Strain identifier
BacDive ID: 8042
Type strain: 
Species: Pseudosporangium ferrugineum
Strain Designation: 3-44-a(19)
Strain history: I. Ara and T. Kudo 3-44-a(19).
NCBI tax ID(s): 439699 (species)
version 8.1 (current version)
General
@ref: 16342
BacDive-ID: 8042
DSM-Number: 45348
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Pseudosporangium ferrugineum 3-44-a is an aerobe, spore-forming, mesophilic bacterium that was isolated from sandy soil at a forest waterfall.
NCBI tax id
- NCBI tax id: 439699
- Matching level: species
strain history
| @ref | history |
|---|---|
| 16342 | <- JCM/RIKEN <- I. Ara and T. Kudo; 3-44-a(19) |
| 67770 | I. Ara and T. Kudo 3-44-a(19). |
doi: 10.13145/bacdive8042.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micromonosporales
- family: Micromonosporaceae
- genus: Pseudosporangium
- species: Pseudosporangium ferrugineum
- full scientific name: Pseudosporangium ferrugineum Ara et al. 2008
synonyms
- @ref: 20215
- synonym: Actinoplanes ferrugineus
@ref: 16342
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micromonosporaceae
genus: Pseudosporangium
species: Pseudosporangium ferrugineum
full scientific name: Pseudosporangium ferrugineum Ara et al. 2008
strain designation: 3-44-a(19)
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 32555 | positive | |
| 69480 | positive | 100 |
pigmentation
- @ref: 32555
- production: yes
multimedia
- @ref: 16342
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45348.jpg
- caption: Medium 535 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 16342 | 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 |
| 16342 | GPHF-MEDIUM (DSMZ Medium 553) | yes | https://mediadive.dsmz.de/medium/553 | Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water |
| 16342 | 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 |
| 16342 | STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) | yes | https://mediadive.dsmz.de/medium/252 | Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water |
| 16342 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://mediadive.dsmz.de/medium/84 | Name: 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 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 16342 | positive | growth | 28 | mesophilic |
| 32555 | positive | growth | 20-37 | |
| 67770 | positive | growth | 28 | mesophilic |
culture pH
- @ref: 32555
- ability: positive
- type: growth
- pH: 05-09
- PH range: alkaliphile
Physiology and metabolism
oxygen tolerance
- @ref: 32555
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32555 | yes | |
| 69481 | yes | 100 |
| 69480 | yes | 100 |
observation
- @ref: 67770
- observation: quinones: MK-9(H6)
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32555 | 22599 | arabinose | + | carbon source |
| 32555 | 17057 | cellobiose | + | carbon source |
| 32555 | 17234 | glucose | + | carbon source |
| 32555 | 17306 | maltose | + | carbon source |
| 32555 | 29864 | mannitol | + | carbon source |
| 32555 | 37684 | mannose | + | carbon source |
| 32555 | 16634 | raffinose | + | carbon source |
| 32555 | 26546 | rhamnose | + | carbon source |
| 32555 | 17992 | sucrose | + | carbon source |
| 32555 | 27082 | trehalose | + | carbon source |
| 32555 | 17151 | xylitol | + | carbon source |
| 32555 | 18222 | xylose | + | carbon source |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 16342 | sandy soil at a forest waterfall | Chokoria, Cox's Bazar | Bangladesh | BGD | Asia |
| 67770 | Sandy soil at a forest waterfall | Chokoria, Cox's Bazar | Bangladesh | BGD | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | |
| #Environmental | #Terrestrial | #Forest |
| #Environmental | #Terrestrial | #Sandy |
| #Environmental | #Terrestrial | #Soil |
Safety information
risk assessment
- @ref: 16342
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16342
- description: Pseudosporangium ferrugineum gene for 16S rRNA, partial sequence
- accession: AB302183
- length: 1513
- database: ena
- NCBI tax ID: 439699
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pseudosporangium ferrugineum strain DSM 45348 | 439699.3 | wgs | patric | 439699 |
| 66792 | Pseudosporangium ferrugineum DSM 45348 | 2728369278 | draft | img | 439699 |
| 67770 | Pseudosporangium ferrugineum DSM 45348 | GCA_003002065 | scaffold | ncbi | 439699 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 16342 | 73.6 | |
| 67770 | 73.6 | high performance liquid chromatography (HPLC) |
| 67770 | 72.5 | genome sequence analysis |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| gram-positive | yes | 89.343 | yes |
| anaerobic | no | 98.835 | yes |
| halophile | no | 95.275 | no |
| spore-forming | yes | 92.041 | yes |
| glucose-util | yes | 90.281 | yes |
| aerobic | yes | 91.648 | yes |
| flagellated | no | 88.603 | no |
| thermophile | no | 98.094 | yes |
| motile | yes | 60.914 | no |
| glucose-ferment | no | 87.927 | no |
External links
@ref: 16342
culture collection no.: DSM 45348, BCC 72027, JCM 14710, MTCC 9007
straininfo link
- @ref: 77470
- straininfo: 406654
literature
- topic: Phylogeny
- Pubmed-ID: 18599710
- title: Pseudosporangium ferrugineum gen. nov., sp. nov., a new member of the family Micromonosporaceae.
- authors: Ara I, Matsumoto A, Bakir MA, Kudo T, Omura S, Takahashi Y
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.65680-0
- year: 2008
- mesh: Bangladesh, Base Composition, DNA, Bacterial/genetics, Micromonosporaceae/*classification/genetics/isolation & purification/ultrastructure, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Species Specificity
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 16342 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45348) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45348 | ||||
| 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 | ||||
| 32555 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28773 | 28776041 | ||
| 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) | ||||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
| 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) | ||||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
| 77470 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID406654.1 | StrainInfo: A central database for resolving microbial strain identifiers |