Geodermatophilus normandii (DSM 45417, CCUG 62814, MTCC 11412)

Name: Geodermatophilus normandii (DSM 45417, CCUG 62814, MTCC 11412)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24057

Type strain

Strain Designation CF5/3

Culture col. no. DSM 45417 CCUG 62814 MTCC 11412 CF5/3 JCM 30064

NCBI tax ID(s) 1137989

Special Collections DSMZ CCUG JCM Literature strains

History <- A. Gorbushina, Bundesanstalt für Materialforschung und -prüfung, Berlin; CF5/3 MTCC 11412 <-- A. A. Gorbushina CF5/3.

Links

Geodermatophilus normandii CF5/3 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from desert sand.

spore-forming Gram-positive motile aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 398540

DSM 45417,CCUG 62814

@ref 20215

Last LPSN update 2026-02-09 11:23:52

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Geodermatophilales

Family Geodermatophilaceae

Genus Geodermatophilus

Species Geodermatophilus normandii

Full scientific name Geodermatophilus normandii Montero-Calasanz et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Motility	Confidence
31067	positive
125439	positive		99

Colony morphology

62905

Incubation period2-3 days

Pigmentation

31067

Productionyes

Multimedia

@ref:	66793
multimedia content:	EM_DSM_45417_1.jpg
multimedia.multimedia content:	EM_DSM_45417_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_45417_2.jpg
multimedia.multimedia content:	EM_DSM_45417_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_45417_3.jpg
multimedia.multimedia content:	EM_DSM_45417_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_45417_4.jpg
multimedia.multimedia content:	EM_DSM_45417_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_45417_5.jpg
multimedia.multimedia content:	EM_DSM_45417_5.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20582	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
20582	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)
20582	positive	growth	28
31067	positive	growth	15-40
62905	positive	growth	30-37
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
31067	positive	growth	6.0-10.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31067	aerobe
62905	aerobe
125438	aerobe	90.185
125439	obligate aerobe	99.9

Spore formation

31067

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31067	NaCl	positive	growth	0-1 %

Observation

@ref	Observation
31067	aggregates in clumps
67770	quinones: MK-9(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31067	30089 ChEBI	acetate	+	carbon source
31067	35391 ChEBI	aspartate	+	carbon source
31067	17057 ChEBI	cellobiose	+	carbon source
31067	23652 ChEBI	dextrin	+	carbon source
31067	15740 ChEBI	formate	+	carbon source
31067	28757 ChEBI	fructose	+	carbon source
31067	28260 ChEBI	galactose	+	carbon source
31067	24265 ChEBI	gluconate	+	carbon source
31067	17234 ChEBI	glucose	+	carbon source
31067	32323 ChEBI	glucuronamide	+	carbon source
31067	29987 ChEBI	glutamate	+	carbon source
31067	17754 ChEBI	glycerol	+	carbon source
31067	17596 ChEBI	inosine	+	carbon source
31067	25115 ChEBI	malate	+	carbon source
31067	17306 ChEBI	maltose	+	carbon source
31067	37684 ChEBI	mannose	+	carbon source
31067	37657 ChEBI	methyl D-glucoside	+	carbon source
31067	51850 ChEBI	methyl pyruvate	+	carbon source
31067	17272 ChEBI	propionate	+	carbon source
31067	26546 ChEBI	rhamnose	+	carbon source
31067	17822 ChEBI	serine	+	carbon source
31067	17992 ChEBI	sucrose	+	carbon source
31067	27082 ChEBI	trehalose	+	carbon source
31067	53423 ChEBI	tween 40	+	carbon source

Enzymes

@ref	Value	Activity	Ec
31067	alkaline phosphatase	+	3.1.3.1
31067	catalase	+	1.11.1.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Desert
#Environmental	#Terrestrial	#Sandy
#Condition	#Xerophilic	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Sampling date
20582	desert sand	Sahara, Ouré Cassoni (15° 42' 44'' N 23° 3' 1'' E)	Chad	TCD	Africa	15.7122	23.0503 15.7122/23.0503
62905	Sand,desert	near Ouré Cussoni	Chad	TCD	Africa			2007
67770	Sand of the Sahara Desert in Ouré Cassoni		Chad	TCD	Africa

Taxonmaps

69479

Global distribution of 16S sequence HE654546 (>99% sequence identity) for Geodermatophilus from Microbeatlas

Aquatic Samples	408
Soil Samples	4562
Animal Samples	721
Plant Samples	1119
Total Samples	6810

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20582	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM318248v1 assembly for Geodermatophilus normandii DSM 45417	contig	GCA_003182485	1137989.5	2585427554	1137989	77.52

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20582	Geodermatophilus normandii partial 16S rRNA gene, culture collection DSM:45417, type strain CF 5/3T	HE654546	1469		1137989

GC content

@ref	GC-content (mol%)	Method
20582	75.5	high performance liquid chromatography (HPLC)
31067	75.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Geodermatophilus normandii DSM 45417
NCBI: GCA_003182485

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	69.10	no
125439	motility	BacteriaNetⓘ	no	65.00	no
125439	gram_stain	BacteriaNetⓘ	positive	99.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Geodermatophilus normandii strain DSM 45417
PATRIC: 1137989.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.81	no
125438	anaerobic	anaerobicⓘ	no	97.32	yes
125438	spore-forming	spore-formingⓘ	yes	65.36	yes
125438	aerobic	aerobicⓘ	yes	90.19	yes
125438	thermophilic	thermophileⓘ	no	95.58	yes
125438	flagellated	motile2+ⓘ	no	64.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Draft Genomes Sequences of 11 Geodermatophilaceae Strains Isolated from Building Stones from New England and Indian Stone Ruins found at historic sites in Tamil Nadu, India.	Ennis NJ, Dharumadurai D, Sevigny JL, Wilmot R, Alnaimat SM, Bryce JG, Thomas WK, Tisa LS.	J Genomics	10.7150/jgen.76121	2022
Phylogeny	Geodermatophilus maliterrae sp. nov., a member of the Geodermatophilaceae isolated from badland surfaces in the Red Desert, Wyoming, USA.	Ben Tekaya S, Nouioui I, Flores GM, Neumann-Schaal M, Bredoire F, Basile F, van Diepen LTA, Ward NL.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006603	2024
Phylogeny	Geodermatophilus daqingensis sp. nov., isolated from petroleum-contaminated soil.	Wang Y, Zhang L, Zhang X, Huang J, Zhao Y, Zhao Y, Liu J, Huang C, Wang J, Hu Y, Ren G, Xu X	Antonie Van Leeuwenhoek	10.1007/s10482-017-0853-3	2017
Phylogeny	Geodermatophilus normandii sp. nov., isolated from Saharan desert sand.	Montero-Calasanz MDC, Goker M, Potter G, Rohde M, Sproer C, Schumann P, Gorbushina AA, Klenk HP	Int J Syst Evol Microbiol	10.1099/ijs.0.051201-0	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 )
#20582	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45417
#27396	IJSEM 3437 2013 ( DOI 10.1099/ijs.0.051201-0 , PubMed 23543496 )
#31067	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 #27396
#62905	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 62814
#66793	Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )
#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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Geodermatophilus normandii (DSM 45417, CCUG 62814, MTCC 11412)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003182485

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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