Name: Niveibacterium umoris DSM 106739
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140139

Type strain:

Species: Niveibacterium umoris

Culture col. no.: DSM 106739, JCM 18716, KACC 17062, MIC 2059

Strain history: K. Y. Jahng MIC2059.

NCBI tax ID(s): 1193620 (species)

SI-ID 406413

DSM 106739

Section

Niveibacterium umoris DSM 106739 is a facultative anaerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from surface water of wetland.

colony-forming
Gram-negative
motile
rod-shaped
facultative anaerobe
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	*Rhodocyclales*
	Family	*Zoogloeaceae*
	Genus	*Niveibacterium*
	Species	**Niveibacterium umoris**
	Full Scientific Name (LPSN)	Niveibacterium umoris Chun et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43805]	Gram stain	negative

[Ref.: #43805]	Cell length	1.6-2.8 µm

[Ref.: #43805]	Cell width	0.2-0.6 µm

[Ref.: #43805]	Cell shape	rod-shaped

[Ref.: #43805]	Motility	yes

[Ref.: #43805]	Flagellum arrangement	polar

[Ref.: #43805]	Colony size	0.5-1 mm
[Ref.: #43805]	Colony color	White
[Ref.: #43805]	Colony shape	circular
[Ref.: #43805]	Incubation period	3 days
[Ref.: #43805]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

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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

[Ref.: #43805]

Culture medium growth

[Ref.: #42746]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #42746]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #42746]

Culture medium composition

expand / minimize

[Ref.: #43805]

Culture medium

Czapek-Dox medium

[Ref.: #43805]

Culture medium growth

[Ref.: #43805]

Culture medium

Deoxycholate agar

[Ref.: #43805]

Culture medium growth

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Culture medium

MacConkey

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Culture medium growth

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Culture medium

Marine agar (MA)

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Culture medium growth

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Culture medium

MRS agar

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Culture medium growth

		Temperature
[Ref.: #42746]	growth	28 °C
[Ref.: #43805]	growth	10-37 °C
[Ref.: #43805]	optimum	30 °C
[Ref.: #67770]	growth	25 °C

[Ref.: #42746]	Temperature range	mesophilic
[Ref.: #43805]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43805]			optimum	7.5
[Ref.: #43805]			growth	6-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43805]

Oxygen tolerance

facultative anaerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43805]		NaCl		growth	0-2	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #43805]	alpha-cyclodextrin ChEBI	+	assimilation
[Ref.: #43805]	alpha-D-glucose ChEBI	+	assimilation
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #43805]	beta-hydroxybutyrate ChEBI	+	assimilation
[Ref.: #43805]	carboxymethylcellulose ChEBI	+	hydrolysis
[Ref.: #43805]	casein	+	hydrolysis
[Ref.: #43805]	cellulose ChEBI	+	hydrolysis
[Ref.: #43805]	D-fructose ChEBI	+	assimilation
[Ref.: #43805]	D-galacturonic acid ChEBI	-	assimilation
[Ref.: #43805]	D-gluconate ChEBI	-	assimilation
[Ref.: #43805]	D-glucosaminic acid ChEBI	-	assimilation
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #43805]	D-glucose 6-phosphate ChEBI	+	assimilation
[Ref.: #43805]	D-glucuronate ChEBI	-	assimilation
[Ref.: #43805]	D-mannitol ChEBI	+	assimilation
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #43805]	D-mannose ChEBI	+	assimilation
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #43805]	D-psicose ChEBI	+	assimilation
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #43805]	dextrin ChEBI	+	assimilation
[Ref.: #43805]	dna ChEBI	+	hydrolysis
[Ref.: #43805]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #43805]	formate ChEBI	+	assimilation
[Ref.: #43805]	gelatin ChEBI	-	hydrolysis
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #43805]	glucuronamide ChEBI	-	assimilation
[Ref.: #43805]	glycogen ChEBI	-	assimilation
[Ref.: #43805]	glycogen ChEBI	+	assimilation
[Ref.: #43805]	L-alaninamide ChEBI	-	assimilation
[Ref.: #43805]	L-alanine 4-nitroanilide	-	assimilation
[Ref.: #43805]	L-alanylglycine ChEBI	-	assimilation
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #43805]	L-asparagine ChEBI	-	assimilation
[Ref.: #43805]	L-aspartate ChEBI	-	assimilation
[Ref.: #43805]	L-fucose ChEBI	-	assimilation
[Ref.: #43805]	L-glutamate ChEBI	-	assimilation
[Ref.: #43805]	L-rhamnose ChEBI	-	assimilation
[Ref.: #43805]	L-serine ChEBI	-	assimilation
[Ref.: #43805]	L-threonine ChEBI	-	assimilation
[Ref.: #43805]	lactate ChEBI	-	assimilation
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #43805]	maltose hydrate	+	assimilation
[Ref.: #43805]	methyl pyruvate ChEBI	+	assimilation
[Ref.: #43805]	N-acetylgalactosamine ChEBI	-	assimilation
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #43805]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #43805]	ribitol ChEBI	-	assimilation
[Ref.: #43805]	starch ChEBI	+	hydrolysis
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #43805]	tween 40 ChEBI	+	assimilation
[Ref.: #43805]	tween 80 ChEBI	+	assimilation
[Ref.: #43805]	tyrosine ChEBI	+	hydrolysis
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity
[Ref.: #43805]	ampicillin ChEBI	yes
[Ref.: #43805]	chloramphenicol ChEBI	yes
[Ref.: #43805]	doxycycline ChEBI	yes
[Ref.: #43805]	erythromycin ChEBI	yes
[Ref.: #43805]	kanamycin ChEBI	yes
[Ref.: #43805]	neomycin ChEBI	yes
[Ref.: #43805]	rifampicin ChEBI	yes
[Ref.: #43805]	streptomycin ChEBI	yes
[Ref.: #43805]	tetracycline ChEBI	yes
[Ref.: #43805]	vancomycin ChEBI	yes

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #43805]	acid phosphatase	+	3.1.3.2
[Ref.: #43805]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43805]	alpha-glucosidase	+	3.2.1.20
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #43805]	beta-galactosidase	-	3.2.1.23
[Ref.: #43805]	beta-glucosidase	-	3.2.1.21
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #43805]	catalase	+	1.11.1.6
[Ref.: #43805]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #43805]	esterase (C 4)	-
[Ref.: #43805]	esterase Lipase (C 8)	+
[Ref.: #43805]	gelatinase	-
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #43805]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43805]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #42746]	24673	+	-	-	-	-	-	-	-	+	+	+	-	-	+	-	-	-	-	-	-	+

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

[Ref.: #42746]	Sample type/isolated from	surface water of wetland
[Ref.: #42746]	Geographic location (country and/or sea, region)	Inland Ungok Wetland
[Ref.: #42746]	Country	Republic of Korea
[Ref.: #42746]	Country ISO 3 Code	KOR
[Ref.: #42746]	Continent	Asia
[Ref.: #42746]	Geographic location	35.4667°/126.6500°

[Ref.: #43805]	Sample type/isolated from	Surface water from the Ungok Wetland of Gochang
[Ref.: #43805]	Geographic location (country and/or sea, region)	Gochang, Jeombuk Province
[Ref.: #43805]	Country	Republic of Korea
[Ref.: #43805]	Country ISO 3 Code	KOR
[Ref.: #43805]	Continent	Asia
[Ref.: #43805]	Geographic location	35.4660°/126.6500°

[Ref.: #67770]	Sample type/isolated from	Ungok Wetland of Gochang in Korea
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Surface water
#Environmental	#Terrestrial	#Wetland (Swamp)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JQ922418 (>99% sequence identity) for Niveibacterium umoris from Microbeatlas

Aquatic Samples	384
Soil Samples	231
Animal Samples	69
Plant Samples	25
Total Samples	709

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

[Ref.: #42746]

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.: #42746]	Niveibacterium umoris strain MIC2059 16S ribosomal RNA gene, partial sequence	JQ922418	1394	ENA	1193620 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Niveibacterium umoris KACC 17062	GCA_017311475	contig	GenBank	1193620 tax ID	*
[Ref.: #66792]	Niveibacterium umoris DSM 106739	GCA_014197015	contig	GenBank	1193620 tax ID	*
[Ref.: #66792]	Niveibacterium umoris strain DSM 106739	1193620.3	wgs	PATRIC	1193620 tax ID	*
[Ref.: #66792]	Niveibacterium umoris strain KACC 17062	1193620.4	wgs	PATRIC	1193620 tax ID	*
[Ref.: #66792]	Niveibacterium umoris DSM 106739	2830054275	draft	JGI IMG/M	1193620 tax ID	*

[Ref.: #67770]

GC-content

65.1 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: Niveibacterium umoris strain DSM 106739 PATRIC: 1193620.3
[Ref.: #69480]	motile	yes	87.345	no
[Ref.: #69480]	gram-positive	no	99.204	yes
[Ref.: #69480]	anaerobic	no	81.032	no
[Ref.: #69480]	aerobic	no	85.153	yes
[Ref.: #69480]	halophile	no	95.902	no
[Ref.: #69480]	spore-forming	no	93.822	no
[Ref.: #69480]	glucose-util	yes	77.748	yes
[Ref.: #69480]	flagellated	yes	91.427	yes
[Ref.: #69480]	thermophile	no	96.352	no
[Ref.: #69480]	glucose-ferment	no	80.726	no

Availability in culture collections External links

[Ref.: #42746]

Culture collection no.

DSM 106739, JCM 18716, KACC 17062, MIC 2059

[Ref.: #96532]

SI-ID 406413

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Niveibacterium microcysteis sp. nov., isolated from a cyanobacterial bloom sample.	Kang M, Park W	Int J Syst Evol Microbiol	10.1099/ijsem.0.004845	2021	*
Phylogeny	Niveibacterium umoris gen. nov., sp. nov., isolated from wetland freshwater.	Chun J, Young Kang J, Cheol Jung Y, Yeop Jahng K	Int J Syst Evol Microbiol	10.1099/ijsem.0.000826	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 )

#42746

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 106739

#43805

Jeesun Chun, Ji Young Kang, Young Cheol Jung, Kwang Yeop Jahng: Niveibacterium umoris gen. nov., sp. nov., isolated from wetland freshwater. IJSEM 66: 997 - 1002 2016 ( DOI 10.1099/ijsem.0.000826 , PubMed 26643899 )

#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;

#68369

Automatically annotated from API 20NE .

#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) .

#96532

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-ID406413.1 )

* These data were automatically processed and therefore are not curated

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Niveibacterium umoris strain DSM 106739

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