Name: Novosphingobium humi R1-4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 141002

Type strain:

Species: Novosphingobium humi

Strain Designation: R1-4

Culture col. no.: KACC 19094, JCM 31879

Strain history: C. O. Jeon; Chung-Ang Univ., South Korea; R1-4.

NCBI tax ID(s): 2282397 (species)

Section

Novosphingobium humi R1-4 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil in military shooting range, Jangseong, Republic of Korea.

Gram-negative
rod-shaped
aerobe
16S sequence
Bacteria

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Erythrobacteraceae*
	Genus	*Novosphingobium*
	Species	**Novosphingobium humi**
	Full Scientific Name (PNU)	Novosphingobium humi Hyeon et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43889]	Gram stain	negative
[Ref.: #43889]	Cell shape	rod-shaped
[Ref.: #43889]	Motility	no

[Ref.: #43889]	Colony color	whitish-yellow
[Ref.: #43889]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

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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

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

Tryptic soy agar

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Culture medium growth

		Temperature
[Ref.: #43889]	growth	15-45 °C
[Ref.: #43889]	optimum	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #43889]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH	pH range
[Ref.: #43889]			optimum	7
[Ref.: #43889]			growth	6.0-9.0	alkaliphile

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43889]		NaCl	no	growth	1	%(w/v)
[Ref.: #43889]		NaCl		minimum	0	%(w/v)

[Ref.: #43889]	Observation	quinone Q-10
[Ref.: #67770]	Observation	quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43889]	adipate ChEBI	-	assimilation
[Ref.: #43889]	casein	-	hydrolysis
[Ref.: #43889]	D-glucose ChEBI	+	assimilation
[Ref.: #43889]	D-mannitol ChEBI	-	assimilation
[Ref.: #43889]	D-mannose ChEBI	-	assimilation
[Ref.: #43889]	decanoate ChEBI	-	assimilation
[Ref.: #43889]	esculin ChEBI	+	hydrolysis
[Ref.: #43889]	gelatin ChEBI	-	hydrolysis
[Ref.: #43889]	glucose ChEBI	-	fermentation
[Ref.: #43889]	L-arabinose ChEBI	-	assimilation
[Ref.: #43889]	malate ChEBI	+	assimilation
[Ref.: #43889]	maltose ChEBI	+	assimilation
[Ref.: #43889]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #43889]	nitrate ChEBI	+	reduction
[Ref.: #43889]	phenylacetate ChEBI	-	assimilation
[Ref.: #43889]	potassium gluconate ChEBI	-	assimilation
[Ref.: #43889]	sodium citrate ChEBI	-	assimilation
[Ref.: #43889]	starch ChEBI	-	hydrolysis
[Ref.: #43889]	tween 20 ChEBI	+	hydrolysis
[Ref.: #43889]	tween 80 ChEBI	-	hydrolysis
[Ref.: #43889]	tyrosine ChEBI	+	hydrolysis
[Ref.: #43889]	urea ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite
[Ref.: #43889]		indole ChEBI

	Enzyme	Enzyme activity	EC number
[Ref.: #43889]	acid phosphatase	+	3.1.3.2
[Ref.: #43889]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43889]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43889]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43889]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43889]	alpha-glucosidase	-	3.2.1.20
[Ref.: #43889]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43889]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43889]	beta-galactosidase	+	3.2.1.23
[Ref.: #43889]	beta-glucosidase	+	3.2.1.21
[Ref.: #43889]	beta-glucuronidase	+	3.2.1.31
[Ref.: #43889]	catalase	-	1.11.1.6
[Ref.: #43889]	cystine arylamidase	-	3.4.11.3
[Ref.: #43889]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43889]	esterase (C 4)	+
[Ref.: #43889]	esterase Lipase (C 8)	+
[Ref.: #43889]	leucine arylamidase	+	3.4.11.1
[Ref.: #43889]	lipase (C 14)	-
[Ref.: #43889]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43889]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43889]	trypsin	-	3.4.21.4
[Ref.: #43889]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43889]

Fatty acid	Percentage
C18:1ω7c / C18:1ω6c	37.8
C16:1ω7c / C16:1ω6c	35.4
C19:0ω8c cyclo	13.2
C16:0	9.4
C14:0 2OH	4.2

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

[Ref.: #43889]	Sample type/isolated from	soil in military shooting range, Jangseong, Republic of Korea
[Ref.: #43889]	Geographic location (country and/or sea, region)	Jangseong
[Ref.: #43889]	Country	Republic of Korea
[Ref.: #43889]	Country ISO 3 Code	KOR
[Ref.: #43889]	Continent	Asia
[Ref.: #43889]	Geographic location	37.2833°/127.4000°
[Ref.: #43889]	Enrichment culture	R2A agar
[Ref.: #43889]	Enrichment culture duration	3 days
[Ref.: #43889]	Enrichment culture temperature	30 ̊C

[Ref.: #67770]	Sample type/isolated from	Soil from a military shooting range
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KY658458 (>99% sequence identity) for Novosphingobium from Microbeatlas

Aquatic Samples	554
Soil Samples	85
Animal Samples	552
Plant Samples	74
Total Samples	1265

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.: #43889]	16S rRNA gene sequence	KY658458		GenBank

[Ref.: #43889]	GC-content	64.4 mol%	real time PCR (RTD-PCR)
[Ref.: #67770]	GC-content	64.4 mol%	thermal denaturation, midpoint method (Tm)

Availability in culture collections External links

[Ref.: #43889]

Culture collection no.

KACC 19094, JCM 31879

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Novosphingobium humi sp. nov., isolated from soil of a military shooting range.	Hyeon JW, Kim K, Son AR, Choi E, Lee SK, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.002089	2017	*
Phylogeny	Novosphingobium umbonatum sp. nov., isolated from a freshwater mesocosm.	Sheu SY, Cai CY, Kwon SW, Chen WM	Int J Syst Evol Microbiol	10.1099/ijsem.0.003889	2020	*

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 )

#43889

Jong Woo Hyeon, Kyungchul Kim, Ah Ryeong Son, Eunmi Choi, Sung Kuk Lee, Che Ok Jeon: Novosphingobium humi sp. nov., isolated from soil of a military shooting range. IJSEM 67: 3083 - 3088 2017 ( DOI 10.1099/ijsem.0.002089 , PubMed 28829033 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

* These data were automatically processed and therefore are not curated

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