Strain identifier
BacDive ID: 133062
Type strain:
Species: Allostreptomyces psammosilenae
Strain history: <- W.-J. Li, Yunnan Univ., Yunnan Inst. Microbiol. (YIM), Kunming, China; YIM DR4008 <- M.-J. Huang
NCBI tax ID(s): 1892865 (species)
General
@ref: 24850
BacDive-ID: 133062
DSM-Number: 42178
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, Gram-positive
description: Allostreptomyces psammosilenae DSM 42178 is a spore-forming, Gram-positive bacterium that builds substrate mycelia and was isolated from surface-sterilized roots of Psammosilene tunicoides.
NCBI tax id
- NCBI tax id: 1892865
- Matching level: species
strain history
- @ref: 24850
- history: <- W.-J. Li, Yunnan Univ., Yunnan Inst. Microbiol. (YIM), Kunming, China; YIM DR4008 <- M.-J. Huang
doi: 10.13145/bacdive133062.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Kitasatosporales
- family: Streptomycetaceae
- genus: Allostreptomyces
- species: Allostreptomyces psammosilenae
- full scientific name: Allostreptomyces psammosilenae Huang et al. 2017
@ref: 24850
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Allostreptomyces
species: Allostreptomyces psammosilenae
full scientific name: Allostreptomyces psammosilenae Huang et al. 2017
type strain: yes
Morphology
cell morphology
@ref | gram stain | motility | confidence |
---|---|---|---|
25169 | positive | ||
69480 | no | 90.556 | |
69480 | positive | 100 |
multicellular morphology
@ref | forms multicellular complex | complex name | complex color | medium name | further description |
---|---|---|---|---|---|
25169 | yes | substrate mycelia | deep orange yellow - black | ISP 2 | extensively branched |
25169 | yes | aerial mycelia | white - light yellow green | ISP 2 | carried straight chains of smooth surfaced spores |
multimedia
- @ref: 24850
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_42178.jpg
- caption: Medium 987 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
24850 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf | |
25169 | ISP 4 | yes | ||
25169 | nutritient agar (NA) | no | ||
24850 | ISP2 MEDIUM (DSMZ Medium 987) | yes | https://mediadive.dsmz.de/medium/987 | Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
25169 | positive | growth | 10-50 | |
25169 | positive | optimum | 28-30 | mesophilic |
24850 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
25169 | positive | growth | 5.0-11.0 | alkaliphile |
25169 | positive | optimum | 7 |
Physiology and metabolism
spore formation
@ref | spore description | type of spore | spore formation | confidence |
---|---|---|---|---|
25169 | chains of smooth surfaced spores on aerial mycelia | spore | yes | |
69481 | yes | 100 | ||
69480 | yes | 100 |
halophily
@ref | salt | tested relation | concentration | growth |
---|---|---|---|---|
25169 | NaCl | optimum | 1 % | |
25169 | NaCl | growth | 0.0-4.0 %(w/v) | positive |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
25169 | 17057 | cellobiose | - | carbon source |
25169 | 15824 | D-fructose | - | carbon source |
25169 | 17924 | D-sorbitol | - | carbon source |
25169 | 65327 | D-xylose | - | carbon source |
25169 | 17234 | glucose | - | carbon source |
25169 | 17754 | glycerol | - | carbon source |
25169 | 17268 | myo-inositol | - | carbon source |
25169 | 16467 | L-arginine | - | nitrogen source |
25169 | 29991 | L-aspartate | - | nitrogen source |
25169 | 16283 | L-cystine | - | nitrogen source |
25169 | 15971 | L-histidine | - | nitrogen source |
25169 | 16828 | L-tryptophan | - | nitrogen source |
25169 | 17716 | lactose | - | carbon source |
25169 | 29864 | mannitol | - | carbon source |
25169 | 26546 | rhamnose | - | carbon source |
25169 | 33942 | ribose | - | carbon source |
25169 | 27922 | sorbose | - | carbon source |
25169 | 17992 | sucrose | - | carbon source |
25169 | 53424 | tween 20 | - | hydrolysis |
25169 | 17151 | xylitol | - | carbon source |
25169 | 17836 | 4-aminobenzoate | + | nitrogen source |
25169 | 16449 | alanine | + | nitrogen source |
25169 | 62968 | cellulose | + | hydrolysis |
25169 | 12936 | D-galactose | + | carbon source |
25169 | 91260 | disodium malate | + | carbon source |
25169 | 5291 | gelatin | + | hydrolysis |
25169 | 30849 | L-arabinose | + | carbon source |
25169 | 29985 | L-glutamate | + | nitrogen source |
25169 | 18050 | L-glutamine | + | nitrogen source |
25169 | 18019 | L-lysine | + | nitrogen source |
25169 | 17295 | L-phenylalanine | + | nitrogen source |
25169 | 16857 | L-threonine | + | nitrogen source |
25169 | 17895 | L-tyrosine | + | nitrogen source |
25169 | 16414 | L-valine | + | nitrogen source |
25169 | 17306 | maltose | + | carbon source |
25169 | 37684 | mannose | + | carbon source |
25169 | 17632 | nitrate | + | reduction |
25169 | 16634 | raffinose | + | carbon source |
25169 | skimmed milk | + | fermentation | |
25169 | 53258 | sodium citrate | + | carbon source |
25169 | 50144 | sodium pyruvate | + | carbon source |
25169 | 28017 | starch | + | hydrolysis |
25169 | 28017 | starch | + | carbon source |
25169 | 27082 | trehalose | + | carbon source |
25169 | 53423 | tween 40 | + | hydrolysis |
25169 | 53425 | tween 60 | + | hydrolysis |
25169 | 53426 | tween 80 | + | hydrolysis |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. | is resistant | resistance conc. |
---|---|---|---|---|---|---|---|
25169 | 2637 | amikacin | yes | yes | 30 µg (disc) | ||
25169 | 3517 | cefuroxime | yes | yes | 30 µg (disc) | ||
25169 | 17698 | chloramphenicol | yes | yes | 30 µg (disc) | ||
25169 | 100241 | ciprofloxacin | yes | yes | 5 µg (disc) | ||
25169 | 48923 | erythromycin | yes | yes | 15 µg (disc) | ||
25169 | 17833 | gentamicin | yes | yes | 10 µg (disc) | ||
25169 | 28368 | novobiocin | yes | yes | 30 µg (disc) | ||
25169 | 17334 | penicillin | yes | yes | 10 Unit (disc) | ||
25169 | 8232 | piperacillin | yes | yes | 100 µg (disc) | ||
25169 | 8309 | polymyxin b | yes | yes | 300 Unit (disc) | ||
25169 | 27902 | tetracycline | yes | yes | 30 µg (disc) | ||
25169 | 86455 | optochin | yes | yes | 5 µg (disc) | ||
25169 | 100246 | norfloxacin | yes | yes | 10 µg (disc) | ||
25169 | 7809 | oxacillin | yes | yes | 1 µg (disc) | ||
25169 | 9332 | sulfamethoxazole | yes | yes | 300 µg (disc) | ||
25169 | 28001 | vancomycin | yes | yes | 30 µg (disc) |
metabolite production
- @ref: 25169
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
25169 | catalase | + | 1.11.1.6 |
25169 | cytochrome oxidase | + | 1.9.3.1 |
25169 | urease | - | 3.5.1.5 |
fatty acid profile
fatty acids
@ref fatty acid percentage 25169 C15:0 anteiso 34.5 25169 C17:0 anteiso 10.3 25169 C16:0 15.6 25169 C15:0 iso 12.6 25169 C16:0 iso 13.2 - type of FA analysis: whole cell analysis
- incubation medium: ISP 2
- incubation temperature: 28
- incubation time: 5
- software version: Sherlock 6.1
- library/peak naming table: TSBA 6
- system: MIS MIDI
- method/protocol: Sasser 1990
- cutoff value:
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature |
---|---|---|---|---|---|---|---|---|---|---|
24850 | surface-sterilized roots of Psammosilene tunicoides | Psammosilene tunicoides | Yunnan, Lijiang | China | CHN | Asia | ||||
25169 | roots of Psammo- silene tunicoides | YECD medium | yeast 0.3 g/L, casein 0.3 g/L, glucose 0.3 g/l; bone meal 0.3 g/L, agar 1.3 g/L, pH 7.2, supplemented with nalidixic acid (25 mg/L) and nystatin (50 mg/L) | 30 days | 28 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Shrub (Scrub) |
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Host Body-Site | #Plant | #Root (Rhizome) |
#Host Body-Site | #Plant | #Sterilized plant part |
taxonmaps
- @ref: 69479
- File name: preview.99_72882.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_31020;97_39238;98_51049;99_72882&stattab=map
- Last taxonomy: Allostreptomyces
- 16S sequence: KX689228
- Sequence Identity:
- Total samples: 506
- soil counts: 239
- aquatic counts: 38
- animal counts: 192
- plant counts: 37
Safety information
risk assessment
- @ref: 24850
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24850
- description: Allostreptomyces psammosilenae strain YIM DR4008 16S ribosomal RNA gene, partial sequence
- accession: KX689228
- length: 1510
- database: ena
- NCBI tax ID: 1892865
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Allostreptomyces psammosilenae DSM 42178 | GCA_013407765 | contig | ncbi | 1892865 |
66792 | Allostreptomyces psammosilenae strain DSM 42178 | 1892865.3 | wgs | patric | 1892865 |
66792 | Allostreptomyces psammosilenae DSM 42178 | 2823648918 | draft | img | 1892865 |
GC content
- @ref: 24850
- GC-content: 75.3
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | no | 92.233 | no |
gram-positive | yes | 90.496 | no |
anaerobic | no | 99.388 | no |
aerobic | yes | 94.052 | no |
halophile | no | 88.638 | no |
spore-forming | yes | 92.988 | yes |
glucose-util | yes | 82.684 | yes |
flagellated | no | 97.574 | no |
thermophile | no | 93.904 | yes |
glucose-ferment | no | 88.821 | no |
External links
@ref: 24850
culture collection no.: DSM 42178, CGMCC 4.7247, YIM DR4008
straininfo link
- @ref: 91327
- straininfo: 400405
literature
- topic: Phylogeny
- Pubmed-ID: 27902296
- title: Allostreptomyces psammosilenae gen. nov., sp. nov., an endophytic actinobacterium isolated from the roots of Psammosilene tunicoides and emended description of the family Streptomycetaceae [Waksman and Henrici (1943)AL] emend. Rainey et al. 1997, emend. Kim et al. 2003, emend. Zhi et al. 2009.
- authors: Huang MJ, Rao MPN, Salam N, Xiao M, Huang HQ, Li WJ
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001617
- year: 2017
- mesh: Bacterial Typing Techniques, Base Composition, Caryophyllaceae/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomycetaceae/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Transcriptome
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
24850 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-42178 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 42178) | |||
25169 | M. J. R. Huang, M. P.,Salam, N.,Xiao, M.,Huang, H. Q.,Li, W. J. | Allostreptomyces psammosilenae gen. nov., sp. nov., an endophytic actinobacterium isolated from the roots of Psammosilene tunicoides and emended description of the family Streptomycetaceae [Waksman and Henrici (1943)AL] emend. Rainey et al. 1997, emend. Kim et al. 2003, emend. Zhi et al. 2009 | 10.1099/ijsem.0.001617 | IJSEM 67: 288-293 2017 | 27902296 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
91327 | Reimer, 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 identifiers | 10.60712/SI-ID400405.1 |