Strain identifier
BacDive ID: 13400
Type strain:
Species: Pseudonocardia acaciae
Strain history: CIP <- 2009, K. Duangmal, Kasetsart Univ., Bangkok, Thailand: strain GMKU095
NCBI tax ID(s): 1123023 (strain), 551276 (species)
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 id | Matching level |
---|---|
551276 | species |
1123023 | strain |
strain history
@ref | history |
---|---|
33650 | 2009, K. Duangmal, Kasetsart Univ., Bangkok, Thailand: strain GMKU095 |
16604 | <- C Suriyachadkun, BIOTEC Culture Collection (BCC); BCC 28481 <- K. Duangmal |
67770 | TISTR 1862 <-- K. Duangmal GMKU095. |
115987 | CIP <- 2009, K. Duangmal, Kasetsart Univ., Bangkok, Thailand: strain GMKU095 |
doi: 10.13145/bacdive13400.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Pseudonocardiales
- family: Pseudonocardiaceae
- genus: 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
@ref | gram stain | motility | confidence | cell shape |
---|---|---|---|---|
29165 | positive | no | ||
69480 | no | 96.109 | ||
69480 | positive | 100 | ||
115987 | positive | no | rod-shaped |
pigmentation
- @ref: 29165
- production: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
16604 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | 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 |
33650 | MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicum | yes | Distilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g) | |
115987 | CIP Medium 116 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16604 | positive | growth | 37 | mesophilic |
29165 | positive | growth | 18-42 | |
29165 | positive | optimum | 37 | mesophilic |
33650 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
29165 | positive | growth | 5.0-8.0 |
29165 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29165 | aerobe |
115987 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
29165 | yes | |
69481 | yes | 100 |
69480 | yes | 99.688 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29165 | NaCl | positive | growth | 0-5 % |
29165 | NaCl | positive | optimum | 2.5 % |
observation
@ref | observation |
---|---|
29165 | aggregates in chains |
67770 | quinones: MK-8(H4) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29165 | 15963 | ribitol | + | carbon source |
29165 | 22599 | arabinose | + | carbon source |
29165 | 28757 | fructose | + | carbon source |
29165 | 17234 | glucose | + | carbon source |
29165 | 17754 | glycerol | + | carbon source |
29165 | 29864 | mannitol | + | carbon source |
29165 | 37684 | mannose | + | carbon source |
29165 | 17268 | myo-inositol | + | carbon source |
29165 | 26546 | rhamnose | + | carbon source |
29165 | 33942 | ribose | + | carbon source |
29165 | 18222 | xylose | + | carbon source |
29165 | 17632 | nitrate | + | reduction |
115987 | 17632 | nitrate | + | reduction |
115987 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 115987
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
29165 | catalase | + | 1.11.1.6 |
29165 | urease | + | 3.5.1.5 |
115987 | oxidase | - | |
115987 | catalase | + | 1.11.1.6 |
115987 | urease | + | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
115987 | - | + | + | - | - | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | host species |
---|---|---|---|---|---|---|
16604 | roots of Acacia auriculiformis A. Cunn. ex. Benth. | Bangkok, Kasetsart University | Thailand | THA | Asia | |
67770 | Roots of Acacia auriculiformis A. Cunn. ex Benth. from Kasetsart Univ. | Bangkok | Thailand | THA | Asia | Acacia auriculiformis |
115987 | Plant, Roots, Acacia auriculiformis | Bangkok | Thailand | THA | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
16604 | 1 | Risk group (German classification) |
115987 | 2 | Risk 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: ena
- NCBI tax ID: 1123023
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudonocardia acaciae DSM 45401 | 1123023.3 | wgs | patric | 1123023 |
66792 | Pseudonocardia acaciae DSM 45401 | 2558860112 | draft | img | 1123023 |
67770 | Pseudonocardia acaciae DSM 45401 | GCA_000620785 | scaffold | ncbi | 1123023 |
GC content
@ref | GC-content | method |
---|---|---|
16604 | 71.6 | |
67770 | 71.6 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | no | 93.096 | no |
flagellated | no | 97.826 | no |
gram-positive | yes | 86.552 | yes |
anaerobic | no | 99.331 | yes |
aerobic | yes | 92.175 | yes |
halophile | no | 89.541 | no |
spore-forming | yes | 77.022 | no |
glucose-util | yes | 88.268 | yes |
thermophile | no | 98.332 | yes |
glucose-ferment | no | 90.229 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19502340 | Pseudonocardia acaciae sp. nov., isolated from roots of Acacia auriculiformis A. Cunn. ex Benth. | Duangmal K, Thamchaipenet A, Matsumoto A, Takahashi Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.007724-0 | 2009 | Acacia/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, Thailand | Genetics |
Phylogeny | 20418409 | Pseudonocardia eucalypti sp. nov., an endophytic actinobacterium with a unique knobby spore surface, isolated from roots of a native Australian eucalyptus tree. | Kaewkla O, Franco CMM | Int J Syst Evol Microbiol | 10.1099/ijs.0.022327-0 | 2010 | Actinomycetales/*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/cytology | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
16604 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45401) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45401 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
29165 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25589 | 28776041 | |
33650 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7875 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
82597 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID362848.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
115987 | Curators of the CIP | Collection of Institut Pasteur (CIP 110060) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110060 |