Name: Symbiobacterium thermophilum T
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 18012

Type strain:

Species: Symbiobacterium thermophilum

Strain Designation: T

Culture col. no.: DSM 24528, IAM 14863, JCM 14929

Strain history: K. Ueda strain T.

NCBI tax ID(s): 292459 (strain), 2734 (species)

SI-ID 88609

IAM 14863, JCM 14929, DSM 24528

Special Collections

DSMZ
JCM

Section

Symbiobacterium thermophilum T is an anaerobe, spore-forming bacterium that was isolated from Compost.

spore-forming
anaerobe
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	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Symbiobacteriaceae*
	Genus	*Symbiobacterium*
	Species	**Symbiobacterium thermophilum**
	Full Scientific Name (LPSN)	Symbiobacterium thermophilum Ohno et al. 2000

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17691]

Culture medium

SYMBIOBACTERIUM THERMOPHILUM MEDIUM (DSMZ Medium 1293)

[Ref.: #17691]

Culture medium growth

[Ref.: #17691]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17691]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #17691]			growth	60 °C
[Ref.: #67770]			growth	60 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #17691]

Oxygen tolerance

anaerobe

[Ref.: #69481]

Ability of spore formation

yes Confidence in %91

[Ref.: #67770]	Observation	Production of Tryptophanase and beta-tyrosinase in association with Bacillus strain S
[Ref.: #67770]	Observation	quinones: MK-6

	Enzymes	Enzyme	EC number
[Ref.: #67770]		tryptophanase	4.1.99.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	aspartate and asparagine metabolism	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]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	purine metabolism	71.28	67 of 94
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	oxidative phosphorylation	70.33	64 of 91
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	lipid metabolism	54.84	17 of 31
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	flavin biosynthesis	40	6 of 15
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	vitamin B12 metabolism	38.24	13 of 34
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
[Ref.: #66794]	heme metabolism	21.43	3 of 14
		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.: #17691]	Sample type/isolated from	Compost
[Ref.: #17691]	Geographic location (country and/or sea, region)	Hiroshima
[Ref.: #17691]	Country	Japan
[Ref.: #17691]	Country ISO 3 Code	JPN
[Ref.: #17691]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Compost in Hiroshima
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered

#Biodegradation

#Composting

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB004913 (>99% sequence identity) for Symbiobacterium thermophilum subclade from Microbeatlas

Aquatic Samples	404
Soil Samples	1451
Animal Samples	4551
Plant Samples	620
Total Samples	7026

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

[Ref.: #17691]

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.: #17691]	Symbiobacterium thermophilum DNA for 16S rRNA	AB004913	1479	GenBank ENA	2734 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Symbiobacterium thermophilum IAM 14863 IAM14863	GCA_000009905	complete	GenBank ENA	292459 tax ID	*
[Ref.: #66792]	Symbiobacterium thermophilum IAM 14863	292459.5	complete	PATRIC	292459 tax ID	*
[Ref.: #66792]	Symbiobacterium thermophilum IAM 14863	637000306	complete	JGI IMG/M	292459 tax ID	*

[Ref.: #17691]	GC-content	68 mol%	sequence analysis
[Ref.: #67770]	GC-content	68.7 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	65.1 mol%	thermal denaturation, midpoint method (Tm)

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: Symbiobacterium thermophilum IAM 14863 IAM14863 NCBI: GCA_000009905.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	91	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Symbiobacterium thermophilum IAM 14863 IAM14863 NCBI: GCA_000009905.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	54.634	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	55.006	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	65.546	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	76.873	no
[Ref.: #69480]	thermophilic	thermophileⓘ	yes	61.512	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	72.5	no

Availability in culture collections External links

[Ref.: #17691]

Culture collection no.

DSM 24528, IAM 14863, JCM 14929

[Ref.: #86999]

SI-ID 88609

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Detection and characterization of a thermophilic biotin biosynthetic enzyme, 7-keto-8-aminopelargonic acid synthase, from various thermophiles.	Kubota T, Izumi Y	Biosci Biotechnol Biochem	10.1271/bbb.110807	2012	*
Enzymology	Essential role of amino acid position 71 in substrate preference by meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum IAM14863.	Zhang Y, Ma Q, Dong M, Zhang X, Chen Y, Gao X, Song Y	Enzyme Microb Technol	10.1016/j.enzmictec.2018.01.001	2018	*
Enzymology	Cloning, expression, purification and preliminary X-ray analysis of a putative metagenome-derived lipase.	Fersini F, Dall'Antonia Y, Chow J, Streit WR, Mueller-Dieckmann J	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/S1744309112025651	2012	*
Phylogeny	Symbiobacterium thermophilum gen. nov., sp. nov., a symbiotic thermophile that depends on co-culture with a Bacillus strain for growth.	Ohno M, Shiratori H, Park MJ, Saitoh Y, Kumon Y, Yamashita N, Hirata A, Nishida H, Ueda K, Beppu T	Int J Syst Evol Microbiol	10.1099/00207713-50-5-1829	2000	*

References

#17691

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24528

#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 )

#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) .

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

#86999

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-ID88609.1 )

* These data were automatically processed and therefore are not curated

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Symbiobacterium thermophilum IAM 14863 IAM14863

Symbiobacterium thermophilum IAM 14863 IAM14863

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