Name: Puniceicoccus vermicola DSM 26450
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17650

Type strain:

Species: Puniceicoccus vermicola

Culture col. no.: DSM 26450, JCM 14086, KCCM 42343, NBRC 101964, IMCC 1545

Strain history: J.-C. Cho IMCC1545.

NCBI tax ID(s): 388746 (species)

SI-ID 293912

NBRC 101964, JCM 14086

Section

Puniceicoccus vermicola DSM 26450 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from intestine of sea polychaeta Periserrula leucophryna.

coccus-shaped
Gram-negative
facultative anaerobe
mesophilic
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	*Puniceicoccus*
	Species	**Puniceicoccus vermicola**
	Full Scientific Name (LPSN)	Puniceicoccus vermicola Choo et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31899]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.997

[Ref.: #31899]	Cell length	0.8 µm

[Ref.: #31899]	Cell width	0.8 µm

[Ref.: #31899]	Cell shape	coccus-shaped

[Ref.: #31899]	Motility	no

[Ref.: #18227]

Incubation period

3-7 days

[Ref.: #31899]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #18227]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)

[Ref.: #18227]

Culture medium growth

[Ref.: #18227]

Culture medium link

Medium recipe at MediaDive

[Ref.: #18227]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #18227]	growth	28 °C
[Ref.: #31899]	growth	08-37 °C
[Ref.: #31899]	optimum	27.5 °C
[Ref.: #67770]	growth	25 °C

[Ref.: #18227]	Temperature range	mesophilic
[Ref.: #31899]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31899]			optimum	9
[Ref.: #31899]			growth	05-12

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31899]

Oxygen tolerance

facultative anaerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.995

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31899]		NaCl		growth	1.0-7.5	%
[Ref.: #31899]		NaCl		optimum	3.25	%

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31899]	2,3-butanediol ChEBI	+	carbon source
[Ref.: #31899]	2-oxopentanoate ChEBI	+	carbon source
[Ref.: #31899]	arabinose ChEBI	+	carbon source
[Ref.: #31899]	cellobiose ChEBI	+	carbon source
[Ref.: #31899]	dextrin ChEBI	+	carbon source
[Ref.: #31899]	DL-carnitine ChEBI	+	carbon source
[Ref.: #31899]	fructose ChEBI	+	carbon source
[Ref.: #31899]	galactose ChEBI	+	carbon source
[Ref.: #31899]	glycerol ChEBI	+	carbon source
[Ref.: #31899]	L-arabitol ChEBI	+	carbon source
[Ref.: #31899]	lactate ChEBI	+	carbon source
[Ref.: #31899]	maltose ChEBI	+	carbon source
[Ref.: #31899]	mannitol ChEBI	+	carbon source
[Ref.: #31899]	mannose ChEBI	+	carbon source
[Ref.: #31899]	methyl D-glucoside ChEBI	+	carbon source
[Ref.: #31899]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #31899]	rhamnose ChEBI	+	carbon source
[Ref.: #31899]	sorbitol ChEBI	+	carbon source
[Ref.: #31899]	succinate ChEBI	+	carbon source
[Ref.: #31899]	sucrose ChEBI	+	carbon source
[Ref.: #31899]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31899]		acid phosphatase	+	3.1.3.2
[Ref.: #31899]		alkaline phosphatase	+	3.1.3.1

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

[Ref.: #18227]	Sample type/isolated from	intestine of sea polychaeta Periserrula leucophryna
[Ref.: #18227]	Host species	Periserrula leucophryna
[Ref.: #18227]	Geographic location (country and/or sea, region)	Yellow Sea
[Ref.: #18227]	Country	Republic of Korea
[Ref.: #18227]	Country ISO 3 Code	KOR
[Ref.: #18227]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Digestive tract of a sea polychaete (Periserrula leucophryna) inhabiting a tidal flat of Donggum Island
[Ref.: #67770]	Host species	Periserrula leucophryna
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Invertebrates (Other)	#Annelida
#Host Body-Site	#Gastrointestinal tract	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ539046 (>99% sequence identity) for Puniceicoccus vermicola subclade from Microbeatlas

Aquatic Samples	61
Soil Samples	1
Animal Samples	1
Plant Samples
Total Samples	63

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

[Ref.: #18227]

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.: #18227]	Puniceicoccus vermicola strain IMCC1545 16S ribosomal RNA gene, partial sequence	DQ539046	1480	ENA	388746 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Puniceicoccus vermicola JCM14086	GCA_014230055	contig	GenBank	388746 tax ID
[Ref.: #66792]	Puniceicoccus vermicola strain JCM14086	388746.3	wgs	PATRIC	388746 tax ID	*
[Ref.: #66792]	Puniceicoccus vermicola DSM 26450	2931345547	draft	JGI IMG/M	388746 tax ID	*

[Ref.: #31899]	GC-content	52.1 mol%
[Ref.: #67770]	GC-content	51.6-52.6 mol%	high performance liquid chromatography (HPLC)

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: Puniceicoccus vermicola strain JCM14086 PATRIC: 388746.3
[Ref.: #69481]	spore-forming	no	77	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Puniceicoccus vermicola strain JCM14086 PATRIC: 388746.3
[Ref.: #69480]	gram-positive	no	97.801	yes
[Ref.: #69480]	anaerobic	no	95.906	yes
[Ref.: #69480]	halophile	no	64.295	no
[Ref.: #69480]	spore-forming	no	94.878	no
[Ref.: #69480]	glucose-util	yes	86.828	no
[Ref.: #69480]	aerobic	no	51.948	yes
[Ref.: #69480]	motile	no	90.865	yes
[Ref.: #69480]	flagellated	no	97.669	no
[Ref.: #69480]	thermophile	no	94.815	no
[Ref.: #69480]	glucose-ferment	no	70.558	no

Availability in culture collections External links

[Ref.: #18227]

Culture collection no.

DSM 26450, JCM 14086, KCCM 42343, NBRC 101964, IMCC 1545

[Ref.: #86641]

SI-ID 293912

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Puniceicoccus vermicola gen. nov., sp. nov., a novel marine bacterium, and description of Puniceicoccaceae fam. nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov. and Opitutae classis nov. in the phylum 'Verrucomicrobia'.	Choo YJ, Lee K, Song J, Cho JC	Int J Syst Evol Microbiol	10.1099/ijs.0.64616-0	2007	*

References

#18227

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26450

#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 )

#31899

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 #28157 (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;

#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 )

#86641

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-ID293912.1 )

#28157

IJSEM 532 2007 ( DOI 10.1099/ijs.0.64616-0 , PubMed 17329779 )

* These data were automatically processed and therefore are not curated

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Puniceicoccus vermicola strain JCM14086

Puniceicoccus vermicola strain JCM14086

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