Name: Pedococcus cremeus V2M2
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 24114

Type strain:

Species: Pedococcus cremeus

Strain Designation: V2M2

Culture col. no.: DSM 28108, CGMCC 1.6963, JCM 17739, NBRC 104261

Strain history: CGMCC 1.6963 <-- J.-Y. Zhang V2M29.

NCBI tax ID(s): 587636 (species)

SI-ID 397118

DSM 28108

Special Collections

Section

Pedococcus cremeus V2M2 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from forest soil.

Gram-positive
rod-shaped
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	*Intrasporangiaceae*
	Genus	*Pedococcus*
	Species	**Pedococcus cremeus**
	Full Scientific Name (LPSN)	Pedococcus cremeus (Zhang et al. 2011) Nouioui et al. 2018

Synonym

Phycicoccus cremeus

Information on morphological and physiological properties Morphology

[Ref.: #29782]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %91.739

[Ref.: #29782]	Cell length	1.75 µm

[Ref.: #29782]	Cell width	0.65 µm

[Ref.: #29782]	Cell shape	rod-shaped

[Ref.: #29782]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %90

[Ref.: #29782]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21151]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #21151]

Culture medium growth

[Ref.: #21151]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21151]

Culture medium composition

expand / minimize

[Ref.: #21151]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #21151]

Culture medium growth

[Ref.: #21151]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21151]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21151]	growth	28 °C
[Ref.: #29782]	growth	14-35 °C
[Ref.: #29782]	optimum	29 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #29782]			optimum	7.5
[Ref.: #29782]			growth	4.1-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29782]

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29782]		NaCl		growth	0-7	%
[Ref.: #29782]		NaCl		optimum	1	%

[Ref.: #29782]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29782]	esculin ChEBI	+	hydrolysis
[Ref.: #29782]	gluconate ChEBI	+	carbon source
[Ref.: #29782]	glucose ChEBI	+	carbon source
[Ref.: #29782]	malate ChEBI	+	carbon source
[Ref.: #29782]	maltose ChEBI	+	carbon source
[Ref.: #29782]	mannitol ChEBI	+	carbon source
[Ref.: #29782]	mannose ChEBI	+	carbon source
[Ref.: #29782]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #29782]	nitrate ChEBI	+	reduction

	Enzyme	Enzyme activity	EC number
[Ref.: #29782]	acid phosphatase	+	3.1.3.2
[Ref.: #29782]	alkaline phosphatase	+	3.1.3.1
[Ref.: #29782]	alpha-galactosidase	+	3.2.1.22
[Ref.: #29782]	catalase	+	1.11.1.6
[Ref.: #29782]	gelatinase	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	myo-inositol biosynthesis	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	purine metabolism	82.98	78 of 94
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	metabolism of disaccharids	81.82	9 of 11
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	pyrimidine metabolism	80	36 of 45
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	tryptophan metabolism	76.32	29 of 38
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	lysine metabolism	69.05	29 of 42
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	oxidative phosphorylation	68.13	62 of 91
[Ref.: #66794]	degradation of sugar acids	68	17 of 25
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	elloramycin biosynthesis	60	3 of 5
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	aclacinomycin biosynthesis	57.14	4 of 7
[Ref.: #66794]	androgen and estrogen metabolism	56.25	9 of 16
[Ref.: #66794]	degradation of pentoses	53.57	15 of 28
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	vitamin B12 metabolism	41.18	14 of 34
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	vitamin B1 metabolism	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	35.29	6 of 17
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #21151]	Sample type/isolated from	forest soil
[Ref.: #21151]	Geographic location (country and/or sea, region)	Changbai Mountain
[Ref.: #21151]	Country	China
[Ref.: #21151]	Country ISO 3 Code	CHN
[Ref.: #21151]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Forest soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Changbai Mountains, Heilongjiang Province
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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

[Ref.: #21151]

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.: #21151]	Phycicoccus cremeus strain V2M29 16S ribosomal RNA gene, partial sequence	FJ529696	1518	GenBank ENA	587636 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Pedococcus cremeus CGMCC 1.6963	GCA_900111375	scaffold	GenBank ENA	587636 tax ID
[Ref.: #66792]	Phycicoccus cremeus strain CGMCC 1.6963	587636.3	wgs	PATRIC	587636 tax ID	*
[Ref.: #66792]	Phycicoccus cremeus CGMCC 1.6963	2671180066	draft	JGI IMG/M	587636 tax ID	*

[Ref.: #29782]	GC-content	72 mol%
[Ref.: #67770]	GC-content	72 mol%	thermal denaturation, midpoint method (Tm)

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: Pedococcus cremeus CGMCC 1.6963 NCBI: GCA_900111375.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	51	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Phycicoccus cremeus strain CGMCC 1.6963 PATRIC: 587636.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	91.739	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	92.621	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	61.191	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	88.882	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.881	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	90	no

Availability in culture collections External links

[Ref.: #21151]

Culture collection no.

DSM 28108, CGMCC 1.6963, JCM 17739, NBRC 104261

[Ref.: #88074]

SI-ID 397118

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phycicoccus cremeus sp. nov., isolated from forest soil, and emended description of the genus Phycicoccus.	Zhang JY, Liu XY, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.020842-0	2010	*

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 )

#21151

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28108

#29782

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 #26162 (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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

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

#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 )

#88074

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-ID397118.1 )

#26162

IJSEM 71 2011 ( DOI 10.1099/ijs.0.020842-0 , PubMed 20154328 )

* These data were automatically processed and therefore are not curated

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Pedococcus cremeus CGMCC 1.6963

Phycicoccus cremeus strain CGMCC 1.6963

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