Name: Undibacterium oligocarboniphilum EM 1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11375

Type strain:

Species: Undibacterium oligocarboniphilum

Strain Designation: EM 1

Culture col. no.: DSM 21777, CCUG 57265

Strain history: <- W. Eder, Roche Diagnostics

NCBI tax ID(s): 666702 (species)

SI-ID 399684

DSM 21777, CCUG 57265

Section

Undibacterium oligocarboniphilum EM 1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from purified water system.

Gram-negative
motile
aerobe
mesophilic
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	*Burkholderiales*
	Family	*Oxalobacteraceae*
	Genus	*Undibacterium*
	Species	**Undibacterium oligocarboniphilum**
	Full Scientific Name (LPSN)	Undibacterium oligocarboniphilum Eder et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #29681]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.995

[Ref.: #29681]	Cell length	1.75 µm

[Ref.: #29681]	Cell width	0.5 µm

[Ref.: #29681]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %98.232

[Ref.: #61264]

Incubation period

1 day

Multimedia content

[Ref.: #15942]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15942]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #15942]

Culture medium growth

[Ref.: #15942]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15942]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15942]	growth	28 °C
[Ref.: #29681]	growth	10-35 °C
[Ref.: #61264]	growth	30-37 °C

[Ref.: #15942]	Temperature range	mesophilic
[Ref.: #61264]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29681]	Oxygen tolerance	aerobe
[Ref.: #61264]	Oxygen tolerance	aerobe

[Ref.: #29681]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29681]	gluconate ChEBI	+	carbon source
[Ref.: #29681]	glucose ChEBI	+	carbon source
[Ref.: #29681]	maltose ChEBI	+	carbon source
[Ref.: #29681]	nitrate ChEBI	+	reduction
[Ref.: #29681]	ribose ChEBI	+	carbon source
[Ref.: #29681]	sucrose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29681]		catalase	+	1.11.1.6
[Ref.: #29681]		cytochrome oxidase	+	1.9.3.1

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

[Ref.: #15942]	Sample type/isolated from	purified water system
[Ref.: #15942]	Geographic location (country and/or sea, region)	Penzberg
[Ref.: #15942]	Country	Germany
[Ref.: #15942]	Country ISO 3 Code	DEU
[Ref.: #15942]	Continent	Europe

[Ref.: #61264]	Sample type/isolated from	Water,purified system
[Ref.: #61264]	Sampling date	2008
[Ref.: #61264]	Country	Germany
[Ref.: #61264]	Country ISO 3 Code	DEU
[Ref.: #61264]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence GQ379228 (>99% sequence identity) for Undibacterium oligocarboniphilum subclade from Microbeatlas

Aquatic Samples	1473
Soil Samples	755
Animal Samples	1998
Plant Samples	450
Total Samples	4676

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

[Ref.: #15942]

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.: #15942]	Undibacterium oligocarboniphilum strain EM 1 16S ribosomal RNA gene, partial sequence	GQ379228	1527	ENA	666702 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Undibacterium oligocarboniphilum EM 1	GCA_013377855	scaffold	GenBank	666702 tax ID	*

[Ref.: #15942]	GC-content	52.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29681]	GC-content	52.4 mol%

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: Undibacterium oligocarboniphilum EM 1 NCBI: GCA_013377855.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Undibacterium oligocarboniphilum EM 1 NCBI: GCA_013377855.1
[Ref.: #69480]	motile	yes	86.677	no
[Ref.: #69480]	flagellated	yes	82.188	no
[Ref.: #69480]	gram-positive	no	98.777	yes
[Ref.: #69480]	anaerobic	no	98.781	yes
[Ref.: #69480]	aerobic	yes	87.984	yes
[Ref.: #69480]	halophile	no	97.171	no
[Ref.: #69480]	spore-forming	no	93.949	no
[Ref.: #69480]	glucose-util	no	59.569	no
[Ref.: #69480]	thermophile	no	95.558	yes
[Ref.: #69480]	glucose-ferment	no	90.514	no

Availability in culture collections External links

[Ref.: #15942]

Culture collection no.

DSM 21777, CCUG 57265

[Ref.: #80605]

SI-ID 399684

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Undibacterium squillarum sp. nov., isolated from a freshwater shrimp culture pond.	Sheu SY, Lin YS, Chen JC, Kwon SW, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.065185-0	2014	*
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

#15942

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21777

#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 )

#29681

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 #26066 (see below)

#61264 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 57265

#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) .

#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) .

#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 )

#80605

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-ID399684.1 )

#26066

IJSEM 384 2011 ( DOI 10.1099/ijs.0.018648-0 , PubMed 20305060 )

* These data were automatically processed and therefore are not curated

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