Strain identifier

BacDive ID: 132577

Type strain: Yes

Species: Isoptericola cucumis

Strain Designation: AP-38

Strain history: CIP <- 2015, P. Kämpfer, Giessen Univ., Giessen, Germany: strain AP-38

NCBI tax ID(s): 1776856 (species)

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General

@ref: 24366

BacDive-ID: 132577

DSM-Number: 101603

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

description: Isoptericola cucumis AP-38 is an obligate aerobe, thermophilic, Gram-positive bacterium that forms circular colonies and was isolated from internal root tissue of cucumber ; grown under greenhouse conditions.

NCBI tax id

  • NCBI tax id: 1776856
  • Matching level: species

strain history

@refhistory
24366<- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany; AP-38 <- G. Wei
67770CCM 8653 <-- S. P. Glaeser; Justus-Liebig-Univ. Giessen, Germany; AP-38.
118808CIP <- 2015, P. Kämpfer, Giessen Univ., Giessen, Germany: strain AP-38

doi: 10.13145/bacdive132577.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Promicromonosporaceae
  • genus: Isoptericola
  • species: Isoptericola cucumis
  • full scientific name: Isoptericola cucumis Kämpfer et al. 2016

@ref: 24366

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Promicromonosporaceae

genus: Isoptericola

species: Isoptericola cucumis

full scientific name: Isoptericola cucumis Kämpfer et al. 2016

strain designation: AP-38

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
43065positive1.5-2.5 µm0.9-1.5 µmrod-shapedno
118808positiverod-shapedno

colony morphology

  • @ref: 43065
  • colony color: yellow
  • colony shape: circular
  • medium used: TSA

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24366TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
43065Trypticase Soy Agar (TSA)yes
24366TRYPTICASE 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
118808CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
43065nogrowth50thermophilic
43065nogrowth5psychrophilic
43065positivegrowth10-45
43065positiveoptimum28mesophilic
24366positivegrowth28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
43065positiveoptimum7
43065positivegrowth5.5-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 43065
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
43065NaClpositivegrowth1-9 %
43065NaClpositivemaximum9 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-9(H2)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
43065casein+hydrolysis
43065gelatin+hydrolysis5291
43065hypoxanthine+hydrolysis17368
43065urea-hydrolysis16199
43065xanthine-hydrolysis15318
43065D-glucose+builds acid from17634
43065raffinose+builds acid from16634
43065D-xylose-builds acid from65327
43065lactose-builds acid from17716
43065sucrose-builds acid from17992
43065D-mannitol-builds acid from16899
43065galactitol-builds acid from16813
43065salicin-builds acid from17814
43065ribitol-builds acid from15963
43065myo-inositol-builds acid from17268
43065D-sorbitol-builds acid from17924
43065L-arabinose-builds acid from30849
43065L-rhamnose-builds acid from62345
43065maltose-builds acid from17306
43065trehalose-builds acid from27082
43065cellobiose-builds acid from17057
43065erythritol-builds acid from17113
43065melibiose-builds acid from28053
43065D-arabitol-builds acid from18333
43065D-arabinose+assimilation17108
43065N-acetylglucosamine+assimilation506227
43065D-fructose+assimilation15824
43065cellobiose+assimilation17057
43065D-galactose+assimilation12936
43065D-gluconate+assimilation8391
43065D-glucose+assimilation17634
43065maltose+assimilation17306
43065D-mannose+assimilation16024
43065L-rhamnose+assimilation62345
43065sucrose+assimilation17992
43065melibiose+assimilation28053
43065arbutin+assimilation18305
43065N-acetylgalactosamine+assimilation28037
43065ribose+assimilation33942
43065ribitol+assimilation15963
43065myo-inositol+assimilation17268
43065D-mannitol+assimilation16899
43065lactose+assimilation17716
43065raffinose+assimilation16634
43065trehalose+assimilation27082
43065D-xylose+assimilation65327
43065salicin-assimilation17814
43065D-sorbitol-assimilation17924
43065nitrate-reduction17632
43065D-arabitol+assimilation18333

enzymes

@refvalueactivityec
43065catalase+1.11.1.6
43065cytochrome oxidase-1.9.3.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43065C14:03
    43065C15:01.4
    43065C16:03.7
    43065C14:0 iso3.3
    43065C15:0 iso12.4
    43065C16:0 iso4.4
    43065C15:0 anteiso66.2
    43065C17:0 anteiso7.5
  • type of FA analysis: whole cell analysis
  • incubation medium: TSA
  • agar/liquid: agar
  • incubation temperature: 28
  • system: MIS MIDI
  • method/protocol: Kämpfer & Kroppenstedt 1996
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
24366internal root tissue of cucumber (Cucumis sativus); grown under greenhouse conditionsCucumis sativusAlabama, AuburnUSAUSANorth America
43065an endophyte from the healthy internal root tissue of cucumber (Cucumis sativus) grown in a greenhouseAuburn, Alabama, USAUSAUSANorth America
67770Root tissue of cucumber (Cucumis sativus)Cucumis sativusAuburn, ALUSAUSANorth America
118808Endophyt, cucumber grown under greenhouse cond.Auburn, Alabama, USAUnited States of AmericaUSANorth America1994-01-03

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3403.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1778;97_2128;98_2608;99_3403&stattab=map
  • Last taxonomy: Isoptericola
  • 16S sequence: KU201961
  • Sequence Identity:
  • Total samples: 1061
  • soil counts: 472
  • aquatic counts: 100
  • animal counts: 365
  • plant counts: 124

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
243661Risk group (German classification)
1188081Risk group (French classification)

Sequence information

16S sequences

  • @ref: 24366
  • description: Isoptericola cucumis strain AP-38 16S ribosomal RNA gene, partial sequence
  • accession: KU201961
  • length: 1443
  • database: ena
  • NCBI tax ID: 1776856

External links

@ref: 24366

culture collection no.: DSM 101603, LMG 29223, CCM 8653, JCM 31758, CIP 110981

straininfo link

  • @ref: 90894
  • straininfo: 400090

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27045419Isoptericola cucumis sp. nov., isolated from the root tissue of cucumber (Cucumis sativus).Kampfer P, Glaeser SP, Kloepper JW, Hu CH, McInroy JA, Martin K, Busse HJInt J Syst Evol Microbiol10.1099/ijsem.0.0010552016Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cucumis sativus/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33398399Puerhibacterium puerhi gen. nov., sp. nov., a novel member of the family Promicromonosporaceae, isolated from Pu-erh tea pile-fermentation.Yang RJ, Zhou, Wang QM, Han L, Peng WS, Liu L, Wang XJ, Yan L, Lv J, Sheng JArch Microbiol10.1007/s00203-020-02151-z2021Actinobacteria/classification/genetics, *Actinomycetales/classification/genetics, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Fermentation, Glycolipids/analysis, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity

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
24366Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101603Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101603)
43065Peter Kämpfer, Stefanie P. Glaeser, Joseph W. Kloepper, Chia-Hui Hu, John A. McInroy, Karin Martin and Hans-Jürgen BusseIsoptericola cucumis sp. nov., isolated from the root tissue of cucumber (Cucumis sativus)10.1099/ijsem.0.001055IJSEM 66: 2784-2788 201627045419
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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/
90894Reimer, 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-ID400090.1
118808Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110981Collection of Institut Pasteur (CIP 110981)