Name: Cryobacterium psychrophilum DSM 4854
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7301

Type strain:

Species: Cryobacterium psychrophilum

Culture col. no.: DSM 4854, ATCC 43563, IAM 12024, IFO 15735, JCM 1463, NBRC 15735, NCIMB 2068, CCM 3311, CGMCC 1.1912, CGMCC 1.4292, CIP 105227, KCTC 3487, LMG 23845, VKM Ac-2100

Strain history: IAM 12024 <-- K. Inoue and K. Komagata 27-O-b.

NCBI tax ID(s): 41988 (species)

Section

Cryobacterium psychrophilum DSM 4854 is a psychrophilic bacterium that was isolated from soil.

psychrophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Cryobacterium*
	Species	**Cryobacterium psychrophilum**
	Full Scientific Name (PNU)	Cryobacterium psychrophilum (ex Inoue and Komagata 1976) Suzuki et al. 1997

Synonym

"Curtobacterium psychrophilum"

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1762]

Culture medium

RICH MEDIUM (DSMZ Medium 736)

[Ref.: #1762]

Culture medium growth

[Ref.: #1762]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #1762]

Culture medium composition

expand / minimize

[Ref.: #39232]

Culture medium

MEDIUM 29- Brain heart agar

[Ref.: #39232]

Culture medium growth

[Ref.: #39232]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #1762]	growth	10-12 °C
[Ref.: #39232]	growth	10 °C
[Ref.: #67770]	growth	10 °C

[Ref.: #1762]	Temperature range	psychrophilic
[Ref.: #39232]	Temperature range	psychrophilic
[Ref.: #67770]	Temperature range	psychrophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #1762]	Murein short key	B07
[Ref.: #1762]	Murein types	B2gamma {Gly} [L-Dab] D-Glu-D-Dab

[Ref.: #67770]

Observation

quinones: MK-10

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	80	8 of 10
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	arginine metabolism	75	18 of 24
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	citric acid cycle	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]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	66.67	6 of 9
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	allantoin degradation	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	degradation of sugar acids	64	16 of 25
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	oxidative phosphorylation	60.44	55 of 91
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	phenol degradation	55	11 of 20
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	daunorubicin biosynthesis	22.22	2 of 9
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		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.: #1762]	Sample type/isolated from	soil
[Ref.: #1762]	Geographic location (country and/or sea, region)	Syowa station
[Ref.: #1762]	Continent	Australia and Oceania

[Ref.: #67770]	Sample type/isolated from	Soil in Showa Station
[Ref.: #67770]	Country	Antarctica
[Ref.: #67770]	Country ISO 3 Code	ATA
[Ref.: #67770]	Continent	Antarctica
* marker position based on {}

Isolation sources categories

#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.: #1762]

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.: #20218]	Cryobacterium psychrophilum 16S rRNA gene, strain DSM 4854	AJ544063	1527	ENA	41988 tax ID	*
[Ref.: #20218]	Cryobacterium psychrophilum partial 16S rRNA gene, type strain DSM 4854	AM410676	1501	ENA	41988 tax ID	*
[Ref.: #1762]	Cryobacterium psychrophilum gene for 16S ribosomal RNA	D45058	1501	ENA	41988 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Cryobacterium psychrophilum strain CGMCC 1.4292	41988.4	wgs	PATRIC	41988 tax ID	*
[Ref.: #66792]	Cryobacterium psychrophilum strain DSM 4854	41988.3	wgs	PATRIC	41988 tax ID	*
[Ref.: #66792]	Cryobacterium psychrophilum DSM 4854	2781126036	draft	JGI IMG/M	41988 tax ID	*
[Ref.: #67770]	Cryobacterium psychrophilum DSM 4854	GCA_004365915	contig	GenBank	41988 tax ID
[Ref.: #67770]	Cryobacterium psychrophilum CGMCC 1.4292	GCA_004403975	contig	GenBank	41988 tax ID
[Ref.: #66792]	Pseudomonas syringae pv. tomato Pst DC 92-1	GCA_019689405	contig	PATRIC	323 tax ID	*

[Ref.: #1762]	GC-content	65 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	66.5 mol%	thermal denaturation, midpoint method (Tm)

Availability in culture collections External links

[Ref.: #1762]

Culture collection no.

DSM 4854, ATCC 43563, IAM 12024, IFO 15735, JCM 1463, NBRC 15735, NCIMB 2068, CCM 3311, CGMCC 1.1912, CGMCC 1.4292, CIP 105227, KCTC 3487, LMG 23845, VKM Ac-2100

[Ref.: #20218]

Associated Passport(s) in StrainInfo

150354, 112818, 112820, 112822, 112819, 332679, 112823

Literature:

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

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Cryobacterium psychrophilum gen. nov., sp. nov., nom. rev., comb. nov., an obligately psychrophilic actinomycete to accommodate "Curtobacterium psychrophilum" Inoue and Komagata 1976.	Suzuki K, Sasaki J, Uramoto M, Nakase T, Komagata K	Int J Syst Bacteriol	10.1099/00207713-47-2-474	1997	*
Phylogeny	Cryobacterium psychrotolerans sp. nov., a novel psychrotolerant bacterium isolated from the China No. 1 glacier.	Zhang DC, Wang HX, Cui HL, Yang Y, Liu HC, Dong XZ, Zhou PJ	Int J Syst Evol Microbiol	10.1099/ijs.0.64750-0	2007	*
Phylogeny	Cryobacterium mesophilum sp. nov., a novel mesophilic bacterium.	Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.65650-0	2008	*
Phylogeny	Cryobacterium roopkundense sp. nov., a psychrophilic bacterium isolated from glacial soil.	Reddy GSN, Pradhan S, Manorama R, Shivaji S	Int J Syst Evol Microbiol	10.1099/ijs.0.011775-0	2009	*
Phylogeny	Naasia aerilata gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from air.	Weon HY, Kim SJ, Jang YH, Hamada M, Tamura T, Ahn JH, Suzuki KI, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.046599-0	2012	*
Phylogeny	Cryobacterium levicorallinum sp. nov., a psychrophilic bacterium isolated from glacier ice.	Liu Q, Liu H, Zhang J, Zhou Y, Xin Y	Int J Syst Evol Microbiol	10.1099/ijs.0.046896-0	2013	*
Phylogeny	Diaminobutyricibacter tongyongensis gen. nov., sp. nov. and Homoserinibacter gongjuensis gen. nov., sp. nov. belong to the family Microbacteriaceae.	Kim SJ, Ahn JH, Weon HY, Hamada M, Suzuki K, Kwon SW	J Microbiol	10.1007/s12275-014-3278-y	2014	*

References

#1762

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4854

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#39232 ; 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) .

#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) .

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Cryobacterium psychrophilum in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF