Varibaculum cambriense R12359 | Type strain | DSM 15806, CCUG 44998, CIP 107344 | BacDiveID:210

Strain identifier

BacDive ID: 210

Type strain:

Species: Varibaculum cambriense

Strain Designation: R12359

Culture col. no.: DSM 15806, CCUG 44998, CIP 107344

Strain history: CIP <- 2002, CCUG <- M.D. Collins, Reading, UK <- V. Hall, Cardiff, UK: strain R12359

NCBI tax ID(s): 1123488 (strain), 184870 (species)

SI-ID 25796

CCUG 44998, CIP 107344, DSM 15806

Other strains from Varibaculum cambriense

V. cambriense CCUG 20976
V. cambriense CCUG 20977
V. cambriense CCUG 34258
V. cambriense CCUG 37510
V. cambriense CCUG 44992
V. cambriense CCUG 45111
V. cambriense CCUG 45112
V. cambriense CCUG 45113
V. cambriense CCUG 46939
V. cambriense CCUG 51839

Section

Varibaculum cambriense R12359 is an anaerobe, mesophilic bacterium that was isolated from human postauricular abscess, 27 years old male.

anaerobe
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Actinomycetales*
	Family	*Actinomycetaceae*
	Genus	*Varibaculum*
	Species	**Varibaculum cambriense**
	Full Scientific Name (LPSN)	Varibaculum cambriense corrig. Hall et al. 2003

Synonym

Varibaculum cambriensis

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #117109]	Cell shape	rod-shaped

[Ref.: #117109]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92.907

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

Culture medium

MEDIUM 6 - Columbia agar with 10 % horse blood

Culture medium growth

Culture medium composition

expand / minimize

[Ref.: #117109]

Culture medium

CIP Medium 6

[Ref.: #117109]

Culture medium growth

[Ref.: #117109]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #6116]			growth	37 °C
[Ref.: #42112]			growth	37 °C
[Ref.: #56585]			growth	37 °C

[Ref.: #6116]	Temperature range	mesophilic
[Ref.: #42112]	Temperature range	mesophilic
[Ref.: #56585]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6116]	Oxygen tolerance	anaerobe
[Ref.: #56585]	Oxygen tolerance	anaerobe
[Ref.: #56585]	Oxygen tolerance	microaerophile
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %97.849

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

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #117109]		cellobiose ChEBI	-	degradation
[Ref.: #117109]		D-arabinose ChEBI	-	degradation
[Ref.: #117109]		D-fructose ChEBI	+	degradation
[Ref.: #117109]		D-glucose ChEBI	-	degradation
[Ref.: #117109]		D-xylose ChEBI	-	degradation
[Ref.: #117109]		esculin ChEBI	-	hydrolysis
[Ref.: #117109]		lactose ChEBI	-	degradation
[Ref.: #117109]		maltose ChEBI	-	degradation
[Ref.: #117109]		nitrate ChEBI	+	reduction
[Ref.: #117109]		nitrite ChEBI	-	reduction
[Ref.: #117109]		salicin ChEBI	-	degradation
[Ref.: #117109]		sucrose ChEBI	-	degradation
[Ref.: #117109]		tributyrin ChEBI	+	hydrolysis
		Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #117109]		indole ChEBI	no

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #68382]		acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68382]		alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]		alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]		alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]		alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]		alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]		alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #117109]		amylase	-
[Ref.: #117109]		beta-galactosidase	-	3.2.1.23
[Ref.: #68382]		beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]		beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]		beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #117109]		caseinase	-	3.4.21.50
[Ref.: #117109]		catalase	+	1.11.1.6
[Ref.: #68382]		cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #117109]		DNase	-
[Ref.: #68382]		esterase (C 4)	-		* from API zym
[Ref.: #68382]		esterase lipase (C 8)	-		* from API zym
[Ref.: #117109]		gelatinase	-
[Ref.: #117109]		lecithinase	-
[Ref.: #68382]		leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #117109]		lipase	-
[Ref.: #68382]		lipase (C 14)	-		* from API zym
[Ref.: #68382]		N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]		naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #117109]		oxidase	-
[Ref.: #117109]		protease	-
[Ref.: #68382]		trypsin	-	3.4.21.4	* from API zym
[Ref.: #117109]		tween esterase	-
[Ref.: #117109]		urease	-	3.5.1.5
[Ref.: #68382]		valine arylamidase	-		* from API zym
		Only first 10 entries are displayed. Click here to see all.

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #117109]	10282	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #6116]	Sample type/isolated from	human postauricular abscess, 27 years old male
[Ref.: #6116]	Geographic location (country and/or sea, region)	London
[Ref.: #6116]	Country	United Kingdom
[Ref.: #6116]	Country ISO 3 Code	GBR
[Ref.: #6116]	Continent	Europe

[Ref.: #56585]	Sample type/isolated from	Human postauricular abscess,27-yr-old male
[Ref.: #56585]	Sampling date	1998
[Ref.: #56585]	Geographic location (country and/or sea, region)	London
[Ref.: #56585]	Country	United Kingdom
[Ref.: #56585]	Country ISO 3 Code	GBR
[Ref.: #56585]	Continent	Europe

[Ref.: #117109]	Sample type/isolated from	Human
[Ref.: #117109]	Geographic location (country and/or sea, region)	Cardiff
[Ref.: #117109]	Country	United Kingdom
[Ref.: #117109]	Country ISO 3 Code	GBR
[Ref.: #117109]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Human	#Male
#Host Body-Site	#Other	#Abscess
#Host Body-Site	#Organ	#Ear

What are isolation sources categories?

Global distribution of 16S sequence AM084231 (>99% sequence identity) for Varibaculum cambriense from Microbeatlas

Aquatic Samples	56
Soil Samples	30
Animal Samples	7804
Plant Samples	2
Total Samples	7892

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

[Ref.: #6116]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #117109]	Biosafety level	1	Risk group (French classification)

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.: #6116]	Varibaculum cambriensis 16S rRNA gene, type strain CCUG 44998T	AJ491326	1510	ENA	184870 tax ID
[Ref.: #20218]	Varibaculum cambriensis partial 16S rRNA gene, strain CCUG 44998	AJ428402	1510	ENA	184870 tax ID	*
[Ref.: #20218]	Varibaculum cambriense partial 16S rRNA gene, isolate CCUG 44998T	AM084231	1509	ENA	184870 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Varibaculum cambriense DSM 15806	GCA_000420065	contig	GenBank	1123488 tax ID	*
[Ref.: #66792]	Varibaculum cambriense DSM 15806	1123488.3	wgs	PATRIC	1123488 tax ID	*
[Ref.: #66792]	Varibaculum cambriense DSM 15806	2524614732	draft	JGI IMG/M	1123488 tax ID	*

GC-content

51.7 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: Varibaculum cambriense DSM 15806 PATRIC: 1123488.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Varibaculum cambriense DSM 15806 PATRIC: 1123488.3
[Ref.: #69480]	motile	no	92.191	no
[Ref.: #69480]	flagellated	no	96.825	no
[Ref.: #69480]	gram-positive	yes	91.42	no
[Ref.: #69480]	anaerobic	yes	73.491	no
[Ref.: #69480]	aerobic	no	98.368	no
[Ref.: #69480]	halophile	no	82.933	no
[Ref.: #69480]	spore-forming	no	97.122	no
[Ref.: #69480]	thermophile	no	95.453	yes
[Ref.: #69480]	glucose-util	yes	78.521	no
[Ref.: #69480]	glucose-ferment	yes	79.261	no

Availability in culture collections External links

Culture collection no.

DSM 15806, CCUG 44998, CIP 107344

SI-ID 25796

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Varibaculum anthropi sp. nov. represented by three genetically different genomovars isolated from clinical material and emended description of the genus Varibaculum.	Glaeser SP, Doijad S, Hijazin M, Chakraborty T, Falsen E, Hall V, Kampfer P	Syst Appl Microbiol	10.1016/j.syapm.2016.09.002	2016	*
Phylogeny	Characterization of some actinomyces-like isolates from human clinical sources: description of Varibaculum cambriensis gen nov, sp nov.	Hall V, Collins MD, Lawson PA, Hutson RA, Falsen E, Inganas E, Duerden B	J Clin Microbiol	10.1128/JCM.41.2.640-644.2003	2003	*

References

#6116

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15806

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#42112 ; Curators of the CIP;
#56585 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 44998

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#68382

Automatically annotated from API zym .

#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 )

#69893

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-ID25796.1 )

#117109 Collection of Institut Pasteur ; Curators of the CIP; CIP 107344
* These data were automatically processed and therefore are not curated

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