Name: Geodermatophilus nigrescens DSM 45408
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5824

Type strain:

Species: Geodermatophilus nigrescens

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

Strain history: S.-K. Tang YIM 75980.

NCBI tax ID(s): 1070870 (species)

SI-ID 399992

DSM 45408

Section

Geodermatophilus nigrescens DSM 45408 is a mesophilic, Gram-positive bacterium that was isolated from soil from a dry-hot river valley.

Gram-positive
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 nigrescens**
	Full Scientific Name (LPSN)	Geodermatophilus nigrescens Nie et al. 2012

Information on morphological and physiological properties Morphology

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

Multimedia content

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Caption:

Medium 65 37°C

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

GPHF-MEDIUM (DSMZ Medium 553)

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

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Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

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Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #16686]			growth	37 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #16686]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

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Ability of spore formation

no Confidence in %95.544

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Observation

quinones: MK-9(H₄)

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

[Ref.: #16686]	Sample type/isolated from	soil from a dry-hot river valley
[Ref.: #16686]	Geographic location (country and/or sea, region)	Yunnan Province, Dongchuan county
[Ref.: #16686]	Country	China
[Ref.: #16686]	Country ISO 3 Code	CHN
[Ref.: #16686]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil from dry-hot river valley in Dongchuan county
[Ref.: #67770]	Geographic location (country and/or sea, region)	Yunnan Province, south-west China
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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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

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

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Biosafety level

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.: #16686]	Geodermatophilus nigrescens strain YIM 75980 16S ribosomal RNA gene, partial sequence	JN656711	1524	ENA	1070870 tax ID
[Ref.: #20218]	Geodermatophilus nigrescens strain YIM 75980 16S ribosomal RNA gene, partial sequence	JN188947	1524	ENA	1070870 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Geodermatophilus nigrescens DSM 45408	GCA_900129495	scaffold	GenBank	1070870 tax ID
[Ref.: #66792]	Geodermatophilus nigrescens strain DSM 45408	1070870.3	wgs	PATRIC	1070870 tax ID	*
[Ref.: #66792]	Geodermatophilus nigrescens DSM 45408	2695420953	draft	JGI IMG/M	1070870 tax ID	*

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GC-content

73.1 mol%

high performance liquid chromatography (HPLC)

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 nigrescens DSM 45408 NCBI: GCA_900129495.1
[Ref.: #69481]	spore-forming	yes	65	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Geodermatophilus nigrescens strain DSM 45408 PATRIC: 1070870.3
[Ref.: #69480]	motile	yes	77.955	no
[Ref.: #69480]	flagellated	no	92.089	no
[Ref.: #69480]	gram-positive	yes	93.589	no
[Ref.: #69480]	anaerobic	no	99.071	no
[Ref.: #69480]	aerobic	yes	91.252	no
[Ref.: #69480]	halophile	no	92.957	no
[Ref.: #69480]	spore-forming	no	68.882	no
[Ref.: #69480]	thermophile	no	99.047	no
[Ref.: #69480]	glucose-util	yes	87.862	no
[Ref.: #69480]	glucose-ferment	no	91.086	no

Availability in culture collections External links

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Culture collection no.

DSM 45408, CCTCC AA 2011015, JCM 18056, YIM 75980

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SI-ID 399992

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*
	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	*

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 )

#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) .

#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 )

#75306

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-ID399992.1 )

* These data were automatically processed and therefore are not curated

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Geodermatophilus nigrescens DSM 45408

Geodermatophilus nigrescens strain DSM 45408

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