Cite this strain

Cellulomonas marina (DSM 24960, CGMCC 4.6945, NBRC 110784)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23832

Type strain

Strain Designation FXJ8.089

Culture col. no. DSM 24960 CGMCC 4.6945 NBRC 110784 FXJ8.089 JCM 30777

NCBI tax ID(s) 988821

Special Collections DSMZ JCM Literature strains

Links

Name and taxonomic classification

Cellulomonas marina FXJ8.089 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from deep-sea water.

Gram-positive motile coccus-shaped facultative anaerobe mesophilic genome sequence 16S sequence Bacteria

SI-ID 405346

DSM 24960

Last LPSN update 2024-12-09 10:45:43

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Cellulomonadaceae

Genus Cellulomonas

Species Cellulomonas marina

Full scientific name Cellulomonas marina Zhang et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
30980	positive	coccus-shaped
125439	positive

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20496	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)		Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
20496	positive	growth	28	mesophilic
30980	positive	growth	04-37
30980	positive	optimum	26.5	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH
30980	positive	optimum	7.5
30980	positive	growth	06-11

Physiology and metabolism

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30980	NaCl	positive	growth	0-3 %

Observation

67770

Observationquinones: MK-9(H₄)

Spore formation

30980

Spore formationno

Enzymes

@ref	Value	Activity	Ec
30980	catalase	+	1.11.1.6
30980	gelatinase	+

Metabolite production

@ref	Chebi-ID	Metabolite	Production
30980	16136 ChEBI	hydrogen sulfide

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30980	17057 ChEBI	cellobiose	+	carbon source
30980	28260 ChEBI	galactose	+	carbon source
30980	17234 ChEBI	glucose	+	carbon source
30980	17754 ChEBI	glycerol	+	carbon source
30980	17716 ChEBI	lactose	+	carbon source
30980	37684 ChEBI	mannose	+	carbon source
30980	17632 ChEBI	nitrate	+	reduction
30980	26546 ChEBI	rhamnose	+	carbon source
30980	33942 ChEBI	ribose	+	carbon source
30980	17992 ChEBI	sucrose	+	carbon source
30980	27082 ChEBI	trehalose	+	carbon source

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	starch degradation	100	10 of 10
66794	vitamin K metabolism	100	5 of 5
66794	threonine metabolism	100	10 of 10
66794	L-lactaldehyde degradation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	cardiolipin biosynthesis	100	7 of 7
66794	sulfoquinovose degradation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	methylglyoxal degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	teichoic acid biosynthesis	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	photosynthesis	92.86	13 of 14
66794	metabolism of disaccharids	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	ketogluconate metabolism	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	pentose phosphate pathway	81.82	9 of 11
66794	factor 420 biosynthesis	80	4 of 5
66794	lipoate biosynthesis	80	4 of 5
66794	pyrimidine metabolism	77.78	35 of 45
66794	serine metabolism	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	alanine metabolism	75.86	22 of 29
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	proline metabolism	72.73	8 of 11
66794	glycolysis	70.59	12 of 17
66794	myo-inositol biosynthesis	70	7 of 10
66794	non-pathway related	68.42	26 of 38
66794	sphingosine metabolism	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	citric acid cycle	64.29	9 of 14
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	degradation of sugar alcohols	62.5	10 of 16
66794	methionine metabolism	61.54	16 of 26
66794	leucine metabolism	61.54	8 of 13
66794	lipid metabolism	61.29	19 of 31
66794	cysteine metabolism	61.11	11 of 18
66794	degradation of hexoses	61.11	11 of 18
66794	oxidative phosphorylation	59.34	54 of 91
66794	arginine metabolism	58.33	14 of 24
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	degradation of pentoses	57.14	16 of 28
66794	glutathione metabolism	57.14	8 of 14
66794	propanol degradation	57.14	4 of 7
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	lysine metabolism	57.14	24 of 42
66794	degradation of sugar acids	56	14 of 25
66794	nitrate assimilation	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	ascorbate metabolism	54.55	12 of 22
66794	urea cycle	53.85	7 of 13
66794	coenzyme M biosynthesis	50	5 of 10
66794	propionate fermentation	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	carotenoid biosynthesis	50	11 of 22
66794	kanosamine biosynthesis II	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	lipid A biosynthesis	44.44	4 of 9
66794	tyrosine metabolism	42.86	6 of 14
66794	3-chlorocatechol degradation	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	sulfate reduction	38.46	5 of 13
66794	vitamin B1 metabolism	38.46	5 of 13
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	CMP-KDO biosynthesis	25	1 of 4
66794	phenol degradation	25	5 of 20
66794	biotin biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	arachidonic acid metabolism	22.22	4 of 18

Oxygen tolerance

@ref	Oxygen tolerance
30980	facultative anaerobe
125439	obligate aerobe

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
20496	deep-sea water	southwest Indian Ocean (49° 39' E 37° 47' S, 2800 m depth)	China	CHN	Asia	-37.7833	49.65 -37.7833/49.65
67770	Deep-sea water from the southwest Indian Ocean (37° 47' S 49° 39' E) at a depth of 2,800 m					-37.7833	49.65 -37.7833/49.65

Safety information

Risk assessment

@ref	Biosafety level	Biosafety level comment
20496	1	Risk group (German classification)

Sequence information

GC content

@ref	GC-content (mol%)	Method
20496	70.3	high performance liquid chromatography (HPLC)
30980	70.3
67770	75.6	genome sequence analysis

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20496	Cellulomonas marina strain FXJ8.089 16S ribosomal RNA gene, partial sequence	JF346422	1445		988821

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Cellulomonas marina NBRC 110784	GCA_016862715	contig		988821
66792	Cellulomonas marina strain CGMCC 4.6945	988821.3	wgs	PATRIC	988821
66792	Cellulomonas marina strain NBRC 110784	988821.4	wgs	PATRIC	988821
66792	Cellulomonas marina CGMCC 4.6945	2675903053	draft	JGI IMG/M	988821
67770	Cellulomonas marina CGMCC 4.6945	GCA_900111925	contig		988821

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Cellulomonas marina NBRC 110784
NCBI: GCA_016862715

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	52.60	no
125439	motility	BacteriaNetⓘ	no	63.70	no
125439	gram_stain	BacteriaNetⓘ	positive	99.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.50	no

Predictions from Diaspora project based on:
Cellulomonas marina strain CGMCC 4.6945
PATRIC: 988821.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.33	yes
125438	anaerobic	anaerobicⓘ	no	93.90	no
125438	aerobic	aerobicⓘ	yes	64.05	yes
125438	spore-forming	spore-formingⓘ	no	71.48	yes
125438	thermophilic	thermophileⓘ	no	94.00	no
125438	flagellated	motile2+ⓘ	no	66.50	no

External links

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Cellulomonas citrea sp. nov., isolated from paddy soil.	Lee HJ, Kim SY, Whang KS	Int J Syst Evol Microbiol	10.1099/ijsem.0.004409	2020
Phylogeny	Cellulomonas marina sp. nov., isolated from deep-sea water.	Zhang L, Xi L, Qiu D, Song L, Dai X, Ruan J, Huang Y	Int J Syst Evol Microbiol	10.1099/ijs.0.048876-0	2013

Straininfo Link

@ref	Straininfo	Culture collections
87857	405346	DSM 24960

Culture collection no.

Culture collection no.
DSM 24960
CGMCC 4.6945
NBRC 110784
FXJ8.089
JCM 30777

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 )
#20496	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24960
#30980	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 #27310 (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;
#87857	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-ID405346.1 )
#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 .

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