Name: Sphaerobacter thermophilus S 6022
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 14090

Type strain:

Species: Sphaerobacter thermophilus

Strain Designation: S 6022

Culture col. no.: DSM 20745, ATCC 49802

Strain history: <- W. Demharter, S 6022

NCBI tax ID(s): 479434 (strain), 2057 (species)

SI-ID 49676

DSM 20745, ATCC 49802, NCIMB 13135

Special Collections

Section

Sphaerobacter thermophilus S 6022 is an obligate aerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from thermophilically treated sewage sludge.

coccus-shaped
colony-forming
Gram-positive
obligate aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Thermomicrobiota*
	Class	*Thermomicrobia*
	Order	*Sphaerobacterales*
	Family	*Sphaerobacteraceae*
	Genus	*Sphaerobacter*
	Species	**Sphaerobacter thermophilus**
	Full Scientific Name (LPSN)	Sphaerobacter thermophilus Demharter et al. 1989

Information on morphological and physiological properties Morphology

[Ref.: #43423]	Gram stain	positive

[Ref.: #43423]	Cell length	1.5-3 µm

[Ref.: #43423]	Cell width	1-1.5 µm

[Ref.: #43423]	Cell shape	coccus-shaped

[Ref.: #43423]	Motility	no

[Ref.: #43423]	Colony size	1-2 mm
[Ref.: #43423]	Colony color	opaque
[Ref.: #43423]	Colony shape	circular
[Ref.: #43423]	Incubation period	3 days
[Ref.: #43423]	Cultivation medium used	Ottow medium

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #9054]

Culture medium

OTTOW MEDIUM (DSMZ Medium 467)

[Ref.: #9054]

Culture medium growth

[Ref.: #9054]

Culture medium link

Medium recipe at MediaDive

[Ref.: #9054]

Culture medium composition

expand / minimize

[Ref.: #43423]

Culture medium

Ottow medium

[Ref.: #43423]

Culture medium growth

		Temperature
[Ref.: #9054]	growth	55 °C
[Ref.: #43423]	growth	40-65 °C
[Ref.: #43423]	optimum	55 °C

	pH	Kind of pH		pH
[Ref.: #43423]			optimum	8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43423]

Oxygen tolerance

obligate aerobe

[Ref.: #43423]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	yes Confidence in %99

[Ref.: #9054]	Murein short key	A21.10
[Ref.: #9054]	Murein types	A3ß L-Orn-ß-Ala

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43423]	casein	-	hydrolysis
[Ref.: #43423]	cellulose ChEBI	-	hydrolysis
[Ref.: #43423]	gelatin ChEBI	-	hydrolysis
[Ref.: #43423]	glucose ChEBI	-	builds acid from
[Ref.: #43423]	starch ChEBI	+	hydrolysis

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #43423]		catalase	+	1.11.1.6
[Ref.: #43423]		cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	4-hydroxymandelate degradation	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	80	8 of 10
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	purine metabolism	72.34	68 of 94
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	phenol degradation	65	13 of 20
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	creatinine degradation	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	bacilysin biosynthesis	60	3 of 5
[Ref.: #66794]	oxidative phosphorylation	54.95	50 of 91
[Ref.: #66794]	degradation of pentoses	53.57	15 of 28
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	alginate biosynthesis	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	allantoin degradation	44.44	4 of 9
[Ref.: #66794]	carotenoid biosynthesis	40.91	9 of 22
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of sugar acids	32	8 of 25
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	vitamin B12 metabolism	29.41	10 of 34
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	daunorubicin biosynthesis	22.22	2 of 9
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #9054]	Sample type/isolated from	thermophilically treated sewage sludge
[Ref.: #9054]	Geographic location (country and/or sea, region)	München
[Ref.: #9054]	Country	Germany
[Ref.: #9054]	Country ISO 3 Code	DEU
[Ref.: #9054]	Continent	Europe

[Ref.: #43423]	Sample type/isolated from	thermal treated municipal sewage sludge
[Ref.: #43423]	Sampling date	between 1973 and 198
[Ref.: #43423]	Geographic location (country and/or sea, region)	Muenchen-Grosslappen, Germany
[Ref.: #43423]	Country	Germany
[Ref.: #43423]	Country ISO 3 Code	DEU
[Ref.: #43423]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Waste	#Sewage sludge
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ420142 (>99% sequence identity) for Sphaerobacter thermophilus subclade from Microbeatlas

Aquatic Samples	464
Soil Samples	3784
Animal Samples	828
Plant Samples	674
Total Samples	5750

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #9054]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Sphaerobacter thermophilus (Corynebacterium spec.) partial 16S rRNA	X53210	1208	GenBank ENA	479434 tax ID	*
[Ref.: #20218]	Sphaerobacter thermophilus 16S rRNA gene, strain DSM 20745T	AJ420142	1500	GenBank ENA	479434 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphaerobacter thermophilus DSM 20745	GCA_000024985	complete	GenBank ENA	479434 tax ID	*
[Ref.: #66792]	Sphaerobacter thermophilus DSM 20745	479434.6	complete	PATRIC	479434 tax ID	*
[Ref.: #66792]	Sphaerobacter thermophilus 4ac11, DSM 20745	646311953	complete	JGI IMG/M	479434 tax ID	*

[Ref.: #9054]	GC-content	66.3 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #9054]	GC-content	65.7 mol%	high performance liquid chromatography (HPLC)
[Ref.: #43423]	GC-content	68.1 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Sphaerobacter thermophilus DSM 20745 DSM 20745 NCBI: GCA_000024985.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	99	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphaerobacter thermophilus DSM 20745 DSM 20745 NCBI: GCA_000024985.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	58.436	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	85.362	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	68.217	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	50.653	no
[Ref.: #69480]	thermophilic	thermophileⓘ	yes	67.056	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	64.041	no

Availability in culture collections External links

[Ref.: #9054]

Culture collection no.

DSM 20745, ATCC 49802

[Ref.: #83258]

SI-ID 49676

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Discovery and Biochemical Characterization of the UDP-Xylose Biosynthesis Pathway in Sphaerobacter thermophilus.	Gu B, Laborda P, Wei S, Duan XC, Song HB, Liu L, Voglmeir J	Protein Pept Lett	10.2174/0929866523666161026115959	2016	*
Genetics	Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022).	Pati A, Labutti K, Pukall R, Nolan M, Glavina Del Rio T, Tice H, Cheng JF, Lucas S, Chen F, Copeland A, Ivanova N, Mavromatis K, Mikhailova N, Pitluck S, Bruce D, Goodwin L, Land M, Hauser L, Chang YJ, Jeffries CD, Chen A, Palaniappan K, Chain P, Brettin T, Sikorski J, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A	Stand Genomic Sci	10.4056/sigs.601105	2010	*

References

#9054

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20745

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#43423

Amrita Pati, Kurt LaButti, Rüdiger Pukall, Matt Nolan, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Susan Lucas, Feng Chen, Alex Copeland, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Sam Pitluck, David Bruce, Lynne Goodwin, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Amy Chen, Krishna Palaniappan, Patrick Chain, Thomas Brettin, Johannes Sikorski, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, Alla Lapidus: Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022). Stand Genomic Sci 2: 49 - 56 2010 ( DOI 10.4056/sigs.601105 , PubMed 21304677 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#83258

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID49676.1 )

* These data were automatically processed and therefore are not curated

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Sphaerobacter thermophilus DSM 20745 DSM 20745

Sphaerobacter thermophilus DSM 20745 DSM 20745

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