Strain identifier

BacDive ID: 132433

Type strain: Yes

Species: Pseudoclavibacter endophyticus

Strain history: <- Wenjun Li

NCBI tax ID(s): 1778590 (species)

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

@ref: 24222

BacDive-ID: 132433

DSM-Number: 29943

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, rod-shaped, colony-forming

description: Pseudoclavibacter endophyticus DSM 29943 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from surface-sterilized healthy roots of Glycyrrhiza uralensis F..

NCBI tax id

  • NCBI tax id: 1778590
  • Matching level: species

strain history

@refhistory
24222<- W.-J. Li, YIM; EGI60007 <- L. Li
67770W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; EGI 60007.
67771<- Wenjun Li

doi: 10.13145/bacdive132433.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Pseudoclavibacter
  • species: Pseudoclavibacter endophyticus
  • full scientific name: Pseudoclavibacter endophyticus Li et al. 2016

@ref: 24222

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Pseudoclavibacter

species: Pseudoclavibacter endophyticus

full scientific name: Pseudoclavibacter endophyticus Li et al. 2016

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43744positive1.1-2.3 µm0.4-0.6 µmrod-shapedno
69480positive100
69480no96.031

colony morphology

  • @ref: 43744
  • colony color: White, opaque
  • colony shape: circular
  • incubation period: 7 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43744GYEAyes
43744LB (Luria-Bertani) MEDIUMyes
43744Reasoner's 2A agar (R2A)yes
43744Trypticase Soy Agar (TSA)yes
24222TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43744positivegrowth10-60
43744positiveoptimum25-35mesophilic
24222positivegrowth28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
43744positivegrowth7-9alkaliphile
43744positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43744aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
43744NaClpositivegrowth0-11 %(w/v)
43744NaClpositiveoptimum4 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4374422599arabinose-builds acid from
4374415824D-fructose-builds acid from
4374416024D-mannose-builds acid from
4374465327D-xylose-builds acid from
4374417234glucose-builds acid from
4374417754glycerol-builds acid from
4374417268myo-inositol-builds acid from
4374429864mannitol-builds acid from
4374428053melibiose-builds acid from
43744506227N-acetylglucosamine-builds acid from
4374426546rhamnose-builds acid from
4374430911sorbitol-builds acid from
4374417992sucrose-builds acid from
437445291gelatin-hydrolysis
4374415588D-malate-respiration
4374416651(S)-lactate-respiration
4374415589L-malate-respiration
43744167632-oxobutanoate-respiration
43744309162-oxoglutarate-respiration
43744645522-hydroxybutyrate-respiration
4374416947citrate-respiration
4374478697D-fructose 6-phosphate-respiration
437448391D-gluconate-respiration
4374414314D-glucose 6-phosphate-respiration
4374417754glycerol-respiration
4374451850methyl pyruvate-respiration
4374417268myo-inositol-respiration
43744506227N-acetylglucosamine-respiration
4374417309pectin-respiration
4374417272propionate-respiration
437444853esculin+fermentation
43744181014-hydroxyphenylacetic acid+respiration
4374430089acetate+respiration
4374413705acetoacetate+respiration
437448295beta-hydroxybutyrate+respiration
4374415824D-fructose+respiration
4374416899D-mannitol+respiration
4374415740formate+respiration
4374429991L-aspartate+respiration
4374429985L-glutamate+respiration

antibiotic resistance

@refmetaboliteis antibioticis sensitiveChEBI
437441 % sodium lactateyesyes
43744troleandomycinyesyes45735
43744lincomycinyesyes6472
43744tetrazolium violetyesyes75193
43744nalidixic acidyesyes100147
43744potassium telluriteyesyes75248
43744aztreonamyesyes161680
43744sodium butyrateyesyes64103
43744sodium bromateyesyes75229

metabolite production

  • @ref: 43744
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

enzymes

@refvalueactivityec
43744catalase+1.11.1.6
43744esterase (C 4)+
43744esterase Lipase (C 8)+
43744leucine arylamidase+3.4.11.1
43744valine arylamidase+
43744cystine arylamidase+3.4.11.3
43744naphthol-AS-BI-phosphohydrolase+
43744chymotrypsin+3.4.4.5
43744beta-glucosidase+3.2.1.21
43744cytochrome oxidase-1.9.3.1
43744lipase (C 14)-
43744alkaline phosphatase-3.1.3.1
43744acid phosphatase-3.1.3.2
43744trypsin-3.4.21.4
43744alpha-galactosidase-3.2.1.22
43744beta-galactosidase-3.2.1.23
43744beta-glucuronidase-3.2.1.31
43744alpha-glucosidase-3.2.1.20
43744beta-D-fucosidase-3.2.1.38
43744alpha-mannosidase-3.2.1.24
43744N-acetyl-beta-glucosaminidase-3.2.1.52
43744urease-3.5.1.5
43744gelatinase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43744C10:0 3OH1.1
    43744C12:010.9
    43744C12:0 3OH2.8
    43744C14:00.8
    43744C16:011.6
    43744C16:1ω5c0.5
    43744C16:1ω7c / C16:1ω6c8.2
    43744C17:00.8
    43744C17:0cyclo13
    43744C17:1ω8c0.9
    43744C18:00.6
    43744C18:1ω7c / C18:1ω6c18.3
    43744C18:1ω9c0.4
    43744C19:0ω8c-cyclo9.3
    43744C11:0 iso 3OH0.3
  • type of FA analysis: whole cell analysis
  • incubation medium: TSA
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Agilent 7890A
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitude
24222surface-sterilized healthy roots of Glycyrrhiza uralensis F.Glycyrrhiza uralensisXinjiang Province, Yili County (43.39° N 83.84° E)ChinaCHNAsia43.3983.84
43744Healthy root of Glycyrrhiza uralensis F. collected from Yili CountyYili County, Xinjiang ProvinceChinaCHNAsia
67770Healthy roots of Glycyrrhiza uralensis F. from Yili CountyGlycyrrhiza uralensisXinjiang Province, north-west ChinaChinaCHNAsia
67771From LiquoriceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Plant#Sterilized plant part
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

Safety information

risk assessment

  • @ref: 24222
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24222
  • description: Pseudoclavibacter endophyticus strain EGI 60007 16S ribosomal RNA gene, partial sequence
  • accession: KP721484
  • length: 1490
  • database: ena
  • NCBI tax ID: 1778590

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoclavibacter endophyticus CGMCC 1.15081GCA_014640595contigncbi1778590
66792Pseudoclavibacter endophyticus strain CGMCC 1.150811778590.4wgspatric1778590
67770Pseudoclavibacter endophyticus EGI 60007GCA_008831085contigncbi1778590

GC content

  • @ref: 24222
  • GC-content: 63.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.006yes
gram-positiveyes92.107no
anaerobicno99.521yes
aerobicyes95.146no
halophileno70.546no
spore-formingno92.695no
thermophileno99.392yes
glucose-utilyes83.863no
flagellatedno97.657yes
glucose-fermentno92.195no

External links

@ref: 24222

culture collection no.: DSM 29943, CGMCC 1.15081, KCTC 39112, EGI 60007, JCM 30633

straininfo link

  • @ref: 90772
  • straininfo: 407283

literature

  • topic: Phylogeny
  • Pubmed-ID: 26739161
  • title: Pseudoclavibacter endophyticus sp. nov., isolated from roots of Glycyrrhiza uralensis.
  • authors: Li YQ, Li L, Fu YS, Cui ZQ, Duan YQ, Salam N, Guo JW, Chen W, Li WJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000876
  • year: 2016

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
24222Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29943Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29943)
43744Yan-Qiong Li, Li Li, Yu-Song Fu, Zhao-Qiong Cui, Yan-Qing Duan, Nimaichand Salam, Jian-Wei Guo, Wei Chen, Wen-Jun LiPseudoclavibacter endophyticus sp. nov., isolated from roots of Glycyrrhiza uralensis10.1099/ijsem.0.000876IJSEM 66: 1287-1292 201626739161
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
90772Reimer, 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-ID407283.1