Geodermatophilus nigrescens (DSM 45408, CCTCC AA 2011015, JCM 18056)

Name: Geodermatophilus nigrescens (DSM 45408, CCTCC AA 2011015, JCM 18056)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5824

Type strain

Culture col. no. DSM 45408 CCTCC AA 2011015 JCM 18056 YIM 75980

NCBI tax ID(s) 1070870

Special Collections DSMZ JCM

Links

Geodermatophilus nigrescens DSM 45408 is a mesophilic prokaryote that was isolated from soil from a dry-hot river valley.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 399992

JCM 18056,DSM 45408

@ref 20215

Last LPSN update 2025-12-16 09:48:10

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Geodermatophilales

Family Geodermatophilaceae

Genus Geodermatophilus

Species Geodermatophilus nigrescens

Full scientific name Geodermatophilus nigrescens Nie et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	98.4

Multimedia

@ref:	16686
multimedia content:	DSM_45408.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45408.jpg
caption:	Medium 65 37°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
16686	GPHF-MEDIUM (DSMZ Medium 553)	Medium recipe at MediaDive	Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
16686	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
16686	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)	Range
16686	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	90.625
125439	obligate aerobe	99.9

Observation

67770

Observationquinones: MK-9(H₄)

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#River (Creek)
#Environmental	#Terrestrial	#Soil
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16686	soil from a dry-hot river valley	Yunnan Province, Dongchuan county	China	CHN	Asia
67770	Soil from dry-hot river valley in Dongchuan county	Yunnan Province, south-west China	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence JN656711 (>99% sequence identity) for Geodermatophilus nigrescens from Microbeatlas

Aquatic Samples	471
Soil Samples	5007
Animal Samples	973
Plant Samples	1373
Total Samples	7824

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16686	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 2695420953 annotated assembly for Geodermatophilus nigrescens DSM 45408	scaffold	GCA_900129495	1070870.3	2695420953	1070870	74.11

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Geodermatophilus nigrescens strain YIM 75980 16S ribosomal RNA gene, partial sequence	JN188947	1524		1070870
16686	Geodermatophilus nigrescens strain YIM 75980 16S ribosomal RNA gene, partial sequence	JN656711	1524		1070870

GC content

@ref	GC-content (mol%)	Method
16686	73.1	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 nigrescens DSM 45408
NCBI: GCA_900129495

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	72.00	no
125439	motility	BacteriaNetⓘ	no	61.50	no
125439	gram_stain	BacteriaNetⓘ	positive	98.40	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 nigrescens strain DSM 45408
PATRIC: 1070870.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.86	no
125438	anaerobic	anaerobicⓘ	no	97.34	no
125438	spore-forming	spore-formingⓘ	yes	63.25	no
125438	aerobic	aerobicⓘ	yes	90.63	no
125438	thermophilic	thermophileⓘ	no	96.50	yes
125438	flagellated	motile2+ⓘ	no	64.50	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
	Testing the Luedemann hypothesis: the discovery of novel antimicrobials from slow-growing microbes from nutrient-limited environments.	Lin B, Woo S, Philbrick A, Bacsa J, Laskey E, Mehra N, Gondil VS, Mei JA, Jones G, Pavelka MS, Dziejman M, Shutter DA, Melander C, Perritt AM, Jakober R, Shen Y, Chang W-C, Quave CL, Dunman PM, Luedemann G.	mSphere	10.1128/msphere.00367-25	2025
Enzymology	Evolution and separation of actinobacterial pyranose and C-glycoside-3-oxidases.	Kostelac A, Taborda A, Martins LO, Haltrich D.	Appl Environ Microbiol	10.1128/aem.01676-23	2024
Phylogeny	Ubiquity, diversity and physiological characteristics of Geodermatophilaceae in Shapotou National Desert Ecological Reserve.	Sun HM, Zhang T, Yu LY, Sen K, Zhang YQ.	Front Microbiol	10.3389/fmicb.2015.01059	2015
	Psi-Footprinting approach for the identification of protein synthesis inhibitor producers.	Handel F, Kulik A, Wex KW, Berscheid A, Saur JS, Winkler A, Wibberg D, Kalinowski J, Brotz-Oesterhelt H, Mast Y	NAR Genom Bioinform	10.1093/nargab/lqac055	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 tzadiensis sp. nov., a UV radiation-resistant bacterium isolated from sand of the Saharan desert.	Montero-Calasanz Mdel C, Goker M, Broughton WJ, Cattaneo A, Favet J, Potter G, Rohde M, Sproer C, Schumann P, Klenk HP, Gorbushina AA.	Syst Appl Microbiol	10.1016/j.syapm.2012.12.005	2013
Phylogeny	Geodermatophilus siccatus sp. nov., isolated from arid sand of the Saharan desert in Chad.	del Carmen Montero-Calasanz M, Goker M, Rohde M, Schumann P, Potter G, Sproer C, Gorbushina AA, Klenk HP.	Antonie Van Leeuwenhoek	10.1007/s10482-012-9824-x	2013
Phylogeny	Geodermatophilus telluris sp. nov., an actinomycete isolated from Saharan desert sand.	Montero-Calasanz MDC, Goker M, Potter G, Rohde M, Sproer C, Schumann P, Klenk HP, Gorbushina AA	Int J Syst Evol Microbiol	10.1099/ijs.0.046888-0	2012
Phylogeny	Geodermatophilus nigrescens sp. nov., isolated from a dry-hot valley.	Nie GX, Ming H, Li S, Zhou EM, Cheng J, Yu TT, Zhang J, Feng HG, Tang SK, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-012-9696-0	2012

References

#16686	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45408
#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 )
#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 nigrescens (DSM 45408, CCTCC AA 2011015, JCM 18056)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900129495

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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