Name: Spirosoma panaciterrae DSM 21099
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 3822

Type strain:

Species: Spirosoma panaciterrae

Culture col. no.: DSM 21099, KCTC 22263, Gsoil 1519

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 1123277 (strain), 496058 (species)

SI-ID 339817

LMG 24496, DSM 21099, KCTC 22263

Section

Spirosoma panaciterrae DSM 21099 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil of a ginseng field.

Gram-negative
rod-shaped
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	*Bacteroidota*
	Class	*Cytophagia*
	Order	*Cytophagales*
	Family	*Spirosomataceae*
	Genus	*Spirosoma*
	Species	**Spirosoma panaciterrae**
	Full Scientific Name (LPSN)	Spirosoma panaciterrae Ten et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #28949]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.993

[Ref.: #28949]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #28949]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %96.359

[Ref.: #28949]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15553]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #15553]

Culture medium growth

[Ref.: #15553]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15553]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15553]	growth	28 °C
[Ref.: #28949]	growth	15-42 °C
[Ref.: #28949]	optimum	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #15553]	Temperature range	mesophilic
[Ref.: #28949]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #28949]			optimum	6.75
[Ref.: #28949]			growth	5.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #28949]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #28949]	Ability of spore formation	no
[Ref.: #67771]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.967

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #28949]		NaCl		growth	<1	%

[Ref.: #28949]	Observation	aggregates in clumps
[Ref.: #67771]	Observation	quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #28949]	arabinose ChEBI	+	carbon source
[Ref.: #28949]	cellobiose ChEBI	+	carbon source
[Ref.: #28949]	glucose ChEBI	+	carbon source
[Ref.: #28949]	maltose ChEBI	+	carbon source
[Ref.: #28949]	mannose ChEBI	+	carbon source
[Ref.: #28949]	melibiose ChEBI	+	carbon source
[Ref.: #28949]	salicin ChEBI	+	carbon source
[Ref.: #28949]	sorbitol ChEBI	+	carbon source
[Ref.: #28949]	sucrose ChEBI	+	carbon source
[Ref.: #28949]	trehalose ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #28949]	acid phosphatase	+	3.1.3.2
[Ref.: #28949]	alkaline phosphatase	+	3.1.3.1
[Ref.: #28949]	alpha-galactosidase	+	3.2.1.22
[Ref.: #28949]	catalase	+	1.11.1.6
[Ref.: #28949]	cytochrome oxidase	+	1.9.3.1
[Ref.: #28949]	gelatinase	+

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

[Ref.: #15553]	Sample type/isolated from	soil of a ginseng field
[Ref.: #15553]	Geographic location (country and/or sea, region)	Pocheon province
[Ref.: #15553]	Country	Republic of Korea
[Ref.: #15553]	Country ISO 3 Code	KOR
[Ref.: #15553]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From soil of ginseng field
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU370956 (>99% sequence identity) for Spirosoma panaciterrae subclade from Microbeatlas

Aquatic Samples	238
Soil Samples	82
Animal Samples	249
Plant Samples	238
Total Samples	807

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

[Ref.: #15553]

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.: #15553]	Spirosoma panaciterrae strain Gsoil 1519 16S ribosomal RNA gene, partial sequence	EU370956	1442	ENA	496058 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Spirosoma panaciterrae DSM 21099	GCA_000374025	scaffold	GenBank	1123277 tax ID	*
[Ref.: #66792]	Spirosoma panaciterrae DSM 21099	1123277.3	wgs	PATRIC	1123277 tax ID	*
[Ref.: #66792]	Spirosoma panaciterrae DSM 21099	2515154167	draft	JGI IMG/M	1123277 tax ID	*

[Ref.: #15553]	GC-content	50.1 mol%	high performance liquid chromatography (HPLC)
[Ref.: #28949]	GC-content	50.1 mol%
[Ref.: #15553]	GC-content	48.9 mol%	sequence analysis

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: Spirosoma panaciterrae DSM 21099 DSM 21099 NCBI: GCA_000374025.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Spirosoma panaciterrae DSM 21099 DSM 21099 NCBI: GCA_000374025.1
[Ref.: #69480]	motile	no	94.124	yes
[Ref.: #69480]	flagellated	no	97.762	yes
[Ref.: #69480]	gram-positive	no	96.74	yes
[Ref.: #69480]	anaerobic	no	99.45	yes
[Ref.: #69480]	aerobic	yes	89.342	yes
[Ref.: #69480]	halophile	no	95.812	no
[Ref.: #69480]	spore-forming	no	92.481	yes
[Ref.: #69480]	glucose-util	yes	83.131	no
[Ref.: #69480]	thermophile	no	99.325	no
[Ref.: #69480]	glucose-ferment	no	88.009	no

Availability in culture collections External links

[Ref.: #15553]

Culture collection no.

DSM 21099, KCTC 22263, Gsoil 1519

[Ref.: #73333]

SI-ID 339817

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Spirosoma metallilatum sp. nov., isolated from an automotive air conditioning system.	Kim DU, Lee H, Lee S, Park S, Yoon JH, Ka JO	Int J Syst Evol Microbiol	10.1099/ijsem.0.002533	2017	*
Phylogeny	Spirosoma terrae sp. nov., Isolated from Soil from Jeju Island, Korea.	Ten LN, Okiria J, Lee JJ, Lee SY, Park S, Lee DS, Kang IK, Kim MK, Jung HY	Curr Microbiol	10.1007/s00284-017-1408-6	2017	*
Phylogeny	Spirosoma harenae sp. nov., a Bacterium Isolated from a Sandy Beach.	Ten LN, Elderiny N, Lee JJ, Lee SY, Park S, Lee DS, Kim MK, Jung HY	Curr Microbiol	10.1007/s00284-017-1363-2	2017	*
Phylogeny	Spirosoma daeguensis sp. nov., isolated from beach soil.	Elderiny N, Ten LN, Lee JJ, Lee SY, Park S, Cho YJ, Kim MK, Jung HY	J Microbiol	10.1007/s12275-017-7211-z	2017	*
Phylogeny	Spirosoma gilvum sp. nov., Isolated from Beach Soil.	Lee JJ, Elderiny N, Lee SY, Lee DS, Kim MK, Ten LN, Jung HY	Curr Microbiol	10.1007/s00284-017-1336-5	2017	*
Phylogeny	Spirosoma swuense sp. nov., isolated from wet soil.	Joo ES, Kim EB, Jeon SH, Srinivasan S, Kim MK	Int J Syst Evol Microbiol	10.1099/ijsem.0.001592	2017	*
Phylogeny	Spirosoma aerolatum sp. nov., isolated from a motor car air conditioning system.	Kim DU, Lee H, Kim SG, Ahn JH, Yoon Park S, Ka JO	Int J Syst Evol Microbiol	10.1099/ijsem.0.000528	2015	*
Phylogeny	Spirosoma montaniterrae sp. nov., an ultraviolet and gamma radiation-resistant bacterium isolated from mountain soil.	Lee JJ, Kang MS, Joo ES, Kim MK, Im WT, Jung HY, Srinivasan S	J Microbiol	10.1007/s12275-015-5008-5	2015	*
Phylogeny	Spirosoma oryzae sp. nov., isolated from rice soil and emended description of the genus Spirosoma.	Ahn JH, Weon HY, Kim SJ, Hong SB, Seok SJ, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.062901-0	2014	*
Phylogeny	Spirosoma radiotolerans sp. nov., a gamma-radiation-resistant bacterium isolated from gamma ray-irradiated soil.	Lee JJ, Srinivasan S, Lim S, Joe M, Im S, Bae SI, Park KR, Han JH, Park SH, Joo BM, Park SJ, Kim MK	Curr Microbiol	10.1007/s00284-014-0584-x	2014	*
Phylogeny	Fibrella aestuarina gen. nov., sp. nov., a filamentous bacterium of the family Cytophagaceae isolated from a tidal flat, and emended description of the genus Rudanella Weon et al. 2008.	Filippini M, Svercel M, Laczko E, Kaech A, Ziegler U, Bagheri HC	Int J Syst Evol Microbiol	10.1099/ijs.0.020503-0	2010	*
Phylogeny	Spirosoma panaciterrae sp. nov., isolated from soil.	Ten LN, Xu JL, Jin FX, Im WT, Oh HM, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.002436-0	2009	*

References

#15553

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21099

#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 )

#28949

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 #25388 (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) .

#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) .

#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 )

#73333

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-ID339817.1 )

#25388

IJSEM 331 2009 ( DOI 10.1099/ijs.0.002436-0 , PubMed 19196773 )

* These data were automatically processed and therefore are not curated

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Spirosoma panaciterrae DSM 21099 DSM 21099

Spirosoma panaciterrae DSM 21099 DSM 21099

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