Varibaculum cambriense (DSM 15806, CCUG 44998, CIP 107344)

Name: Varibaculum cambriense (DSM 15806, CCUG 44998, CIP 107344)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 210

Type strain

Strain Designation R12359

Culture col. no. DSM 15806 CCUG 44998 CIP 107344 R12359

NCBI tax ID(s) 1123488 184870

Special Collections DSMZ CCUG CIP

History <- E. Falsen, CCUG <- M. D. Collins, Univ. of Reading <- V. Hall CIP <- 2002, CCUG <- M.D. Collins, Reading, UK <- V. Hall, Cardiff, UK: strain R12359

Links

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

rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 25796

NCTC-14293,CCUG 44998,CIP 107344,DSM 15806

@ref 20215

Last LPSN update 2026-02-09 11:17:49

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Actinomycetales

Family Actinomycetaceae

Genus Varibaculum

Species Varibaculum cambriense

Full scientific name Varibaculum cambriense corrig. Hall et al. 2003

Synonyms (1)

Varibaculum cambriensis

BacDive ID	Other strains from **Varibaculum cambriense** (10)	Type strain
143685	V. cambriense CCUG 20976
143686	V. cambriense CCUG 20977
147803	V. cambriense CCUG 34258
149327	V. cambriense CCUG 37510
151827	V. cambriense CCUG 44992
151882	V. cambriense CCUG 45111
151883	V. cambriense CCUG 45112
151884	V. cambriense CCUG 45113
152496	V. cambriense CCUG 46939
153984	V. cambriense CCUG 51839

Morphology

Cell morphology

@ref	Cell shape	Motility	Confidence
117109	rod-shaped
125438			91.875

Colony morphology

Multimedia

@ref:	66793
multimedia content:	EM_DSM_15806_1.jpg
multimedia.multimedia content:	EM_DSM_15806_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_15806_2.jpg
multimedia.multimedia content:	EM_DSM_15806_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_15806_3.jpg
multimedia.multimedia content:	EM_DSM_15806_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_15806_4.jpg
multimedia.multimedia content:	EM_DSM_15806_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_15806_5.jpg
multimedia.multimedia content:	EM_DSM_15806_5.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6116	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)	Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
6116	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
42112	MEDIUM 6 - Columbia agar with 10 % horse blood		Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
117109	CIP Medium 6	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6116	positive	growth	37
42112	positive	growth	37
56585	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
6116	anaerobe
56585	anaerobe
56585	microaerophile

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
117109	17057 ChEBI	cellobiose	-	degradation
117109	17108 ChEBI	D-arabinose	-	degradation
117109	15824 ChEBI	D-fructose	+	degradation
117109	17634 ChEBI	D-glucose	-	degradation
117109	65327 ChEBI	D-xylose	-	degradation
117109	4853 ChEBI	esculin	-	hydrolysis
117109	17716 ChEBI	lactose	-	degradation
117109	17306 ChEBI	maltose	-	degradation
117109	17632 ChEBI	nitrate	+	reduction
117109	16301 ChEBI	nitrite	-	reduction
117109	17814 ChEBI	salicin	-	degradation
117109	17992 ChEBI	sucrose	-	degradation
117109	35020 ChEBI	tributyrin	+	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
117109	35581 ChEBI	indole

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
117109	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
117109	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
117109	caseinase	-	3.4.21.50
117109	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
117109	DNase	-
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
117109	gelatinase	-
117109	lecithinase	-
68382	leucine arylamidase	-	3.4.11.1	from API zym
117109	lipase	-
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
117109	oxidase	-
117109	protease	-
68382	trypsin	-	3.4.21.4	from API zym
117109	tween esterase	-
117109	urease	-	3.5.1.5
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
117109	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	#Male
#Host Body-Site	#Other	#Abscess
#Host Body-Site	#Organ	#Ear

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
6116	human postauricular abscess, 27 years old male		London	United Kingdom	GBR	Europe
56585	Human postauricular abscess,27-yr-old male	1998	London	United Kingdom	GBR	Europe
117109	Human		Cardiff	United Kingdom	GBR	Europe

Taxonmaps

69479

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6116	2	Risk group (German classification) According to TRBA 466
117109	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	ASM42006v1 assembly for Varibaculum cambriense DSM 15806	contig	GCA_000420065	1123488.3	2524614732	1123488	76.5

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Varibaculum cambriensis partial 16S rRNA gene, strain CCUG 44998	AJ428402	1510	184870
20218	Varibaculum cambriense partial 16S rRNA gene, isolate CCUG 44998T	AM084231	1509	184870
6116	Varibaculum cambriensis 16S rRNA gene, type strain CCUG 44998T	AJ491326	1510	184870

GC content

6116

GC-content (mol%)51.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Varibaculum cambriense DSM 15806
NCBI: GCA_000420065

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	85.60	no
125439	motility	BacteriaNetⓘ	no	54.10	no
125439	gram_stain	BacteriaNetⓘ	variable	67.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	78.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Varibaculum cambriense DSM 15806
PATRIC: 1123488.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.49	no
125438	anaerobic	anaerobicⓘ	no	65.54	no
125438	spore-forming	spore-formingⓘ	no	81.29	no
125438	aerobic	aerobicⓘ	no	83.45	no
125438	thermophilic	thermophileⓘ	no	95.19	yes
125438	flagellated	motile2+ⓘ	no	91.88	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations.	Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, Lynch SV.	OMICS	10.1089/omi.2009.0100	2010
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
Genetics	Varibaculum massiliense sp. nov., a new bacterium isolated from human urine with culturomics.	Niang EHA, Lo CI, Brahimi S, Armstrong N, Raoult D, Fournier PE, Fenollar F.	New Microbes New Infect	10.1016/j.nmni.2019.100591	2019
	Arcanobacterium ihumii sp. nov., Varibaculum vaginae sp. nov. and Tessaracoccus timonensis sp. nov., isolated from vaginal swabs from healthy Senegalese women.	Fall NS, Lo CI, Fournier PE, Sokhna C, Raoult D, Fenollar F, Lagier JC.	New Microbes New Infect	10.1016/j.nmni.2019.100585	2019
Phylogeny	Tenacibaculum lutimaris sp. nov., isolated from a tidal flat in the Yellow Sea, Korea.	Yoon JH, Kang SJ, Oh TK.	Int J Syst Evol Microbiol	10.1099/ijs.0.63416-0	2005
	Varibaculum timonense sp. nov., a new bacterial species isolated from human stool sample.	Lo CI, Niang EHA, Guilhot E, Raoult D, Fournier PE, Fenollar F.	New Microbes New Infect	10.1016/j.nmni.2019.100575	2019
Genetics	'Prevotella ihumii' sp. nov. and 'Varibaculum timonense' sp. nov., two new bacterial species isolated from a fresh human stool specimen.	Guilhot E, Lagier JC, Raoult D, Khelaifia S.	New Microbes New Infect	10.1016/j.nmni.2017.03.002	2017
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

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 .
#117109	Collection of Institut Pasteur ; Curators of the CIP; CIP 107344
#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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Varibaculum cambriense (DSM 15806, CCUG 44998, CIP 107344)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000420065

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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