Name: Serinicoccus profundi 0714S6-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6284

Type strain:

Species: Serinicoccus profundi

Strain Designation: 0714S6-1

Culture col. no.: DSM 21363, CGMCC 4.5582, NBRC 110789, MCCC 1A05965, JCM 17740

Strain history: CGMCC 4.5582 <-- J. Xu 0714S6-1 (=MCCC 1A05965).

NCBI tax ID(s): 1043205 (strain), 1078471 (species)

Section

Serinicoccus profundi 0714S6-1 is an aerobe, Gram-positive, coccus-shaped bacterium that was isolated from deep-sea sediment.

coccus-shaped
Gram-positive
aerobe
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	*Micrococcales*
	Family	*Ornithinimicrobiaceae*
	Genus	*Serinicoccus*
	Species	**Serinicoccus profundi**
	Full Scientific Name (LPSN)	Serinicoccus profundi Xiao et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #29748]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #29748]	Cell shape	coccus-shaped

[Ref.: #29748]	Motility	no

[Ref.: #21354]	Colony color	Corn yellow (1006)
[Ref.: #21354]	Incubation period	10-14 days
[Ref.: #21354]	Cultivation medium used	ISP 2

[Ref.: #21354]	Colony color	Signal yellow (1003)
[Ref.: #21354]	Incubation period	10-14 days
[Ref.: #21354]	Cultivation medium used	ISP 3

[Ref.: #21354]	Colony color	Signal yellow (1003)
[Ref.: #21354]	Incubation period	10-14 days
[Ref.: #21354]	Cultivation medium used	ISP 4

[Ref.: #21354]	Colony color	Signal yellow (1003)
[Ref.: #21354]	Incubation period	10-14 days
[Ref.: #21354]	Cultivation medium used	ISP 5

[Ref.: #21354]	Colony color	Brown beige (1011)
[Ref.: #21354]	Incubation period	10-14 days
[Ref.: #21354]	Cultivation medium used	ISP 7

[Ref.: #21354]	Colony color	Ochre yellow (1024)
[Ref.: #21354]	Incubation period	10-14 days
[Ref.: #21354]	Cultivation medium used	suter with tyrosine

[Ref.: #21354]	Colony color	Lemon yellow (1012)
[Ref.: #21354]	Incubation period	10-14 days
[Ref.: #21354]	Cultivation medium used	suter without tyrosine

[Ref.: #29748]

Pigment production

yes

[Ref.: #21354]	Multicellular complex forming ability	no
[Ref.: #21354]	Medium Name (multicellularity)	ISP 2

[Ref.: #21354]	Multicellular complex forming ability	no
[Ref.: #21354]	Medium Name (multicellularity)	ISP 3

[Ref.: #21354]	Multicellular complex forming ability	no
[Ref.: #21354]	Medium Name (multicellularity)	ISP 4

[Ref.: #21354]	Multicellular complex forming ability	no
[Ref.: #21354]	Medium Name (multicellularity)	ISP 5

[Ref.: #21354]	Multicellular complex forming ability	no
[Ref.: #21354]	Medium Name (multicellularity)	ISP 7

[Ref.: #21354]	Multicellular complex forming ability	no
[Ref.: #21354]	Medium Name (multicellularity)	Suter with tyrosine

[Ref.: #21354]	Multicellular complex forming ability	no
[Ref.: #21354]	Medium Name (multicellularity)	Suter without tyrosine

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21354]

Culture medium

ISP 2

[Ref.: #21354]

Culture medium growth

[Ref.: #21354]

Culture medium composition

expand / minimize

[Ref.: #21354]

Culture medium

ISP 3

[Ref.: #21354]

Culture medium growth

[Ref.: #21354]

Culture medium composition

expand / minimize

[Ref.: #21354]

Culture medium

ISP 4

[Ref.: #21354]

Culture medium growth

[Ref.: #21354]

Culture medium composition

expand / minimize

[Ref.: #21354]

Culture medium

ISP 5

[Ref.: #21354]

Culture medium growth

[Ref.: #21354]

Culture medium composition

expand / minimize

[Ref.: #21354]

Culture medium

ISP 7

[Ref.: #21354]

Culture medium growth

[Ref.: #21354]

Culture medium composition

expand / minimize

[Ref.: #21354]

Culture medium

suter with tyrosine

[Ref.: #21354]

Culture medium growth

[Ref.: #21354]

Culture medium composition

expand / minimize

[Ref.: #21354]

Culture medium

suter without tyrosine

[Ref.: #21354]

Culture medium growth

[Ref.: #21354]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #29748]	growth	10-35 °C
[Ref.: #29748]	optimum	30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #29748]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29748]			optimum	7
[Ref.: #29748]			growth	06-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29748]

Oxygen tolerance

aerobe

[Ref.: #29748]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %92
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.989

	Salt		Salt conc.
[Ref.: #21354]	NaCl	maximum	10	%
[Ref.: #29748]	NaCl	growth	0-14	%
[Ref.: #29748]	NaCl	optimum	4	%

[Ref.: #29748]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29748]	2,3-butanediol ChEBI	+	carbon source
[Ref.: #29748]	2-oxopentanoate ChEBI	+	carbon source
[Ref.: #21354]	arabinose ChEBI	-
[Ref.: #29748]	arabinose ChEBI	+	carbon source
[Ref.: #21354]	cellulose ChEBI	-
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #29748]	dextrin ChEBI	+	carbon source
[Ref.: #29748]	esculin ChEBI	+	hydrolysis
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #21354]	fructose ChEBI	+
[Ref.: #29748]	fructose ChEBI	+	carbon source
[Ref.: #68379]	gelatin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #29748]	gluconate ChEBI	+	carbon source
[Ref.: #21354]	glucose ChEBI	+
[Ref.: #29748]	glucose ChEBI	+	carbon source
[Ref.: #29748]	glycerol ChEBI	+	carbon source
[Ref.: #29748]	glycogen ChEBI	+	carbon source
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #29748]	inosine ChEBI	+	carbon source
[Ref.: #29748]	L-alaninamide ChEBI	+	carbon source
[Ref.: #29748]	lactate ChEBI	+	carbon source
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #29748]	malate ChEBI	+	carbon source
[Ref.: #29748]	maltose ChEBI	+	carbon source
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #21354]	mannose ChEBI	+/-
[Ref.: #29748]	mannose ChEBI	+	carbon source
[Ref.: #29748]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #21354]	myo-inositol ChEBI	-
[Ref.: #29748]	nitrate ChEBI	+	reduction
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #29748]	pyruvate ChEBI	+	carbon source
[Ref.: #21354]	raffinose ChEBI	+
[Ref.: #29748]	raffinose ChEBI	+	carbon source
[Ref.: #21354]	rhamnose ChEBI	-
[Ref.: #29748]	ribose ChEBI	+	carbon source
[Ref.: #29748]	sorbitol ChEBI	+	carbon source
[Ref.: #29748]	succinate ChEBI	+	carbon source
[Ref.: #21354]	sucrose ChEBI	-
[Ref.: #29748]	sucrose ChEBI	+	carbon source
[Ref.: #68379]	sucrose ChEBI	+	fermentation	* from API Coryne
[Ref.: #29748]	thymidine ChEBI	+	carbon source
[Ref.: #29748]	trehalose ChEBI	+	carbon source
[Ref.: #29748]	tween 40 ChEBI	+	carbon source
[Ref.: #29748]	tween 80 ChEBI	+	carbon source
[Ref.: #68379]	urea ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #29748]	uridine ChEBI	+	carbon source
[Ref.: #21354]	xylose ChEBI	+
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #29748]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym, API Coryne
[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, API Coryne
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym, API Coryne
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68379]	beta-glucosidase	-	3.2.1.21	* from API Coryne
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym, API Coryne
[Ref.: #29748]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #29748]	gelatinase	+
[Ref.: #68379]	gelatinase	+		* from API Coryne
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym, API Coryne
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68379]	pyrrolidonyl arylamidase	+	3.4.19.3	* from API Coryne
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #68379]	urease	+	3.5.1.5	* from API Coryne
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Coryne:

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

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #21354]	483	-	+/-	+	+	-	-	+	+	-	+	+	not determinedn.d.	-	-	-	-	-	-	+	-	not determinedn.d.

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.: #21354]	995	not determinedn.d.	+	+	+	-	+	+	+	+	+	+	+	-	-	-	+	+	+	-	-

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

[Ref.: #15653]	Sample type/isolated from	deep-sea sediment
[Ref.: #15653]	Geographic location (country and/or sea, region)	Indian Ocean
[Ref.: #15653]	Country	Indian Ocean
[Ref.: #15653]	Continent	Asia
[Ref.: #15653]	Geographic location	-55.2400°/9.0300°

[Ref.: #67770]	Sample type/isolated from	Deep-sea (5,368 m) sediment of the Indian Ocean
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

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

[Ref.: #15653]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #15653]	Serinicoccus profundi MCCC 1A05965 16S ribosomal RNA gene, partial sequence	EU603762	1490	ENA	1043205 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Serinicoccus profundi MCCC 1A05965	GCA_000224715	contig	GenBank	1043205 tax ID
[Ref.: #66792]	Serinicoccus profundi CGMCC 4.5582	GCA_008001015	complete	GenBank	1078471 tax ID	*
[Ref.: #66792]	Serinicoccus profundi strain CGMCC 4.5582	1078471.4	complete	PATRIC	1078471 tax ID	*
[Ref.: #66792]	Serinicoccus profundi CGMCC 4.5582	2884004160	complete	JGI IMG/M	1078471 tax ID	*

[Ref.: #15653]	GC-content	72 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29748]	GC-content	72 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: Serinicoccus profundi strain CGMCC 4.5582 PATRIC: 1078471.4
[Ref.: #69481]	spore-forming	no	92	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Serinicoccus profundi CGMCC 4.5582 NCBI: GCA_008001015.1
[Ref.: #69480]	motile	no	93.885	yes
[Ref.: #69480]	flagellated	no	98.717	no
[Ref.: #69480]	gram-positive	yes	91.056	no
[Ref.: #69480]	anaerobic	no	99.133	no
[Ref.: #69480]	aerobic	yes	92.282	yes
[Ref.: #69480]	halophile	no	75.543	no
[Ref.: #69480]	spore-forming	no	93.147	no
[Ref.: #69480]	glucose-util	yes	90.465	yes
[Ref.: #69480]	thermophile	no	96.019	yes
[Ref.: #69480]	glucose-ferment	no	88.69	yes

Availability in culture collections External links

[Ref.: #15653]

Culture collection no.

DSM 21363, CGMCC 4.5582, NBRC 110789, MCCC 1A05965, JCM 17740

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Ornithinimicrobium pratense sp. nov., isolated from meadow soil.	Guo Q, Wang B, Zhou Z, Ke X, Zhang L, Chen M, Lin M, Wang W, Zhang W, Li X	Int J Syst Evol Microbiol	10.1099/ijsem.0.004557	2020	*
Phylogeny	Serinicoccus hydrothermalis sp. nov., isolated from shallow-sea hydrothermal systems off Kueishantao Island.	Zhang Q, Ye J, Yu L, Lin D, Tang K	Int J Syst Evol Microbiol	10.1099/ijsem.0.004145	2020	*
Phylogeny	Serinicoccus sediminis sp. nov., isolated from tidal flat sediment.	Lee DW, Yoo Y, Lee H, Kwon BO, Khim JS, Yim UH, Kim BS, Kim GH, Kim JJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003415	2019	*
Genetics	Genome sequence of Serinicoccus profundi, a novel actinomycete isolated from deep-sea sediment.	Xiao J, Luo Y, Xu J	J Bacteriol	10.1128/JB.06119-11	2011	*
Phylogeny	Serinicoccus chungangensis sp. nov., isolated from tidal flat sediment, and emended description of the genus Serinicoccus.	Traiwan J, Park MH, Kim W	Int J Syst Evol Microbiol	10.1099/ijs.0.025635-0	2010	*
Phylogeny	Serinicoccus profundi sp. nov., an actinomycete isolated from deep-sea sediment, and emended description of the genus Serinicoccus.	Xiao J, Luo Y, Xie S, Xu J	Int J Syst Evol Microbiol	10.1099/ijs.0.019976-0	2010	*
Phylogeny	Serinicoccus kebangsaanensis sp. nov: A new bacterium isolated from the toxic diatom, Nitzschia navis-varingica.	Yusof A, Sahrani FK, Ahmad A, Usup G, Bunawan H	New Microbes New Infect	10.1016/j.nmni.2022.101005	2022	*

References

#15653

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21363

#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 )

#21354

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#29748

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 #26130 (see below)

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#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 )

#26130

IJSEM 16 2013 ( DOI 10.1099/ijs.0.019976-0 , PubMed 20118285 )

* These data were automatically processed and therefore are not curated

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Serinicoccus profundi strain CGMCC 4.5582

Serinicoccus profundi CGMCC 4.5582

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