Geodermatophilus amargosae (DSM 46136, ATCC 25081, CBS 236.69)

Name: Geodermatophilus amargosae (DSM 46136, ATCC 25081, CBS 236.69)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5818

Type strain

Strain Designation G12, G96

Culture col. no. DSM 46136 ATCC 25081 CBS 236.69 CCUG 62971 IFO 13316 11 more

NCBI tax ID(s) 1296565

Special Collections DSMZ CCUG JCM KCTC

Links

Geodermatophilus amargosae G12 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from desert soil.

Gram-positive aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 125967

ATCC 25081,DSM 46136,IFO 13316,IMET 9240,JCM 3153,NRRL B-3578,CBS 236.69,KCTC 9360,NBRC 13316,CCUG 62971

@ref 20215

Last LPSN update 2025-12-16 09:48:09

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Geodermatophilales

Family Geodermatophilaceae

Genus Geodermatophilus

Species Geodermatophilus amargosae

Full scientific name Geodermatophilus amargosae Montero-Calasanz et al. 2014

Synonyms (1)

"Geodermatophilus obscurus subsp. amargosae"

Morphology

Cell morphology

@ref	Gram stain	Confidence
67771	positive
125439	positive	99

Colony morphology

62920

Incubation period6-10 days

Multimedia

@ref:	66793
multimedia content:	EM_DSM_46136_1.jpg
multimedia.multimedia content:	EM_DSM_46136_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_46136_2.jpg
multimedia.multimedia content:	EM_DSM_46136_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_46136_3.jpg
multimedia.multimedia content:	EM_DSM_46136_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_46136_4.jpg
multimedia.multimedia content:	EM_DSM_46136_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_46136_5.jpg
multimedia.multimedia content:	EM_DSM_46136_5.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_46136_6.jpg
multimedia.multimedia content:	EM_DSM_46136_6.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
12459	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)	Range
12459	positive	growth	28	mesophilic
62920	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic
67771	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
62920	aerobe
67771	aerobe
125439	obligate aerobe	99.8

Compound production

20216

CompoundActinorhodin

Observation

67770

Observationquinones: MK-9(H₄)

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Sampling date
12459	desert soil	Nevada, Amargosa Desert	USA	USA	North America
62920	Soil,desert		USA	USA	North America	1976
67770	Soil, Amargosa Desert	NV	USA	USA	North America
67771	From soil	Amargosa desert	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence HF679056 (>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
12459	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	IMG-taxon 2599185195 annotated assembly for Geodermatophilus amargosae DSM 46136	scaffold	GCA_900116515	1296565.3	2599185195	1296565	62.52

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
12459	Geodermatophilus amargosae partial 16S rRNA gene, strain DSM 46136, isolate G96	HF679056	1513		1296565

GC content

@ref	GC-content (mol%)	Method
12459	73.0	high performance liquid chromatography (HPLC)
67770	73	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Geodermatophilus amargosae DSM 46136
NCBI: GCA_900116515

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	64.60	no
125439	motility	BacteriaNetⓘ	no	66.40	no
125439	gram_stain	BacteriaNetⓘ	positive	99.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Geodermatophilus amargosae strain DSM 46136
PATRIC: 1296565.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.44	yes
125438	anaerobic	anaerobicⓘ	no	98.23	yes
125438	spore-forming	spore-formingⓘ	yes	67.02	no
125438	aerobic	aerobicⓘ	yes	89.08	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
Enzymology	Biochemical Characterization of Pyranose Oxidase from Streptomyces canus-Towards a Better Understanding of Pyranose Oxidase Homologues in Bacteria.	Kostelac A, Sutzl L, Puc J, Furlanetto V, Divne C, Haltrich D.	Int J Mol Sci	10.3390/ijms232113595	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 aquaeductus sp. nov., isolated from the ruins of Hadrian's aqueduct.	Hezbri K, Ghodhbane-Gtari F, Del Carmen Montero-Calasanz M, Sghaier H, Rohde M, Sproer C, Schumann P, Klenk HP, Gtari M.	Antonie Van Leeuwenhoek	10.1007/s10482-015-0461-z	2015
Phylogeny	Description of Geodermatophilus amargosae sp. nov., to accommodate the not validly named Geodermatophilus obscurus subsp. amargosae (Luedemann, 1968).	Montero-Calasanz Mdel C, Goker M, Rohde M, Sproer C, Schumann P, Mayilraj S, Goodfellow M, Klenk HP	Curr Microbiol	10.1007/s00284-013-0479-2	2013

References

#12459	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 46136
#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 )
#20216	Curators of the HKI: Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) . Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI):
#62920	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 62971
#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;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 amargosae (DSM 46136, ATCC 25081, CBS 236.69)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Compound production

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900116515

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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