Name: Novosphingobium colocasiae Teta.03
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140931

Type strain:

Species: Novosphingobium colocasiae

Strain Designation: Teta.03

Culture col. no.: LMG 27385, KCTC 32255

NCBI tax ID(s): 1256513 (species)

SI-ID 386839

LMG 27385, KCTC 32255

Section

Novosphingobium colocasiae Teta.03 is an aerobe, chemoheterotroph, Gram-negative bacterium that forms circular colonies and was isolated from The water of a taro field in Luye Township in the vicinity of Taitung city.

colony-forming
Gram-negative
rod-shaped
aerobe
chemoheterotroph
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	*Erythrobacteraceae*
	Genus	*Novosphingobium*
	Species	**Novosphingobium colocasiae**
	Full Scientific Name (LPSN)	Novosphingobium colocasiae Chen et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43808]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.974

[Ref.: #43808]	Cell length	0.8-1 µm

[Ref.: #43808]	Cell width	0.3-0.5 µm

[Ref.: #43808]	Cell shape	rod-shaped

[Ref.: #43808]	Motility	no

[Ref.: #43808]	Colony size	1-1.9 mm
[Ref.: #43808]	Colony color	Bright yellow
[Ref.: #43808]	Colony shape	circular
[Ref.: #43808]	Incubation period	2 days
[Ref.: #43808]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

LB (Luria-Bertani) MEDIUM

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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

Trypticase soy agar

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Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #43808]			growth	10-37 °C
[Ref.: #43808]			optimum	20 °C

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Temperature range

psychrophilic

	pH	Kind of pH		pH
[Ref.: #43808]			optimum	7-8
[Ref.: #43808]			growth	3-9

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

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Nutrition type

chemoheterotroph

[Ref.: #43808]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.992

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Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43808]		NaCl		growth	0-1	%(w/v)
[Ref.: #43808]		NaCl		optimum	0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43808]	2-oxobutanoate ChEBI	+	carbon source
[Ref.: #43808]	2-oxoglutarate ChEBI	+	carbon source
[Ref.: #43808]	2-oxopentanoate ChEBI	+	carbon source
[Ref.: #43808]	acetate ChEBI	+	carbon source
[Ref.: #43808]	adipate ChEBI	-	assimilation
[Ref.: #43808]	alpha-D-glucose ChEBI	+	carbon source
[Ref.: #43808]	arabinose ChEBI	-	assimilation
[Ref.: #43808]	beta-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #43808]	bromosuccinate ChEBI	+	carbon source
[Ref.: #43808]	carboxymethylcellulose ChEBI	+	hydrolysis
[Ref.: #43808]	casein	-	hydrolysis
[Ref.: #43808]	cellobiose ChEBI	+	carbon source
[Ref.: #43808]	chitin ChEBI	-	hydrolysis
[Ref.: #43808]	citrate ChEBI	-	assimilation
[Ref.: #43808]	corn oil	-	hydrolysis
[Ref.: #43808]	D-alanine ChEBI	+	carbon source
[Ref.: #43808]	D-fructose ChEBI	+	carbon source
[Ref.: #43808]	D-glucose ChEBI	-	builds acid from
[Ref.: #43808]	decanoate ChEBI	-	assimilation
[Ref.: #43808]	dextrin ChEBI	+	carbon source
[Ref.: #43808]	dna ChEBI	-	hydrolysis
[Ref.: #43808]	esculin ChEBI	+	hydrolysis
[Ref.: #43808]	gelatin ChEBI	-	hydrolysis
[Ref.: #43808]	gluconate ChEBI	-	assimilation
[Ref.: #43808]	glucose ChEBI	-	fermentation
[Ref.: #43808]	glucose ChEBI	+	assimilation
[Ref.: #43808]	glycyl L-aspartic acid ChEBI	+	carbon source
[Ref.: #43808]	glycyl-l-glutamate ChEBI	+	carbon source
[Ref.: #43808]	L-alaninamide ChEBI	+	carbon source
[Ref.: #43808]	L-alanine 4-nitroanilide	+	carbon source
[Ref.: #43808]	L-alanylglycine ChEBI	+	carbon source
[Ref.: #43808]	L-asparagine ChEBI	+	carbon source
[Ref.: #43808]	L-glutamate ChEBI	+	carbon source
[Ref.: #43808]	L-leucine ChEBI	+	carbon source
[Ref.: #43808]	L-ornithine ChEBI	+	carbon source
[Ref.: #43808]	L-proline ChEBI	+	carbon source
[Ref.: #43808]	lactate ChEBI	+	carbon source
[Ref.: #43808]	malate ChEBI	-	assimilation
[Ref.: #43808]	maltose hydrate	+	assimilation
[Ref.: #43808]	mannitol ChEBI	-	assimilation
[Ref.: #43808]	mannose ChEBI	-	assimilation
[Ref.: #43808]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #43808]	monomethyl succinate ChEBI	+	carbon source
[Ref.: #43808]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #43808]	nitrate ChEBI	-	reduction
[Ref.: #43808]	phenylacetate ChEBI	-	assimilation
[Ref.: #43808]	starch ChEBI	-	hydrolysis
[Ref.: #43808]	succinamate ChEBI	+	carbon source
[Ref.: #43808]	sucrose ChEBI	+	carbon source
[Ref.: #43808]	tween 20 ChEBI	-	hydrolysis
[Ref.: #43808]	tween 40 ChEBI	+	hydrolysis
[Ref.: #43808]	tween 60 ChEBI	+	hydrolysis
[Ref.: #43808]	tween 80 ChEBI	-	hydrolysis
[Ref.: #43808]	tween 80 ChEBI	+	carbon source
[Ref.: #43808]	urea ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #43808]	ampicillin ChEBI	yes	10	µg (disc)
[Ref.: #43808]	chloramphenicol ChEBI	yes	30	µg (disc)
[Ref.: #43808]	gentamicin ChEBI	yes	10	µg (disc)
[Ref.: #43808]	kanamycin ChEBI	yes	30	µg (disc)
[Ref.: #43808]	nalidixic acid ChEBI				yes	30	µg (disc)
[Ref.: #43808]	novobiocin ChEBI	yes	30	µg (disc)
[Ref.: #43808]	penicillin g ChEBI	yes	10	Unit (disc)
[Ref.: #43808]	rifampicin ChEBI	yes	5	µg (disc)
[Ref.: #43808]	streptomycin ChEBI				yes	10	µg (disc)
[Ref.: #43808]	sulfamethoxazole ChEBI				yes	23.75	µg (disc)
[Ref.: #43808]	tetracycline ChEBI	yes	30	µg (disc)
[Ref.: #43808]	trimethoprim ChEBI				yes	1.25	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43808]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43808]	acid phosphatase	+	3.1.3.2
[Ref.: #43808]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43808]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43808]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43808]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43808]	alpha-glucosidase	-	3.2.1.20
[Ref.: #43808]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43808]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43808]	beta-galactosidase	-	3.2.1.23
[Ref.: #43808]	beta-glucosidase	+	3.2.1.21
[Ref.: #43808]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43808]	catalase	+	1.11.1.6
[Ref.: #43808]	cystine arylamidase	-	3.4.11.3
[Ref.: #43808]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43808]	esterase (C 4)	+
[Ref.: #43808]	esterase Lipase (C 8)	+
[Ref.: #43808]	leucine arylamidase	+	3.4.11.1
[Ref.: #43808]	lipase (C 14)	+
[Ref.: #43808]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43808]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43808]	trypsin	-	3.4.21.4
[Ref.: #43808]	urease	-	3.5.1.5
[Ref.: #43808]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43808]

Fatty acid	Percentage
C18:1ω7c	45.5
C16:1ω7c / C16:1ω6c	19.8
C16:0	12.2
C16:0 2OH	6.5
C18:0	4.3
C14:0 2OH	3.2
C16:1ω5c	2.1
11-methyl C18:1ω7c	1.6
C17:1ω6c	1.4
C14:0	1.1

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

[Ref.: #43808]	Sample type/isolated from	The water of a taro field in Luye Township in the vicinity of Taitung city
[Ref.: #43808]	Geographic location (country and/or sea, region)	Taitung city
[Ref.: #43808]	Country	Taiwan
[Ref.: #43808]	Country ISO 3 Code	TWN
[Ref.: #43808]	Continent	Asia
[Ref.: #43808]	Geographic location	22.9450°/121.1550°
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Environmental	#Aquatic	-
#Host	#Plants	#Herbaceous plants (Grass,Crops)

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.: #43808]	16S rRNA gene sequence	HF548595		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Novosphingobium colocasiae KCTC 32255	GCA_014652555	scaffold	GenBank	1256513 tax ID	*
[Ref.: #66792]	Novosphingobium colocasiae strain KCTC 32255	1256513.3	wgs	PATRIC	1256513 tax ID	*

[Ref.: #43808]

GC-content

65 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 GenomeNet Sporulation v. 1 based on: Novosphingobium colocasiae KCTC 32255 NCBI: GCA_014652555.1
[Ref.: #69481]	spore-forming	no	89	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Novosphingobium colocasiae KCTC 32255 NCBI: GCA_014652555.1
[Ref.: #69480]	motile	no	53.277	yes
[Ref.: #69480]	flagellated	no	86.189	no
[Ref.: #69480]	gram-positive	no	97.586	yes
[Ref.: #69480]	anaerobic	no	98.607	yes
[Ref.: #69480]	aerobic	yes	89.192	no
[Ref.: #69480]	halophile	no	97.206	yes
[Ref.: #69480]	spore-forming	no	93.895	yes
[Ref.: #69480]	glucose-util	yes	89.688	yes
[Ref.: #69480]	thermophile	no	95.231	yes
[Ref.: #69480]	glucose-ferment	no	91.317	no

Availability in culture collections External links

[Ref.: #43808]

Culture collection no.

LMG 27385, KCTC 32255

[Ref.: #96815]

SI-ID 386839

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Novosphingobium colocasiae sp. nov., isolated from a taro field.	Chen WM, Chen JC, Huang CW, Young CC, Sheu SY	Int J Syst Evol Microbiol	10.1099/ijsem.0.000771	2015	*

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 )

#43808

Wen-Ming Chen, Jhen-Ci Chen, Cheng-Wen Huang, Chiu-Chung Young, Shih-Yi Sheu: Novosphingobium colocasiae sp. nov., isolated from a taro field. IJSEM 66: 673 - 679 2016 ( DOI 10.1099/ijsem.0.000771 , PubMed 26582085 )

#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 )

#96815

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-ID386839.1 )

* These data were automatically processed and therefore are not curated

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Novosphingobium colocasiae KCTC 32255

Novosphingobium colocasiae KCTC 32255

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