Strain identifier
BacDive ID: 64
Type strain: 
Species: Stella humosa
Strain history: <- VKM
NCBI tax ID(s): 94 (species)
version 8.1 (current version)
General
@ref: 2352
BacDive-ID: 64
DSM-Number: 5900
keywords: genome sequence, 16S sequence, Bacteria, chemoorganotroph, mesophilic, Gram-negative, star-shaped, colony-forming
description: Stella humosa DSM 5900 is a chemoorganotroph, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from soil.
NCBI tax id
- NCBI tax id: 94
- Matching level: species
strain history
- @ref: 2352
- history: <- VKM
doi: 10.13145/bacdive64.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodospirillales
- family: Stellaceae
- genus: Stella
- species: Stella humosa
- full scientific name: Stella humosa Vasilyeva 1985
@ref: 2352
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Stellaceae
genus: Stella
species: Stella humosa
full scientific name: Stella humosa Vasilyeva 1985
type strain: yes
Morphology
cell morphology
- @ref: 23248
- gram stain: negative
- cell length: 0.7-3.0 µm
- cell shape: star-shaped
- motility: no
colony morphology
- @ref: 23248
- colony size: 2.5 mm
- colony color: greyish white
- colony shape: circular
- incubation period: 14 days
Culture and growth conditions
culture medium
- @ref: 2352
- name: ANCALOMICROBIUM MEDIUM (DSMZ Medium 603)
- growth: yes
- link: https://mediadive.dsmz.de/medium/603
- composition: Name: ANCALOMICROBIUM MEDIUM (DSMZ Medium 603) Composition: Agar 15.0 g/l MgSO4 x 7 H2O 0.588119 g/l (NH4)2SO4 0.247525 g/l Glucose 0.247525 g/l Nitrilotriacetic acid 0.19802 g/l Na2HPO4 0.070297 g/l CaCl2 x 2 H2O 0.0660396 g/l ZnSO4 x 7 H2O 0.00108416 g/l FeSO4 x 7 H2O 0.00049505 g/l Na-EDTA 0.000247525 g/l (NH4)6Mo7O24 x 4 H2O 0.000183168 g/l MnSO4 x H2O 0.000152475 g/l Calcium pantothenate 4.95049e-05 g/l Nicotinamide 4.95049e-05 g/l Riboflavin 4.95049e-05 g/l Thiamine-HCl x 2 H2O 4.95049e-05 g/l CuSO4 x 5 H2O 3.88119e-05 g/l Co(NO3)2 x 6 H2O 2.45545e-05 g/l Biotin 1.9802e-05 g/l Folic acid 1.9802e-05 g/l Na2B4O7 x 10 H2O 1.75248e-05 g/l Vitamin B12 9.90099e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 2352 | positive | growth | 28-30 | mesophilic |
| 23248 | positive | optimum | 28-30 | mesophilic |
culture pH
- @ref: 23248
- ability: positive
- type: growth
- pH: 7
Physiology and metabolism
nutrition type
- @ref: 23248
- type: chemoorganotroph
spore formation
- @ref: 23248
- spore formation: no
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 23248 | 30916 | 2-oxoglutarate | - | growth |
| 23248 | 17968 | butyrate | - | growth |
| 23248 | 15570 | D-alanine | - | growth |
| 23248 | 15740 | formate | - | growth |
| 23248 | 29806 | fumarate | - | growth |
| 23248 | 24265 | gluconate | - | growth |
| 23248 | 16977 | L-alanine | - | growth |
| 23248 | 16467 | L-arginine | - | growth |
| 23248 | 17196 | L-asparagine | - | growth |
| 23248 | 29991 | L-aspartate | - | growth |
| 23248 | 18050 | L-glutamine | - | growth |
| 23248 | 15971 | L-histidine | - | growth |
| 23248 | 17115 | L-serine | - | growth |
| 23248 | 26986 | threonine | - | growth |
| 23248 | 31011 | valerate | - | growth |
| 23248 | 62968 | cellulose | - | hydrolysis |
| 23248 | 5291 | gelatin | - | hydrolysis |
| 23248 | 28017 | starch | - | hydrolysis |
| 23248 | 30089 | acetate | + | growth |
| 23248 | 16947 | citrate | + | growth |
| 23248 | 17561 | L-cysteine | + | growth |
| 23248 | 16283 | L-cystine | + | growth |
| 23248 | 29985 | L-glutamate | + | growth |
| 23248 | 18019 | L-lysine | + | growth |
| 23248 | 24996 | lactate | + | growth |
| 23248 | 25115 | malate | + | growth |
| 23248 | 15361 | pyruvate | + | growth |
| 23248 | 30031 | succinate | + | growth |
antibiotic resistance
| @ref | ChEBI | metabolite | is antibiotic | is intermediate | intermediate conc. | is sensitive | sensitivity conc. |
|---|---|---|---|---|---|---|---|
| 23248 | 7935 | paromomycin sulfate | yes | yes | 2-10 µg/mL | ||
| 23248 | 17334 | penicillin | yes | yes | 8 µg/mL | ||
| 23248 | 7507 | neomycin | yes | yes | 0.5-1 µg/mL |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 23248 | catalase | + | 1.11.1.6 |
| 23248 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 2352 | soil | Krasnodar | Russia | RUS | Europe |
| 23248 | Virgin chernozem |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_141379.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_634;96_20993;97_26151;98_33233;99_141379&stattab=map
- Last taxonomy: Stella humosa
- 16S sequence: AJ535710
- Sequence Identity:
- Total samples: 81
- soil counts: 12
- aquatic counts: 46
- animal counts: 15
- plant counts: 8
Safety information
risk assessment
- @ref: 2352
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Stella humosa 16S rRNA gene, strain DSM5900
- accession: AJ535710
- length: 1447
- database: ena
- NCBI tax ID: 94
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Stella humosa DSM 5900 | GCA_003751345 | contig | ncbi | 94 |
| 66792 | Stella humosa ATCC 43930 | GCA_006738645 | complete | ncbi | 94 |
| 66792 | Stella humosa strain ATCC 43930 | 94.5 | complete | patric | 94 |
| 66792 | Stella humosa strain DSM 5900 | 94.4 | wgs | patric | 94 |
| 66792 | Stella humosa DSM 5900 | 2788499841 | draft | img | 94 |
GC content
- @ref: 23248
- GC-content: 72.70
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 87.41 | yes |
| flagellated | no | 94.246 | yes |
| gram-positive | no | 98.413 | no |
| anaerobic | no | 98.499 | no |
| aerobic | yes | 94.043 | no |
| halophile | no | 90.738 | no |
| spore-forming | no | 95.574 | yes |
| thermophile | no | 97.215 | no |
| glucose-util | yes | 77.022 | no |
| glucose-ferment | no | 90.399 | no |
External links
@ref: 2352
culture collection no.: DSM 5900, ATCC 43930, AUCM B-1137, BKM B-1137, DSM 3698, VKM B-1137
straininfo link
- @ref: 69748
- straininfo: 42130
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15143003 | Phylogenetic relationships of the genera Stella, Labrys and Angulomicrobium within the 'Alphaproteobacteria' and description of Angulomicrobium amanitiforme sp. nov. | Fritz I, Strompl C, Abraham WR | Int J Syst Evol Microbiol | 10.1099/ijs.0.02746-0 | 2004 | Acetobacteraceae/*classification/genetics/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Genes, Bacterial, Hyphomicrobiaceae/*classification/genetics/metabolism, Lipids/analysis, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics | Metabolism |
| Genetics | 31395645 | Complete Genome Sequences of Three Star-Shaped Bacteria, Stella humosa, Stella vacuolata, and Stella Species ATCC 35155. | Shibai A, Maeda T, Kawada M, Kotani H, Sakata N, Furusawa C | Microbiol Resour Announc | 10.1128/MRA.00719-19 | 2019 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 2352 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5900) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5900 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 23248 | L. V. VASILYEVA | 10.1099/00207713-35-4-518 | Stella, a New Genus of Soil Prosthecobacteria, with Proposals for Stella humosa sp. nov. and Stella vacuolata sp. nov. | IJSEM 35: 518-521 1985 | ||
| 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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 69748 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42130.1 | StrainInfo: A central database for resolving microbial strain identifiers |