Strain identifier

BacDive ID: 159626

Type strain: Yes

Species: Streptomyces cavernae

Strain history: <- W.-J. Li, Sun Yat-Sen University, Guangzhou, China; SYSU K10008 <- B. Fang, Sun Yat-Sen University, Guangzhou, China; SYSU K10008

NCBI tax ID(s): 2259034 (species)

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General

@ref: 66461

BacDive-ID: 159626

DSM-Number: 104115

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

description: Streptomyces cavernae DSM 104115 is an aerobe, spore-forming, mesophilic bacterium that builds aerial hyphae and was isolated from karst cave soil.

NCBI tax id

  • NCBI tax id: 2259034
  • Matching level: species

strain history

  • @ref: 66461
  • history: <- W.-J. Li, Sun Yat-Sen University, Guangzhou, China; SYSU K10008 <- B. Fang, Sun Yat-Sen University, Guangzhou, China; SYSU K10008

doi: 10.13145/bacdive159626.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kitasatosporales
  • family: Streptomycetaceae
  • genus: Streptomyces
  • species: Streptomyces cavernae
  • full scientific name: Streptomyces cavernae Fang et al. 2020

@ref: 66461

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Streptomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces cavernae

full scientific name: Streptomyces cavernae Fang et al. 2019

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotility
69480positive100
69497positiveno

colony morphology

@refcolony colormedium used
69272Beige (1001), light ivory (1015)suter with tyrosine
69272Light ivory (1015)ISP 3
69272Light ivory (1015)suter without tyrosine
69272Light ivory (1015), sand yellow (1002)ISP 7
69272Oyster white (1013), ochre yellow (1024)ISP 5
69272Sand yellow (1002)ISP 2
69272Sand yellow (1002)ISP 6
69497ISP 2

multicellular morphology

@refforms multicellular complexcomplex namemedium namecomplex colorfurther description
69272noAerial myceliumISP 2
69272noAerial myceliumISP 3
69272noAerial myceliumISP 5
69272noAerial myceliumISP 6
69272noAerial myceliumISP 7
69272noAerial myceliumsuter with tyrosine
69272noAerial myceliumsuter without tyrosine
69497yesaerial hyphaeISP 3blackyellowish-brown extensively branched substrate mycelia

pigmentation

@refproductionname
69272noMelanin
69272nosoluble pigment

multimedia

  • @ref: 66461
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_104115.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
66461GYM 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
69497ISP 5yes
69497ISP 6yes
69497ISP 7yes
69497ISP 2yes

culture temp

@refgrowthtypetemperaturerange
66461positivegrowth28mesophilic
69497positivegrowth20.0-37.0
69497positiveoptimum28mesophilic

culture pH

  • @ref: 69497
  • ability: positive
  • type: growth
  • pH: 6.0-10.0

Physiology and metabolism

oxygen tolerance

  • @ref: 69497
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69480yes100
69481yes100

halophily

@refsaltgrowthtested relationconcentration
69272NaClpositivegrowth0-2.5 %
69497NaClpositivegrowth0.0-6.0 %(w/v)

observation

@refobservation
69497The polar lipid profile consists of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside.
69497ll-Diaminopimelic acid is the diagnostic diamino acid in cell-wall peptidoglycan.
69497The predominant menaquinone is MK-9(H6).

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6927222599arabinose+growth
6927262968cellulose+growth
6927228757fructose+growth
6927217234glucose+growth
6927217268inositol+growth
6927237684mannose+growth
6927216634raffinose+growth
6927226546rhamnose+growth
6927217992sucrose+growth
6927218222xylose+growth
6949728017starch-hydrolysis
6949753424tween 20-hydrolysis
6949753423tween 40-hydrolysis
6949753425tween 60-hydrolysis
6949716467L-arginine-nitrogen source
6949717561L-cysteine-nitrogen source
6949718019L-lysine-nitrogen source
6949716828L-tryptophan-nitrogen source
6949717632nitrate-reduction
6949717057cellobiose+carbon source
6949715824D-fructose+carbon source
6949712936D-galactose+carbon source
6949717634D-glucose+carbon source
6949716899D-mannitol+carbon source
6949716024D-mannose+carbon source
6949716988D-ribose+carbon source
6949717924D-sorbitol+carbon source
6949765327D-xylose+carbon source
6949717754glycerol+carbon source
6949730849L-arabinose+carbon source
6949762345L-rhamnose+carbon source
6949717716lactose+carbon source
6949717306maltose+carbon source
6949717268myo-inositol+carbon source
6949716634raffinose+carbon source
6949717992sucrose+carbon source
6949717151xylitol+carbon source
6949762968cellulose+hydrolysis
694975291gelatin+hydrolysis
6949753426tween 80+hydrolysis
6949715428glycine+nitrogen source
6949716977L-alanine+nitrogen source
6949729991L-aspartate+nitrogen source
6949729985L-glutamate+nitrogen source
6949718050L-glutamine+nitrogen source
6949715971L-histidine+nitrogen source
6949716643L-methionine+nitrogen source
6949717295L-phenylalanine+nitrogen source
6949717115L-serine+nitrogen source
6949716857L-threonine+nitrogen source
6949717895L-tyrosine+nitrogen source
6949716414L-valine+nitrogen source
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 69497
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
69497catalase+1.11.1.6
69497urease+3.5.1.5
69497cytochrome oxidase-1.9.3.1
68382alkaline phosphatase+3.1.3.1
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    69497anteiso-C15:015
    69497C16:020.4
    69497C16:1 w7c / C16:1 w6c10.2
    69497iso-C16:019
  • type of FA analysis: whole cell analysis
  • incubation medium: ISP 2
  • incubation temperature: 28
  • incubation time: 7
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69272+--+-+--+-+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69272++/-+/--+++/-+/--++++-++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
66461karst cave soilXingyiChinaCHNAsia
69497soil sample karst caveXingyi County, Guizhou ProvinceChinaCHNAsia25.15104.767humic acid-vitamin agarsupplemented with cycloheximide (50 mg/l) and nalidixic acid (20 mg/l)14 days28dilution plate method

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Geologic
#Environmental#Terrestrial#Soil

Sequence information

16S sequences

  • @ref: 66461
  • description: Streptomyces sp. SYSU K10008 16S ribosomal RNA gene, partial sequence
  • accession: MH553382
  • length: 1517
  • database: ena
  • NCBI tax ID: 2259034

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
69272Streptomyces cavernae SYSU K10008GCA_004023625scaffoldncbi2259034
69497genome sequenceRPDJ00000000ncbi2259034

GC content

@refGC-contentmethod
6646170.5sequence analysis
6949770.5genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.436no
flagellatedno98.116no
gram-positiveyes84.071no
anaerobicno98.955no
aerobicyes92.025no
halophileno92.541no
spore-formingyes94.02no
thermophileno98.994no
glucose-utilyes92.386yes
glucose-fermentno89.431yes

External links

@ref: 66461

culture collection no.: DSM 104115, KCTC 39850, SYSU K10008

straininfo link

  • @ref: 112100
  • straininfo: 408132

literature

  • topic: Phylogeny
  • Pubmed-ID: 31613202
  • title: Streptomyces cavernae sp. nov., a novel actinobacterium isolated from a karst cave sediment sample.
  • authors: Fang BZ, Han MX, Jiao JY, Xie YG, Zhang XT, Liu L, Zhang ZT, Xiao M, Li WJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003724
  • year: 2020
  • mesh: Bacterial Typing Techniques, Base Composition, Caves/*microbiology, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcatalogue
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
66461Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104115Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104115)
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69272Wink, J.Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweighttps://cdn.dsmz.de/wink/DSM%20104115.pdf
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
69497Bei Li, Yuying Li, Ronghua Liu, Chunxu Xue, Xiaoyu Zhu, Xiaorong Tian, Xiaolei Wang, Jinchang Liang, Yanfen Zheng, Xiao-Hua ZhangStreptomyces cavernae sp. nov., a novel actinobacterium isolated from a karst cave sediment sample10.1099/ijsem.0.003724
112100Reimer, 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-ID408132.1