Name: Cerasicoccus arenae YM26-026
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 134262

Type strain:

Species: Cerasicoccus arenae

Strain Designation: YM26-026

Culture col. no.: MBIC 082805, KCTC 12870, CIP 109746, MBIC 08280

Strain history: CIP <- 2007, KCTC <- J. Yoon, Tokyo Univ., Tokyo, Japan: strain YM26-026

NCBI tax ID(s): 424488 (species)

SI-ID 309529

KCTC 12870, NBRC 103621, CIP 109746

Special Collections

Section

Cerasicoccus arenae YM26-026 is an aerobe, Gram-negative, coccus-shaped bacterium that was isolated from Environment, Marine sand.

coccus-shaped
Gram-negative
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	*Verrucomicrobiota*
	Class	*Opitutia*
	Order	*Puniceicoccales*
	Family	*Puniceicoccaceae*
	Genus	*Cerasicoccus*
	Species	**Cerasicoccus arenae**
	Full Scientific Name (LPSN)	Cerasicoccus arenae Yoon et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32194]	Gram stain	negative
[Ref.: #116483]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %95.418

[Ref.: #32194]	Cell length	0.9 µm

[Ref.: #32194]	Cell width	0.9 µm

[Ref.: #32194]	Cell shape	coccus-shaped
[Ref.: #116483]	Cell shape	coccus-shaped

[Ref.: #32194]	Motility	no
[Ref.: #116483]	Motility	no

[Ref.: #32194]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #33916]

Culture medium

Marine agar (MA)

[Ref.: #33916]

Culture medium growth

[Ref.: #33916]

Culture medium composition

expand / minimize

[Ref.: #116483]

Culture medium

CIP Medium 13

[Ref.: #116483]

Culture medium growth

[Ref.: #116483]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #32194]	growth	10-30 °C
[Ref.: #32194]	optimum	27.5 °C
[Ref.: #33916]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #32194]			optimum	7.5
[Ref.: #32194]			growth	06-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32194]

Oxygen tolerance

aerobe

[Ref.: #32194]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32194]		NaCl		growth	<8	%

[Ref.: #32194]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32194]	5-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #32194]	arabinose ChEBI	+	carbon source
[Ref.: #32194]	esculin ChEBI	+	hydrolysis
[Ref.: #32194]	fructose ChEBI	+	carbon source
[Ref.: #32194]	galactose ChEBI	+	carbon source
[Ref.: #32194]	glucose ChEBI	+	carbon source
[Ref.: #32194]	lactose ChEBI	+	carbon source
[Ref.: #32194]	mannose ChEBI	+	carbon source
[Ref.: #116483]	nitrate ChEBI	-	reduction
[Ref.: #116483]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #116483]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #32194]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[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
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #32194]	catalase	+	1.11.1.6
[Ref.: #116483]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #32194]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[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
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #116483]	oxidase	+/-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #116483]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #116483]	12082	-	+	+	+	-	-	-	-	-	-	-	+	-	+	-	-	-	-	-	+

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

[Ref.: #116483]	Sample type/isolated from	Environment, Marine sand
[Ref.: #116483]	Geographic location (country and/or sea, region)	Iwate
[Ref.: #116483]	Country	Japan
[Ref.: #116483]	Country ISO 3 Code	JPN
[Ref.: #116483]	Continent	Asia
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence AB292183 (>99% sequence identity) for Cerasicoccus arenae subclade from Microbeatlas

Aquatic Samples	15
Soil Samples	2
Animal Samples
Plant Samples
Total Samples	17

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

[Ref.: #116483]

Biosafety level

Risk group (French classification)

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.: #32194]	Cerasicoccus arenae gene for 16S rRNA, partial sequence	AB292183	1469	GenBank ENA	424488 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Cerasicoccus arenae KCTC 12870	GCA_016595555	contig	GenBank ENA	424488 tax ID	*
[Ref.: #66792]	Cerasicoccus arenae KCTC 12870	GCA_014651635	scaffold	GenBank ENA	424488 tax ID	*
[Ref.: #66792]	Cerasicoccus arenae strain KCTC 12870	424488.4	wgs	PATRIC	424488 tax ID	*
[Ref.: #66792]	Cerasicoccus arenae strain KCTC 12870	424488.3	wgs	PATRIC	424488 tax ID	*

[Ref.: #32194]

GC-content

54 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Cerasicoccus arenae KCTC 12870 NCBI: GCA_014651635.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Cerasicoccus arenae KCTC 12870 NCBI: GCA_014651635.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	95.418	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	87.944	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	63.958	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	84.036	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	88.468	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	73.385	yes

Availability in culture collections External links

[Ref.: #32194]

Culture collection no.

MBIC 082805, KCTC 12870, CIP 109746, MBIC 08280

[Ref.: #91849]

SI-ID 309529

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Cerasicoccus maritimus sp. nov. and Cerasicoccus frondis sp. nov., two peptidoglycan-less marine verrucomicrobial species, and description of Verrucomicrobia phyl. nov., nom. rev.	Yoon J, Matsuo Y, Matsuda S, Kasai H, Yokota A	J Gen Appl Microbiol	10.2323/jgam.56.213	2010	*
Phylogeny	Cerasicoccus arenae gen. nov., sp. nov., a carotenoid-producing marine representative of the family Puniceicoccaceae within the phylum 'Verrucomicrobia', isolated from marine sand.	Yoon J, Matsuo Y, Matsuda S, Adachi K, Kasai H, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.65102-0	2007	*

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 )

#32194

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 #28436 (see below)

#33916 ; 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) .

#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 .

#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 )

#91849

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID309529.1 )

#116483 Collection of Institut Pasteur ; Curators of the CIP; CIP 109746

#28436

IJSEM 2067 2007 ( DOI 10.1099/ijs.0.65102-0 , PubMed 17766873 )

* These data were automatically processed and therefore are not curated

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Cerasicoccus arenae KCTC 12870

Cerasicoccus arenae KCTC 12870

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