Strain identifier
BacDive ID: 5820
Type strain:
Species: Geodermatophilus arenarius
Strain Designation: CF5/4
Strain history: MTCC 11413 <-- A. A. Gorbushina CF5/4.
NCBI tax ID(s): 1137990 (species)
General
@ref: 16550
BacDive-ID: 5820
DSM-Number: 45418
keywords: 16S sequence, Bacteria, aerobe, mesophilic
description: Geodermatophilus arenarius CF5/4 is an aerobe, mesophilic bacterium that was isolated from desert sand.
NCBI tax id
- NCBI tax id: 1137990
- Matching level: species
strain history
@ref | history |
---|---|
16550 | <- A. Gorbushina, Bundesanstalt für Materialforschung und -prüfung, Berlin; CF5/4 |
67770 | MTCC 11413 <-- A. A. Gorbushina CF5/4. |
doi: 10.13145/bacdive5820.20230509.8.1
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 arenarius
- full scientific name: Geodermatophilus arenarius Montero-Calasanz et al. 2013
@ref: 16550
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Geodermatophilaceae
genus: Geodermatophilus
species: Geodermatophilus arenarius
full scientific name: Geodermatophilus arenarius Montero-Calasanz et al. 2013
strain designation: CF5/4
type strain: yes
Morphology
colony morphology
- @ref: 62896
- incubation period: 1-2 days
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_45418_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_45418_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_45418_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_45418_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_45418_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
16550 | 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 |
16550 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
16550 | 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 |
---|---|---|---|---|
16550 | positive | growth | 28 | mesophilic |
62896 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 62896
- oxygen tolerance: aerobe
observation
- @ref: 67770
- observation: quinones: MK-9(H4)
fatty acid profile
fatty acids
@ref fatty acid percentage ECL 62896 C15:0 2.3 15 62896 C16:0 1.7 16 62896 C17:0 1.2 17 62896 C13:0 3OH/C15:1 i I/H 1.4 14.469 62896 C14:0 ISO 1.2 13.618 62896 C15:0 ANTEISO 1.7 14.711 62896 C15:0 ISO 27.1 14.621 62896 C15:1 ω6c 1 14.856 62896 C16:0 iso 26.6 15.626 62896 C16:1 ISO H 10.7 15.461 62896 C16:1 ω3c 1.7 15.933 62896 C16:1 ω7c 2.5 15.819 62896 C17:0 anteiso 2.3 16.722 62896 C17:0 iso 2.9 16.629 62896 C17:1 ω8c 7.5 16.792 62896 C17:1 ω9c ISO 4.9 16.416 62896 C18:1 ω9c 1.1 17.769 62896 Unidentified 2.4 14.927 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date |
---|---|---|---|---|---|---|
16550 | desert sand | Saharan, Ouré Cassoni | Chad | TCD | Africa | |
62896 | arid desert soil | Ouré Cassoni | Chad | TCD | Africa | 2007 |
67770 | Sand of the Sahara Desert near Ouré Cassoni | Chad | TCD | Africa |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Desert |
#Environmental | #Terrestrial | #Sandy |
#Condition | #Xerophilic |
taxonmaps
- @ref: 69479
- File name: preview.99_156662.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_2039;97_3177;98_103257;99_156662&stattab=map
- Last taxonomy: Geodermatophilus arenarius subclade
- 16S sequence: HE654547
- Sequence Identity:
- Total samples: 613
- soil counts: 487
- aquatic counts: 44
- animal counts: 50
- plant counts: 32
Safety information
risk assessment
- @ref: 16550
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16550
- description: Geodermatophilus arenarius partial 16S rRNA gene, type strain CF 5/4T
- accession: HE654547
- length: 1511
- database: ena
- NCBI tax ID: 1137990
GC content
- @ref: 16550
- GC-content: 75.9
- method: high performance liquid chromatography (HPLC)
External links
@ref: 16550
culture collection no.: DSM 45418, CCUG 62763, MTCC 11413, JCM 30063
straininfo link
- @ref: 75302
- straininfo: 405995
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23081798 | Geodermatophilus arenarius sp. nov., a xerophilic actinomycete isolated from Saharan desert sand in Chad. | Montero-Calasanz MC, Goker M, Potter G, Rohde M, Sproer C, Schumann P, Gorbushina AA, Klenk HP | Extremophiles | 10.1007/s00792-012-0486-4 | 2012 | Actinomycetales/*classification/cytology/genetics/*isolation & purification, Africa, Northern, Bacterial Typing Techniques, Base Composition, Chad, Desert Climate, Geologic Sediments/chemistry/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Silicon Dioxide | Enzymology |
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 |
---|---|---|---|---|---|---|
16550 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45418) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45418 | |||
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 | |||
62896 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 62763) | https://www.ccug.se/strain?id=62763 | |||
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 | |||
75302 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID405995.1 | StrainInfo: A central database for resolving microbial strain identifiers |