Strain identifier

BacDive ID: 13324

Type strain: Yes

Species: Pseudonocardia autotrophica

Strain Designation: 394, Kodai

Strain history: CIP <- 2001, CCM <- R. E. Gordon <- H. G. Schlegel <- P. Hirsch <- A. Takamiya

NCBI tax ID(s): 2074 (species)

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General

@ref: 130

BacDive-ID: 13324

DSM-Number: 535

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, human pathogen

description: Pseudonocardia autotrophica 394 is an obligate aerobe, spore-forming, mesophilic human pathogen that was isolated from phosphate buffer.

NCBI tax id

  • NCBI tax id: 2074
  • Matching level: species

strain history

@refhistory
130<- IMG <- P. Hirsch, 394 <- A. Takamiya, Kodai
67770KCC S-0348 <-- IFO 12743 <-- SAJ <-- ISP 5011 <-- A. Takamiya aa-1-1.
116652CIP <- 2001, CCM <- R. E. Gordon <- H. G. Schlegel <- P. Hirsch <- A. Takamiya

doi: 10.13145/bacdive13324.20230509.8.1

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 autotrophica
  • full scientific name: Pseudonocardia autotrophica (Takamiya and Tubaki 1956) Warwick et al. 1994

  • synonyms

    @refsynonym
    20215Proactinomyces autotrophicus
    20215Streptomyces autotrophicus
    20215Nocardia autotrophica
    20215Amycolata autotrophica

@ref: 130

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia autotrophica

full scientific name: Pseudonocardia autotrophica (Takamiya and Tubaki 1956) Warwick et al. 1994 emend. Nouioui et al. 2018

strain designation: 394, Kodai

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.22
69480100positive
116652nopositiverod-shaped

colony morphology

  • @ref: 116652

multimedia

  • @ref: 130
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_535.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
33085MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
130TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yesName: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/535
130GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yesName: 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 waterhttps://mediadive.dsmz.de/medium/65
116652CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
33085positivegrowth30mesophilic
130positivegrowth28mesophilic
67770positivegrowth28mesophilic
116652positivegrowth10-37
116652nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116652
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480no93.248

halophily

@refsaltgrowthtested relationconcentration
116652NaClpositivegrowth4 %
116652NaClnogrowth0 %
116652NaClnogrowth2 %
116652NaClnogrowth6 %
116652NaClnogrowth8 %
116652NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4), MK-8(H2), MK-8(H4)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
116652esculin-hydrolysis4853
116652hippurate-hydrolysis606565
116652nitrate+reduction17632
116652nitrite-reduction16301
116652nitrate-respiration17632

antibiotic resistance

  • @ref: 116652
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116652
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11665215688acetoin-
11665217234glucose-

enzymes

@refvalueactivityec
116652oxidase-
116652beta-galactosidase+3.2.1.23
116652alcohol dehydrogenase-1.1.1.1
116652gelatinase-
116652amylase-
116652DNase-
116652caseinase-3.4.21.50
116652catalase+1.11.1.6
116652tween esterase-
116652gamma-glutamyltransferase-2.3.2.2
116652lecithinase-
116652lipase-
116652lysine decarboxylase-4.1.1.18
116652ornithine decarboxylase-4.1.1.17
116652phenylalanine ammonia-lyase-4.3.1.24
116652tryptophan deaminase-
116652urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
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 zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116652-+++-++--------+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116652-----------------------------------------+/-------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116652+++++--+--+----+---+++---++----+++++++--+-------++------++-+--+--++---++---+---++-----+-+-++---+++-

Isolation, sampling and environmental information

isolation

@refsample type
130phosphate buffer
116652Contaminant in a phosphate buffer solution

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Laboratory

taxonmaps

  • @ref: 69479
  • File name: preview.99_32456.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_175;97_435;98_24033;99_32456&stattab=map
  • Last taxonomy: Pseudonocardia
  • 16S sequence: EU928972
  • Sequence Identity:
  • Total samples: 339
  • soil counts: 68
  • aquatic counts: 61
  • animal counts: 190
  • plant counts: 20

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
130yes, in single cases1Risk group (German classification)
1166522Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudonocardia autotrophica 16S ribosomal RNA gene, partial sequenceEU9289721380ena2074
20218Amycolata autotrophica (Nocardia a.) partial 16S rRNAX542881332ena2074
20218Pseudonocardia autotrophica 16S rRNA gene, strain IMSNU 20050TAJ2528241512ena2074

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudonocardia autotrophica NBRC 12743GCA_003945385completencbi2074
66792Pseudonocardia autotrophica strain DSM 5352074.6wgspatric2074
66792Pseudonocardia autotrophica strain DSM 5352074.12wgspatric2074
66792Pseudonocardia autotrophica strain NBRC 127432074.11wgspatric2074
66792Pseudonocardia autotrophica NBRC 127432856823606completeimg2074
66792Pseudonocardia autotrophica DSM 5352756170255draftimg2074
66792Pseudonocardia autotrophica DSM 5352856837300draftimg2074
67770Pseudonocardia autotrophica DSM 535GCA_002119215contigncbi2074
67770Pseudonocardia autotrophica DSM 535GCA_004361965contigncbi2074

GC content

@refGC-contentmethod
6777073genome sequence analysis
6777072thermal denaturation, midpoint method (Tm)
6777070thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno91.629no
flagellatedno97.777no
gram-positiveyes87.557no
anaerobicno98.865no
aerobicyes93.607no
halophileno82.455no
spore-formingyes68.254no
glucose-utilyes90.445no
glucose-fermentno93.364no
thermophileno99.071no

External links

@ref: 130

culture collection no.: DSM 535, ATCC 19727, CBS 466.68, DSM 40011, DSM 43210, IFO 12743, ISP 5011, KCC S-0348, NBRC 12743, RIA 1008, JCM 4348, BCRC 12444, CCM 2750, CECT 3301, CGMCC 4.1211, CGMCC 4.1297, CIP 107114, IMET 7646, IMSNU 11005, IMSNU 20050, KCTC 1816, KCTC 9564, KCTC 9574, NCIMB 9810, NRRL B-11275, VKM Ac-941

straininfo link

  • @ref: 82524
  • straininfo: 88622

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism15752735A gene cluster for the fatty acid catabolism from Pseudonocardia autotrophica BCRC12444.Chen CH, Cheng JC, Cho YC, Hsu WHBiochem Biophys Res Commun10.1016/j.bbrc.2005.02.0522005Actinomycetales/classification/*genetics/*metabolism, Amino Acid Sequence, Bacterial Proteins/chemistry/genetics/*metabolism, Catalysis, Fatty Acids/genetics/*metabolism, Molecular Sequence Data, Multigene Family/*physiology, Repressor Proteins/chemistry/genetics/*metabolism, Species Specificity, Transcription Factors/chemistry/genetics/*metabolismPhylogeny
Phylogeny19244441Pseudonocardia endophytica sp. nov., isolated from the pharmaceutical plant Lobelia clavata.Chen HH, Qin S, Li J, Zhang YQ, Xu LH, Jiang CL, Kim CJ, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.64740-02009Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis/isolation & purification, DNA, Ribosomal/analysis, Genes, rRNA, Lobelia/*microbiology, Medicine, Chinese Traditional, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plants, Medicinal/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityEnzymology
Enzymology19450562Purification, characterization, and directed evolution study of a vitamin D3 hydroxylase from Pseudonocardia autotrophica.Fujii Y, Kabumoto H, Nishimura K, Fujii T, Yanai S, Takeda K, Tamura N, Arisawa A, Tamura TBiochem Biophys Res Commun10.1016/j.bbrc.2009.05.0332009Actinomycetales/*enzymology, Amino Acid Sequence, Cholestanetriol 26-Monooxygenase/*chemistry/*genetics/isolation & purification/metabolism, Cloning, Molecular, *Directed Molecular Evolution, Molecular Sequence DataGenetics
Enzymology21144838Construction of a novel expression vector in Pseudonocardia autotrophica and its application to efficient biotransformation of compactin to pravastatin, a specific HMG-CoA reductase inhibitor.Fujii Y, Norihisa K, Fujii T, Aritoku Y, Kagawa Y, Sallam KI, Johdo O, Arisawa A, Tamura TBiochem Biophys Res Commun10.1016/j.bbrc.2010.12.0132010Acetone/pharmacology, Base Sequence, Biotransformation, Cloning, Molecular, Cytochrome P-450 Enzyme System/*genetics, Gene Expression/drug effects, Genetic Engineering, Genetic Vectors/*genetics, Hydroxymethylglutaryl-CoA Reductase Inhibitors/*metabolism, Industrial Microbiology/methods, Lovastatin/*analogs & derivatives/metabolism, Molecular Sequence Data, Plasmids/genetics, Pravastatin/*biosynthesis, Promoter Regions, Genetic/drug effects, Replication Origin, Streptomyces/genetics/*metabolismMetabolism
Phylogeny22733061Pseudonocardia nantongensis sp. nov., a novel endophytic actinomycete isolated from the coastal halophyte Tamarix chinensis Lour.Xing K, Qin S, Bian GK, Zhang YJ, Zhang WD, Dai CC, Liu CH, Li WJ, Jiang JHAntonie Van Leeuwenhoek10.1007/s10482-012-9764-52012Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Endophytes/*classification/genetics/*isolation & purification/physiology, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/microbiology, Sequence Analysis, DNA, Tamaricaceae/*microbiology, Ubiquinone/analysisEnzymology
Genetics28705965Draft Genome Sequences of Three Actinobacteria Strains Presenting New Candidate Organisms with High Potentials for Specific P450 Cytochromes.Grumaz C, Vainshtein Y, Kirstahler P, Luetz S, Kittelmann M, Schroer K, Eggimann FK, Czaja R, Vogel A, Hilberath T, Worsch A, Girhard M, Urlacher VB, Sandberg M, Sohn KGenome Announc10.1128/genomeA.00532-172017
Genetics30533676Complete Genome Sequence of an Efficient Vitamin D3-Hydroxylating Bacterium, Pseudonocardia autotrophica NBRC 12743.Yoshida K, Yasutake Y, Tamura TMicrobiol Resour Announc10.1128/MRA.01105-182018

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
130Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 535)https://www.dsmz.de/collection/catalogue/details/culture/DSM-535
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
33085Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4514
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82524Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88622.1StrainInfo: A central database for resolving microbial strain identifiers
116652Curators of the CIPCollection of Institut Pasteur (CIP 107114)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107114