Cryobacterium levicorallinum (DSM 28143, CGMCC 1.11211, Hh34)

Name: Cryobacterium levicorallinum (DSM 28143, CGMCC 1.11211, Hh34)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24187

Type strain

Strain Designation Hh34

Culture col. no. DSM 28143 CGMCC 1.11211 Hh34 NBRC 107883

NCBI tax ID(s) 995038

Special Collections DSMZ Literature strains

Links

Cryobacterium levicorallinum Hh34 is an aerobe, psychrophilic, Gram-positive prokaryote that was isolated from ice in glacier.

Gram-positive rod-shaped aerobe psychrophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 402409

NBRC 107883,DSM 28143

@ref 20215

Last LPSN update 2025-12-16 09:52:48

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Cryobacterium

Species Cryobacterium levicorallinum

Full scientific name Cryobacterium levicorallinum Liu et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
30890	positive	0.93 µm	0.43 µm	rod-shaped

Colony morphology

20519

Incubation period3-7 days

Pigmentation

30890

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20519	PP-MEDIUM (DSMZ Medium 513)		Medium recipe at MediaDive	Name: PP-MEDIUM (DSMZ Medium 513) Composition: Agar 15.0 g/l Polypeptone 10.0 g/l Yeast extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
20519	positive	growth	10	psychrophilic
30890	positive	growth	0-18	psychrophilic
30890	positive	optimum	11	psychrophilic

Culture pH

@ref	Ability	Type	PH	PH range
30890	positive	growth	6.0-12.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30890	aerobe
125439	obligate aerobe	93

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30890	NaCl	positive	growth	0-3 %

Observation

30890

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30890	30089 ChEBI	acetate	+	carbon source
30890	22599 ChEBI	arabinose	+	carbon source
30890	17057 ChEBI	cellobiose	+	carbon source
30890	28757 ChEBI	fructose	+	carbon source
30890	28260 ChEBI	galactose	+	carbon source
30890	24265 ChEBI	gluconate	+	carbon source
30890	17234 ChEBI	glucose	+	carbon source
30890	17754 ChEBI	glycerol	+	carbon source
30890	25115 ChEBI	malate	+	carbon source
30890	17306 ChEBI	maltose	+	carbon source
30890	29864 ChEBI	mannitol	+	carbon source
30890	37684 ChEBI	mannose	+	carbon source
30890	17632 ChEBI	nitrate	+	reduction
30890	33942 ChEBI	ribose	+	carbon source
30890	30911 ChEBI	sorbitol	+	carbon source
30890	17992 ChEBI	sucrose	+	carbon source
30890	27082 ChEBI	trehalose	+	carbon source
30890	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30890	catalase	+	1.11.1.6

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	lipoate biosynthesis	100	5 of 5
66794	phenylmercury acetate degradation	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	starch degradation	100	10 of 10
66794	L-lactaldehyde degradation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	cardiolipin biosynthesis	100	7 of 7
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	teichoic acid biosynthesis	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	cyanate degradation	100	3 of 3
66794	ribulose monophosphate pathway	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	pentose phosphate pathway	100	11 of 11
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	cellulose degradation	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	vitamin K metabolism	100	5 of 5
66794	Entner Doudoroff pathway	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	ketogluconate metabolism	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	citric acid cycle	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	purine metabolism	82.98	78 of 94
66794	glycolysis	82.35	14 of 17
66794	proline metabolism	81.82	9 of 11
66794	metabolism of disaccharids	81.82	9 of 11
66794	factor 420 biosynthesis	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	pyrimidine metabolism	80	36 of 45
66794	alanine metabolism	79.31	23 of 29
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	heme metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	d-mannose degradation	77.78	7 of 9
66794	histidine metabolism	75.86	22 of 29
66794	isoleucine metabolism	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	tryptophan metabolism	68.42	26 of 38
66794	enterobactin biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	non-pathway related	65.79	25 of 38
66794	degradation of sugar acids	64	16 of 25
66794	oxidative phosphorylation	63.74	58 of 91
66794	degradation of sugar alcohols	62.5	10 of 16
66794	arginine metabolism	62.5	15 of 24
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	methionine metabolism	61.54	16 of 26
66794	degradation of pentoses	60.71	17 of 28
66794	3-chlorocatechol degradation	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	phenol degradation	60	12 of 20
66794	gallate degradation	60	3 of 5
66794	lipid metabolism	58.06	18 of 31
66794	glutathione metabolism	57.14	8 of 14
66794	lysine metabolism	57.14	24 of 42
66794	cysteine metabolism	55.56	10 of 18
66794	urea cycle	53.85	7 of 13
66794	tyrosine metabolism	50	7 of 14
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	cyclohexanol degradation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	carotenoid biosynthesis	50	11 of 22
66794	glycine metabolism	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	resorcinol degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	sulfate reduction	46.15	6 of 13
66794	d-xylose degradation	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	degradation of hexoses	44.44	8 of 18
66794	nitrate assimilation	44.44	4 of 9
66794	mevalonate metabolism	42.86	3 of 7
66794	glycine betaine biosynthesis	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	carnitine metabolism	37.5	3 of 8
66794	vitamin B6 metabolism	36.36	4 of 11
66794	polyamine pathway	34.78	8 of 23
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	lipid A biosynthesis	33.33	3 of 9
66794	allantoin degradation	33.33	3 of 9
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	cholesterol biosynthesis	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	lactate fermentation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	daunorubicin biosynthesis	22.22	2 of 9
66794	vitamin B12 metabolism	20.59	7 of 34

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Glacier
#Environmental	#Aquatic	#Ice

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
20519	ice in glacier	No.1 Glacier in Xingjiang Uygur Autonomous Region, north-west China	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20519	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM440240v1 assembly for Cryobacterium levicorallinum Hh34	contig	GCA_004402405	995038.5	8117581345	995038	70.11
66792	IMG-taxon 2663762754 annotated assembly for Cryobacterium levicorallinum GMCC 1.11211	scaffold	GCA_900113585	995038.3	2663762754	995038	69.78
66792	ASM799235v1 assembly for Cryobacterium levicorallinum NBRC 107883	contig	GCA_007992355	995038.7	8110920627	995038	63.42

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20519	Cryobacterium levicorallinum strain Hh34 16S ribosomal RNA gene, partial sequence	JF267312	1478		995038

GC content

20519

GC-content (mol%)63.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Cryobacterium levicorallinum NBRC 107883
NCBI: GCA_007992355

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	88.20	no
125439	motility	BacteriaNetⓘ	no	55.20	no
125439	gram_stain	BacteriaNetⓘ	positive	66.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Cryobacterium levicorallinum strain Hh34
PATRIC: 995038.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.11	yes
125438	anaerobic	anaerobicⓘ	no	96.04	yes
125438	aerobic	aerobicⓘ	yes	88.14	yes
125438	spore-forming	spore-formingⓘ	no	72.35	no
125438	thermophilic	thermophileⓘ	no	90.91	no
125438	flagellated	motile2+ⓘ	no	79.10	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genomic Insights of Cryobacterium Isolated From Ice Core Reveal Genome Dynamics for Adaptation in Glacier.	Liu Y, Shen L, Zeng Y, Xing T, Xu B, Wang N.	Front Microbiol	10.3389/fmicb.2020.01530	2020
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

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 )
#20519	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28143
#30890	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 #27220 (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 )
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Cryobacterium levicorallinum (DSM 28143, CGMCC 1.11211, Hh34)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004402405

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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