Strain identifier

BacDive ID: 132134

Type strain: Yes

Species: Kibdelosporangium phytohabitans

Strain history: <- S Qin, Xuzhou Normal Univ., China

NCBI tax ID(s): 860235 (species)

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General

@ref: 23924

BacDive-ID: 132134

DSM-Number: 104448

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

description: Kibdelosporangium phytohabitans DSM 104448 is an aerobe, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from root of the oil-seed plant Jatropha curcas L.

NCBI tax id

  • NCBI tax id: 860235
  • Matching level: species

strain history

@refhistory
23924<- J. Liu, CCTCC; CCTCC AA 2010001
67770KCTC 19775 <-- S. Qin; Jiangsu Normal Univ., China; KLBMP 1111.
67771<- S Qin, Xuzhou Normal Univ., China

doi: 10.13145/bacdive132134.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Kibdelosporangium
  • species: Kibdelosporangium phytohabitans
  • full scientific name: Kibdelosporangium phytohabitans Xing et al. 2012

@ref: 23924

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Kibdelosporangium

species: Kibdelosporangium phytohabitans

full scientific name: Kibdelosporangium phytohabitans Xing et al. 2012 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

  • @ref: 67771
  • gram stain: positive

colony morphology

@refcolony colormedium used
69275Beige (1001), grey brown (8019)ISP 5
69275Grey brown (8019)ISP 2
69275Grey brown (8019)ISP 7
69275Grey brown (8019), olive grey (7002)ISP 6
69275Ivory (1014)suter without tyrosine
69275Light ivory (1015)ISP 3
69275Pale brown (8025), grey brown (8019)ISP 4
69275Sepia brown (8014), pale brown (8025)suter with tyrosine

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69275yesAerial myceliumSignal white (9003)ISP 2
69275yesAerial myceliumSignal white (9003)ISP 3
69275yesAerial myceliumSignal white (9003)ISP 4
69275yesAerial myceliumSignal white (9003)ISP 5
69275noAerial myceliumISP 6
69275yesAerial myceliumSignal white (9003)ISP 7
69275yesAerial myceliumSignal white (9003)suter with tyrosine
69275yesAerial myceliumSignal white (9003)suter without tyrosine

pigmentation

@refproductionnamecolor
69275yesMelanin
69275yessoluble pigmentJet black (9005)

multimedia

  • @ref: 23924
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_104448.jpg
  • caption: Medium 987 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 23924
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
23924positivegrowth28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

halophily

  • @ref: 69275
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2.5 %

observation

@refobservation
67770quinones: MK-9(H4)
67771quinones: MK-9(H_4_)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6927522599arabinose-growth
6927562968cellulose+/-growth
6927528757fructose+/-growth
6927517234glucose+growth
6927517268inositol+growth
6927537684mannose+/-growth
6927516634raffinose+/-growth
6927526546rhamnose+/-growth
6927517992sucrose+growth
6927518222xylose+growth
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

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
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69275-+-+--++--+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69275++/-++/-+++/-+++-+/---++++-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
23924root of the oil-seed plant Jatropha curcas LJatropha curcasSichuan provinceChinaCHNAsia
67770Healthy root of Jatropha curcas L., an oil-seed traditional Chinese medicinal plantJatropha curcascity of Panzhihua, Sichuan Province, south-west ChinaChinaCHNAsia
67771From plantSichuanChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3692.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_415;97_470;98_541;99_3692&stattab=map
  • Last taxonomy: Kibdelosporangium
  • 16S sequence: HM153787
  • Sequence Identity:
  • Total samples: 203
  • soil counts: 176
  • aquatic counts: 4
  • animal counts: 15
  • plant counts: 8

Safety information

risk assessment

  • @ref: 23924
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 23924
  • description: Kibdelosporangium phytohabitans strain KLBMP 1111 16S ribosomal RNA gene, partial sequence
  • accession: HM153787
  • length: 1436
  • database: ena
  • NCBI tax ID: 860235

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kibdelosporangium phytohabitans DSM 104448GCA_014873115contigncbi860235
66792Kibdelosporangium phytohabitans strain DSM 104448860235.7wgspatric860235
66792Kibdelosporangium phytohabitans strain KLBMP1111860235.4completepatric860235
66792Kibdelosporangium phytohabitans DSM 1044482873434522draftimg860235
67770Kibdelosporangium phytohabitans KLBMP1111GCA_001302585completencbi860235

GC content

@refGC-contentmethod
2392467.2
6777068.4genome sequence analysis
6777067.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno91.478no
flagellatedno96.827no
gram-positiveyes84.811yes
anaerobicno99.146yes
halophileno89.682no
spore-formingyes93.542no
thermophileno99.014yes
glucose-utilyes87.733yes
aerobicyes90.225yes
glucose-fermentno90.404yes

External links

@ref: 23924

culture collection no.: DSM 104448, CCTCC AA 2010001, KCTC 19775, KLBMP 1111, JCM 31487

straininfo link

  • @ref: 90490
  • straininfo: 407738

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21989686Kibdelosporangium phytohabitans sp. nov., a novel endophytic actinomycete isolated from oil-seed plant Jatropha curcas L. containing 1-aminocyclopropane-1-carboxylic acid deaminase.Xing K, Bian GK, Qin S, Klenk HP, Yuan B, Zhang YJ, Li WJ, Jiang JHAntonie Van Leeuwenhoek10.1007/s10482-011-9652-42011Actinomycetales/classification/*enzymology/genetics/*isolation & purification, Amino Acids, Cyclic/metabolism, Bacterial Proteins/genetics/*metabolism, Carbon-Carbon Lyases/genetics/*metabolism, China, Endophytes/classification/*enzymology/genetics/*isolation & purification, Fatty Acids/metabolism, Jatropha/metabolism/*microbiology, Molecular Sequence Data, Phylogeny, Plant Roots/metabolism/microbiologyMetabolism
Genetics26516119Complete genome sequence of Kibdelosporangium phytohabitans KLBMP 1111(T), a plant growth promoting endophytic actinomycete isolated from oil-seed plant Jatropha curcas L.Qin S, Feng WW, Xing K, Bai JL, Yuan B, Liu WJ, Jiang JHJ Biotechnol10.1016/j.jbiotec.2015.10.0172015Actinomycetales/*genetics/*isolation & purification, Base Sequence, Endophytes/*genetics, *Genome, Bacterial, Jatropha/*growth & development/*microbiology, Plant Oils, Seeds/*microbiologyEnzymology

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
23924Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104448Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104448)
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69275Wink, J.Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweighttps://cdn.dsmz.de/wink/DSM%20104448.pdf
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/
90490Reimer, 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-ID407738.1