Strain identifier

BacDive ID: 133062

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refgram stainmotilityconfidence
25169positive
69480no90.556
69480positive100

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium namefurther description
25169yessubstrate myceliadeep orange yellow - blackISP 2extensively branched
25169yesaerial myceliawhite - light yellow greenISP 2carried 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

@refnamegrowthlinkcomposition
24850GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf
25169ISP 4yes
25169nutritient agar (NA)no
24850ISP2 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
25169positivegrowth10-50
25169positiveoptimum28-30mesophilic
24850positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
25169positivegrowth5.0-11.0alkaliphile
25169positiveoptimum7

Physiology and metabolism

spore formation

@refspore descriptiontype of sporespore formationconfidence
25169chains of smooth surfaced spores on aerial myceliasporeyes
69481yes100
69480yes100

halophily

@refsalttested relationconcentrationgrowth
25169NaCloptimum1 %
25169NaClgrowth0.0-4.0 %(w/v)positive

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2516917057cellobiose-carbon source
2516915824D-fructose-carbon source
2516917924D-sorbitol-carbon source
2516965327D-xylose-carbon source
2516917234glucose-carbon source
2516917754glycerol-carbon source
2516917268myo-inositol-carbon source
2516916467L-arginine-nitrogen source
2516929991L-aspartate-nitrogen source
2516916283L-cystine-nitrogen source
2516915971L-histidine-nitrogen source
2516916828L-tryptophan-nitrogen source
2516917716lactose-carbon source
2516929864mannitol-carbon source
2516926546rhamnose-carbon source
2516933942ribose-carbon source
2516927922sorbose-carbon source
2516917992sucrose-carbon source
2516953424tween 20-hydrolysis
2516917151xylitol-carbon source
25169178364-aminobenzoate+nitrogen source
2516916449alanine+nitrogen source
2516962968cellulose+hydrolysis
2516912936D-galactose+carbon source
2516991260disodium malate+carbon source
251695291gelatin+hydrolysis
2516930849L-arabinose+carbon source
2516929985L-glutamate+nitrogen source
2516918050L-glutamine+nitrogen source
2516918019L-lysine+nitrogen source
2516917295L-phenylalanine+nitrogen source
2516916857L-threonine+nitrogen source
2516917895L-tyrosine+nitrogen source
2516916414L-valine+nitrogen source
2516917306maltose+carbon source
2516937684mannose+carbon source
2516917632nitrate+reduction
2516916634raffinose+carbon source
25169skimmed milk+fermentation
2516953258sodium citrate+carbon source
2516950144sodium pyruvate+carbon source
2516928017starch+hydrolysis
2516928017starch+carbon source
2516927082trehalose+carbon source
2516953423tween 40+hydrolysis
2516953425tween 60+hydrolysis
2516953426tween 80+hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
251692637amikacinyesyes30 µg (disc)
251693517cefuroximeyesyes30 µg (disc)
2516917698chloramphenicolyesyes30 µg (disc)
25169100241ciprofloxacinyesyes5 µg (disc)
2516948923erythromycinyesyes15 µg (disc)
2516917833gentamicinyesyes10 µg (disc)
2516928368novobiocinyesyes30 µg (disc)
2516917334penicillinyesyes10 Unit (disc)
251698232piperacillinyesyes100 µg (disc)
251698309polymyxin byesyes300 Unit (disc)
2516927902tetracyclineyesyes30 µg (disc)
2516986455optochinyesyes5 µg (disc)
25169100246norfloxacinyesyes10 µg (disc)
251697809oxacillinyesyes1 µg (disc)
251699332sulfamethoxazoleyesyes300 µg (disc)
2516928001vancomycinyesyes30 µg (disc)

metabolite production

  • @ref: 25169
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
25169catalase+1.11.1.6
25169cytochrome oxidase+1.9.3.1
25169urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25169C15:0 anteiso34.5
    25169C17:0 anteiso10.3
    25169C16:015.6
    25169C15:0 iso12.6
    25169C16:0 iso13.2
  • 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

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
24850surface-sterilized roots of Psammosilene tunicoidesPsammosilene tunicoidesYunnan, LijiangChinaCHNAsia
25169roots of Psammo- silene tunicoidesYECD mediumyeast 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 days28

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Allostreptomyces psammosilenae DSM 42178GCA_013407765contigncbi1892865
66792Allostreptomyces psammosilenae strain DSM 421781892865.3wgspatric1892865
66792Allostreptomyces psammosilenae DSM 421782823648918draftimg1892865

GC content

  • @ref: 24850
  • GC-content: 75.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.233no
gram-positiveyes90.496no
anaerobicno99.388no
aerobicyes94.052no
halophileno88.638no
spore-formingyes92.988yes
glucose-utilyes82.684yes
flagellatedno97.574no
thermophileno93.904yes
glucose-fermentno88.821no

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

@idauthorstitledoi/urlcataloguejournalpubmed
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
24850Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-42178Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 42178)
25169M. 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. 200910.1099/ijsem.0.001617IJSEM 67: 288-293 201727902296
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
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
91327Reimer, 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-ID400405.1