Name: Silvimonas terrae KM-45
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 10501

Type strain:

Species: Silvimonas terrae

Strain Designation: KM-45

Culture col. no.: DSM 18233, KCTC 12358, NBRC 100961, JCM 21671, IAM 15217

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 300266 (species)

SI-ID 232848

KCTC 12358, NBRC 100961, DSM 18233, JCM 21671, IAM 15217

Section

Silvimonas terrae KM-45 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from forest soil.

Gram-negative
motile
rod-shaped
facultative anaerobe
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	*Betaproteobacteria*
	Order	*Neisseriales*
	Family	*Chromobacteriaceae*
	Genus	*Silvimonas*
	Species	**Silvimonas terrae**
	Full Scientific Name (LPSN)	Silvimonas terrae Yang et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31576]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.99

[Ref.: #31576]	Cell length	1.65 µm

[Ref.: #31576]	Cell width	0.65 µm

[Ref.: #31576]	Cell shape	rod-shaped

[Ref.: #31576]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %96.285

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7446]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7446]

Culture medium growth

[Ref.: #7446]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7446]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7446]	growth	28 °C
[Ref.: #31576]	growth	15-40 °C
[Ref.: #31576]	optimum	27.5 °C
[Ref.: #67770]	growth	30 °C
[Ref.: #67771]	growth	28 °C

[Ref.: #7446]	Temperature range	mesophilic
[Ref.: #31576]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31576]			optimum	7
[Ref.: #31576]			growth	6.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31576]	Oxygen tolerance	facultative anaerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.993

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31576]		NaCl		growth	<2	%
[Ref.: #31576]		NaCl		optimum	1	%

[Ref.: #31576]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: Q-8
[Ref.: #67771]	Observation	quinones: Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31576]	arabinose ChEBI	+	carbon source
[Ref.: #31576]	fucose ChEBI	+	carbon source
[Ref.: #31576]	gluconate ChEBI	+	carbon source
[Ref.: #31576]	maltose ChEBI	+	carbon source
[Ref.: #31576]	mannitol ChEBI	+	carbon source
[Ref.: #31576]	mannose ChEBI	+	carbon source
[Ref.: #31576]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #31576]	nitrate ChEBI	+	reduction
[Ref.: #31576]	rhamnose ChEBI	+	carbon source
[Ref.: #31576]	sucrose ChEBI	+	carbon source

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

[Ref.: #7446]	Sample type/isolated from	forest soil
[Ref.: #7446]	Geographic location (country and/or sea, region)	near Daejeon
[Ref.: #7446]	Country	Republic of Korea
[Ref.: #7446]	Country ISO 3 Code	KOR
[Ref.: #7446]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Forest soil collected near KAIST
[Ref.: #67770]	Geographic location (country and/or sea, region)	Daejeon
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From forest soil
[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	#Forest
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB194302 (>99% sequence identity) for Silvimonas from Microbeatlas

Aquatic Samples	9
Soil Samples	116
Animal Samples	5
Plant Samples
Total Samples	130

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

[Ref.: #7446]

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.: #7446]	Silvimonas terrae gene for 16S rRNA, partial sequence	AB194302	1491	ENA	300266 tax ID
[Ref.: #20218]	Silvimonas terrae gene for 16S rRNA, partial sequence, strain: NBRC 100961	AB681298	1459	ENA	300266 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Silvimonas terrae DSM 18233	GCA_014202765	scaffold	GenBank	300266 tax ID	*
[Ref.: #66792]	Silvimonas terrae strain DSM 18233	300266.6	wgs	PATRIC	300266 tax ID	*
[Ref.: #66792]	Silvimonas terrae DSM 18233	2861607078	draft	JGI IMG/M	300266 tax ID	*

[Ref.: #7446]	GC-content	58 mol%	high performance liquid chromatography (HPLC)
[Ref.: #31576]	GC-content	58 mol%

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: Silvimonas terrae DSM 18233 NCBI: GCA_014202765.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Silvimonas terrae DSM 18233 NCBI: GCA_014202765.1
[Ref.: #69480]	flagellated	yes	64.728	no
[Ref.: #69480]	gram-positive	no	97.817	yes
[Ref.: #69480]	anaerobic	no	99.013	yes
[Ref.: #69480]	aerobic	yes	69.715	no
[Ref.: #69480]	halophile	no	94.868	no
[Ref.: #69480]	spore-forming	no	95.023	no
[Ref.: #69480]	glucose-util	yes	94.849	no
[Ref.: #69480]	thermophile	no	99.4	yes
[Ref.: #69480]	motile	yes	92.028	yes
[Ref.: #69480]	glucose-ferment	no	76.186	no

Availability in culture collections External links

[Ref.: #7446]

Culture collection no.

DSM 18233, KCTC 12358, NBRC 100961, JCM 21671, IAM 15217

[Ref.: #79778]

SI-ID 232848

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Amantichitinum ursilacus gen. nov., sp. nov., a chitin-degrading bacterium isolated from soil.	Moss KS, Hartmann SC, Muller I, Fritz C, Krugener S, Zibek S, Hirth T, Rupp S	Int J Syst Evol Microbiol	10.1099/ijs.0.034447-0	2012	*
Phylogeny	Silvimonas iriomotensis sp. nov. and Silvimonas amylolytica sp. nov., new members of the class Betaproteobacteria isolated from the subtropical zone in Japan.	Muramatsu Y, Suzuki KI, Nakagawa Y	Int J Syst Evol Microbiol	10.1099/ijs.0.011007-0	2009	*
Phylogeny	Chitinilyticum aquatile gen. nov., sp. nov., a chitinolytic bacterium isolated from a freshwater pond used for Pacific white shrimp culture.	Chang SC, Chen WM, Wang JT, Wu MC	Int J Syst Evol Microbiol	10.1099/ijs.0.65168-0	2007	*
Phylogeny	Deefgea rivuli gen. nov., sp. nov., a member of the class Betaproteobacteria.	Stackebrandt E, Lang E, Cousin S, Pauker O, Brambilla E, Kroppenstedt R, Lunsdorf H	Int J Syst Evol Microbiol	10.1099/ijs.0.64771-0	2007	*
Phylogeny	Silvimonas terrae gen. nov., sp. nov., a novel chitin-degrading facultative anaerobe belonging to the 'Betaproteobacteria'.	Yang HC, Im WT, An DS, Park WS, Kim IS, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.63837-0	2005	*

References

#7446

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18233

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#31576

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 #27865 (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) .

#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 )

#79778

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-ID232848.1 )

#27865

IJSEM 2329 2005 ( DOI 10.1099/ijs.0.63837-0 , PubMed 16280491 )

* These data were automatically processed and therefore are not curated

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Silvimonas terrae DSM 18233

Silvimonas terrae DSM 18233

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