Atopobacter phocae (CIP 106392, CCUG 42358, ATCC BAA-285)

Name: Atopobacter phocae (CIP 106392, CCUG 42358, ATCC BAA-285)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 138666

Type strain

Culture col. no. CIP 106392 CCUG 42358 ATCC BAA-285

NCBI tax ID(s) 1336234 136492

Special Collections CCUG CIP

History CIP <- 2000, CCUG <- P. Lawson, FST, Reading, UK <- G. Foster, Inverness, UK

Links

Atopobacter phocae CIP 106392 is a facultative anaerobe, mesophilic, Gram-positive prokaryote of the family Carnobacteriaceae.

Gram-positive coccus-shaped facultative anaerobe mesophilic genome sequence

Name and taxonomic classification

SI-ID 45454

ATCC BAA-285,CCUG 42358,CIP 106392,NCIMB 703064,NCFB3064

@ref 20215

Last LPSN update 2025-12-16 10:03:07

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Carnobacteriaceae

Genus Atopobacter

Species Atopobacter phocae

Full scientific name Atopobacter phocae Lawson et al. 2000

BacDive ID	Other strains from **Atopobacter phocae** (3)	Type strain
150858	A. phocae CCUG 42577
151132	A. phocae CCUG 43341
151663	A. phocae CCUG 44562

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
40304	positive	coccus-shaped

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
40304	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)
40304	CIP Medium 6			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
40304	positive	growth	37	mesophilic
40304	positive	growth	25-41
40304	negative	growth	10
40304	negative	growth	45

Physiology and metabolism

Oxygen tolerance

40304

Oxygen tolerancefacultative anaerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
40304	NaCl		growth	6.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
40304	4853 ChEBI	esculin	-	hydrolysis
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
40304	606565 ChEBI	hippurate	-	hydrolysis
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
40304	17632 ChEBI	nitrate	-	reduction
40304	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	+	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	+	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Antibiotic resistance

@ref	ChEBI	Metabolite	Is sensitive	Is resistant
40304		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
40304	86455	optochin

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
40304	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
40304	alcohol dehydrogenase	+	1.1.1.1
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
40304	beta-galactosidase	-	3.2.1.23
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
40304	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
40304	gamma-glutamyltransferase	-	2.3.2.2
68382	leucine arylamidase	-	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
40304	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
40304	ornithine decarboxylase	-	4.1.1.17
40304	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
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
40304	-	+	+	+	-	-	-	-	-	-	+	+	-	-	-	+	-	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
40304	not determinedn.d.	-	-	-	-	+	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	+	-	-	+/-	-	-	+	-	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Aquatic mammal
#Host Body-Site	#Oral cavity and airways	#Lung
#Host Body-Site	#Gastrointestinal tract	#Small intestine
#Host	#Juvenile	-

Isolation

@ref	Sample type	Sampling date	Country	Country ISO 3 Code	Continent
40304			United Kingdom	GBR	Europe
55403	Seal,common seal pup,lung,small intestine,etc.	1994	United Kingdom	GBR	Europe
40304	Seal		United Kingdom	GBR	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
40304	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM52667v1 assembly for Atopobacter phocae ATCC BAA-285	contig	GCA_000526675	1336234.3	2546825536	1336234	61.29

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
	Draft Genome Sequence of Atopobacter sp. Strain AH10, Isolated from a Vaginal Swab from Macaca fascicularis.	Chang DH, Seo HS, Park KR, Lee SK, Jeong KJ, Jeong H, Kim BC.	Microbiol Resour Announc	10.1128/mra.01643-18	2019
Phylogeny	Atopobacter phocae gen. nov., sp. nov., a novel bacterium isolated from common seals.	Lawson PA, Foster G, Falsen E, Ohlen M, Collins MD	Int J Syst Evol Microbiol	10.1099/00207713-50-5-1755	2000

References

#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 )
#40304	Collection of Institut Pasteur ; Curators of the CIP; CIP 106392
#55403	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 42358
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Atopobacter phocae (CIP 106392, CCUG 42358, ATCC BAA-285)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite tests

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000526675

Genome-based predictions

Literature

Literature

References

BacDive

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