Phocicoccus pinnipedialis (DSM 17030, CCUG 42722, CIP 107946)

Name: Phocicoccus pinnipedialis (DSM 17030, CCUG 42722, CIP 107946)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14410

Type strain

Strain Designation A/G14/99/10

Culture col. no. DSM 17030 CCUG 42722 CIP 107946 A/G14/99/10

NCBI tax ID(s) 110845

Special Collections DSMZ CCUG CIP Literature strains

History <- CCUG <- M.D.Collins, Reading, <- L. Hoyles, Reading, UK <- G.Foster, A/G14/99/10 CIP <- 2003, CCUG <- M.D. Collins, Reading, UK <- L. Hoyles, Reading, UK <- G. Foster, Inverness, UK, strain A/G14/99/10

Links

Phocicoccus pinnipedialis A/G14/99/10 is a microaerophile, Gram-positive, coccus-shaped bacterium that was isolated from Seal mouth, female southern elephant seal.

Gram-positive coccus-shaped microaerophile genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 87820

CCUG 42722,CIP 107946,DSM 17030

@ref 20215

Last LPSN update 2026-02-09 11:21:24

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Staphylococcaceae

Genus Phocicoccus

Species Phocicoccus pinnipedialis

Full scientific name Phocicoccus pinnipedialis (Hoyles et al. 2004) Bello et al. 2024

Synonyms (1)

Jeotgalicoccus pinnipedialis

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
30016	positive	coccus-shaped
121837	positive	coccus-shaped
125438	positive		90.811

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6694	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
6694	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
34311	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)
121837	CIP Medium 45	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6694	positive	growth	37
30016	positive	growth	25-42
30016	positive	optimum	33.5
34311	positive	growth	37
55531	positive	growth	37
121837	positive	growth	25-41
121837	negative	growth	10
121837	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
6694	microaerophile
6694	aerobe
30016	facultative anaerobe
55531	aerobe
121837	obligate aerobe

Spore formation

30016

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30016	NaCl	positive	growth	02-06 %
30016	NaCl	positive	optimum	4 %
121837	NaCl	positive	growth	6.5 %

Observation

30016

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
121837	4853 ChEBI	esculin	+	hydrolysis
30016	5291 ChEBI	gelatin	+	carbon source
121837	606565 ChEBI	hippurate	+	hydrolysis
121837	17632 ChEBI	nitrate	-	reduction
121837	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
121837	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
121837	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
30016	acid phosphatase	+	3.1.3.2
68382	acid phosphatase	-	3.1.3.2	from API zym
121837	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
68382	beta-galactosidase	-	3.2.1.23	from API zym
121837	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
30016	catalase	+	1.11.1.6
121837	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
30016	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
121837	gamma-glutamyltransferase	+	2.3.2.2
30016	gelatinase	+
68382	leucine arylamidase	-	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
121837	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
121837	ornithine decarboxylase	-	4.1.1.17
121837	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
121837	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
121837	not determinedn.d.	+	+	+	+	+	-	+	-	-	+	+	+	+	+	+	-	-	+	+	+	+	+	-	+	+	-	-	-	-	-	-	+	-	+	-	-	+	-	+	-	-	-	-	+	-	-	-	-	-	+	+	-	+	+	+	+	-	+	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	+	-	-	+	+	-	-	+	+	+	+	-	+	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Patient	-
#Host	#Mammals	-
#Host Body-Site	#Oral cavity and airways	#Mouth
#Host	#Human	#Female

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
6694	Seal mouth, female southern elephant seal		South Orkneys	Antarctica	ATA	Australia and Oceania
55531	Seal mouth,female southern elephant seal	1993	South Orkneys	Antarctica	ATA	Australia and Oceania
121837	Swab from the mouth of a female southern elephant seal	1993	South Orkneys, Scotland	United Kingdom	GBR	Europe

Taxonmaps

69479

Global distribution of 16S sequence AJ251530 (>99% sequence identity) for Jeotgalicoccus pinnipedialis from Microbeatlas

Aquatic Samples	14
Soil Samples	142
Animal Samples	441
Plant Samples	5
Total Samples	602

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6694	1	Risk group (German classification) According to TRBA 466
121837	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	ASM1787364v1 assembly for Phocicoccus pinnipedialis DSM 17030	contig	GCA_017873645	110845.4	2913376348	110845	74.33
124043	ASM4266503v1 assembly for Phocicoccus pinnipedialis CCUG 42722	scaffold	GCA_042665035			110845	71.81
66792	CIP107946 assembly for Phocicoccus pinnipedialis CIP 107946	contig	GCA_903994035	110845.3	8065627521	110845	62.46

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6694	Jeotgalicoccus pinnipedialis partial 16S rRNA gene, type strain CCUG 42722T	AJ251530	1419		110845

GC content

6694

GC-content (mol%)38.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Jeotgalicoccus pinnipedialis CIP 107946
NCBI: GCA_903994035

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	72.90	no
125439	gram_stain	BacteriaNetⓘ	variable	70.00	no
125439	motility	BacteriaNetⓘ	no	54.00	no
125439	spore_formation	BacteriaNetⓘ	no	72.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Jeotgalicoccus pinnipedialis strain CIP107946
PATRIC: 110845.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.81	yes
125438	anaerobic	anaerobicⓘ	no	93.49	no
125438	spore-forming	spore-formingⓘ	no	84.26	yes
125438	aerobic	aerobicⓘ	yes	62.81	no
125438	thermophilic	thermophileⓘ	no	93.72	yes
125438	flagellated	motile2+ⓘ	no	88.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Jeotgalicoccus schoeneichii sp. nov. isolated from exhaust air of a pig barn.	Glaeser SP, Kleinhagauer T, Jackel U, Klug K, Kampfer P	Int J Syst Evol Microbiol	10.1099/ijsem.0.001230	2016
Phylogeny	Jeotgalicoccus pinnipedialis sp. nov., from a southern elephant seal (Mirounga leonina).	Hoyles L, Collins MD, Foster G, Falsen E, Schumann P	Int J Syst Evol Microbiol	10.1099/ijs.0.02833-0	2004

References

#6694	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17030
#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 )
#26380	IJSEM 745 2004 ( DOI 10.1099/ijs.0.02833-0 , PubMed 15143018 )
#30016	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 #26380
#34311	; Curators of the CIP;
#55531	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 42722
#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) .
#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 .
#121837	Collection of Institut Pasteur ; Curators of the CIP; CIP 107946
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Phocicoccus pinnipedialis (DSM 17030, CCUG 42722, CIP 107946)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite tests

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_017873645

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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