Name: Sphingomicrobium arenosum KCTC 62233
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 159873

Type strain:

Species: Sphingomicrobium arenosum

Culture col. no.: KCTC 62233, NBRC 113094, CAU 1457

Strain history: <- Wonyong Kim, Chung-Ang Univ.

NCBI tax ID(s): 2233861 (species)

Section

Sphingomicrobium arenosum KCTC 62233 is an obligate aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from marine sand.

colony-forming
Gram-negative
motile
rod-shaped
mesophilic
obligate aerobe
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 arenosum**
	Full Scientific Name (LPSN)	Sphingomicrobium arenosum Zhang et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #66616]	Gram stain	negative

[Ref.: #66616]	Cell length	0.7-1.9 µm

[Ref.: #66616]	Cell width	0.1-0.4 µm

[Ref.: #66616]	Cell shape	rod-shaped

[Ref.: #66616]	Motility	yes

[Ref.: #66616]	Flagellum arrangement	monotrichous, polar

[Ref.: #66616]	Colony size	0.5 mm
[Ref.: #66616]	Colony color	dar-orange
[Ref.: #66616]	Colony shape	circular
[Ref.: #66616]	Incubation period	3 days
[Ref.: #66616]	Cultivation medium used	Marine agar (MA)

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Marine agar (MA)

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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

BHI

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Culture medium growth

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Culture medium

GYE

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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

tryptic soy agar (TSA)

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Culture medium growth

		Temperature
[Ref.: #66616]	optimum	30 °C
[Ref.: #66616]	growth	20-37 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #66616]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #66616]			optimum	6
[Ref.: #66616]			growth	5.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #66616]	Oxygen tolerance	obligate aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66616]		NaCl		growth	0-7	%
[Ref.: #66616]		NaCl		optimum	2	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66616]	adipate ChEBI	+	assimilation
[Ref.: #66616]	alpha-D-glucose ChEBI	+	carbon source
[Ref.: #66616]	amygdalin ChEBI	-	builds acid from
[Ref.: #66616]	arbutin ChEBI	-	builds acid from
[Ref.: #66616]	casein	-	hydrolysis
[Ref.: #66616]	cellobiose ChEBI	-	builds acid from
[Ref.: #66616]	citric acid ChEBI	+	assimilation
[Ref.: #66616]	D-arabinose ChEBI	-	builds acid from
[Ref.: #66616]	D-arabitol ChEBI	-	builds acid from
[Ref.: #66616]	D-fructose ChEBI	-	builds acid from
[Ref.: #66616]	D-fructose ChEBI	+	carbon source
[Ref.: #66616]	D-fucose ChEBI	-	builds acid from
[Ref.: #66616]	D-galactose ChEBI	+	builds acid from
[Ref.: #66616]	D-galactose ChEBI	+	carbon source
[Ref.: #66616]	D-glucose ChEBI	+	assimilation
[Ref.: #66616]	D-glucose ChEBI	-	builds acid from
[Ref.: #66616]	D-lyxose ChEBI	-	builds acid from
[Ref.: #66616]	D-mannitol ChEBI	+	assimilation
[Ref.: #66616]	D-mannitol ChEBI	-	builds acid from
[Ref.: #66616]	D-mannitol ChEBI	+	carbon source
[Ref.: #66616]	D-mannose ChEBI	+	assimilation
[Ref.: #66616]	D-mannose ChEBI	-	builds acid from
[Ref.: #66616]	D-ribose ChEBI	-	builds acid from
[Ref.: #66616]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #66616]	D-sorbitol ChEBI	+	carbon source
[Ref.: #66616]	D-tagatose ChEBI	-	builds acid from
[Ref.: #66616]	D-xylose ChEBI	-	builds acid from
[Ref.: #66616]	erythritol ChEBI	-	builds acid from
[Ref.: #66616]	esculin ferric citrate	+	builds acid from
[Ref.: #66616]	galactitol ChEBI	-	builds acid from
[Ref.: #66616]	gelatin ChEBI	-	hydrolysis
[Ref.: #66616]	gentiobiose ChEBI	-	builds acid from
[Ref.: #66616]	glycerol ChEBI	-	builds acid from
[Ref.: #66616]	glycogen ChEBI	-	builds acid from
[Ref.: #66616]	inulin ChEBI	-	builds acid from
[Ref.: #66616]	L-arabinose ChEBI	+	assimilation
[Ref.: #66616]	L-arabinose ChEBI	+	builds acid from
[Ref.: #66616]	L-arabinose ChEBI	+	carbon source
[Ref.: #66616]	L-arabitol ChEBI	-	builds acid from
[Ref.: #66616]	L-fucose ChEBI	-	builds acid from
[Ref.: #66616]	L-histidine ChEBI	+	carbon source
[Ref.: #66616]	L-leucine ChEBI	+	carbon source
[Ref.: #66616]	L-ornithine ChEBI	+	carbon source
[Ref.: #66616]	L-phenylalanine ChEBI	+	carbon source
[Ref.: #66616]	L-proline ChEBI	+	carbon source
[Ref.: #66616]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #66616]	L-rhamnose ChEBI	+	carbon source
[Ref.: #66616]	L-sorbose ChEBI	-	builds acid from
[Ref.: #66616]	L-threonine ChEBI	+	carbon source
[Ref.: #66616]	L-xylose ChEBI	-	builds acid from
[Ref.: #66616]	lactose ChEBI	-	builds acid from
[Ref.: #66616]	lactose ChEBI	+	carbon source
[Ref.: #66616]	malate ChEBI	+	assimilation
[Ref.: #66616]	maltose ChEBI	+	assimilation
[Ref.: #66616]	maltose ChEBI	-	builds acid from
[Ref.: #66616]	maltose ChEBI	+	carbon source
[Ref.: #66616]	melezitose ChEBI	-	builds acid from
[Ref.: #66616]	melibiose ChEBI	-	builds acid from
[Ref.: #66616]	melibiose ChEBI	+	carbon source
[Ref.: #66616]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #66616]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #66616]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #66616]	myo-inositol ChEBI	-	builds acid from
[Ref.: #66616]	myo-inositol ChEBI	+	carbon source
[Ref.: #66616]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #66616]	nitrate ChEBI	-	reduction
[Ref.: #66616]	potassium 2-dehydro-D-gluconate	-	builds acid from
[Ref.: #66616]	potassium 5-dehydro-D-gluconate	+	builds acid from
[Ref.: #66616]	potassium gluconate ChEBI	+	assimilation
[Ref.: #66616]	potassium gluconate ChEBI	+	builds acid from
[Ref.: #66616]	raffinose ChEBI	+	builds acid from
[Ref.: #66616]	raffinose ChEBI	+	carbon source
[Ref.: #66616]	ribitol ChEBI	-	builds acid from
[Ref.: #66616]	ribitol ChEBI	+	carbon source
[Ref.: #66616]	salicin ChEBI	-	builds acid from
[Ref.: #66616]	sodium citrate ChEBI	+	assimilation
[Ref.: #66616]	starch ChEBI	-	builds acid from
[Ref.: #66616]	starch ChEBI	-	hydrolysis
[Ref.: #66616]	sucrose ChEBI	-	builds acid from
[Ref.: #66616]	sucrose ChEBI	+	carbon source
[Ref.: #66616]	trehalose ChEBI	-	builds acid from
[Ref.: #66616]	turanose ChEBI	-	builds acid from
[Ref.: #66616]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #66616]	acid phosphatase	+	3.1.3.2
[Ref.: #66616]	alkaline phosphatase	+	3.1.3.1
[Ref.: #66616]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #66616]	alpha-fucosidase	-	3.2.1.51
[Ref.: #66616]	alpha-galactosidase	-	3.2.1.22
[Ref.: #66616]	alpha-glucosidase	-	3.2.1.20
[Ref.: #66616]	alpha-mannosidase	-	3.2.1.24
[Ref.: #66616]	arginine dihydrolase	+	3.5.3.6
[Ref.: #66616]	beta-galactosidase	-	3.2.1.23
[Ref.: #66616]	beta-glucosidase	-	3.2.1.21
[Ref.: #66616]	beta-glucuronidase	-	3.2.1.31
[Ref.: #66616]	catalase	+	1.11.1.6
[Ref.: #66616]	cystine arylamidase	+	3.4.11.3
[Ref.: #66616]	cytochrome oxidase	+	1.9.3.1
[Ref.: #66616]	esterase (C 4)	+
[Ref.: #66616]	esterase Lipase (C 8)	+
[Ref.: #66616]	leucine arylamidase	+	3.4.11.1
[Ref.: #66616]	lipase (C 14)	+
[Ref.: #66616]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #66616]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #66616]	ornithine decarboxylase	+	4.1.1.17
[Ref.: #66616]	trypsin	+	3.4.21.4
[Ref.: #66616]	urease	+	3.5.1.5
[Ref.: #66616]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

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Fatty acid	Percentage
C18:1 w7c / C18:1 w6c	51.7
C18:1 w7c 11-methyl	10.1
C16:0	8.8
C16:1 w7c / C16:1 w6c	8.2
C18:0	5.1
C18:1 2OH	4.6
C17:1 w6c	3.8
C18:1 w5c	3.5
C17:0	1.5
C16:1 w5c	1
C20:1 w7c	0.9
Unknown ECL 18.846 / C19:1w6c / C19:0w10c cyclo	0.6

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

[Ref.: #66616]	Sample type/isolated from	marine sand
[Ref.: #66616]	Geographic location (country and/or sea, region)	Modo
[Ref.: #66616]	Country	Republic of Korea
[Ref.: #66616]	Country ISO 3 Code	KOR
[Ref.: #66616]	Continent	Asia
[Ref.: #66616]	Geographic location	37.5367°/126.4140°
[Ref.: #66616]	Enrichment culture	MA
[Ref.: #66616]	Enrichment culture composition	supplemented with cycloheximide (50 mg/l) and nalidixic acid (20 mg/l)
[Ref.: #66616]	Enrichment culture duration	7 days
[Ref.: #66616]	Enrichment culture temperature	30 ̊C
[Ref.: #66616]	Isolation/enrichment procedure	1 g of sample was serially diluted with 10 ml sterilized 0.85 %(w/v) sodium chloride solution an 100 µl of each serial dilution was plated on marine agar

[Ref.: #67771]	Sample type/isolated from	From mud
[Ref.: #67771]	Geographic location (country and/or sea, region)	Modo
[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	#Aquatic	#Marine
#Environmental	#Terrestrial	#Sandy

What are isolation sources categories?

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.: #66616]	Sphingomicrobium sp. strain CAU 1457 16S ribosomal RNA gene, partial sequence	MH091576	1480	ENA	2233861 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingomicrobium arenosum NBRC 113094	GCA_026157085	contig	GenBank	2233861 tax ID	*

[Ref.: #66616]

GC-content

68.80 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingomicrobium arenosum NBRC 113094 NCBI: GCA_026157085.1
[Ref.: #69480]	motile	no	79.082	yes
[Ref.: #69480]	flagellated	no	93.768	yes
[Ref.: #69480]	gram-positive	no	97.107	yes
[Ref.: #69480]	anaerobic	no	97.774	yes
[Ref.: #69480]	aerobic	yes	83.942	no
[Ref.: #69480]	halophile	no	84.65	no
[Ref.: #69480]	spore-forming	no	95.56	no
[Ref.: #69480]	glucose-ferment	no	89.358	no
[Ref.: #69480]	thermophile	no	96.066	yes
[Ref.: #69480]	glucose-util	yes	88.664	no

Availability in culture collections External links

[Ref.: #66616]

Culture collection no.

KCTC 62233, NBRC 113094, CAU 1457

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomicrobium arenosum sp. nov., isolated from marine sediment.	Zhang Q, Kanjanasuntree R, Kim JH, Yoon JH, Sukhoom A, Kantachote D, Kim W	Int J Syst Evol Microbiol	10.1099/ijsem.0.002875	2018	*

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 )

#66616

Qi Zhang, Rungravee Kanjanasuntree, Jong-Hwa Kim, Jung-Hoon Yoon, Ampaitip Sukhoom, Duangporn Kantachote and Wonyong Kim: Sphingomicrobium arenosum sp. nov., isolated from marine sediment. IJSEM 68: 2551 - 2556 2018 ( DOI 10.1099/ijsem.0.002875 , PubMed 29927368 )

#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;

#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) .

* These data were automatically processed and therefore are not curated

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Sphingomicrobium arenosum NBRC 113094

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