Strain identifier

BacDive ID: 13384

Type strain: Yes

Species: Pseudonocardia alaniniphila

Strain Designation: Y-16303

Strain history: CIP <- 2002, W.J. Li, Yunnan Univ., Kunming, China: strain Y-16303 <- CCTCC <- C.L. Jiang

NCBI tax ID(s): 75291 (species)

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General

@ref: 11856

BacDive-ID: 13384

DSM-Number: 44660

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive

description: Pseudonocardia alaniniphila Y-16303 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from primval forest soil.

NCBI tax id

  • NCBI tax id: 75291
  • Matching level: species

strain history

@refhistory
11856<- W.-J. Li; Y-16303 <- CIP <- CCTCC <- C.-L. Jiang
67770AS 4.1536 <-- C. L. Jiang Y-16303.
116174CIP <- 2002, W.J. Li, Yunnan Univ., Kunming, China: strain Y-16303 <- CCTCC <- C.L. Jiang

doi: 10.13145/bacdive13384.20230509.8.1

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 alaniniphila
  • full scientific name: Pseudonocardia alaniniphila (Xu et al. 1999) Huang et al. 2002

  • synonyms

    • @ref: 20215
    • synonym: Actinobispora alaniniphila

@ref: 11856

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia alaniniphila

full scientific name: Pseudonocardia alaniniphila (Xu et al. 1999) Huang et al. 2002

strain designation: Y-16303

type strain: yes

Morphology

cell morphology

  • @ref: 116174
  • gram stain: positive
  • motility: no

multimedia

  • @ref: 11856
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44660.jpg
  • caption: Medium 553 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11856GYM 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
33777MEDIUM 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)
116174CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperaturerange
11856positivegrowth28mesophilic
33777positivegrowth30mesophilic
67770positivegrowth28mesophilic
116174positivegrowth25-41
116174nogrowth10psychrophilic
116174nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116174
  • oxygen tolerance: facultative anaerobe

halophily

  • @ref: 116174
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11617416947citrate-carbon source
1161744853esculin-hydrolysis
116174606565hippurate-hydrolysis
11617417632nitrate+reduction
11617416301nitrite-reduction
11617417632nitrate+respiration

metabolite production

  • @ref: 116174
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11617415688acetoin+
11617417234glucose-

enzymes

@refvalueactivityec
116174oxidase-
116174beta-galactosidase-3.2.1.23
116174alcohol dehydrogenase+1.1.1.1
116174gelatinase-
116174catalase+1.11.1.6
116174gamma-glutamyltransferase-2.3.2.2
116174lysine decarboxylase-4.1.1.18
116174ornithine decarboxylase-4.1.1.17
116174phenylalanine ammonia-lyase-4.3.1.24
116174tryptophan deaminase-
116174urease-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
116174-+--------++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11856primval forest soilYunnan, XichouChinaCHNAsia
67770SoilXichou, YunnanChinaCHNAsia
116174Environment, SoilXichou, YunnanChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_24954.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1626;97_1946;98_18760;99_24954&stattab=map
  • Last taxonomy: Pseudonocardia
  • 16S sequence: FR733722
  • Sequence Identity:
  • Total samples: 3998
  • soil counts: 2822
  • aquatic counts: 175
  • animal counts: 266
  • plant counts: 735

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
118561Risk group (German classification)
1161742Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudonocardia alaniniphila partial 16S rRNA gene, type strain DSM44660TFR7337221512ena75291
67770Actinobispora alaniniphila 16S ribosomal RNA gene, partial sequenceAF0567081557ena75291
67770Actinobispora alaniniphila 16S ribosomal RNA gene, partial sequenceAF3257261400ena75291
67770Pseudonocardia alaniniphila strain YIM 16303 16S ribosomal RNA gene, partial sequenceEU7225191514ena75291

Genome sequences

  • @ref: 66792
  • description: Pseudonocardia alaniniphila Y-16303
  • accession: GCA_022524485
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 75291

GC content

  • @ref: 67770
  • GC-content: 69.3
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno98.207no
gram-positiveyes87.49no
anaerobicno98.675no
aerobicyes90.365no
halophileno93.626no
spore-formingyes70.719no
motileno91.838no
glucose-fermentno86.477no
thermophileno98.832yes
glucose-utilyes85.958no

External links

@ref: 11856

culture collection no.: DSM 44660, AS 4.1536, CCTCC AA 97001, CIP 107367, JCM 11837, CGMCC 4.1536

straininfo link

  • @ref: 82581
  • straininfo: 100470

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10319514Three new species of the genus Actinobispora of the family Pseudonocardiaceae, Actinobispora alaniniphila sp. nov., Actinobispora aurantiaca sp. nov. and Actinobispora xinjiangensis sp. nov.Xu LH, Jin X, Mao PH, Lu ZF, Cui XL, Jiang CLInt J Syst Bacteriol10.1099/00207713-49-2-8811999Actinomycetales/*classification/cytology/genetics/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/physiologyGenetics
Phylogeny28151383Pseudonocardia profundimaris sp. nov., isolated from marine sediment.Zhang G, Wang L, Li J, Zhou YInt J Syst Evol Microbiol10.1099/ijsem.0.0018492017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Glycolipids/chemistry, Nucleic Acid Hybridization, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11856Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44660)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44660
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
33777Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4795
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
82581Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100470.1StrainInfo: A central database for resolving microbial strain identifiers
116174Curators of the CIPCollection of Institut Pasteur (CIP 107367)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107367