Name: Sphingomicrobium lutaoense CC-TBT-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14298

Type strain:

Species: Sphingomicrobium lutaoense

Strain Designation: CC-TBT-3

Culture col. no.: DSM 24194, CCM 7794

Strain history: <- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany; CC-TBT-3 <- A. B. Arun, Yenepoya Univ., Mangalore, India

NCBI tax ID(s): 515949 (species)

SI-ID 399702

DSM 24194

Section

Sphingomicrobium lutaoense CC-TBT-3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from water from coastal hot spring.

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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingomicrobium*
	Species	**Sphingomicrobium lutaoense**
	Full Scientific Name (LPSN)	Sphingomicrobium lutaoense Kämpfer et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30362]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.972

[Ref.: #30362]	Cell length	1.5 µm

[Ref.: #30362]	Cell width	1 µm

[Ref.: #30362]	Cell shape	rod-shaped

[Ref.: #30362]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17541]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)

[Ref.: #17541]

Culture medium growth

[Ref.: #17541]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17541]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #17541]			growth	28 °C
[Ref.: #30362]			growth	20-40 °C

[Ref.: #17541]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #30362]			growth	6.5-10.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30362]

Oxygen tolerance

aerobe

[Ref.: #30362]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.993

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30362]		NaCl		growth	1-7	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30362]		3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #30362]		pyruvate ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30362]		cytochrome oxidase	+	1.9.3.1

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

[Ref.: #17541]	Sample type/isolated from	water from coastal hot spring
[Ref.: #17541]	Geographic location (country and/or sea, region)	Taituang, Green Island (22° 39' N 121° 29' E)
[Ref.: #17541]	Country	Taiwan
[Ref.: #17541]	Country ISO 3 Code	TWN
[Ref.: #17541]	Continent	Asia
[Ref.: #17541]	Geographic location	22.6500°/121.4830°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Thermal spring
#Environmental	#Terrestrial	#Coast
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

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

[Ref.: #17541]

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.: #17541]	Sphingomicrobium lutaoense strain CC-TBT-3 16S ribosomal RNA gene, partial sequence	EU564841	1462	ENA	515949 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingomicrobium lutaoense DSM 24194	GCA_014195685	scaffold	GenBank	515949 tax ID	*
[Ref.: #66792]	Sphingomicrobium lutaoense strain DSM 24194	515949.3	wgs	PATRIC	515949 tax ID	*
[Ref.: #66792]	Sphingomicrobium lutaoense DSM 24194	2828014108	draft	JGI IMG/M	515949 tax ID	*
[Ref.: #66792]	Sphingomicrobium lutaoense DSM 24194	GCA_026157185	scaffold	GenBank	515949 tax ID	*

[Ref.: #17541]	GC-content	63.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30362]	GC-content	63.4 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: Sphingomicrobium lutaoense DSM 24194 NCBI: GCA_014195685.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingomicrobium lutaoense DSM 24194 NCBI: GCA_014195685.1
[Ref.: #69480]	flagellated	no	94.005	no
[Ref.: #69480]	gram-positive	no	97.318	yes
[Ref.: #69480]	anaerobic	no	98.741	no
[Ref.: #69480]	aerobic	yes	86.563	yes
[Ref.: #69480]	halophile	no	84.877	no
[Ref.: #69480]	spore-forming	no	95.547	yes
[Ref.: #69480]	glucose-util	yes	85.447	no
[Ref.: #69480]	motile	no	81.722	yes
[Ref.: #69480]	glucose-ferment	no	90.053	no
[Ref.: #69480]	thermophile	no	96.825	yes

Availability in culture collections External links

[Ref.: #17541]

Culture collection no.

DSM 24194, CCM 7794

[Ref.: #83451]

SI-ID 399702

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomicrobium marinum sp. nov. and Sphingomicrobium flavum sp. nov., isolated from surface seawater, and emended description of the genus Sphingomicrobium.	Shahina M, Hameed A, Lin SY, Hsu YH, Liu YC, Huang YM, Lin JC, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.052837-0	2013	*
Phylogeny	Sphingomicrobium astaxanthinifaciens sp. nov., an astaxanthin-producing glycolipid-rich bacterium isolated from surface seawater and emended description of the genus Sphingomicrobium.	Shahina M, Hameed A, Lin SY, Hsu YH, Liu YC, Cheng IC, Lee MR, Lai WA, Lee RJ, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.047704-0	2013	*
Phylogeny	Sphingomicrobium lutaoense gen. nov., sp. nov., isolated from a coastal hot spring.	Kampfer P, Arun AB, Young CC, Busse HJ, Kassmannhuber J, Rossello-Mora R, Geueke B, Rekha PD, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.034413-0	2011	*
Phylogeny	Sphingomicrobium nitratireducens sp. nov., isolated from a tidal flat in Guangxi.	You H, Xu L, Kong YH, Sun C, Zhou P, Xu XW	Arch Microbiol	10.1007/s00203-022-03273-2	2022	*

References

#17541

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24194

#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 )

#30362

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 #26702 (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) .

#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 )

#83451

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-ID399702.1 )

#26702

IJSEM 1326 2012 ( DOI 10.1099/ijs.0.034413-0 , PubMed 21828023 )

* These data were automatically processed and therefore are not curated

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Sphingomicrobium lutaoense DSM 24194

Sphingomicrobium lutaoense DSM 24194

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