Cite this strain

Geodermatophilus marinus (DSM 106570, CCTCC AA 2018014, LHW52908)

BacDive ID 159073

Type strain

Strain Designation LHW52908

Culture col. no. DSM 106570 CCTCC AA 2018014 LHW52908

NCBI tax ID(s) 1663241

Special Collections DSMZ Wink compendium Literature strains

Links

Geodermatophilus marinus LHW52908 is a bacterium that was isolated from marine sponge.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 406866

DSM 106570

@ref 20215

Last LPSN update 2026-02-09 11:38:30

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Geodermatophilales

Family Geodermatophilaceae

Genus Geodermatophilus

Species Geodermatophilus marinus

Full scientific name Geodermatophilus marinus Li et al. 2019

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	99

Colony morphology

@ref	Colony color
68138	black
69320	Light ivory (1015)
69320	Ochre yellow (1024)
69320	Pastel orange (2003)
69320	Pastel orange (2003)
69320	Pastel yellow (1034)
69320	Reed green (6013)

Multicellular morphology

@ref	Complex name	Medium name
69320	Aerial mycelium	ISP 2
69320	Aerial mycelium	ISP 3
69320	Aerial mycelium	ISP 4
69320	Aerial mycelium	ISP 5
69320	Aerial mycelium	ISP 6
69320	Aerial mycelium	ISP 7

Pigmentation

@ref	Production	Name
69320		melanin pigment
69320		soluble pigment

Multimedia

@ref:	65896
multimedia content:	DSM_106570.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_106570.jpg
caption:	Medium 621 8x 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
65896	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
65896	GEO-MEDIUM (DSMZ Medium 714)	Medium recipe at MediaDive	Name: GEO-MEDIUM (DSMZ Medium 714) Composition: Agar 15.0 g/l CaCO3 1.0 g/l Starch 1.0 g/l Glucose 1.0 g/l Yeast extract 1.0 g/l Distilled water
65896	PYGV AGAR (DSMZ Medium 621)	Medium recipe at MediaDive	Name: PYGV AGAR (DSMZ Medium 621) Composition: Agar 15.0 g/l MgSO4 x 7 H2O 0.625264 g/l Glucose 0.25 g/l Peptone 0.25 g/l Yeast extract 0.25 g/l Nitrilotriacetic acid 0.210526 g/l CaCl2 x 2 H2O 0.0703158 g/l FeSO4 x 7 H2O 0.00208422 g/l Na2MoO4 x 2 H2O 0.000266736 g/l Pyridoxine hydrochloride 0.0001 g/l p-Aminobenzoic acid 5e-05 g/l D-Calcium pantothenate 5e-05 g/l Nicotinamide 5e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l Riboflavine 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Vitamin B12 1e-06 g/l Metall salt sol. 44 Distilled water
65896	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 20.0 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)
65896	positive	growth	28
68138	positive	growth	20-40

Culture pH

@ref	Ability	Type	PH
68138	positive	growth	7.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
68138	NaCl	positive	growth	0-5 %
69320	NaCl	positive	growth	0-2.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68138	16708 ChEBI	adenine	+	nitrogen source
69320	22599 ChEBI	arabinose	+	growth
68138	85146 ChEBI	carboxymethylcellulose	-	degradation
68138	17057 ChEBI	cellobiose	+/-	carbon source
69320	62968 ChEBI	cellulose	+	growth
68138	17108 ChEBI	D-arabinose	-	carbon source
68138	15824 ChEBI	D-fructose	+	carbon source
68138	12936 ChEBI	D-galactose	+	carbon source
68138	17634 ChEBI	D-glucose	+	carbon source
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68138	16899 ChEBI	D-mannitol	+/-	carbon source
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68138	16024 ChEBI	D-mannose	+	carbon source
68138	16988 ChEBI	D-ribose	-	carbon source
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68138	17924 ChEBI	D-sorbitol	-	carbon source
68138	65327 ChEBI	D-xylose	+/-	carbon source
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68138	4853 ChEBI	esculin	-	degradation
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
69320	28757 ChEBI	fructose	-	growth
68138	16813 ChEBI	galactitol	-	carbon source
68138	5291 ChEBI	gelatin	+	degradation
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
69320	17234 ChEBI	glucose	+	growth
68138	17754 ChEBI	glycerol	+	carbon source
68138	15428 ChEBI	glycine	+/-	nitrogen source
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68138	24741 ChEBI	hydroxyproline	+/-	nitrogen source
68138	17368 ChEBI	hypoxanthine	+/-	nitrogen source
69320	17268 ChEBI	inositol	+	growth
68138	16977 ChEBI	L-alanine	-	nitrogen source
68138	30849 ChEBI	L-arabinose	-	carbon source
68138	16467 ChEBI	L-arginine	-	nitrogen source
68138	17196 ChEBI	L-asparagine	+/-	nitrogen source
68138	29991 ChEBI	L-aspartate	-	nitrogen source
68138	17561 ChEBI	L-cysteine	-	nitrogen source
68138	29985 ChEBI	L-glutamate	-	nitrogen source
68138	18050 ChEBI	L-glutamine	-	nitrogen source
68138	15971 ChEBI	L-histidine	+	nitrogen source
68138	15603 ChEBI	L-leucine	-	nitrogen source
68138	18019 ChEBI	L-lysine	+/-	nitrogen source
68138	16643 ChEBI	L-methionine	-	nitrogen source
68138	17295 ChEBI	L-phenylalanine	-	nitrogen source
68138	17203 ChEBI	L-proline	-	nitrogen source
68138	62345 ChEBI	L-rhamnose	-	carbon source
68138	17115 ChEBI	L-serine	+/-	nitrogen source
68138	16857 ChEBI	L-threonine	+/-	nitrogen source
68138	16828 ChEBI	L-tryptophan	+/-	nitrogen source
68138	17895 ChEBI	L-tyrosine	+/-	nitrogen source
68138	90608 ChEBI	L-valine 2-naphthylamide	+/-	nitrogen source
68138	17716 ChEBI	lactose	+/-	carbon source
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68138	17306 ChEBI	maltose	-	carbon source
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
69320	37684 ChEBI	mannose	-	growth
68138	28053 ChEBI	melibiose	-	carbon source
68138		milk	-	assimilation
68138	17268 ChEBI	myo-inositol	+/-	carbon source
68138	17632 ChEBI	nitrate	-	reduction
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
68138	16634 ChEBI	raffinose	-	carbon source
69320	16634 ChEBI	raffinose	+	growth
69320	26546 ChEBI	rhamnose	+	growth
68138	32954 ChEBI	sodium acetate	+	carbon source
68138	53258 ChEBI	sodium citrate	-	carbon source
68138	50144 ChEBI	sodium pyruvate	+/-	carbon source
68138	28017 ChEBI	starch	-	hydrolysis
68138	17992 ChEBI	sucrose	+/-	carbon source
69320	17992 ChEBI	sucrose	+	growth
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68138	27082 ChEBI	trehalose	-	carbon source
68138	53424 ChEBI	tween 20	-	degradation
68138	53423 ChEBI	tween 40	-	degradation
68138	53425 ChEBI	tween 60	-	degradation
68138	53426 ChEBI	tween 80	-	degradation
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
68138	15318 ChEBI	xanthine	-	nitrogen source
68138	17151 ChEBI	xylitol	-	carbon source
69320	18222 ChEBI	xylose	+	growth

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68138	16136 ChEBI	hydrogen sulfide
68138	89634 ChEBI	melanin

Enzymes

@ref	Value	Activity	Ec
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-glucosidase	+	3.2.1.21	from API zym
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
68138	catalase	+	1.11.1.6
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	-		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68379	urease	-	3.5.1.5	from API Coryne
68382	valine arylamidase	+		from API zym

Fatty acid profile

Metadata FA analysis

@ref

68138

Fatty acid	Percentage
C16:0 iso	54.8
C16:1 iso H	24
C15:0 iso	6.9
C14:0 iso	3.9
C16:1 w7c/C16:1 w6c	2.7
C17:1 w8c	1.5
C18:1 w9c	1.3
C17:0 10-methyl	0.8
C17:1 w9c iso/C16:0 10-methyl	0.7
C18:0 iso	0.7
C16:0	0.6
C17:0 iso	0.5
C18:0	0.4
C15:1 iso H/C13:0 3OH	0.4
C15:0 anteiso	0.3
C15:1 w6c	0.3
C14:0	0.3

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
69320	-	-	-	+	-	-	+	-	-	-	-	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
69320	not determinedn.d.	+/-	+	+	+/-	+	+	+/-	+/-	-	+/-	+/-	-	-	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Host	#Invertebrates (Other)	#Porifera (Sponges)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
65896	marine sponge	Hainan Province, Xisha Islands, Chinese Exclusive Economic Zone (16° 45' N, 112° 21' E)	China	CHN	Asia	16.75	112.35 16.75/112.35
68138	Tissues of sponge Leucetta chagosensi		China	CHN	Asia	16.75	112.35 16.75/112.35

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
68138	ASM342864v1 assembly for Geodermatophilus sp. LHW52908	scaffold	GCA_003428645	2303986.3	2834224877	2303986	62.87

Genome browser: GCA_003428645

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
65896	Geodermatophilus sp. strain LHW52908 16S ribosomal RNA gene, partial sequence	MG200147	1467		52020

GC content

@ref	GC-content (mol%)	Method
68138	75.6	genome sequence analysis
65896	75.6	sequence analysis

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Geodermatophilus sp. LHW52908
NCBI: GCA_003428645

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	52.30	no
125439	motility	BacteriaNetⓘ	no	68.40	no
125439	gram_stain	BacteriaNetⓘ	positive	99.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.90	no

Predictions from Diaspora project based on:
Geodermatophilus sp. LHW52908 LHW52908
NCBI: GCA_003428645.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.78	no
125438	anaerobic	anaerobicⓘ	no	96.77	no
125438	aerobic	aerobicⓘ	yes	87.81	no
125438	spore-forming	spore-formingⓘ	yes	63.49	no
125438	thermophilic	thermophileⓘ	no	94.33	yes
125438	flagellated	motile2+ⓘ	no	62.83	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Geodermatophilus marinus sp. nov., isolated from the marine sponge Leucetta chagosensis.	Li L, Zhang D, Tang WZ, Lin HW, Lu YH.	Int J Syst Evol Microbiol	10.1099/ijsem.0.003478	2019

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 )
#65896	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 106570
#68138	Lei Li, Die Zhang, Wei-zhuo Tang, Hou-wen Lin and Yan-hua Lu: Geodermatophilus marinus sp. nov., isolated from the marine sponge Leucetta chagosensis. IJSEM 69: 2966 - 2971 2019 ( DOI 10.1099/ijsem.0.003478 )
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#69320	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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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Geodermatophilus marinus (DSM 106570, CCTCC AA 2018014, LHW52908)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Metabolite utilization

Metabolite production

Enzymes

Fatty acid profile?

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003428645

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media

Fatty acid profile