Strain identifier

BacDive ID: 134322

Type strain: Yes

Species: Streptacidiphilus melanogenes

Strain Designation: SB-B34

Strain history: <- SB Kim, Chungnam Natl. Univ.

NCBI tax ID(s): 411235 (species)

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General

@ref: 64723

BacDive-ID: 134322

DSM-Number: 108659

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

description: Streptacidiphilus melanogenes SB-B34 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 411235
  • Matching level: species

strain history

@refhistory
64723<- NBRC; NBRC 103184 <- S. B. Kim and S. H. Cho, School Biosci. Biotechnol., Chungnam Natl. Univ., Republic of Korea; SB-B34
67770KCTC 19280 <-- S. B. Kim SB-B34.
67771<- SB Kim, Chungnam Natl. Univ.

doi: 10.13145/bacdive134322.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kitasatosporales
  • family: Streptomycetaceae
  • genus: Streptacidiphilus
  • species: Streptacidiphilus melanogenes
  • full scientific name: Streptacidiphilus melanogenes Cho et al. 2008

@ref: 64723

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptacidiphilus

species: Streptacidiphilus melanogenes

full scientific name: Streptacidiphilus melanogenes Cho et al. 2008 emend. Nouioui et al. 2018

strain designation: SB-B34

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
67771positive
69480no96.148
69480positive100

pigmentation

  • @ref: 32427
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64723ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
64723GYM 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
64723ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
64723positivegrowth28mesophilic
32427positivegrowth28-35mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

  • @ref: 32427
  • ability: positive
  • type: growth
  • pH: 03-08
  • PH range: acidophile

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32427yes
69481yes100
69480yes100

observation

  • @ref: 67770
  • observation: quinones: MK-9(H8), MK-9(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3242729016arginine+carbon source
3242724265gluconate+carbon source
3242717754glycerol+carbon source
3242728053melibiose+carbon source
3242717268myo-inositol+carbon source
3242730911sorbitol+carbon source
3242717992sucrose+carbon source
3242718222xylose+carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
32427soil
64723soil of Pinus thunbergiiSambong, Tae-an, ChungnamRepublic of KoreaKORAsia
67770Pinus-associated soilSambong, near the coastal areas of Tae-An, ChungnamRepublic of KoreaKORAsiaPinus
67771From `Pinus` soilRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_3777.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_1291;97_2062;98_2532;99_3777&stattab=map
  • Last taxonomy: Streptacidiphilus
  • 16S sequence: DQ994689
  • Sequence Identity:
  • Total samples: 486
  • soil counts: 433
  • aquatic counts: 17
  • animal counts: 19
  • plant counts: 17

Safety information

risk assessment

  • @ref: 64723
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64723
  • description: Streptacidiphilus melanogenes strain SB-B34 16S ribosomal RNA gene, partial sequence
  • accession: DQ994689
  • length: 1428
  • database: ena
  • NCBI tax ID: 411235

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptacidiphilus melanogenes NBRC 103184411235.3wgspatric411235
66792Streptacidiphilus melanogenes NBRC 1031842706794556draftimg411235
67770Streptacidiphilus melanogenes NBRC 103184GCA_000787835scaffoldncbi411235

GC content

  • @ref: 67770
  • GC-content: 72
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes89.869yes
anaerobicno98.862yes
halophileno93.477no
spore-formingyes91.871no
glucose-utilyes87.762no
aerobicyes92.793yes
flagellatedno98.078no
motileno94.169no
thermophileno98.766no
glucose-fermentno89.23no

External links

@ref: 64723

culture collection no.: NBRC 103184, KCTC 19280, DSM 108659, JCM 16224

straininfo link

  • @ref: 91897
  • straininfo: 404206

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18599696Streptacidiphilus anmyonensis sp. nov., Streptacidiphilus rugosus sp. nov. and Streptacidiphilus melanogenes sp. nov., acidophilic actinobacteria isolated from Pinus soils.Cho SH, Han JH, Ko HY, Kim SBInt J Syst Evol Microbiol10.1099/ijs.0.65480-02008Actinobacteria/*classification/genetics/growth & development/isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, *Pinus, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species SpecificityGenetics
Phylogeny29620496Streptacidiphilus monticola sp. nov., a novel actinomycete isolated from soil.Song W, Duan L, Jin L, Zhao J, Jiang S, Sun T, Guo XW, Xiang W, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0027512018Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny30102143Streptacidiphilus pinicola sp. nov., isolated from pine grove soil.Roh SG, Kim MK, Park S, Yun BR, Park J, Kim MJ, Kim YS, Kim SBInt J Syst Evol Microbiol10.1099/ijsem.0.0029572018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, *Phylogeny, Pinus/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Streptomycetaceae/*classification/genetics/isolation & purificationTranscriptome
Phylogeny34106822Streptacidiphilus fuscans sp. nov., a novel actinobacterium isolated from the root of pumpkin (Cucurbita moschata).Yu B, Han C, Zhao J, Zhang Y, Shan Q, Wu Y, Ju H, Xiang W, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0048242021Actinobacteria/genetics/growth & development/*isolation & purification/ultrastructure, Base Sequence, Cucurbita/*microbiology, DNA, Bacterial/genetics, Genome, Bacterial, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
32427Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172865028776041
64723Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-108659Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 108659)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91897Reimer, 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 identifiers10.60712/SI-ID404206.1