Name: Vulcaniibacterium tengchongense DSM 25623
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24686

Type strain:

Species: Vulcaniibacterium tengchongense

Culture col. no.: DSM 25623, CCTCC AB 2011152, YIM 77520, JCM 17893

Strain history: S.-K. Tang YIM 77520.

NCBI tax ID(s): 1273429 (species)

SI-ID 407654

DSM 25623

Section

Vulcaniibacterium tengchongense DSM 25623 is a mesophilic, Gram-negative bacterium that was isolated from geothermally heated soil.

Gram-negative
mesophilic
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	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Vulcaniibacterium*
	Species	**Vulcaniibacterium tengchongense**
	Full Scientific Name (LPSN)	Vulcaniibacterium tengchongense Yu et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.986

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21313]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)

[Ref.: #21313]

Culture medium growth

[Ref.: #21313]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21313]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #21313]			growth	37 °C
[Ref.: #67770]			growth	45 °C

[Ref.: #21313]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %93
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.926

[Ref.: #67770]

Observation

quinones: Q-8

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	lipid A biosynthesis	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	D-cycloserine biosynthesis	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	oxidative phosphorylation	35.16	32 of 91
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	vitamin B12 metabolism	20.59	7 of 34
		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.: #21313]	Sample type/isolated from	geothermally heated soil
[Ref.: #21313]	Geographic location (country and/or sea, region)	Yunnan Province, Tengchong, Rehai National Park (N 24.95002°, W 98.43742°)
[Ref.: #21313]	Country	China
[Ref.: #21313]	Country ISO 3 Code	CHN
[Ref.: #21313]	Continent	Asia
[Ref.: #21313]	Geographic location	24.9503°/98.4374°

[Ref.: #67770]	Sample type/isolated from	Geothermally heated soil at Rehai National Park
[Ref.: #67770]	Geographic location (country and/or sea, region)	Tengchong, Yunnan Province
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Condition	#Thermophilic (>45°C)	-
#Environmental	#Aquatic	-

What are isolation sources categories?

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

[Ref.: #21313]

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.: #21313]	Lysobacter sp. YIM 77520 16S ribosomal RNA gene, partial sequence	JX964994	1539	ENA	1273429 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Vulcaniibacterium tengchongense YIM 77520	GCA_008033455	contig	GenBank	1273429 tax ID
[Ref.: #66792]	Vulcaniibacterium tengchongense DSM 25623	GCA_003814555	scaffold	GenBank	1273429 tax ID	*
[Ref.: #66792]	Vulcaniibacterium tengchongense strain DSM 25623	1273429.3	wgs	PATRIC	1273429 tax ID	*
[Ref.: #66792]	Vulcaniibacterium tengchongense strain YIM 77520	1273429.4	wgs	PATRIC	1273429 tax ID	*
[Ref.: #66792]	Vulcaniibacterium tengchongense DSM 25623	2786546141	draft	JGI IMG/M	1273429 tax ID	*

[Ref.: #21313]

GC-content

66.9 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Vulcaniibacterium tengchongense DSM 25623 NCBI: GCA_003814555.1
[Ref.: #69481]	spore-forming	no	93	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Vulcaniibacterium tengchongense DSM 25623 NCBI: GCA_003814555.1
[Ref.: #69480]	motile	yes	83.695	no
[Ref.: #69480]	flagellated	no	86.376	no
[Ref.: #69480]	gram-positive	no	98.558	no
[Ref.: #69480]	anaerobic	no	98.702	no
[Ref.: #69480]	aerobic	yes	92.147	no
[Ref.: #69480]	halophile	no	94.939	no
[Ref.: #69480]	spore-forming	no	95.704	no
[Ref.: #69480]	thermophile	no	92.159	no
[Ref.: #69480]	glucose-util	yes	92.977	no
[Ref.: #69480]	glucose-ferment	no	88.098	no

Availability in culture collections External links

[Ref.: #21313]

Culture collection no.

DSM 25623, CCTCC AB 2011152, YIM 77520, JCM 17893

[Ref.: #88522]

SI-ID 407654

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Vulcaniibacterium gelatinicum sp. nov., a moderately thermophilic bacterium isolated from a hot spring.	Niu XK, Narsing Rao MP, Dong ZY, Kan Y, Li QR, Huang J, Zhao L, Wang MZ, Shen ZP, Kang YQ, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003934	2020	*
Phylogeny	Vulcaniibacterium tengchongense gen. nov., sp. nov. isolated from a geothermally heated soil sample, and reclassification of Lysobacter thermophilus Wei et al. 2012 as Vulcaniibacterium thermophilum comb. nov.	Yu TT, Zhou EM, Yin YR, Yao JC, Ming H, Dong L, Li S, Nie GX, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-013-9959-4	2013	*

References

#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 )

#21313

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25623

#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;

#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 )

#88522

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-ID407654.1 )

* These data were automatically processed and therefore are not curated

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