Strain identifier

BacDive ID: 5824

Type strain: Yes

Species: Geodermatophilus nigrescens

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

NCBI tax ID(s): 1070870 (species)

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General

@ref: 16686

BacDive-ID: 5824

DSM-Number: 45408

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

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

NCBI tax id

  • NCBI tax id: 1070870
  • Matching level: species

strain history

@refhistory
16686<- S.-K. Tang, YIM; YIM 75980 <- J. Zhang
67770S.-K. Tang YIM 75980.

doi: 10.13145/bacdive5824.20230509.8.1

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 nigrescens
  • full scientific name: Geodermatophilus nigrescens Nie et al. 2012

@ref: 16686

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Geodermatophilaceae

genus: Geodermatophilus

species: Geodermatophilus nigrescens

full scientific name: Geodermatophilus nigrescens Nie et al. 2012 emend. Montero-Calasanz et al. 2017

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

multimedia

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

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16686GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf
16686TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
16686GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: 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

@refgrowthtypetemperaturerange
16686positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 95.544

observation

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

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16686soil from a dry-hot river valleyYunnan Province, Dongchuan countyChinaCHNAsia
67770Soil from dry-hot river valley in Dongchuan countyYunnan Province, south-west ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#River (Creek)
#Environmental#Terrestrial#Soil
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_8098.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_2039;97_2459;98_3041;99_8098&stattab=map
  • Last taxonomy: Geodermatophilus nigrescens
  • 16S sequence: JN656711
  • Sequence Identity:
  • Total samples: 7824
  • soil counts: 5007
  • aquatic counts: 471
  • animal counts: 973
  • plant counts: 1373

Safety information

risk assessment

  • @ref: 16686
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Geodermatophilus nigrescens strain YIM 75980 16S ribosomal RNA gene, partial sequenceJN1889471524ena1070870
16686Geodermatophilus nigrescens strain YIM 75980 16S ribosomal RNA gene, partial sequenceJN6567111524ena1070870

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Geodermatophilus nigrescens strain DSM 454081070870.3wgspatric1070870
66792Geodermatophilus nigrescens DSM 454082695420953draftimg1070870
67770Geodermatophilus nigrescens DSM 45408GCA_900129495scaffoldncbi1070870

GC content

  • @ref: 16686
  • GC-content: 73.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes65no
motileyes77.955no
flagellatedno92.089no
gram-positiveyes93.589no
anaerobicno99.071no
aerobicyes91.252no
halophileno92.957no
spore-formingno68.882no
thermophileno99.047no
glucose-utilyes87.862no
glucose-fermentno91.086no

External links

@ref: 16686

culture collection no.: DSM 45408, CCTCC AA 2011015, JCM 18056, YIM 75980

straininfo link

  • @ref: 75306
  • straininfo: 399992

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22273761Geodermatophilus 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 WJAntonie Van Leeuwenhoek10.1007/s10482-012-9696-02012Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, China, Cluster Analysis, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny23159748Geodermatophilus 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 AAInt J Syst Evol Microbiol10.1099/ijs.0.046888-02012Actinomycetales/*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/analysisGenetics
35855324Psi-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 YNAR Genom Bioinform10.1093/nargab/lqac0552022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16686Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45408)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45408
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
75306Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399992.1StrainInfo: A central database for resolving microbial strain identifiers