Strain identifier

BacDive ID: 13400

Type strain: Yes

Species: Pseudonocardia acaciae

Strain history: CIP <- 2009, K. Duangmal, Kasetsart Univ., Bangkok, Thailand: strain GMKU095

NCBI tax ID(s): 1123023 (strain), 551276 (species)

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General

@ref: 16604

BacDive-ID: 13400

DSM-Number: 45401

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

description: Pseudonocardia acaciae DSM 45401 is an aerobe, spore-forming, mesophilic bacterium that was isolated from roots of Acacia auriculiformis A. Cunn. ex. Benth..

NCBI tax id

NCBI tax idMatching level
1123023strain
551276species

strain history

@refhistory
336502009, K. Duangmal, Kasetsart Univ., Bangkok, Thailand: strain GMKU095
16604<- C Suriyachadkun, BIOTEC Culture Collection (BCC); BCC 28481 <- K. Duangmal
67770TISTR 1862 <-- K. Duangmal GMKU095.
115987CIP <- 2009, K. Duangmal, Kasetsart Univ., Bangkok, Thailand: strain GMKU095

doi: 10.13145/bacdive13400.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Pseudonocardia
  • species: Pseudonocardia acaciae
  • full scientific name: Pseudonocardia acaciae Duangmal et al. 2009

@ref: 16604

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia acaciae

full scientific name: Pseudonocardia acaciae Duangmal et al. 2009

type strain: yes

Morphology

cell morphology

@refgram stainmotilitycell shapeconfidence
29165positiveno
115987positivenorod-shaped
125438no90.1
125439no91.3
125439positive99.9

pigmentation

  • @ref: 29165
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16604GYM 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
33650MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicumyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
115987CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperature
16604positivegrowth37
29165positivegrowth18-42
29165positiveoptimum37
33650positivegrowth37
67770positivegrowth37

culture pH

@refabilitytypepH
29165positivegrowth5.0-8.0
29165positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
29165aerobe
115987facultative anaerobe
125439obligate aerobe99.3

spore formation

@refspore formationconfidence
29165yes
125439yes91.1

halophily

@refsaltgrowthtested relationconcentration
29165NaClpositivegrowth0-5 %
29165NaClpositiveoptimum2.5 %

observation

@refobservation
29165aggregates in chains
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2916515963ribitol+carbon source
2916522599arabinose+carbon source
2916528757fructose+carbon source
2916517234glucose+carbon source
2916517754glycerol+carbon source
2916529864mannitol+carbon source
2916537684mannose+carbon source
2916517268myo-inositol+carbon source
2916526546rhamnose+carbon source
2916533942ribose+carbon source
2916518222xylose+carbon source
2916517632nitrate+reduction
11598717632nitrate+reduction
11598716301nitrite-reduction

metabolite production

  • @ref: 115987
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29165catalase+1.11.1.6
29165urease+3.5.1.5
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
115987oxidase-
115987catalase+1.11.1.6
115987urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
115987-++-------++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
16604roots of Acacia auriculiformis A. Cunn. ex. Benth.Bangkok, Kasetsart UniversityThailandTHAAsia
67770Roots of Acacia auriculiformis A. Cunn. ex Benth. from Kasetsart Univ.BangkokThailandTHAAsiaAcacia auriculiformis
115987Plant, Roots, Acacia auriculiformisBangkokThailandTHAAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6643.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_3149;97_3857;98_4899;99_6643&stattab=map
  • Last taxonomy: Pseudonocardia acaciae subclade
  • 16S sequence: EU921261
  • Sequence Identity:
  • Total samples: 1430
  • soil counts: 964
  • aquatic counts: 89
  • animal counts: 115
  • plant counts: 262

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
166041Risk group (German classification)
1159872Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16604
  • description: Pseudonocardia acaciae strain GMKU095 16S ribosomal RNA gene, partial sequence
  • accession: EU921261
  • length: 1483
  • database: nuccore
  • NCBI tax ID: 1123023

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudonocardia acaciae DSM 454011123023.3wgspatric1123023
66792Pseudonocardia acaciae DSM 454012558860112draftimg1123023
67770Pseudonocardia acaciae DSM 45401GCA_000620785scaffoldncbi1123023

GC content

@refGC-contentmethod
1660471.6
6777071.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.3
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.9
125439BacteriaNetmotilityAbility to perform movementno91.3
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes91.1
125438gram-positivegram-positivePositive reaction to Gram-stainingyes88.714yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.127yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes71.309yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes85.424no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96yes
125438motile2+flagellatedAbility to perform flagellated movementno90.1yes

External links

@ref: 16604

culture collection no.: DSM 45401, BCC 28481, NBRC 104274, NRRL B-24609, GMKU 095, TISTR 1862, JCM 16707, CIP 110060

straininfo link

  • @ref: 82597
  • straininfo: 362848

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19502340Pseudonocardia acaciae sp. nov., isolated from roots of Acacia auriculiformis A. Cunn. ex Benth.Duangmal K, Thamchaipenet A, Matsumoto A, Takahashi YInt J Syst Evol Microbiol10.1099/ijs.0.007724-02009Acacia/classification/genetics/*microbiology/physiology, Actinomycetales/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA Gyrase/genetics, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, Plant Roots/*microbiology, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, ThailandGenetics
Phylogeny20418409Pseudonocardia eucalypti sp. nov., an endophytic actinobacterium with a unique knobby spore surface, isolated from roots of a native Australian eucalyptus tree.Kaewkla O, Franco CMMInt J Syst Evol Microbiol10.1099/ijs.0.022327-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Australia, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Eucalyptus/*microbiology, Molecular Sequence Data, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial/cytologyGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16604Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45401)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45401
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
29165Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2558928776041
33650Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7875
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
82597Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362848.1StrainInfo: A central database for resolving microbial strain identifiers
115987Curators of the CIPCollection of Institut Pasteur (CIP 110060)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110060
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1