Supplementary figures
Additional file 1 to: “Complete genome sequence of DSM 30083T, the
type strain (U5/41T) of Escherichia coli, and a proposal for delineating
subspecies in microbial taxonomy”
Authors: Jan P. Meier-Kolthoff, Richard L. Hahnke, Jörn Petersen, Carmen Scheuner, Victoria
Michael, Anne Fiebig, Christina Rohde, Manfred Rohde, Berthold Fartmann, Lynne A. Goodwin,
Olga Chertkov, Tatiparthi B. Reddy, Amrita Pati, Natalia N. Ivanova, Victor Markowitz, Nikos
C. Kyrpides, Tanja Woyke, Markus Göker*, Hans-Peter Klenk
*Corresponding author: Markus Göker <[email protected]>
1
Figure S1 - 1: Phylogenetic tree highlighting the position of E. coli relative to the
type strains of the other species within the genus Escherichia. The
tree was inferred from 1,433 aligned characters of the 16S rRNA gene
sequence under the maximum likelihood (ML) criterion as previously
described (Göker et al. 2011). Shimwellia blattae was included in the
data set for use as outgroup taxon. The branches are scaled in terms
of the expected number of substitutions per site. Numbers adjacent
to the branches are support values from 1,000 ML bootstrap replicates (left) and from 1,000 maximum-parsimony bootstrap replicates
(right) if larger than 60% (Göker et al. 2011). Lineages with type
strain genome sequencing projects registered in GOLD (Pagani et al.
2012) are labeled with one asterisk, those also listed as ’Complete and
Published’ with two asterisks.
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Number of comparisons
3000
Number of
comparisons
3000
2500
2000
2000
1000
1500
0
1000
500
0
0
10
20
30
40
50
60
70
80
90
dDDH (in %)
Figure S1 - 2: Histogram of all pairwise digital DDH similarities between all pairs
of strains contained in the data set (see Supplement File S2).
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100
Figure S1 - 3: Whole-genome phylogeny inferred using the latest GBDP version (Meier-Kolthoff et
al. 2013) and rooted with Shimwellia blattae. The only difference between this tree
and the one shown in Figure 7 of the main manuscript is that here all outgroup
organisms are shown: Escherichia albertii, Escherichia hermannii, Shimwellia blattae,
and Escherichia fergusonii ). Refer to Figure 7 of the main manuscript for further
information.
A
B
C
Figure S1 - 4: API 20E test of E. coli strains DSM 30083T and DSM 18039. At the DSMZ,
strain DSM 30083T was tested for the first time with API 20E test stripes at
37◦ C for 24 h in 1979 (A), and additionally on McCognay agar, chinablue and
ENDO agar (B). Strain DSM 18039 differed from DSM 30083T in being positive
for ornithine decarboxylase activity (C). Abbreviations of substrates are listed
in the manufacturer protocol (bioMérieux, Nürtingen, Germany).
Count
0
5
10 15 20
50
200
Value
150
250
Color Key
and Histogram
100
300
PM01
A01 (Negative Control)
D04 (1,2−Propanediol)
E05 (Tween 80)
D11 (Sucrose)
E09 (Adonitol)
E06 (a−Hydroxy−Glutaric Acid−g−Lactone)
G07 (Acetoacetic Acid)
F04 (D−Threonine)
H05 (D−Psicose)
F11 (D−Cellobiose)
H12 (Ethanolamine)
D02 (D−Aspartic Acid)
F03 (myo−Inositol)
H11 (b−Phenylethylamine)
H04 (Tyramine)
G02 (Tricarballylic Acid)
F02 (Citric Acid)
H02 (p−Hydroxy−Phenylacetic Acid)
H03 (m−Hydroxy−Phenylacetic Acid)
C11 (D−Melibiose)
G09 (Mono−Methyl Succinate)
F10 (Glyoxylic Acid)
D03 (D−Glucosaminic Acid)
D05 (Tween 40)
C05 (Tween 20)
B12 (L−Glutamic Acid)
D07 (a−Keto−Butyric Acid)
E02 (m−Tartaric Acid)
B08 (D−Xylose)
A04 (D−Saccharic Acid)
A12 (Dulcitol)
B10 (Sodium Formate)
E07 (a−Hydroxy−Butyric Acid)
F08 (Mucic Acid)
H07 (Glucuronamide)
C09 (D−Glucose)
E10 (Maltotriose)
B11 (D−Mannitol)
B09 (L−Lactic Acid)
G11 (D−Malic Acid)
G10 (Methyl Pyruvate)
F06 (Bromo−Succinic Acid)
C08 (Acetic Acid)
E01 (L−Glutamine)
G04 (L−Threonine)
B07 (D,L−a−Glycerol−Phosphate)
F07 (Propionic Acid)
D09 (a−D−Lactose)
E11 (2'−Deoxy−Adenosine)
C07 (D−Fructose)
G12 (L−Malic Acid)
E04 (D−Fructose−6−Phosphate)
F09 (Glycolic Acid)
G08 (N−Acetyl−b−D−Mannosamine)
G01 (Gly−Glu)
A03 (N−Acetyl−D−Glucosamine)
B03 (Glycerol)
B02 (D−Sorbitol)
G03 (L−Serine)
E08 (b−Methyl−D−Glucoside)
D01 (L−Asparagine)
A07 (L−Aspartic Acid)
H01 (Gly−Pro)
F05 (Fumaric Acid)
G05 (L−Alanine)
A05 (Succinic Acid)
F01 (Gly−Asp)
A09 (D−Alanine)
H08 (Pyruvic Acid)
G06 (Ala−Gly)
C03 (D,L−Malic Acid)
C12 (Thymidine)
C06 (L−Rhamnose)
B05 (D−Glucuronic Acid)
H10 (D−Galacturonic Acid)
C04 (D−Ribose)
C01 (D−Glucose−6−Phosphate)
H06 (L−Lyxose)
B01 (D−Serine)
F12 (Inosine)
A02 (L−Arabinose)
H09 (L−Galactonic Acid−g−Lactone)
A06 (D−Galactose)
D12 (Uridine)
A08 (L−Proline)
B04 (L−Fucose)
B06 (D−Gluconic Acid)
D06 (a−Keto−Glutaric Acid)
A10 (D−Trehalose)
D10 (Lactulose)
C02 (D−Galactonic Acid−g−Lactone)
D08 (a−Methyl−D−Galactoside)
C10 (D−Maltose)
E03 (a−D−Glucose−1−Phosphate)
A11 (D−Mannose)
E12 (Adenosine)
30083 24−A
30083 8−A
18039 24−A
18039 20−A
Figure S1 - 5: Heat map of the phenotype microarray results, microplate PM-01, for the type strain of
E. coli compared to strain DSM 18039. Data were analysed with OPM version 1.1.2,
using the maximum curve height parameter for plotting, inferred using smoothing
splines.
Count
0
5
10 15 20
50
200
Value
150
250
Color Key
and Histogram
100
300
PM02
G02 (L−Alaninamide)
F01 (D−Lactic Acid Methyl Ester)
E08 (b−Hydroxy−Butyric Acid)
D01 (D−Raffinose)
D04 (L−Sorbose)
D06 (D−Tagatose)
B05 (D−Arabinose)
B01 (N−Acetyl−D−Galactosamine)
C03 (D−Lactitol)
B02 (N−Acetyl−Neuraminic Acid)
C09 (b−Methyl−D−Glucuronic Acid)
C07 (b−Methyl−D−Galactoside)
B12 (3−O−b−D−Galactopyranosyl−D−Arabinose)
B03 (b−D−Allose)
F03 (Melibionic Acid)
A06 (Dextrin)
E05 (D−Glucosamine)
H09 (Dihydroxy−Acetone)
E06 (2−Hydroxy−Benzoic Acid)
G09 (L−Isoleucine)
E11 (Itaconic Acid)
G07 (L−Homoserine)
G06 (L−Histidine)
E07 (4−Hydroxy−Benzoic Acid)
F08 (Sebacic Acid)
F11 (D−Tartaric Acid)
B09 (2−Deoxy−D−Ribose)
G10 (L−Leucine)
E09 (g−Hydroxy−Butyric Acid)
G08 (L−Hydroxyproline)
B10 (m−Erythritol)
E04 (D−Citramalic Acid)
F04 (Oxalic Acid)
G04 (L−Arginine)
B06 (D−Arabitol)
D08 (Xylitol)
D09 (N−Acetyl−D−Glucosaminitol)
G11 (L−Lysine)
H01 (L−Ornithine)
D11 (d−Amino−Valeric Acid)
E01 (Capric Acid)
H04 (L−Valine)
H03 (L−Pyroglutamic Acid)
H07 (D,L−Octopamine)
H08 (Putrescine)
F06 (Quinic Acid)
E10 (a−Keto−Valeric Acid)
F07 (D−Ribono−1,4−Lactone)
H05 (D,L−Carnitine)
E12 (5−Keto−D−Gluconic Acid)
B08 (Arbutin)
A12 (Pectin)
F09 (Sorbic Acid)
H06 (Butylamine [sec])
B07 (L−Arabitol)
D10 (g−Amino−n−Butyric Acid)
C11 (b−Methyl−D−Xylopyranoside)
C10 (a−Methyl−D−Mannoside)
A09 (Inulin)
G12 (L−Methionine)
A05 (g−Cyclodextrin)
C08 (3−O−Methyl−D−Glucose)
H10 (2,3−Butanediol)
B04 (Amygdalin)
C02 (L−Glucose)
D03 (Sedoheptulosan)
D05 (Stachyose)
F12 (L−Tartaric Acid)
G01 (Acetamide)
E02 (Caproic Acid)
E03 (Citraconic Acid)
C06 (a−Methyl−D−Glucoside)
H02 (L−Phenylalanine)
B11 (D−Fucose)
G03 (N−Acetyl−L−Glutamic Acid)
A02 (Chondroitin Sulfate C)
G05 (Glycine)
C12 (Palatinose)
F10 (Succinamic Acid)
A10 (Laminarin)
A11 (Mannan)
A08 (Glycogen)
D07 (Turanose)
H12 (3−Hydroxy−2−Butanone)
D02 (D−Salicin)
A01 (Negative Control)
H11 (2,3−Butanedione)
A04 (b−Cyclodextrin)
A07 (Gelatin)
A03 (a−Cyclodextrin)
F05 (Oxalomalic Acid)
C04 (D−Melezitose)
F02 (Malonic Acid)
C01 (b−Gentiobiose)
D12 (Butyric Acid)
C05 (Maltitol)
30083 24−B
30083 8−B
18039 24−B
18039 20−B
Figure S1 - 6: Heat map of the phenotype microarray results, microplate PM-02, for the type strain of
E. coli compared to strain DSM 18039. Data were analysed with OPM version 1.1.2,
using the maximum curve height parameter for plotting, inferred using smoothing
splines.
References
Göker M, Cleland D, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S,
Cheng JF, Tapia R, et al. Complete genome sequence of Isosphaera pallida type strain (IS1BT ).
Stand Genomic Sci 2011; 4:63-71.
Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC.
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and
their associated metadata. Nucleic Acids Res 2012; 40:D571-579.
Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation
with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14: 60,
(doi:10.1186/1471-2105-14-60).
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