Undibacterium pigrum (DSM 19792, CCUG 49009, CIP 109318)

Name: Undibacterium pigrum (DSM 19792, CCUG 49009, CIP 109318)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11373

Type strain

Strain Designation CMB NF1b

Culture col. no. DSM 19792 CCUG 49009 CIP 109318 UCCCB16 CMB NF1b

NCBI tax ID(s) 401470

Special Collections DSMZ CCUG CIP Literature strains UCCCB

History <- P. Kämpfer, Univ. Giessen <- E. Falsen, CCUG Göteborg Kampfer P. Justus-Liebig-Universitat Giessen < Falsen E., Culture Collection University Of Gothenburg CIP <- 2006, CCUG <- 2004, F. Persson, Göteborg Univ., Göteborg, Sweden: strain CMB NF1b

Links

Undibacterium pigrum CMB NF1b is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from drinking water.

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

Name and taxonomic classification

SI-ID 215181

CCUG 49009,CIP 109318,DSM 19792

@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 pigrum

Full scientific name Undibacterium pigrum Kämpfer et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
32000	negative	rod-shaped
121831	negative	rod-shaped
125439	negative		98.6
125438	negative		99

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8321	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
37510	MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati		Distilled water make up to (1000.000 ml);R2A agar (18.200 g)
121831	CIP Medium 566	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
8321	positive	growth	25
37510	positive	growth	25
58435	positive	growth	22
67772	positive	minimum	4
67772	positive	optimum	22
67772	positive	maximum	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32000	aerobe
58435	aerobe
121831	obligate aerobe
125439	obligate aerobe	99

Spore formation

@ref	Spore formation	Confidence
32000
125439		98.7

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
121831	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
121831	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
121831	35581 ChEBI	indole

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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
121831	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
32000	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		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
121831	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
121831	urease	+	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	acetate fermentation	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	L-lactaldehyde degradation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	butanoate fermentation	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	ubiquinone biosynthesis	100	7 of 7
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	NAD metabolism	94.44	17 of 18
66794	phenylalanine metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	lipid metabolism	87.1	27 of 31
66794	heme metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	alanine metabolism	82.76	24 of 29
66794	pyrimidine metabolism	82.22	37 of 45
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	purine metabolism	81.91	77 of 94
66794	proline metabolism	81.82	9 of 11
66794	cellulose degradation	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	gallate degradation	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	glutathione metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	methionine metabolism	76.92	20 of 26
66794	vitamin B1 metabolism	76.92	10 of 13
66794	leucine metabolism	76.92	10 of 13
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	vitamin B6 metabolism	72.73	8 of 11
66794	cysteine metabolism	72.22	13 of 18
66794	citric acid cycle	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tyrosine metabolism	71.43	10 of 14
66794	arginine metabolism	70.83	17 of 24
66794	glycolysis	70.59	12 of 17
66794	sulfate reduction	69.23	9 of 13
66794	lysine metabolism	69.05	29 of 42
66794	tryptophan metabolism	68.42	26 of 38
66794	non-pathway related	68.42	26 of 38
66794	ascorbate metabolism	68.18	15 of 22
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	oxidative phosphorylation	65.93	60 of 91
66794	phenol degradation	65	13 of 20
66794	degradation of sugar acids	64	16 of 25
66794	pentose phosphate pathway	63.64	7 of 11
66794	histidine metabolism	62.07	18 of 29
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	3-phenylpropionate degradation	60	9 of 15
66794	lipoate biosynthesis	60	3 of 5
66794	starch degradation	60	6 of 10
66794	glycogen metabolism	60	3 of 5
66794	polyamine pathway	56.52	13 of 23
66794	degradation of sugar alcohols	56.25	9 of 16
66794	nitrate assimilation	55.56	5 of 9
66794	urea cycle	53.85	7 of 13
66794	androgen and estrogen metabolism	50	8 of 16
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	pantothenate biosynthesis	50	3 of 6
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	quinate degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	ethanol fermentation	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	vitamin B12 metabolism	47.06	16 of 34
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	d-xylose degradation	45.45	5 of 11
66794	allantoin degradation	44.44	4 of 9
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	arachidonic acid metabolism	44.44	8 of 18
66794	3-chlorocatechol degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	vitamin K metabolism	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	degradation of pentoses	39.29	11 of 28
66794	degradation of hexoses	38.89	7 of 18
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	metabolism of disaccharids	36.36	4 of 11
66794	carotenoid biosynthesis	36.36	8 of 22
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	coenzyme M biosynthesis	30	3 of 10
66794	myo-inositol biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	methanogenesis from CO2	25	3 of 12
66794	toluene degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	chlorophyll metabolism	22.22	4 of 18

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
121831	-	+	+	+	-	+	+	-	+	-	+	+	-	-	-	+	-	-	-	-

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
8321	+	-	-	-	-	+	+	-	+	-	+	-	-	+	+	-	-	-	-	-	+

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
8321	drinking water			Sweden	SWE	Europe
58435	Water,biofilm,drinking water	2004-03-10	Göteborg,Lackarebäcks vattenverk	Sweden	SWE	Europe
67772	Water, biofilm, drinking water	2004	Västergötland and Bohuslän, Gothenburg	Sweden	SWE	Europe	57.7	11.9667 57.7/11.9667
121831	Environment, Water, biofilm, drinking water		Göteborg	Sweden	SWE	Europe			2004

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8321	1	Risk group (German classification) According to TRBA 466
67772	1
121831	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	ASM320181v1 assembly for Undibacterium pigrum DSM 19792	scaffold	GCA_003201815	401470.3	2770939554	401470	66.63

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8321	Undibacterium pigrum partial 16S rRNA gene, type strain CCUG 49009T	AM397630	1434		401470

GC content

32000

GC-content (mol%)50.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Undibacterium pigrum DSM 19792
NCBI: GCA_003201815

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.70	no
125439	motility	BacteriaNetⓘ	yes	71.80	no
125439	gram_stain	BacteriaNetⓘ	negative	98.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Undibacterium pigrum DSM 19792
NCBI: GCA_003201815.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	94.88	yes
125438	aerobic	aerobicⓘ	yes	84.25	yes
125438	spore-forming	spore-formingⓘ	no	85.28	yes
125438	thermophilic	thermophileⓘ	no	98.49	yes
125438	flagellated	motile2+ⓘ	yes	82.46	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Co-occurrence of enzyme domains guides the discovery of an oxazolone synthetase.	de Rond T, Asay JE, Moore BS.	Nat Chem Biol	10.1038/s41589-021-00808-4	2021
Metabolism	Biofilm Formation and Degradation of Commercially Available Biodegradable Plastic Films by Bacterial Consortiums in Freshwater Environments.	Morohoshi T, Oi T, Aiso H, Suzuki T, Okura T, Sato S.	Microbes Environ	10.1264/jsme2.me18033	2018
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
Phylogeny	Undibacterium pigrum gen. nov., sp. nov., isolated from drinking water.	Kampfer P, Rossello-Mora R, Hermansson M, Persson F, Huber B, Falsen E, Busse HJ	Int J Syst Evol Microbiol	10.1099/ijs.0.64785-0	2007

References

#8321	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19792
#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 )
#28254	IJSEM 1510 2007 ( DOI 10.1099/ijs.0.64785-0 , PubMed 17625185 )
#32000	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28254
#37510	; Curators of the CIP;
#58435	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 49009
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 .
#121831	Collection of Institut Pasteur ; Curators of the CIP; CIP 109318
#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 pigrum (DSM 19792, CCUG 49009, CIP 109318)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

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_003201815

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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