Undibacterium parvum (DSM 23061, CCUG 49012, CIP 109317)

Name: Undibacterium parvum (DSM 23061, CCUG 49012, CIP 109317)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11374

Type strain

Strain Designation CMB NF2a

Culture col. no. DSM 23061 CCUG 49012 CIP 109317 UCCCB17 CMB NF2a

NCBI tax ID(s) 401471

Special Collections DSMZ CCUG CIP UCCCB

History <- CCUG <- F. Persson, Univ. Göteborg, Sweden The type strain CCUG 49012 (= DSM 23061) was previouly described by Kämpfer et al. 2007 as a second genomovar of Undibacterium pigrum because of the lack of differentiating characters. CIP <- 2006, CCUG, Undibacterium pigrum <- 2004, F. Persson, Göteborg Univ., Göteborg, Sweden: strain CMB NF2a

Links

Undibacterium parvum CMB NF2a is an aerobe, Gram-negative, motile bacterium that was isolated from drinking water.

Gram-negative motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 215184

CCUG 49012,CIP 109317,DSM 23061

@ref 20215

Last LPSN update 2026-02-09 11:20:32

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Oxalobacteraceae

Genus Undibacterium

Species Undibacterium parvum

Full scientific name Undibacterium parvum Eder et al. 2011

Synonyms (1)

"Neoundibacterium parvum"

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
121604	negative	rod-shaped
125439	negative		98.5
125438	negative		97

Colony morphology

58437

Incubation period5 days

Multimedia

@ref:	16684
multimedia content:	DSM_23061.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_23061.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
16684	REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)	Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
32695	MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati		Distilled water make up to (1000.000 ml);R2A agar (18.200 g)
121604	CIP Medium 566	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
16684	positive	growth	22
32695	positive	growth	22
58437	positive	growth	22
67772	positive	minimum	5
67772	positive	optimum	22
67772	positive	maximum	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
58437	aerobe
125439	obligate aerobe	97.7

Spore formation

@ref	Spore formation	Confidence
125439		95.9
125438		90.087

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
121604	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
121604	16301 ChEBI	nitrite	-	reduction
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
121604	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
121604	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68382	esterase (C 4)	-		from API zym
68369	gelatinase	-		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121604	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
121604	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
58437	-	+	-	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-
121604	-	+	-	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
58437	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Isolation date
16684	drinking water		Göteborg	Sweden	SWE	Europe
58437	Water,biofilm,drinking water	2004-03-10	Göteborg	Sweden	SWE	Europe
67772	Water, biofilm, drinking water	2004	Västergötland and Bohuslän, Gothenburg	Sweden	SWE	Europe	57.7	11.9667 57.7/11.9667
121604	Environment, Water, biofilm, drinking water		Göteborg	Sweden	SWE	Europe			2004

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16684	1	Risk group (German classification) According to TRBA 466
67772	1
121604	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM395573v1 assembly for Undibacterium parvum DSM 23061	complete	GCA_003955735	401471.8	2836680013	401471	97.75

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16684	Undibacterium parvum partial 16S rRNA gene, type strain CCUG 49012T	AM397629	1442		401471

GC content

@ref	GC-content (mol%)	Method
16684	50.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Undibacterium parvum strain DSM 23061
PATRIC: 401471.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.90	no
125439	motility	BacteriaNetⓘ	yes	82.50	no
125439	gram_stain	BacteriaNetⓘ	negative	98.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Undibacterium parvum DSM 23061
NCBI: GCA_003955735.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.00	no
125438	anaerobic	anaerobicⓘ	no	95.45	no
125438	aerobic	aerobicⓘ	yes	84.33	yes
125438	spore-forming	spore-formingⓘ	no	90.09	no
125438	thermophilic	thermophileⓘ	no	96.70	no
125438	flagellated	motile2+ⓘ	yes	83.90	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Identification and characterization of a novel extracellular polyhydroxyalkanoate depolymerase in the complete genome sequence of Undibacterium sp. KW1 and YM2 strains.	Morohoshi T, Oi T, Suzuki T, Sato S.	PLoS One	10.1371/journal.pone.0232698	2020
	Blood microbiome is associated with changes in portal hypertension after successful direct-acting antiviral therapy in patients with HCV-related cirrhosis.	Virseda-Berdices A, Brochado-Kith O, Diez C, Hontanon V, Berenguer J, Gonzalez-Garcia J, Rojo D, Fernandez-Rodriguez A, Ibanez-Samaniego L, Llop-Herrera E, Olveira A, Perez-Latorre L, Barbas C, Rava M, Resino S, Jimenez-Sousa MA.	J Antimicrob Chemother	10.1093/jac/dkab444	2022
	Longitudinal analysis of exposure to a low concentration of oxytetracycline on the zebrafish gut microbiome.	Kayani MUR, Yu K, Qiu Y, Yu X, Chen L, Huang L.	Front Microbiol	10.3389/fmicb.2022.985065	2022
Metabolism	Diversity of Iron Oxidizers in Groundwater-Fed Rapid Sand Filters: Evidence of Fe(II)-Dependent Growth by Curvibacter and Undibacterium spp.	Gulay A, Cekic Y, Musovic S, Albrechtsen HJ, Smets BF.	Front Microbiol	10.3389/fmicb.2018.02808	2018
Phylogeny	Undibacterium piscinae sp. nov., isolated from Korean shiner intestine.	Lee SY, Kang W, Kim PS, Kim HS, Sung H, Shin NR, Whon TW, Yun JH, Lee JY, Lee JY, Jung MJ, Jeong YS, Tak EJ, Han JE, Hyun DW, Kang MS, Lee KE, Lee BH, Bae JW	Int J Syst Evol Microbiol	10.1099/ijsem.0.003604	2019
Phylogeny	Description of Undibacterium oligocarboniphilum sp. nov., isolated from purified water, and Undibacterium pigrum strain CCUG 49012 as the type strain of Undibacterium parvum sp. nov., and emended descriptions of the genus Undibacterium and the species Undibacterium pigrum.	Eder W, Wanner G, Ludwig W, Busse HJ, Ziemke-Kageler F, Lang E	Int J Syst Evol Microbiol	10.1099/ijs.0.018648-0	2010

References

#16684	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23061
#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 )
#32695	; Curators of the CIP;
#58437	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 49012
#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) .
#67772	The University of Coimbra Bacteria Culture Collection (UCCCB) ; Curators of the UCCCB;
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#121604	Collection of Institut Pasteur ; Curators of the CIP; CIP 109317
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Undibacterium parvum (DSM 23061, CCUG 49012, CIP 109317)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003955735

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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