Name: Spelaeicoccus albus D3-40
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23809

Type strain:

Species: Spelaeicoccus albus

Strain Designation: D3-40

Culture col. no.: DSM 26341, KCTC 29141, JCM 31495

Strain history: <- SD Lee, Jeju Natl. Univ.

NCBI tax ID(s): 1280376 (species)

SI-ID 408044

DSM 26341

Section

Spelaeicoccus albus D3-40 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil of a natural cave.

coccus-shaped
Gram-positive
aerobe
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Brevibacteriaceae*
	Genus	*Spelaeicoccus*
	Species	**Spelaeicoccus albus**
	Full Scientific Name (LPSN)	Spelaeicoccus albus Lee 2013

Information on morphological and physiological properties Morphology

[Ref.: #31048]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive

[Ref.: #31048]	Cell length	0.75 µm

[Ref.: #31048]	Cell width	0.75 µm

[Ref.: #31048]	Cell shape	coccus-shaped

[Ref.: #31048]	Motility	no

[Ref.: #31048]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21288]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #21288]

Culture medium growth

[Ref.: #21288]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21288]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21288]	growth	30 °C
[Ref.: #31048]	growth	10-37 °C
[Ref.: #31048]	optimum	29 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #21288]	Temperature range	mesophilic
[Ref.: #31048]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31048]			optimum	7
[Ref.: #31048]			growth	05-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31048]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #31048]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31048]		NaCl		growth	0-6	%
[Ref.: #31048]		NaCl		optimum	1.5	%

[Ref.: #31048]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: MK-9(H₂)
[Ref.: #67771]	Observation	quinones: MK-9(H2)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31048]	citrate ChEBI	+	carbon source
[Ref.: #31048]	esculin ChEBI	+	hydrolysis
[Ref.: #31048]	glucose ChEBI	+	carbon source
[Ref.: #31048]	mannitol ChEBI	+	carbon source
[Ref.: #31048]	mannose ChEBI	+	carbon source
[Ref.: #31048]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #31048]	nitrate ChEBI	+	reduction

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31048]		acid phosphatase	+	3.1.3.2
[Ref.: #31048]		catalase	+	1.11.1.6

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

[Ref.: #21288]	Sample type/isolated from	soil of a natural cave
[Ref.: #21288]	Geographic location (country and/or sea, region)	Jeju
[Ref.: #21288]	Country	Republic of Korea
[Ref.: #21288]	Country ISO 3 Code	KOR
[Ref.: #21288]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil of a natural cave
[Ref.: #67770]	Geographic location (country and/or sea, region)	Jeju
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From natural cave soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Jeju
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Geologic
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HF570029 (>99% sequence identity) for Spelaeicoccus albus subclade from Microbeatlas

Aquatic Samples	52
Soil Samples	85
Animal Samples	312
Plant Samples	24
Total Samples	473

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

[Ref.: #21288]

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.: #21288]	Spelaeicoccus albus partial 16S rRNA gene, type strain d3-40T	HF570029	1397	ENA	1280376 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Spelaeicoccus albus DSM 26341	GCA_013409065	contig	GenBank	1280376 tax ID
[Ref.: #66792]	Spelaeicoccus albus strain DSM 26341	1280376.3	wgs	PATRIC	1280376 tax ID	*
[Ref.: #66792]	Spelaeicoccus albus DSM 26341	2833989251	draft	JGI IMG/M	1280376 tax ID	*
[Ref.: #66792]	Spelaeicoccus albus DSM 26341	GCA_021729195	contig	GenBank	1280376 tax ID	*

[Ref.: #21288]	GC-content	64.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #31048]	GC-content	64.3 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Spelaeicoccus albus strain DSM 26341 PATRIC: 1280376.3
[Ref.: #69480]	motile	no	90.001	yes
[Ref.: #69480]	gram-positive	yes	92.983	yes
[Ref.: #69480]	anaerobic	no	99.537	no
[Ref.: #69480]	aerobic	yes	93.845	yes
[Ref.: #69480]	halophile	no	61.635	yes
[Ref.: #69480]	spore-forming	no	92.189	no
[Ref.: #69480]	thermophile	no	94.737	no
[Ref.: #69480]	glucose-util	yes	87.977	no
[Ref.: #69480]	flagellated	no	97.939	yes
[Ref.: #69480]	glucose-ferment	no	88.565	no

Availability in culture collections External links

[Ref.: #21288]

Culture collection no.

DSM 26341, KCTC 29141, JCM 31495

[Ref.: #87839]

SI-ID 408044

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Spelaeicoccus albus gen. nov., sp. nov., an actinobacterium isolated from a natural cave.	Lee SD	Int J Syst Evol Microbiol	10.1099/ijs.0.050732-0	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 )

#21288

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26341

#31048

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27378 (see below)

#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) .

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

#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) .

#87839

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-ID408044.1 )

#27378

IJSEM 3958 2013 ( DOI 10.1099/ijs.0.050732-0 , PubMed 23811133 )

* These data were automatically processed and therefore are not curated

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Spelaeicoccus albus strain DSM 26341

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