Name: Stackebrandtia cavernae DSM 100594
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132431

Type strain:

Species: Stackebrandtia cavernae

Culture col. no.: DSM 100594, CCTCC AA 2015021, KCTC 39599, YIM ART06

Strain history: <- Wenjun Li

NCBI tax ID(s): 1766802 (species)

SI-ID 401667

DSM 100594

Section

Stackebrandtia cavernae DSM 100594 is an obligate aerobe, Gram-positive bacterium that was isolated from dissoluble rock from palisades of a karst cave.

Gram-positive
obligate aerobe
16S sequence
Bacteria

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Glycomycetales*
	Family	*Glycomycetaceae*
	Genus	*Stackebrandtia*
	Species	**Stackebrandtia cavernae**
	Full Scientific Name (LPSN)	Stackebrandtia cavernae Zhang et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43753]	Gram stain	positive

Multimedia content

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Caption:

Medium 554 28°C

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

R2A MEDIUM (DSMZ Medium 830)

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

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Culture medium

ISP2

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Culture medium growth

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Culture medium

ISP3

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Culture medium growth

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Culture medium

ISP5

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Culture medium growth

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Culture medium

Nutrient agar (NA)

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Culture medium growth

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

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Culture medium growth

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Culture medium

N-Z-AMINE-MEDIUM (DSMZ Medium 554)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

		Temperature
[Ref.: #24220]	growth	28 °C
[Ref.: #43753]	growth	15-35 °C
[Ref.: #43753]	optimum	28-30 °C
[Ref.: #67771]	growth	28 °C

[Ref.: #24220]	Temperature range	mesophilic
[Ref.: #43753]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43753]			optimum	7-8
[Ref.: #43753]			growth	6-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43753]	Oxygen tolerance	obligate aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43753]		NaCl		growth	0-4	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43753]	alanine ChEBI	+	nitrogen source
[Ref.: #43753]	alpha-lactose ChEBI	+	carbon source
[Ref.: #43753]	cellulose ChEBI	-	hydrolysis
[Ref.: #43753]	D-galactose ChEBI	-	carbon source
[Ref.: #43753]	D-galactose ChEBI	-	nitrogen source
[Ref.: #43753]	D-glucose ChEBI	-	carbon source
[Ref.: #43753]	D-glucose ChEBI	-	nitrogen source
[Ref.: #43753]	D-mannose ChEBI	-	carbon source
[Ref.: #43753]	D-mannose ChEBI	-	nitrogen source
[Ref.: #43753]	D-sorbitol ChEBI	-	carbon source
[Ref.: #43753]	D-sorbitol ChEBI	-	nitrogen source
[Ref.: #43753]	galactitol ChEBI	+	carbon source
[Ref.: #43753]	gelatin ChEBI	-	hydrolysis
[Ref.: #43753]	glycine ChEBI	+	nitrogen source
[Ref.: #43753]	L-arabinose ChEBI	+	carbon source
[Ref.: #43753]	L-arginine ChEBI	+	nitrogen source
[Ref.: #43753]	L-aspartate ChEBI	+	nitrogen source
[Ref.: #43753]	L-cysteine ChEBI	+	nitrogen source
[Ref.: #43753]	L-cystine ChEBI	-	carbon source
[Ref.: #43753]	L-cystine ChEBI	-	nitrogen source
[Ref.: #43753]	L-glutamate ChEBI	+	nitrogen source
[Ref.: #43753]	L-glutamine ChEBI	-	carbon source
[Ref.: #43753]	L-glutamine ChEBI	-	nitrogen source
[Ref.: #43753]	L-histidine ChEBI	+	nitrogen source
[Ref.: #43753]	L-isoleucine ChEBI	+	nitrogen source
[Ref.: #43753]	L-leucine ChEBI	+	nitrogen source
[Ref.: #43753]	L-lysine ChEBI	+	nitrogen source
[Ref.: #43753]	L-ornithine ChEBI	+	nitrogen source
[Ref.: #43753]	L-phenylalanine ChEBI	+	nitrogen source
[Ref.: #43753]	L-proline ChEBI	+	nitrogen source
[Ref.: #43753]	L-serine ChEBI	+	nitrogen source
[Ref.: #43753]	L-threonine ChEBI	+	nitrogen source
[Ref.: #43753]	L-tryptophan ChEBI	-	carbon source
[Ref.: #43753]	L-tryptophan ChEBI	-	nitrogen source
[Ref.: #43753]	L-tyrosine ChEBI	+	nitrogen source
[Ref.: #43753]	L-valine ChEBI	+	nitrogen source
[Ref.: #43753]	maltose ChEBI	+	carbon source
[Ref.: #43753]	mannitol ChEBI	+	carbon source
[Ref.: #43753]	methionine ChEBI	+	nitrogen source
[Ref.: #43753]	nitrate ChEBI	+	reduction
[Ref.: #43753]	potassium nitrate ChEBI	+	nitrogen source
[Ref.: #43753]	propionamide ChEBI	+	nitrogen source
[Ref.: #43753]	raffinose ChEBI	-	carbon source
[Ref.: #43753]	raffinose ChEBI	-	nitrogen source
[Ref.: #43753]	raffinose ChEBI	+	carbon source
[Ref.: #43753]	starch ChEBI	-	hydrolysis
[Ref.: #43753]	starch ChEBI	+	carbon source
[Ref.: #43753]	sucrose ChEBI	+	carbon source
[Ref.: #43753]	trehalose ChEBI	-	carbon source
[Ref.: #43753]	trehalose ChEBI	-	nitrogen source
[Ref.: #43753]	tween 20 ChEBI	-	hydrolysis
[Ref.: #43753]	tween 40 ChEBI	-	hydrolysis
[Ref.: #43753]	tween 60 ChEBI	-	hydrolysis
[Ref.: #43753]	tween 80 ChEBI	+	hydrolysis
[Ref.: #43753]	tyrosine ChEBI	+	nitrogen source
[Ref.: #43753]	xanthine ChEBI	+	nitrogen source
[Ref.: #43753]	xylitol ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43753]		hydrogen sulfide ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43753]	catalase	+	1.11.1.6
[Ref.: #43753]	cytochrome oxidase	-	1.9.3.1
[Ref.: #43753]	urease	-	3.5.1.5

Fatty acid profile

Metadata FA analysis

Reference

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Fatty acid	Percentage
C15:0 iso	24.6
C17:0 iso 3OH	17.8
C16:1ω7c / C16:1ω6c	16.4
C15:0 iso 3OH	6.4
C15:1 iso G	6.4
C16:0 iso 3OH	5.8
C16:0 3OH	4.8
C15:0 3OH	2.7
C15:0 anteiso	2.2
C16:0 iso	1.8
C16:0	1.7
C17:0 2OH	1.5

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

[Ref.: #24220]	Sample type/isolated from	dissoluble rock from palisades of a karst cave
[Ref.: #24220]	Geographic location (country and/or sea, region)	Guizhou province
[Ref.: #24220]	Country	China
[Ref.: #24220]	Country ISO 3 Code	CHN
[Ref.: #24220]	Continent	Asia

[Ref.: #43753]	Sample type/isolated from	A dissoluble rock soil sample collected from palisades of a karst cave
[Ref.: #43753]	Geographic location (country and/or sea, region)	Guizhou Province
[Ref.: #43753]	Country	China
[Ref.: #43753]	Country ISO 3 Code	CHN
[Ref.: #43753]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	rock sample of karst cave
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Built environment	-
#Environmental	#Terrestrial	#Geologic
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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Global distribution of 16S sequence KT312956 (>99% sequence identity) for Stackebrandtia cavernae subclade from Microbeatlas

Aquatic Samples	22
Soil Samples	371
Animal Samples	131
Plant Samples	59
Total Samples	583

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

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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.: #24220]	Stackebrandtia cavernae strain YIM ART06 16S ribosomal RNA gene, partial sequence	KT312956	1537	ENA	1766802 tax ID

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GC-content

71 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

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Culture collection no.

DSM 100594, CCTCC AA 2015021, KCTC 39599, YIM ART06

[Ref.: #90770]

SI-ID 401667

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Stackebrandtia cavernae sp. nov., a novel actinobacterium isolated from a karst cave sample.	Zhang WQ, Li YQ, Liu L, Salam N, Fang BZ, Wei DQ, Han MX, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.000859	2015	*

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 )

#24220

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100594

#43753

Wan-Qin Zhang, Yu-Qian Li, Lan Liu, Nimaichand Salam, Bao-Zhu Fang, Dao-Qiao Wei, Ming-Xian Han, Wen-Jun Li: Stackebrandtia cavernae sp. nov., a novel actinobacterium isolated from a karst cave sample. IJSEM 66: 1206 - 1211 2016 ( DOI 10.1099/ijsem.0.000859 , PubMed 26703216 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

#90770

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-ID401667.1 )

* These data were automatically processed and therefore are not curated

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