Archive BacDiveID:10.13145/bacdive5821.20230509.8.1

Strain identifier

BacDive ID: 5821

Type strain:

Species: Geodermatophilus siccatus

Strain Designation: CF6/1

Strain history: MTCC 11414 <-- A. A. Gorbushina CF6/1.

NCBI tax ID(s): 1137991 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 16551

BacDive-ID: 5821

DSM-Number: 45419

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive

description: Geodermatophilus siccatus CF6/1 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from desert sand.

NCBI tax id

NCBI tax id: 1137991
Matching level: species

strain history

@ref	history
16551	<- A. Gorbushina, Bundesanstalt für Materialforschung und -prüfung, Berlin; CF6/1
67770	MTCC 11414 <-- A. A. Gorbushina CF6/1.

doi: 10.13145/bacdive5821.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/actinomycetota
domain: Bacteria
phylum: Actinomycetota
class: Actinomycetes
order: Geodermatophilales
family: Geodermatophilaceae
genus: Geodermatophilus
species: Geodermatophilus siccatus
full scientific name: Geodermatophilus siccatus Montero-Calasanz et al. 2013

@ref: 16551

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Geodermatophilaceae

genus: Geodermatophilus

species: Geodermatophilus siccatus

full scientific name: Geodermatophilus siccatus Montero-Calasanz et al. 2013 emend. Montero-Calasanz et al. 2017

strain designation: CF6/1

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: positive
confidence: 100

colony morphology

@ref: 62898
incubation period: 3-4 days

multimedia

@ref	multimedia content	caption	intellectual property rights
66793	EM_DSM_45419_1.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_45419_2.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_45419_3.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_45419_4.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_45419_5.jpg	electron microscopic image	© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
16551	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	yes	https://mediadive.dsmz.de/medium/65	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
16551	R2A MEDIUM (DSMZ Medium 830)	yes	https://mediadive.dsmz.de/medium/830	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
16551	positive	growth	28	mesophilic
62898	positive	growth	30-37	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

oxygen tolerance

@ref: 62898
oxygen tolerance: aerobe

spore formation

@ref: 69480
spore formation: no
confidence: 92.531

observation

@ref: 67770
observation: quinones: MK-9(H₄)

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent	sampling date
16551	desert sand	Sahara, near Ourba	Chad	TCD	Africa
62898	Sand,desert	Ourba,Sahara Desert	Chad	TCD	Africa	2007
67770	Sand of the Sahara Desert near to Ourba		Chad	TCD	Africa

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Desert
#Environmental	#Terrestrial	#Sandy
#Condition	#Xerophilic

taxonmaps

@ref: 69479
File name: preview.99_5352.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_2039;97_3177;98_3990;99_5352&stattab=map
Last taxonomy: Geodermatophilus
16S sequence: HE654548
Sequence Identity:
Total samples: 1553
soil counts: 1025
aquatic counts: 218
animal counts: 141
plant counts: 169

Safety information

risk assessment

@ref: 16551
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 16551
description: Geodermatophilus siccatus partial 16S rRNA gene, strain DSM 45419, type strain CF6/1T
accession: HE654548
length: 1472
database: ena
NCBI tax ID: 1137991

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Geodermatophilus siccatus strain DSM 45419	1137991.3	wgs	patric	1137991
66792	Geodermatophilus siccatus DSM 45419	2599185192	draft	img	1137991
67770	Geodermatophilus siccatus DSM 45419	GCA_900103785	scaffold	ncbi	1137991

GC content

@ref: 16551
GC-content: 74.9
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	82	no
motile	yes	72.996	no
flagellated	no	90.811	no
gram-positive	yes	91.166	no
anaerobic	no	98.637	yes
aerobic	yes	89.74	no
halophile	no	85.36	no
spore-forming	no	60.169	no
glucose-util	yes	86.615	no
thermophile	no	97.536	yes
glucose-ferment	no	89.681	no

External links

@ref: 16551

culture collection no.: DSM 45419, CCUG 62765, MTCC 11414, JCM 30066

straininfo link

@ref: 75303
straininfo: 405405

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	23076796	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	2012	Actinomycetales/classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Chad, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Desert Climate, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature, Vitamin K 2/analysis	Genetics
Phylogeny	23159748	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	Actinomycetales/classification/genetics/isolation & purification, Africa, Northern, Bacterial Typing Techniques, Base Composition, Chad, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Silicon Dioxide, Soil Microbiology, Vitamin K 2/analogs & derivatives/analysis	Genetics

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
16551	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45419)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-45419
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
62898	Curators of the CCUG	Culture Collection University of Gothenburg (CCUG) (CCUG 62765)	https://www.ccug.se/strain?id=62765
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793	Mukherjee et al.		10.1038/nbt.3886	GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life	35: 676-683 2017	28604660
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
75303	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID405405.1	StrainInfo: A central database for resolving microbial strain identifiers