Cryobacterium roopkundense (DSM 21065, JCM 15131, CCUG 55701)

Name: Cryobacterium roopkundense (DSM 21065, JCM 15131, CCUG 55701)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7304

Type strain

Strain Designation Rug 17

Culture col. no. DSM 21065 JCM 15131 CCUG 55701 Rug 17 CGMCC 1.10672

NCBI tax ID(s) 1001240

Special Collections DSMZ CCUG JCM Literature strains

History DSMZ <- S. Shivaji, CCMB; Rug 17 JCM <-- S. Shivaji RuGl7.

Links

Cryobacterium roopkundense Rug 17 is an aerobe, Gram-positive, motile bacterium that was isolated from glacial lake.

Gram-positive motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 272340

LMG 24851,JCM 15131

@ref 20215

Last LPSN update 2026-05-29 08:26:37

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Cryobacterium

Species Cryobacterium roopkundense

Full scientific name Cryobacterium roopkundense Reddy et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
29373	positive	2.5 µm	0.8 µm	rod-shaped

Pigmentation

29373

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
29373	positive	growth	0-18
29373	positive	optimum	15-18
29373	positive	optimum	16.5
60699	positive	growth	8
67770	positive	growth	15

Culture pH

@ref	Ability	Type	PH
29373	positive	optimum	7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29373	aerobe
60699	aerobe
125439	facultative anaerobe	90.388

Observation

67770

Observationquinones: MK-10, MK-11, MK-12

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29373	16947 ChEBI	citrate	+	carbon source
29373	15792 ChEBI	malonate	+	carbon source
29373	17632 ChEBI	nitrate	+	reduction

Enzymes

@ref	Value	Activity	Ec
29373	catalase	+	1.11.1.6
29373	gelatinase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	starch degradation	100	10 of 10
66794	kanosamine biosynthesis II	100	2 of 2
66794	pentose phosphate pathway	100	11 of 11
66794	ribulose monophosphate pathway	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	glycogen metabolism	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	cardiolipin biosynthesis	100	7 of 7
66794	palmitate biosynthesis	100	22 of 22
66794	threonine metabolism	100	10 of 10
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	formaldehyde oxidation	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	ketogluconate metabolism	100	8 of 8
66794	lipoate biosynthesis	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	Entner Doudoroff pathway	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	d-mannose degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
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	NAD metabolism	83.33	15 of 18
66794	proline metabolism	81.82	9 of 11
66794	flavin biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	3-chlorocatechol degradation	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	alanine metabolism	75.86	22 of 29
66794	gluconeogenesis	75	6 of 8
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	purine metabolism	73.4	69 of 94
66794	pyrimidine metabolism	73.33	33 of 45
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	degradation of sugar alcohols	68.75	11 of 16
66794	degradation of sugar acids	68	17 of 25
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	tryptophan metabolism	65.79	25 of 38
66794	heme metabolism	64.29	9 of 14
66794	glutathione metabolism	64.29	9 of 14
66794	oxidative phosphorylation	62.64	57 of 91
66794	arginine metabolism	62.5	15 of 24
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	histidine metabolism	62.07	18 of 29
66794	urea cycle	61.54	8 of 13
66794	vitamin B1 metabolism	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	gallate degradation	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	O-antigen biosynthesis	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	non-pathway related	57.89	22 of 38
66794	methionine metabolism	57.69	15 of 26
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	lipid metabolism	54.84	17 of 31
66794	metabolism of disaccharids	54.55	6 of 11
66794	ascorbate metabolism	54.55	12 of 22
66794	degradation of pentoses	53.57	15 of 28
66794	phenylmercury acetate degradation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	toluene degradation	50	2 of 4
66794	lysine metabolism	50	21 of 42
66794	glycine metabolism	50	5 of 10
66794	lactate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	androgen and estrogen metabolism	50	8 of 16
66794	glycogen biosynthesis	50	2 of 4
66794	sulfate reduction	46.15	6 of 13
66794	d-xylose degradation	45.45	5 of 11
66794	vitamin B6 metabolism	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	allantoin degradation	44.44	4 of 9
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	bile acid biosynthesis, neutral pathway	41.18	7 of 17
66794	carotenoid biosynthesis	40.91	9 of 22
66794	D-cycloserine biosynthesis	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	arachidonate biosynthesis	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	tyrosine metabolism	35.71	5 of 14
66794	polyamine pathway	34.78	8 of 23
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	lipid A biosynthesis	33.33	3 of 9
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	methanogenesis from CO2	25	3 of 12
66794	biotin biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	chlorophyll metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Glacier
#Environmental	#Aquatic	#Lake (large)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15539	glacial lake	Roopkund, Himalayan region	India	IND	Asia
60699	Water,glacier	Himalayan region,Lake Roopkund	India	IND	Asia
67770	Soil at the periphery of the glacial Lake Roopkund in the Himalayan mountain range		India	IND	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF467640 (>99% sequence identity) for Cryobacterium from Microbeatlas

Aquatic Samples	1295
Soil Samples	1037
Animal Samples	250
Plant Samples	164
Total Samples	2746

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15539	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1420040v1 assembly for Cryobacterium roopkundense DSM 21065	contig	GCA_014200405	1001240.6	2844826561	1001240	77.66
67770	ASM76416v1 assembly for Cryobacterium roopkundense RuG17	contig	GCA_000764165	1001240.4	2636416111	1001240	32.85

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15539	Cryobacterium roopkundense strain RuGl7 16S ribosomal RNA gene, partial sequence	EF467640	1459		1001240

GC content

15539

GC-content (mol%)64.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1420040v1 assembly for Cryobacterium roopkundense DSM 21065
NCBI: GCA_014200405

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	90.39	no
125439	gram_stain	BacteriaNetⓘ	positive	83.02	no
125439	motility	BacteriaNetⓘ	no	85.27	no
125439	spore_formation	BacteriaNetⓘ	no	85.72	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Cryobacterium roopkundense strain DSM 21065
PATRIC: 1001240.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.86	yes
125438	anaerobic	anaerobicⓘ	no	97.56	yes
125438	spore-forming	spore-formingⓘ	no	62.37	no
125438	aerobic	aerobicⓘ	yes	87.53	yes
125438	thermophilic	thermophileⓘ	no	90.83	yes
125438	flagellated	motile2+ⓘ	no	80.64	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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	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

References

#15539	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21065
#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 )
#25781	IJSEM 866 2010 ( DOI 10.1099/ijs.0.011775-0 , PubMed 19661491 )
#29373	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 #25781
#60699	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55701
#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;
#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 .
#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 roopkundense (DSM 21065, JCM 15131, CCUG 55701)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014200405

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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