8

    Translation, ribosomal structure and biogenesis

A

    0

    0.0

    RNA processing and modification

K

    230

    8.8

    Transcription

L

    156

    6.0

    Replication, recombination and repair

B

    1

    0.0

    Chromatin structure and dynamics

D

    33

    1.3

    Cell cycle control, cell division, chromosome partitioning

Y

    0

    0.0

    Nuclear structure

V

    98

    3.8

    Defense mechanisms

T

    162

    6.2

    Signal transduction mechanisms

M

    170

    6.5

    Cell wall/membrane/envelope biogenesis

N

    68

    2.6

    Cell motility

Z

    0

    0.0

    Cytoskeleton

W

    0

    0.0

    Extracellular structures

U

    43

    1.7

    Intracellular trafficking, secretion, and vesicular transport

O

    74

    2.8

    Posttranslational modification, protein turnover, chaperones

C

    156

    6.0

    Energy production and conversion

G

    78

    3.0

    Carbohydrate transport and metabolism

E

    214

    8.2

    Amino acid transport and metabolism

F

    65

    2.5

    Nucleotide transport and metabolism

H

    140

    5.4

    Coenzyme transport and metabolism

I

    49

    1.9

    Lipid transport and metabolism

P

    195

    7.5

    Inorganic ion transport and metabolism

Q

    27

    1.0

    Secondary metabolites biosynthesis, transport and catabolism

R

    282

    10.8

    General function prediction only

S

    220

    8.4

    Function unknown

-

    1,040

    30.2

    Not in COGs

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Maren Schröder (DSMZ) for growing S. glycolicus 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, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2.


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.

References

  1. Euzéby JP. List of bacterial names with standing in nomenclature: A folder available on the internet. Int J Syst Bacteriol. 1997; 47:590-592 View ArticlePubMed
  2. Boone DR, Castenholz RW, Garrity GM, eds. 2001. Bergey’s Manual of Systematic Bacteriology, 2nd ed. Springer-Verlag. New York, NY.
  3. Friedrich M, Springer N, Ludwig W and Schink B. Phylogenetic position of Desulfofustis glycolicus gen. nov. sp. nov. and Syntrophobotulus glycolicus gen. nov. sp. nov., two new strict anaerobes growing with glycolic acid. Int J Syst Bacteriol. 1996; 46:1065-1069 View ArticlePubMed
  4. Whittingham CP and Pritchard GG. The production of glycolate during photosynthesis in Chlorella. Proc R Soc Lond. 1963; 157:366-382 View Article
  5. Codd GA and Smith BM. Glycolate formation and excretion by the purple photosynthetic bacterium Rhodospirillum rubrum. FEBS Lett. 1974; 48:105-108 View ArticlePubMed
  6. Codd GA, Bowien B and Schlegel HG. Glycolate production and excretion by Alcaligenes eutrophus. Arch Microbiol. 1976; 110:167-171 View ArticlePubMed
  7. Beudeker RF, Kuenen JG and Codd GA. Glycolate metabolism in the obligate chemolithotroph Thiobacillus neapolitanus grown in continuous culture. J Gen Microbiol. 1981; 126:337-346
  8. Friedrich M, Laderer U and Schink B. Fermentative degradation of glycolic acid by defined syntrophic cocultures. Arch Microbiol. 1991; 156:398-404 View Article
  9. Altschul SF, Gish W, Miller W, Myers EW and Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215:403-410PubMed
  10. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P and Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006; 72:5069-5072 View ArticlePubMed
  11. Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems 1980; 14:130-137.
  12. Schlötelburg C, von Wintzingerode C, Hauck R, von Wintzingerode F, Hegemann W and Göbel UB. Microbial structure of an anaerobic bioreactor population that continuously dechlorinates 1,2-dichloropropane. FEMS Microbiol Ecol. 2002; 39:229-237 View ArticlePubMed
  13. Lee C, Grasso C and Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics. 2002; 18:452-464 View ArticlePubMed
  14. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000; 17:540-552PubMed
  15. Stamatakis A, Hoover P and Rougemont J. A rapid bootstrap algorithm for the RAxML web-servers. Syst Biol. 2008; 57:758-771 View ArticlePubMed
  16. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME and Stamatakis A. How many bootstrap replicates are necessary? Lect Notes Comput Sci. 2009; 5541:184-200 View Article
  17. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 b10. Sinauer Associates, Sunderland, 2002.
  18. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM and 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 View ArticlePubMed
  19. Spring S, Lapidus A, Schröder M, Gleim D, Sims D, Meincke L, Glavina Del Rio T, Tice H, Copeland A and Cheng JF. Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575T). Stand Genomic Sci. 2009; 1:242-253 View ArticlePubMed
  20. Kosaka T, Kato S, Shimoyama T, Ishii S, Abe T and Watanabe K. The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota. Genome Res. 2008; 18:442-448 View ArticlePubMed
  21. Nonaka H, Keresztes G, Shinoda Y, Ikenaga Y, Abe M, Naito K, Inatomi K, Furukawa K, Inui M and Yukawa H. Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195. J Bacteriol. 2006; 188:2262-2274 View ArticlePubMed
  22. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ and Angiuoli SV. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008; 26:541-547 View ArticlePubMed
  23. Garrity G. NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser. Microbiol Today. 2010; 37:9
  24. Woese CR, Kandler O and 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 View ArticlePubMed
  25. Gibbons NE and Murray RGE. Proposals Concerning the Higher Taxa of Bacteria. Int J Syst Bacteriol. 1978; 28:1-6 View Article
  26. Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 119-169.
  27. . List of new names and new combinations previously effectively, but not validly, published. List no. 132. Int J Syst Evol Microbiol. 2010; 60:469-472 View Article
  28. Rainey FA. Class II. Clostridia class nov. In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 3, Springer-Verlag, New York, 2009, p. 736.
  29. Skerman VBD, McGowan V and Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol. 1980; 30:225-420 View Article
  30. Prévot AR. In: Hauderoy P, Ehringer G, Guillot G, Magrou. J., Prévot AR, Rosset D, Urbain A (eds), Dictionnaire des Bactéries Pathogènes, Second Edition, Masson et Cie, Paris, 1953, p. 1-692.
  31. Rogosa M. Peptococcaceae, a new family to include the Gram-positive, anaerobic cocci of the genera Peptococcus, Peptostreptococcus and Ruminococcus. Int J Syst Bacteriol. 1971; 21:234-237 View Article
  32. BAuA 2005. Classification of bacteria and archaea in risk groups. TRBA 466 p. 336; Web Site
  33. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS and Eppig JT. Gene Ontology: tool for the unification of biology. Nat Genet. 2000; 25:25-29 View ArticlePubMed
  34. Friedrich M and Schink B. Hydrogen formation from glycolate driven by reversed electron transport in membrane vesicles of a syntrophic glycolate-oxidizing bacterium. Eur J Biochem. 1993; 217:233-240 View ArticlePubMed
  35. Friedrich M and Schink B. Electron transport phosphorylation driven by glyoxylate respiration with hydrogen as electron donor in membrane vesicles of a glyoxylate-fermenting bacterium. Arch Microbiol. 1995; 163:268-275 View ArticlePubMed
  36. Klenk HP and Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol. 2010; 33:175-182 View ArticlePubMed
  37. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M and Tindall BJ. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 2009; 462:1056-1060 View ArticlePubMed
  38. List of growth media used at DSMZ: Web Site
  39. Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch A, Berendsohn WG and Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreservation and Biobanking. 2011; 9:51-55 View Article
  40. Zerbino DR and Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008; 18:821-829 View ArticlePubMed
  41. Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F and Lucas S. Complete genome sequence of Kytococcus sedentarius type strain (541T). Stand Genomic Sci. 2009; 1:12-20 View ArticlePubMed
  42. 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.
  43. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW and Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010; 11:119 View ArticlePubMed
  44. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A and Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods. 2010; 7:455-457 View ArticlePubMed
  45. Markowitz VM, Ivanova NN, Chen IMA, Chu K and Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009; 25:2271-2278 View ArticlePubMed