Strain identifier

BacDive ID: 13369

Type strain: Yes

Species: Pseudonocardia asaccharolytica

Strain Designation: 580

Strain history: CIP <- 1998, A. Lipski, Osnabrück Univ., Osnabrück, Germany: strain 580

NCBI tax ID(s): 1123024 (strain), 54010 (species)

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General

@ref: 11620

BacDive-ID: 13369

DSM-Number: 44247

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

description: Pseudonocardia asaccharolytica 580 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from biofilter of waste gases.

NCBI tax id

NCBI tax idMatching level
54010species
1123024strain

strain history

@refhistory
11620<- K. Reichert, 580
372181998, A. Lipski, Univ. Osnabrück, Germany: strain 580
67770A. Lipski 580.
116516CIP <- 1998, A. Lipski, Osnabrück Univ., Osnabrück, Germany: strain 580

doi: 10.13145/bacdive13369.20230509.8.1

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 asaccharolytica
  • full scientific name: Pseudonocardia asaccharolytica Reichert et al. 1998

@ref: 11620

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia asaccharolytica

full scientific name: Pseudonocardia asaccharolytica Reichert et al. 1998 emend. Nouioui et al. 2018

strain designation: 580

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
116516positiverod-shapedno

multimedia

  • @ref: 11620
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44247.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11620TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
37218MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116516CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
11620positivegrowth28mesophilic
37218positivegrowth30mesophilic
67770positivegrowth25mesophilic
116516positivegrowth25-37mesophilic
116516nogrowth10psychrophilic
116516nogrowth41thermophilic
116516nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116516
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
116516NaClpositivegrowth2 %
116516NaClnogrowth0 %
116516NaClnogrowth4 %
116516NaClnogrowth6 %
116516NaClnogrowth8 %
116516NaClnogrowth10 %

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
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-tagatose-builds acid from16443
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
116516esculin-hydrolysis4853
116516hippurate+hydrolysis606565
116516nitrate+reduction17632
116516nitrite-reduction16301

metabolite production

  • @ref: 116516
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11651615688acetoin-
11651617234glucose-

enzymes

@refvalueactivityec
116516oxidase-
116516beta-galactosidase-3.2.1.23
116516alcohol dehydrogenase-1.1.1.1
116516gelatinase-
116516DNase-
116516caseinase-3.4.21.50
116516catalase+1.11.1.6
116516tween esterase-
116516gamma-glutamyltransferase-2.3.2.2
116516lecithinase-
116516lipase-
116516lysine decarboxylase-4.1.1.18
116516ornithine decarboxylase-4.1.1.17
116516phenylalanine ammonia-lyase-4.3.1.24
116516protease-
116516tryptophan deaminase-
116516urease-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
116516--++-+----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116516-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116516----------------------------------------+-------------+---------------------------------+------+---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
11620biofilter of waste gases
67770Tree-bark compost from biofilters
116516Experimental biofilterBrögbern, LingenGermanyDEUEurope1994

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioremediation#Biofilter
#Engineered#Waste#Waste gas

taxonmaps

  • @ref: 69479
  • File name: preview.99_3033.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1593;97_1901;98_2333;99_3033&stattab=map
  • Last taxonomy: Pseudonocardia asaccharolytica subclade
  • 16S sequence: Y08536
  • Sequence Identity:
  • Total samples: 389
  • soil counts: 266
  • aquatic counts: 13
  • animal counts: 38
  • plant counts: 72

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
116201Risk group (German classification)
1165162Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: P.asaccharolytica 16S rRNA gene
  • accession: Y08536
  • length: 1514
  • database: ena
  • NCBI tax ID: 54010

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudonocardia asaccharolytica DSM 442471123024.3wgspatric1123024
66792Pseudonocardia asaccharolytica DSM 44247 = NBRC 162241123024.5wgspatric1123024
66792Pseudonocardia asaccharolytica DSM 442472522572182draftimg1123024
67770Pseudonocardia asaccharolytica DSM 44247 = NBRC 16224GCA_000423625scaffoldncbi1123024
67770Pseudonocardia asaccharolytica DSM 44247 = NBRC 16224GCA_007989065contigncbi1123024

GC content

  • @ref: 67770
  • GC-content: 71.8
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes84no
motileno94.32no
flagellatedno98.568no
gram-positiveyes88.474no
anaerobicno97.636no
aerobicyes91.402no
halophileno88.017no
spore-formingyes66.411no
glucose-utilyes79.146no
thermophileno89.521yes
glucose-fermentno92.588no

External links

@ref: 11620

culture collection no.: DSM 44247, IFO 16224, NBRC 16224, JCM 10410, CGMCC 4.1535, CIP 105685, IMSNU 22142, NCIMB 13544

straininfo link

  • @ref: 82567
  • straininfo: 50532

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9731282Pseudonocardia asaccharolytica sp. nov. and Pseudonocardia sulfidoxydans sp. nov., two new dimethyl disulfide-degrading actinomycetes and emended description of the genus Pseudonocardia.Reichert K, Lipski A, Pradella S, Stackebrandt E, Altendorf KInt J Syst Bacteriol10.1099/00207713-48-2-4411998Actinomycetales/*classification/isolation & purification/metabolism/ultrastructure, Base Sequence, DNA, Bacterial, Disulfides/metabolism, Molecular Sequence Data, PhylogenyMetabolism
Phylogeny22899021Pseudonocardia hispaniensis sp. nov., a novel actinomycete isolated from industrial wastewater activated sludge.Cuesta G, Soler A, Alonso JL, Ruvira MA, Lucena T, Arahal DR, Goodfellow MAntonie Van Leeuwenhoek10.1007/s10482-012-9792-12012Actinomycetales/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, *Industrial Waste, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Spain, Vitamin K 2/analysis, Waste Water/*microbiologyGenetics
Metabolism276238201,4-Dioxane degradation potential of members of the genera Pseudonocardia and Rhodococcus.Inoue D, Tsunoda T, Sawada K, Yamamoto N, Saito Y, Sei K, Ike MBiodegradation10.1007/s10532-016-9772-72016Actinomycetales/*metabolism, Biodegradation, Environmental, Dioxanes/*metabolism, Furans/metabolism, Rhodococcus/*metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11620Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44247)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44247
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
37218Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17731
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)
82567Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50532.1StrainInfo: A central database for resolving microbial strain identifiers
116516Curators of the CIPCollection of Institut Pasteur (CIP 105685)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105685