Geodermatophilus dictyosporus G-5 | Type strain | DSM 43161, ATCC 25080, CBS 234.69, CCUG 62970, IFO 13317, KCC A-0154, MTCC 11558, NBRC 13317, NBRC 1331, JCM 3154, IMET 9241, IMSNU 22090, KCTC 9074, NRRL B-3579, RIA 945, VKM Ac-659 | BacDiveID:5816

Strain identifier

BacDive ID: 5816

Type strain:

Species: Geodermatophilus dictyosporus

Strain Designation: G-5

Culture col. no.: DSM 43161, ATCC 25080, CBS 234.69, CCUG 62970, IFO 13317, KCC A-0154, MTCC 11558, NBRC 13317, NBRC 1331, JCM 3154, IMET 9241, IMSNU 22090, KCTC 9074, NRRL B-3579, RIA 945, VKM Ac-659

Strain history: KCC A-0154 <-- G. M. Luedemann G-5.

NCBI tax ID(s): 1523247 (species)

SI-ID 265321

ATCC 25080, DSM 43161, IFO 13317, JCM 3154, IMET 9241, KCTC 9074, NRRL B-3579, VKM Ac-659, CBS 234.69, NBRC 13317, KACC 20038, CBS234.19

Other strains from Geodermatophilus dictyosporus

G. dictyosporus G16, DSM 44208

Section

Geodermatophilus dictyosporus G-5 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

Gram-positive
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 dictyosporus**
	Full Scientific Name (LPSN)	Geodermatophilus dictyosporus Montero-Calasanz et al. 2015

Synonym

"Geodermatophilus obscurus subsp. dictyosporus"

Information on morphological and physiological properties Morphology

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

Incubation period

6-10 days

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

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

Culture medium

CZAPEK PEPTONE AGAR (DSMZ Medium 83)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #10829]			growth	28 °C
[Ref.: #62919]			growth	30 °C
[Ref.: #67770]			growth	28 °C

[Ref.: #10829]	Temperature range	mesophilic
[Ref.: #62919]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

Oxygen tolerance

aerobe

Observation

quinones: MK-9(H₄)

	Pathway	Enzyme coverage	Annotated reactions	External links
	Pathway annotation	Computationally determined by
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	myo-inositol biosynthesis	100	10 of 10
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	arginine metabolism	75	18 of 24
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	tryptophan metabolism	73.68	28 of 38
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	lysine metabolism	66.67	28 of 42
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	allantoin degradation	66.67	6 of 9
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	oxidative phosphorylation	64.84	59 of 91
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	carotenoid biosynthesis	63.64	14 of 22
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	creatinine degradation	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	58.82	10 of 17
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	androgen and estrogen metabolism	56.25	9 of 16
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	lipid A biosynthesis	55.56	5 of 9
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	grixazone biosynthesis	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	degradation of sugar acids	40	10 of 25
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
[Ref.: #66794]	daunorubicin biosynthesis	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #10829]	Sample type/isolated from	soil
[Ref.: #10829]	Geographic location (country and/or sea, region)	California, Westgard Pass
[Ref.: #10829]	Country	USA
[Ref.: #10829]	Country ISO 3 Code	USA
[Ref.: #10829]	Continent	North America

[Ref.: #62919]	Sample type/isolated from	Soil,desert
[Ref.: #62919]	Sampling date	1989
[Ref.: #62919]	Geographic location (country and/or sea, region)	California,Westgard Pass
[Ref.: #62919]	Country	USA
[Ref.: #62919]	Country ISO 3 Code	USA
[Ref.: #62919]	Continent	North America

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Westgard Pass, CA
[Ref.: #67770]	Country	USA
[Ref.: #67770]	Country ISO 3 Code	USA
[Ref.: #67770]	Continent	North America
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

Global distribution of 16S sequence X92355 (>99% sequence identity) for Geodermatophilus from Microbeatlas

Aquatic Samples	58
Soil Samples	565
Animal Samples	210
Plant Samples	37
Total Samples	870

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.: #67770]	Geodermatophilus obscurus dictyosporus 16S ribosomal RNA (16S rRNA) gene	L40621	1411	ENA	1523247 tax ID
[Ref.: #10829]	Geodermatophilus dictyosporus partial 16S rRNA gene, type strain G-5T	HF970584	1517	ENA	1523247 tax ID
[Ref.: #20218]	Geodermatophilus obscurus subsp. dictyosporus 16S ribosomal RNA (strain DSM43161)	X92355	1469	ENA	1523247 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Geodermatophilus obscurus DSM 43161	GCA_900115395	scaffold	GenBank	1861 tax ID
[Ref.: #66792]	Geodermatophilus obscurus strain DSM 43161	1861.3	wgs	PATRIC	1861 tax ID	*
[Ref.: #66792]	Geodermatophilus dictyosporus DSM 43161	2599185183	draft	JGI IMG/M	1861 tax ID	*

[Ref.: #10829]	GC-content	75.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	74.4 mol%	thermal denaturation, midpoint method (Tm)

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 obscurus DSM 43161 NCBI: GCA_900115395.1
[Ref.: #69481]	spore-forming	no	58	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Geodermatophilus obscurus strain DSM 43161 PATRIC: 1861.3
[Ref.: #69480]	motile	yes	80.85	no
[Ref.: #69480]	gram-positive	yes	90.647	no
[Ref.: #69480]	anaerobic	no	99.072	no
[Ref.: #69480]	aerobic	yes	91.858	yes
[Ref.: #69480]	halophile	no	86.438	no
[Ref.: #69480]	spore-forming	no	62.646	no
[Ref.: #69480]	glucose-util	yes	88.042	no
[Ref.: #69480]	flagellated	no	91.966	no
[Ref.: #69480]	thermophile	no	99.21	no
[Ref.: #69480]	glucose-ferment	no	86.776	no

Availability in culture collections External links

Culture collection no.

DSM 43161, ATCC 25080, CBS 234.69, CCUG 62970, IFO 13317, KCC A-0154, MTCC 11558, NBRC 13317, NBRC 1331, JCM 3154, IMET 9241, IMSNU 22090, KCTC 9074, NRRL B-3579, RIA 945, VKM Ac-659

SI-ID 265321

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description of gamma radiation-resistant Geodermatophilus dictyosporus sp. nov. to accommodate the not validly named Geodermatophilus obscurus subsp. dictyosporus (Luedemann, 1968).	Montero-Calasanz Mdel C, Hezbri K, Goker M, Sghaier H, Rohde M, Sproer C, Schumann P, Klenk HP	Extremophiles	10.1007/s00792-014-0708-z	2014	*

References

#10829

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 43161

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#62919 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 62970

#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 )

#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 .

#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 )

#75298

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-ID265321.1 )

* These data were automatically processed and therefore are not curated

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