Open Access

Complete genome sequence of the sulfur-oxidizing chemolithoautotrophic Sulfurovum lithotrophicum 42BKTT

Standards in Genomic Sciences201712:54

https://doi.org/10.1186/s40793-017-0265-z

Received: 2 January 2017

Accepted: 23 August 2017

Published: 6 September 2017

Abstract

A sulfur-oxidizing chemolithoautotrophic bacterium, Sulfurovum lithotrophicum 42BKTT, isolated from hydrothermal sediments in Okinawa, Japan, has been used industrially for CO2 bio-mitigation owing to its ability to convert CO2 into C5H8NO4 at a high rate of specific mitigation (0.42 g CO2/cell/h). The genome of S. lithotrophicum 42BKTT comprised of a single chromosome of 2217,891 bp with 2217 genes, including 2146 protein-coding genes and 54 RNA genes. Here, we present its complete genome-sequence information, including information about the genes encoding enzymes involved in CO2 fixation and sulfur oxidation.

Keywords

Complete genomeSulfur-oxidizing bacteriumChemolithoautotrophCO2 bio-mitigation Sulfurovum lithotrophicum

Introduction

Epsilonproteobacteria are well-known chemolithoautotrophic bacteria found in deep-sea hydrothermal fields that play significant roles in sulfur, nitrogen, and hydrogen flux [1, 2].

Sulfurovum lithotrophicum 42BKTT is a sulfur-oxidizing member of Epsilonproteobacteria that was isolated from deep-sea hydrothermal sediments in Okinawa, Japan [3]. Strain 42BKTT is a Gram-negative, non-motile, and coccoid-to-short-rod-shaped bacterium that utilizes CO2 as a carbon source, S or S2O3 2− as electron donors, and O2 and NO3 as electron acceptors [3, 4]. Recent studies have focused on its potential industrial applications for CO2 bio-mitigation, reporting that this strain could convert CO2 into C5H8NO4 at a high specific mitigation rate of ~0.42 g CO2/cell/h [4].

The CO2-bio-mitigation ability of S. lithotrophicum can be improved and optimized through genetic engineering; however, the present lack of genetic knowledge of S. lithotrophicum renders the genetic engineering of this strain difficult. Here, we presented a preliminary description and the general features of S. lithotrophicum 42BKTT, along with its genome-sequence annotations and interactions with other Sulfurovum species. This information would be helpful for improving the use of chemolithoautotrophic bacteria, including Sulfurovum species, in industrial applications in CO2 bio-mitigation.

Organism information

Classification and features

A representative 16S rRNA gene of S. lithotrophicum 42BKTT was compared with that of other species using NCBI BLAST [5]. Figure 1 shows the phylogenetic tree with S. lithotrophicum 42BKTT, constructed based on the 16S rRNA sequence. This strain shared 99.1% (1393/1406 bp) and 95.1% (1312/1379) sequence identity with the 16S rRNA genes of Sulfurovum sp. NBC37–1 [6] and Sulfurovum aggregans Monchim33T, respectively.
Fig. 1

Phylogenetic tree showing the relative position of Sulfurovum lithotrophicum 42BKTT, based 16S rRNA gene sequence. All sites were informative and free of gaps. Evolutionary history was inferred using the neighbor-joining method [35]. The tree was built using the maximum composite-likelihood method [36]. The percentage of replicate trees with the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the corresponding branches [37]. Evolutionary analyses were conducted in MEGA6 [38]. Corresponding GenBank accession numbers are shown in brackets next to the strain name

S. lithotrophicum 42BKTT is a Gram-negative, non-motile, coccoid-to-short-rod-shaped bacterium that is 0.5–1.2 μm in length and 0.4–0.8 μm in width (Fig. 2). The 42BKTT strain is a mesophilic, facultative anaerobe that requires sea salt to grow and can use NH4Cl as a nitrogen source. Normal growth occurs at a temperature of 10–40 °C, pH of 5.0–9.0, and salinity of 5–60 g/l [3]. The basic details of its genome sequence are shown in Table 1.
Fig. 2

Scanning electron micrograph of Sulfurovum lithotrophicum 42BKTT

Table 1

Classification and general features of Sulfurovum lithotrophicum strain 42BKTT [11]

MIGS ID

Property

Term

Evidence codea

 

Classification

Domain Bacteria

TAS [29]

  

Phylum Proteobacteria

TAS [30]

  

Class Epsilonproteobacteria

TAS [31]

  

Order Campylobacterales

TAS [32]

  

Family Helicobacteraceae

TAS [33]

  

Genus Sulfurovum

TAS [3]

  

Species Sulfurovum lithotrophicum

TAS [3]

  

Type strain: 42BKTT (CP011308)

TAS [3]

 

Gram stain

Negative

TAS [3]

 

Cell shape

Coccoid to short rods

TAS [3]

 

Motility

None-motile

TAS [3]

 

Sporulation

Not reported

NAS

 

Temperature range

10–40 °C

TAS [3]

 

Optimum temperature

28–30 °C

TAS [3]

 

pH range; Optimum

6.5–7.0

TAS [3]

 

Carbon source

Sodium bicarbonate

TAS [4]

MIGS-6

Habitat

Deep-sea hydrothermal vent

TAS [3]

MIGS-6.3

Salinity

0.5–6% NaCl (w/v)

TAS [3]

MIGS-22

Oxygen requirement

Facultatively anaerobic

TAS [3]

MIGS-15

Biotic relationship

Symbiont

TAS [3]

MIGS-14

Pathogenicity

Not reported

NAS

MIGS-4

Geographic location

Okinawa, Japan

TAS [3]

MIGS-5

Sample collection

April 2002

TAS [3]

MIGS-4.1

Latitude

27° 47·38′ N

TAS [3]

MIGS-4.2

Longitude

126° 53·87′ E

TAS [3]

MIGS-4.4

Altitude

−1033 m

TAS [3]

aEvidence codes - 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 [34]

Chemotaxonomic data

The major cellular fatty acids that were present in strain 42BKTT included C16: 1 (53.7%), C16: 0 (31.3%), and C18: 0 (15.0%) [3]. It did not contain C14:0, C14:1, or C18:1, whereas S. aggregans Monchim33T contains 7.7, 5.9, and 9.4%, respectively, of these fatty acids [3, 7], and Sulfurimonas autotrophica OK 10T, another chemolithoautotrophic bacteria, contains 8.4% of C14:0 and 9.4% of C18:1 [8]. S. lithotrophicum 42BKTT can fix CO2 via the reductive tricarboxylic acid (TCA) cycle, although the gene encoding phosphoenolpyruvate (PEP) carboxylase is not annotated in its genome. Sulfur or S2O3 2− are oxidized by bacteria of the genus Sulfurovum ; S. lithotrophicum 42BKTT can oxidize S2− only using a sulfide-quinone reductase, whereas Sulfurovum sp. NBC37–1 oxidizes S2− using a sulfide-quinone reductase or a sulfide dehydrogenase.

Genome sequencing information

Genome project history

S. lithotrophicum 42BKTT was selected for sequencing based on its ability to convert CO2 into C5H8NO4 , which can be industrially used for CO2 bio-mitigation. The draft sequencing and annotation were performed by ChunLab, Inc. (Seoul, Korea). The genome project was deposited in the Genomes OnLine Database [9] under the accession number Gp0118364. The complete genome sequence was also deposited in GenBank [10] under the accession number CP011308. Table 2 contains the details of the project and its association with MIGS version 2.0 compliance [11].
Table 2

Project information

MIGS ID

Property

Term

MIGS 31

Finishing quality

Completely finished

MIGS 28

Libraries used

Illumina 300-bp paired-end library,

PacBio 20 K library

MIGS 29

Sequencing platforms

Miseq PE 300, PacBio 10 K

MIGS 31.2

Fold coverage

852.21×

MIGS 30

Assemblers

CLC Genomics Workbench v.7.5.1,

SMRT Analysis v.2.3

MIGS 32

Gene-calling method

Prodigal 2.6.2

 

Locus Tag

YH65

 

Genbank ID

CP011308.1

 

Genbank Date of Release

08/20/2015

 

GOLD ID

Gp0118364

 

BIOPROJECT

PRJNA279430

MIGS 13

Source-material identifier

42BKTT/ ATCC BAA-797T

 

Project relevance

CO2 fixation

Growth conditions and genomic DNA preparation

S. lithotrophicum 42BKTT was grown in a 125-mL serum bottle (Wheaton Industries, Millville, NJ, USA) with 20 mL of MJ basal medium and filled with a CO2/N2 gas mixture. The bottle was incubated at 29 °C while shaking at 120 rpm (Green Shaker, Vision Scientific Co., Daejeon, Korea) [4]. Genomic DNA was isolated using a QIAmp DNA mini kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions.

Genome sequencing and assembly

The genomic library was sequenced using an Illumina MiSeq PE 300 and PacBio 10 K with the Illumina 300-bp paired-end library (Illumina, San Diego, CA, USA) and the PacBio 20 K library (Pacific Biosciences, Menlo Park, CA, USA), respectively. The generated paired-end sequencing reads (total read length: 2217,891 bp) were assembled using the CLC Genomics Workbench version 7.5.1 (CLC Bio, Aarhus, Denmark) and PacBio SMRT Analysis version 2.3 (Pacific Biosciences), resulting in one contig with an average genome coverage of 852.21 × .

Genome annotation

The genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline [12], which was designed to annotate bacterial genomes. Genome annotation was performed by predicting protein-coding, rRNA, tRNA, ncRNA, and pseudo genes. Phobius [13] was used to predict signal-peptide genes, and TMHMM Server version 2.0 [14] was used to predict transmembrane helix genes [15, 16]. Protein families [17] were investigated using Pfam 29.0 [18], and GeneMarkS+ [19], which uses alignment data for gene prediction, was used as an annotation tool [20].

Genome properties

The genome of S. lithotrophicum 42BKTT comprised a single circular chromosome of 2217,891 bp with a GC content of 44.26%. Among the 2217 genes predicted, 2146 (96.80%) were protein-coding DNA sequences, 17 of which were pseudogenes. Among the CDSs, 89.66% were grouped into cluster of orthologous group functional categories. The genome contained a CRISPR array and 54 RNA genes, including 44 tRNAs, 9 rRNAs, and one ncRNA. The properties and statistics of the genome are summarized in Fig. 3 and Tables 3 and 4, 5.
Fig. 3

Genome map of Sulfurovum lithotrophicum 42BKTT. From the outer to the inner circle: RNA regions (rRNA, red; tRNA, lavender), CDS on the reverse strand (colored based on COG categories), CDS on the forward strand (colored based on COG categories), G + C skew (blue/goldenrod), and GC ratio (green/red)

Table 3

Genome statistics

Attribute

Value

% of total

Genome size (bp)

2217,891

100.00

DNA coding (bp)

2,028,222

91.44

DNA G + C (bp)

981,638

44.26

DNA scaffolds

1

 

Total genes

2217

100.00

Protein-coding genes

2146

96.80

RNA genes

54

2.44

Pseudo genes

17

0.77

Genes in internal clusters

NA

NA

Genes with function prediction

1559

70.32

Genes assigned to COGs

1979

89.26

Genes with Pfam domains

1770

79.84

Genes with signal peptides

412

18.58

Genes with transmembrane helices

513

23.14

CRISPR repeats

1

 
Table 4

Number of genes associated with the general COG functional categories

Code

Value

% agea

Description

J

138

6.43

Translation, ribosomal structure, and biogenesis

A

0

0.00

RNA processing and modification

K

47

2.19

Transcription

L

94

4.38

Replication, recombination, and repair

B

1

0.05

Chromatin structure and dynamics

D

14

0.65

Cell cycle control, cell division, chromosome partitioning

V

18

0.84

Defense mechanisms

T

88

4.10

Signal-transduction mechanisms

M

144

6.71

Cell wall/membrane/envelope biogenesis

N

6

0.28

Cell motility

U

39

1.82

Intracellular trafficking and secretion

O

95

4.43

Post-translational modification, protein turnover, chaperones

C

138

6.43

Energy production and conversion

G

53

2.47

Carbohydrate transport and metabolism

E

119

5.55

Amino acid transport and metabolism

F

60

2.80

Nucleotide transport and metabolism

H

85

3.96

Coenzyme transport and metabolism

I

43

2.00

Lipid transport and metabolism

P

106

4.94

Inorganic ion transport and metabolism

Q

22

1.03

Secondary metabolites biosynthesis, transport and catabolism

R

143

6.66

General function prediction only

S

526

24.51

Function unknown

-

238

11.09

Not in COGs

aPercentage of the total number of protein-coding genes in the genome

Table 5

Species in the genus Sulfurovum

Species (isolation source)

Genome size (Mb)

Accession no.

CDS

GC (%)

Reference

Sulfurovum lithotrophicum 42BKTT

(Deep-sea hydrothermal sediment)

2.21

CP011308

2092

44.3

This report

Sulfurovum sp. NBC37–1

(Deep-sea hydrothermal vent)

2.56

AP009179

2466

43.8

[6]

Candidatus Sulfurovum sediminum AR

(Marine sediment)

2.12

AJLE01000000

2114

39.2

[26]

Insights from the genome sequence

S. lithotrophicum 42BKTT is a sulfur-oxidizing bacterium that can fix CO2 through the reductive TCA cycle. Here, we focused on investigating its abilities for CO2 fixation and sulfur oxidation (sox), based on its genome sequence.

So far, six pathways have been associated with CO2 fixation: the Calvin-Benson-Bassham or reductive pentose pathway, the reductive TCA cycle or reverse citric acid cycle, the reductive acetyl CoA or Wood-Ljungdahl pathway, the 3-hydroxypropionate pathway or malyl CoA pathway, the 3-hydroxypropionate/4-hydroxy-butyrate cycle, and the dicarboxylate/4-hydroxybutyrate cycle [21, 22]. Similar to the majority of Epsilonproteobacteria , S. lithotrophicum 42BKTT can also grow chemoautotrophically through its adenosine triphosphate citrate lyase, 2-oxoglutarate:ferredoxin oxidoreductase, and pyruvate:ferredoxin oxidoreductase via the reductive TCA cycle [2325]. We annotated these three key enzymes, as well as other relevant enzymes such as malate dehydrogenase, fumarate hydratase, fumarate reductase, isocitrate dehydrogenase, aconitate hydratase, PEP synthase, and PEP carboxylase, in the genome sequence of 42BKTT. Notably, Sulfurovum sp. NBC37–1 and Candidatus Sulfurovum sediminum AR could also assimilate CO2 via the reductive TCA cycle [6, 26].

S. lithotrophicum 42BKTT is known to oxidize or S2S O3 2− via a sox system using SoxB, SoxXA, SoxYZ, and Sox(CD)2 periplasmic proteins [27]. These enzymes catalyze the oxidation of S or S2O3 2− using horse cytochrome c as the final electron acceptor [28]. Here, we confirmed the presence of SoxA, SoxB, SoxZ, SoxY, and SoxX genes in the 42BKTT genome.

Conclusions

To the best of our knowledge, this is the first report describing the genome sequence of S. lithotrophicum 42BKTT, which comprised a circular chromosome of 2217,891 bp (44.26% GC content) with 2217 genes, among which 2146 were CDSs, 17 were pseudogenes, and 54 were RNA genes. S. lithotrophicum 42BKTT assimilates CO2 via the reductive TCA cycle and oxidizes S or S2O3 2− via the sox system. The details of the genome sequence of this strain could provide potential strategies to enhance the industrial application of such bacteria for CO2 bio-mitigation.

Abbreviations

CDS: 

Coding DNA sequence

COG: 

Cluster of orthologous group

PEP: 

Phosphoenolpyruvate

TCA: 

Tricarboxylic acid

Declarations

Funding

This study was supported by a grant from the KRIBB Research Initiative Program, and Industrial Strategic Technology Development Program (10067772, Development of bio-glutaric acid based plasticizers) funded by the Ministry of Trade, Industry & Energy (MOTIE, Korea).

Authors’ contributions

WJ and GP performed the microbial cultivation and genomic DNA isolation. LP and HL performed the phylogenetic analysis. WJ, LP, and NL performed sequencing and data analysis. WJ, LP, and JA drafted the manuscript. DL, HK, IA, CL, HL, and JA edited the manuscript. All the authors have read and approved the final manuscript.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Authors’ Affiliations

(1)
Biotechnology Process Engineering Center, KRIBB
(2)
Bioprocess Department, University of Science and Technology
(3)
Chemical Engineering Study Program, Faculty of Industrial Technology, Institut Teknologi Bandung
(4)
Department of Chemical and Biomolecular Engineering, National University of Singapore
(5)
Department of Chemical and Biomolecular Engineering, Yonsei University

References

  1. Nakagawa S, Takai K, Inagaki F, Hirayama H, Nunoura T, Horikoshi K, Sako Y. Distribution, phylogenetic diversity and physiological characteristics of epsilon-Proteobacteria in a deep-sea hydrothermal field. Environ Microbiol. 2005;7:1619–32.View ArticlePubMedGoogle Scholar
  2. Huber JA, Butterfield DA, Baross JA. Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption. FEMS Microbiol Ecol. 2003;43:393–409.View ArticlePubMedGoogle Scholar
  3. Inagaki F, Takai K, Nealson KH, Horikoshi K. Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the epsilon-Proteobacteria isolated from Okinawa trough hydrothermal sediments. Int J Syst Evol Microbiol. 2004;54:1477–82.View ArticlePubMedGoogle Scholar
  4. Kwon HS, Lee JH, Kim T, Kim JJ, Jeon P, Lee CH, Ahn IS. Biofixation of a high-concentration of carbon dioxide using a deep-sea bacterium: Sulfurovum lithotrophicum 42BKTT. RSC Adv. 2015;5:7151–9.View ArticleGoogle Scholar
  5. NCBI BLAST. https://blast.ncbi.nlm.nih.gov/Blast.cgi. Accessed 17 Jan 2017.
  6. Nakagawa S, Takaki Y, Shimamura S, Reysenbach AL, Takai K, Horikoshi K. Deep-sea vent epsilon-proteobacterial genomes provide insights into emergence of pathogens. Proc Natl Acad Sci U S A. 2007;104:12146–50.View ArticlePubMedPubMed CentralGoogle Scholar
  7. Mino S, Kudo H, Arai T, Sawabe T, Takai K, Nakagawa S. Sulfurovum aggregans sp. nov.,a hydrogen-oxidizing, thiosulfate-reducing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent chimney, and an emended description of the genus Sulfurovum. Int J Syst Evol Microbiol. 2014;64:3195–201.View ArticlePubMedGoogle Scholar
  8. Inagaki F, Takai K, Kobayashi H, Nealson KH, Horikoshi K. Sulfurimonas autotrophica gen. nov., sp. nov., a novel sulfur-oxidizing epsilon-proteobacterium isolated from hydrothermal sediments in the Mid-Okinawa Trough. Int J Syst Evol Microbiol. 2003;53:1801–5.View ArticlePubMedGoogle Scholar
  9. Genomes OnLine Database. https://gold.jgi.doe.gov/. Accessed 17 Jan 2017.
  10. GenBank. https://www.ncbi.nlm.nih.gov/genbank/. Accessed 17 Jan 2017.
  11. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ. Angiuoli SV and others. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26:541–7.View ArticlePubMedPubMed CentralGoogle Scholar
  12. NCBI Prokaryotic Genome Annotation Pipeline. https://www.ncbi.nlm.nih.gov/genome/annotation_prok/. Accessed 17 Jan 2017.
  13. Phobius. http://phobius.sbc.su.se/. Accessed 17 Jan 2017.
  14. TMHMM Server version 2.0. http://www.cbs.dtu.dk/services/TMHMM/. Accessed 17 Jan 2017.
  15. Kall L, Krogh A, Sonnhammer EL. Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server. Nucleic Acids Res. 2007;35:W429–32.View ArticlePubMedPubMed CentralGoogle Scholar
  16. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305:567–80.View ArticlePubMedGoogle Scholar
  17. Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer ELL. The Pfam protein families database. Nucleic Acids Res. 2000;28:263–6.View ArticlePubMedPubMed CentralGoogle Scholar
  18. Pfam 29.0. http://pfam.xfam.org/. Accessed 17 Jan 2017.
  19. GeneMarkS+. http://exon.gatech.edu/Genemark/genemarks.cgi. Accessed 17 Jan 2017.
  20. 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;29:2607–18.View ArticlePubMedPubMed CentralGoogle Scholar
  21. Saini R, Kapoor R, Kumar R, Siddiqi TO, Kumar A. CO(2) utilizing microbes--a comprehensive review. Biotechnol Adv. 2011;29:949–60.View ArticlePubMedGoogle Scholar
  22. Kanao T, Fukui T, Atomi H, Imanaka T. ATP-citrate lyase from the green sulfur bacterium Chlorobium limicola is a heteromeric enzyme composed of two distinct gene products. Eur J Biochem. 2001;268:1670–8.View ArticlePubMedGoogle Scholar
  23. Hügler M, Gärtner A, Imhoff JF. Functional genes as markers for sulfur cycling and CO2 fixation in microbial communities of hydrothermal vents of the Logatchev field. FEMS Microbiol Ecol. 2010;73:526–37.PubMedGoogle Scholar
  24. Hugler M, Wirsen CO, Fuchs G, Taylor CD, Sievert SM. Evidence for autotrophic CO2 fixation via the reductive tricarboxylic acid cycle by members of the epsilon subdivision of proteobacteria. J Bacteriol. 2005;187:3020–7.View ArticlePubMedPubMed CentralGoogle Scholar
  25. Takai K, Campbell BJ, Cary SC, Suzuki M, Oida H, Nunoura T, Hirayama H, Nakagawa S, Suzuki Y, Inagaki F, et al. Enzymatic and genetic characterization of carbon and energy metabolisms by deep-sea hydrothermal chemolithoautotrophic isolates of Epsilonproteobacteria. Appl Environ Microbiol. 2005;71:7310–20.View ArticlePubMedPubMed CentralGoogle Scholar
  26. Park SJ, Ghai R, Martin-Cuadrado AB, Rodriguez-Valera F, Jung MY, Kim JG, Rhee SK. Draft genome sequence of the sulfur-oxidizing bacterium “Candidatus Sulfurovum sediminum” AR, which belongs to the Epsilonproteobacteria. J Bacteriol. 2012;194:4128–9.View ArticlePubMedPubMed CentralGoogle Scholar
  27. Friedrich CG, Bardischewsky F, Rother D, Quentmeier A, Fischer J. Prokaryotic sulfur oxidation. Curr Opin Microbiol. 2005;8:253–9.View ArticlePubMedGoogle Scholar
  28. Bardischewsky F, Quentmeier A, Rother D, Hellwig P, Kostka S, Friedrich CG. Sulfur dehydrogenase of Paracoccus pantotrophus: the heme-2 domain of the molybdoprotein cytochrome c complex is dispensable for catalytic activity. Biochemistry. 2005;44:7024–34.View ArticlePubMedGoogle Scholar
  29. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1980;87:4576–9.View ArticleGoogle Scholar
  30. Garrity GM, Bell JA, LT. Phylum. XIV. Proteobacteria phyl. nov. Bergey’s manual of systematic bacteriology 2005, 2, Part B: 1.Google Scholar
  31. Garrity GM, Bell JA, Lilburn T. Class V. Epsilonproteobacteria class. nov. Bergey’s manual of systematic bacteriology. 2005, 2, Part C: 1145.View ArticleGoogle Scholar
  32. Garrity GM, Bell JA, Lilburn T. Order I. Campylobacterales ord. nov. Bergey’s manual of systematic bacteriology 2005, 2, Part C: 1145.View ArticleGoogle Scholar
  33. Garrity GM, Bell JA, Lilburn T. Family II. Helicobacteraceae fam. nov. Bergey’s manual of systematic bacteriology. 2005, 2, Part C: 1168.Google Scholar
  34. 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;25:25–9.View ArticlePubMedPubMed CentralGoogle Scholar
  35. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–25.PubMedGoogle Scholar
  36. Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A. 2004;101:11030–5.View ArticlePubMedPubMed CentralGoogle Scholar
  37. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39:783–91.View ArticlePubMedGoogle Scholar
  38. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30:2725–9.View ArticlePubMedPubMed CentralGoogle Scholar

Copyright

© The Author(s). 2017