Geodermatophilus normandii CF5/3 | Type strain | DSM 45417, CCUG 62814, MTCC 11412, JCM 30064 | BacDiveID:24057

Strain identifier

BacDive ID: 24057

Type strain:

Species: Geodermatophilus normandii

Strain Designation: CF5/3

Culture col. no.: DSM 45417, CCUG 62814, MTCC 11412, JCM 30064

Strain history: MTCC 11412 <-- A. A. Gorbushina CF5/3.

NCBI tax ID(s): 1137989 (species)

SI-ID 398540

DSM 45417, CCUG 62814

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Geodermatophilales*
	Family	*Geodermatophilaceae*
	Genus	*Geodermatophilus*
	Species	**Geodermatophilus normandii**
	Full Scientific Name (LPSN)	Geodermatophilus normandii Montero-Calasanz et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #31067]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #31067]	Motility	yes

Incubation period

2-3 days

Pigment production

yes

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

R2A MEDIUM (DSMZ Medium 830)

Culture medium growth

Culture medium link

Medium recipe provided by DSMZ

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #20582]			growth	28 °C
[Ref.: #31067]			growth	15-40 °C
[Ref.: #62905]			growth	30-37 °C
[Ref.: #67770]			growth	28 °C

[Ref.: #20582]	Temperature range	mesophilic
[Ref.: #62905]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31067]			growth	6.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31067]	Oxygen tolerance	aerobe
[Ref.: #62905]	Oxygen tolerance	aerobe

Ability of spore formation

yes

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31067]		NaCl		growth	0-1	%

[Ref.: #31067]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: MK-9(H₄)

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31067]		acetate ChEBI	+	carbon source
[Ref.: #31067]		aspartate ChEBI	+	carbon source
[Ref.: #31067]		cellobiose ChEBI	+	carbon source
[Ref.: #31067]		dextrin ChEBI	+	carbon source
[Ref.: #31067]		formate ChEBI	+	carbon source
[Ref.: #31067]		fructose ChEBI	+	carbon source
[Ref.: #31067]		galactose ChEBI	+	carbon source
[Ref.: #31067]		gluconate ChEBI	+	carbon source
[Ref.: #31067]		glucose ChEBI	+	carbon source
[Ref.: #31067]		glucuronamide ChEBI	+	carbon source
[Ref.: #31067]		glutamate ChEBI	+	carbon source
[Ref.: #31067]		glycerol ChEBI	+	carbon source
[Ref.: #31067]		inosine ChEBI	+	carbon source
[Ref.: #31067]		malate ChEBI	+	carbon source
[Ref.: #31067]		maltose ChEBI	+	carbon source
[Ref.: #31067]		mannose ChEBI	+	carbon source
[Ref.: #31067]		methyl D-glucoside ChEBI	+	carbon source
[Ref.: #31067]		methyl pyruvate ChEBI	+	carbon source
[Ref.: #31067]		propionate ChEBI	+	carbon source
[Ref.: #31067]		rhamnose ChEBI	+	carbon source
[Ref.: #31067]		serine ChEBI	+	carbon source
[Ref.: #31067]		sucrose ChEBI	+	carbon source
[Ref.: #31067]		trehalose ChEBI	+	carbon source
[Ref.: #31067]		tween 40 ChEBI	+	carbon source
		Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31067]		alkaline phosphatase	+	3.1.3.1
[Ref.: #31067]		catalase	+	1.11.1.6

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #20582]	Sample type/isolated from	desert sand
[Ref.: #20582]	Geographic location (country and/or sea, region)	Sahara, Ouré Cassoni (15° 42' 44'' N 23° 3' 1'' E)
[Ref.: #20582]	Country	Chad
[Ref.: #20582]	Country ISO 3 Code	TCD
[Ref.: #20582]	Continent	Africa
[Ref.: #20582]	Geographic location	15.7122°/23.0503°

[Ref.: #62905]	Sample type/isolated from	Sand,desert
[Ref.: #62905]	Sampling date	2007
[Ref.: #62905]	Geographic location (country and/or sea, region)	near Ouré Cussoni
[Ref.: #62905]	Country	Chad
[Ref.: #62905]	Country ISO 3 Code	TCD
[Ref.: #62905]	Continent	Africa

[Ref.: #67770]	Sample type/isolated from	Sand of the Sahara Desert in Ouré Cassoni
[Ref.: #67770]	Country	Chad
[Ref.: #67770]	Country ISO 3 Code	TCD
[Ref.: #67770]	Continent	Africa
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Desert
#Environmental	#Terrestrial	#Sandy
#Condition	#Xerophilic	-

What are isolation sources categories?

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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

Biosafety level

1

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20582]	Geodermatophilus normandii partial 16S rRNA gene, culture collection DSM:45417, type strain CF 5/3T	HE654546	1469	ENA	1137989 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Geodermatophilus normandii DSM 45417	GCA_003182485	contig	GenBank	1137989 tax ID
[Ref.: #66792]	Geodermatophilus normandii strain DSM 45417	1137989.5	wgs	PATRIC	1137989 tax ID	*
[Ref.: #66792]	Geodermatophilus normandii DSM 45417	2585427554	draft	JGI IMG/M	1137989 tax ID	*

[Ref.: #20582]	GC-content	75.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #31067]	GC-content	75.5 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Geodermatophilus normandii strain DSM 45417 PATRIC: 1137989.5
[Ref.: #69481]	spore-forming	yes	83	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Geodermatophilus normandii strain DSM 45417 PATRIC: 1137989.5
[Ref.: #69480]	motile	yes	76.437	yes
[Ref.: #69480]	flagellated	no	92.286	no
[Ref.: #69480]	gram-positive	yes	93.687	no
[Ref.: #69480]	anaerobic	no	99.006	yes
[Ref.: #69480]	aerobic	yes	95.006	yes
[Ref.: #69480]	halophile	no	91.157	no
[Ref.: #69480]	spore-forming	no	65.513	yes
[Ref.: #69480]	glucose-util	yes	88.31	yes
[Ref.: #69480]	glucose-ferment	no	90.273	no
[Ref.: #69480]	thermophile	no	98.047	no

Availability in culture collections External links

Culture collection no.

DSM 45417, CCUG 62814, MTCC 11412, JCM 30064

SI-ID 398540

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
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

#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 (see below)

#62905 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 62814

#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) .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#88028

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-ID398540.1 )

#27396

IJSEM 3437 2013 ( DOI 10.1099/ijs.0.051201-0 , PubMed 23543496 )

* These data were automatically processed and therefore are not curated

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