Arcanobacterium phocisimile (DSM 26142, CCM 8430, LMG 27073)

Name: Arcanobacterium phocisimile (DSM 26142, CCM 8430, LMG 27073)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 22902

Type strain

Strain Designation 2698

Culture col. no. DSM 26142 CCM 8430 LMG 27073 2698 CIP 110543

NCBI tax ID(s) 1302235

Special Collections DSMZ Literature strains CIP

History 2012, P. Kämpfer, Giessen Univ., Giessen, Germany: strain 2698 <- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany; strain 2698 CIP <- 2012, P. Kämpfer, Giessen Univ., Giessen, Germany: strain 2698

Links

Arcanobacterium phocisimile 2698 is an anaerobe, Gram-positive, rod-shaped bacterium that was isolated from vaginal swab of a harbour seal.

Gram-positive rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 380918

LMG 27073,CCM 8430,CIP 110543,DSM 26142

@ref 20215

Last LPSN update 2026-02-09 11:23:36

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Actinomycetales

Family Actinomycetaceae

Genus Arcanobacterium

Species Arcanobacterium phocisimile

Full scientific name Arcanobacterium phocisimile Hijazin et al. 2013

BacDive ID	Other strains from **Arcanobacterium phocisimile** (1)	Type strain
138946	A. phocisimile 4112, CIP 110544

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30836	positive	1.5 µm	0.5 µm	rod-shaped
125438					92
125439	positive				96.1
125439					96.5
121804	positive			rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
37605	MEDIUM 45 - for Columbia agar with sheep blood		Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
19334	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
19334	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
121804	CIP Medium 45	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
19334	positive	growth	37
37605	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
19334	anaerobe
19334	microaerophile
30836	microaerophile
125439	microaerophile	96.9

Spore formation

@ref	Spore formation	Confidence
30836
125439		95

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
30836	28087 ChEBI	glycogen	+	carbon source
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
30836	17716 ChEBI	lactose	+	carbon source
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	+	fermentation	from API rID32A
30836	33942 ChEBI	ribose	+	carbon source
30836	17992 ChEBI	sucrose	+	carbon source
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
30836	alkaline phosphatase	+	3.1.3.1
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
30836	catalase	+	1.11.1.6
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	+	3.4.11.5	from API rID32A
30836	pyrazinamidase	+	3.5.1.B15
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
19334	-	-	-	+	-	+	-	-	-	-	+	+	-	-	-	-	-	+/-	+	-	-	+/-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Patient	#Swab
#Host	#Mammals	-
#Host Body-Site	#Urogenital tract	#Vagina

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
19334	vaginal swab of a harbour seal	North Sea	Germany	DEU	Europe
121804	Harbour seals	North Sea	Germany	DEU	Europe	2004

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
19334	yes, in single cases	1	Risk group (German classification) According to TRBA 466
121804		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	ASM1690467v1 assembly for Arcanobacterium phocisimile DSM 26142	complete	GCA_016904675	1302235.3	3001711770	1302235	96.51

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19334	Arcanobacterium phocisimile partial 16S rRNA gene, type strain 2698T	FN562996	1337		1302235

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Arcanobacterium phocisimile strain DSM 26142
PATRIC: 1302235.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.00	no
125439	motility	BacteriaNetⓘ	no	96.50	no
125439	gram_stain	BacteriaNetⓘ	positive	96.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	microaerophile	96.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Arcanobacterium phocisimile DSM 26142
NCBI: GCA_016904675.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.34	yes
125438	anaerobic	anaerobicⓘ	no	80.50	no
125438	aerobic	aerobicⓘ	no	75.82	no
125438	spore-forming	spore-formingⓘ	no	88.92	yes
125438	thermophilic	thermophileⓘ	no	93.00	yes
125438	flagellated	motile2+ⓘ	no	92.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Identification of Trueperella pyogenes isolated from bovine mastitis by Fourier transform infrared spectroscopy.	Nagib S, Rau J, Sammra O, Lammler C, Schlez K, Zschock M, Prenger-Berninghoff E, Klein G, Abdulmawjood A.	PLoS One	10.1371/journal.pone.0104654	2014
Genetics	Complete Genome Sequence of Arcanobacterium phocisimile Strain DSM 26142, Isolated from a Harbor Seal.	Borowiak M, Alssahen M, Malorny B, Lammler C, Siebert U, Plotz M, Abdulmawjood A	Microbiol Resour Announc	10.1128/MRA.00215-21	2021
Phylogeny	Arcanobacterium pinnipediorum sp. nov., isolated from a harbour seal.	Sammra O, Balbutskaya A, Ulbegi-Mohyla H, Nagib S, Lammler C, Kampfer P, Glaeser SP, Golke J, Busse HJ, Prenger-Berninghoff E, Siebert U, Abdulmawjood A, Klein G	Int J Syst Evol Microbiol	10.1099/ijsem.0.000609	2015
Phylogeny	Arcanobacterium phocisimile sp. nov., isolated from harbour seals.	Hijazin M, Sammra O, Ulbegi-Mohyla H, Nagib S, Alber J, Lammler C, Kampfer P, Glaeser SP, Busse HJ, Kassmannhuber J, Prenger-Berninghoff E, Weiss R, Siebert U, Hassan AA, Abdulmawjood A, Zschock M	Int J Syst Evol Microbiol	10.1099/ijs.0.045591-0	2012

References

#19334	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26142
#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 )
#27166	IJSEM 2019 2013 ( DOI 10.1099/ijs.0.045591-0 , PubMed 23041640 )
#30836	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 #27166
#37605	; Curators of the CIP;
#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) .
#68380	Automatically annotated from API rID32A .
#121804	Collection of Institut Pasteur ; Curators of the CIP; CIP 110543
#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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Arcanobacterium phocisimile (DSM 26142, CCM 8430, LMG 27073)

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

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_016904675

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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