Strain identifier

BacDive ID: 16624

Type strain: Yes

Species: Sphaerisporangium melleum

Strain Designation: 3-28(8)

Strain history: I. Ara 3-28(8).

NCBI tax ID(s): 321316 (species)

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General

@ref: 12207

BacDive-ID: 16624

DSM-Number: 44954

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

description: Sphaerisporangium melleum 3-28 is a spore-forming, mesophilic bacterium that was isolated from sandy soil.

NCBI tax id

  • NCBI tax id: 321316
  • Matching level: species

strain history

@refhistory
12207<- T. Kudo (Sphaerosporangium melleum) <- I. Ara; 3-28(8)
67770I. Ara 3-28(8).

doi: 10.13145/bacdive16624.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Streptosporangiaceae
  • genus: Sphaerisporangium
  • species: Sphaerisporangium melleum
  • full scientific name: Sphaerisporangium melleum corrig. Ara and Kudo 2007
  • synonyms

    • @ref: 20215
    • synonym: Sphaerosporangium melleum

@ref: 12207

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Sphaerisporangium

species: Sphaerisporangium melleum

full scientific name: Sphaerisporangium melleum Ara and Kudo 2007

strain designation: 3-28(8)

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.993
69480100positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12207GYM 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
12207ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
12207positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

observation

  • @ref: 67770
  • observation: quinones: MK-9(III,VIII-H4), MK-9(H6)

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12207sandy soilChokoriaBangladeshBGDAsia
67770Sandy soil at a forest-side waterfallChokoria, Cox's BazarBangladeshBGDAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Sandy
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 12207
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12207
  • description: Sphaerisporangium melleum gene for 16S rRNA, partial sequence, strain: 3-28(8)
  • accession: AB208714
  • length: 1503
  • database: ena
  • NCBI tax ID: 321316

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphaerisporangium melleum NBRC 107356GCA_016863375contigncbi321316
66792Sphaerisporangium melleum JCM 13064GCA_014646695scaffoldncbi321316
66792Sphaerisporangium melleum strain JCM 13064321316.3wgspatric321316
66792Sphaerisporangium melleum strain NBRC 107356321316.4wgspatric321316

GC content

@refGC-contentmethod
1220771
6777071high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.868no
gram-positiveyes85.479no
anaerobicno98.483no
aerobicyes87.96no
halophileno93.119no
spore-formingyes94.113no
thermophileno97.834yes
glucose-utilyes89.028no
motileno92.395no
glucose-fermentno91.354no

External links

@ref: 12207

culture collection no.: DSM 44954, JCM 13064, NBRC 107356, BCC 36478, CGMCC 4.5528

straininfo link

  • @ref: 85645
  • straininfo: 297460

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25294725Sphaerisporangium dianthi sp. nov., an endophytic actinomycete isolated from a root of Dianthus chinensis L.Xing J, Liu C, Zhang Y, He H, Zhou Y, Li L, Zhao J, Liu S, Wang X, Xiang WAntonie Van Leeuwenhoek10.1007/s10482-014-0298-x2014Actinobacteria/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Dianthus/*microbiology, Endophytes/*classification/genetics/*isolation & purification, Fatty Acids/analysis, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phylogeny, Plant Roots/microbiology, Plants, Medicinal/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisEnzymology
Phylogeny25963939Sphaerisporangium corydalis sp. nov., isolated from the root of Corydalis yanhusuo L.Wang X, Liu C, Cheng J, Zhang Y, Ma Z, Li L, Wang X, Xiang WAntonie Van Leeuwenhoek10.1007/s10482-015-0471-x2015Actinobacteria/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Cell Wall/chemistry, China, Cluster Analysis, Corydalis/*microbiology, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics

Reference

@idauthorscataloguedoi/urltitle
12207Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44954)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44954
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
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/
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
85645Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297460.1StrainInfo: A central database for resolving microbial strain identifiers