Strain identifier

BacDive ID: 11192

Type strain: Yes

Species: Allonocardiopsis opalescens

Strain Designation: I10A-01259

Strain history: <- YQ Zhang, IMB, CAMS & Peking Union Medical College, China

NCBI tax ID(s): 1144618 (species)

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General

@ref: 17742

BacDive-ID: 11192

DSM-Number: 45601

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

description: Allonocardiopsis opalescens I10A-01259 is an aerobe, spore-forming, mesophilic bacterium that was isolated from From fruit of Lonicera maackii Maxim..

NCBI tax id

  • NCBI tax id: 1144618
  • Matching level: species

strain history

@refhistory
17742<- Y.-Q. Zhang, Chinese Academy Medical Sci. and Peking Union Medical College, Beijing, China; I10A-01259 <- H.-J. Du
67770KCTC 19844 <-- Y.-Q. Zhang; Inst. of Med. Biotechnol., Chin. Acad. Med. Sci. & Peking Union Med. Coll., China; I10A-01259.
67771<- YQ Zhang, IMB, CAMS & Peking Union Medical College, China

doi: 10.13145/bacdive11192.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Streptosporangiales, not assigned to family
  • genus: Allonocardiopsis
  • species: Allonocardiopsis opalescens
  • full scientific name: Allonocardiopsis opalescens Du et al. 2013

@ref: 17742

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiales, not assigned to family

genus: Allonocardiopsis

species: Allonocardiopsis opalescens

full scientific name: Allonocardiopsis opalescens Du et al. 2013 emend. Nouioui et al. 2018

strain designation: I10A-01259

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30666positiverod-shaped
67771positive
69480no97.721
69480positive100

colony morphology

@refcolony colormedium used
69411Ivory (1014)ISP 2
69411Ivory (1014)ISP 3
69411Ivory (1014)ISP 6
69411Ivory (1014) and sand yellow (1002)ISP 4
69411Light ivory (1015)ISP 5
69411Light ivory (1015)suter with tyrosine
69411Light ivory (1015)suter without tyrosine
69411Oyster white (1013)ISP 7

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69411noAerial myceliumISP 2
69411noAerial myceliumISP 3
69411noAerial myceliumISP 4
69411noAerial myceliumISP 5
69411noAerial myceliumISP 6
69411noAerial myceliumISP 7
69411noAerial myceliumsuter with tyrosine
69411noAerial myceliumsuter without tyrosine

pigmentation

@refproductionnamecolor
30666no
69411noMelanin
69411yessoluble pigmentIvory(1014), golden yellow (1004)

multimedia

@refmultimedia contentcaptionintellectual property rights
69411DSM_45601_image3.jpegPlates (535, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69411DSM_45601_image4.jpegPlates (535, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17742TRYPTICASE 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
17742GYM 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

culture temp

@refgrowthtypetemperaturerange
17742positivegrowth28mesophilic
30666positivegrowth20-40
30666positiveoptimum28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30666positivegrowth05-11alkaliphile
30666positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30666aerobe
67771aerobe

spore formation

@refspore formationconfidence
30666yes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
30666NaClpositivegrowth0-10 %
69411NaClpositivegrowth0-2.5 %

observation

@refobservation
30666aggregates in chains
67770quinones: MK-9, MK-11, MK-12, MK-10
67771quinones: MK-9, MK-11, MK-12, MK-10(minor)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3066630089acetate+carbon source
3066617057cellobiose+carbon source
3066623652dextrin+carbon source
3066615740formate+carbon source
3066628757fructose+carbon source
3066633984fucose+carbon source
3066624265gluconate+carbon source
3066617234glucose+carbon source
3066617306maltose+carbon source
3066629864mannitol+carbon source
3066637684mannose+carbon source
3066637657methyl D-glucoside+carbon source
3066617268myo-inositol+carbon source
3066630031succinate+carbon source
3066617992sucrose+carbon source
3066627082trehalose+carbon source
6941122599arabinose+growth
6941162968cellulose+/-growth
6941128757fructose+growth
6941117234glucose+growth
6941117268inositol+growth
6941137684mannose+growth
6941116634raffinose+/-growth
6941126546rhamnose+growth
6941117992sucrose+/-growth
6941118222xylose+growth
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
30666acid phosphatase+3.1.3.2
30666alkaline phosphatase+3.1.3.1
30666catalase+1.11.1.6
30666gelatinase+
30666urease+3.5.1.5
68379gelatinase+
68379urease+3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase+3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69411-+++-++++++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69411++/-++/-+++/-+/-+++/-+++++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
67771From fruit of Lonicera maackii (Rupr.)Maxim.BeijingChinaCHNAsia
17742surface-sterilized red fruit of Lonicera maackii (Rupr.) Maxim.BeijingChinaCHNAsiaLonicera maackii
67770Surface-sterilized red fruit of Lonicera maackii (Rupr.) Maxim., a medicinal plantsuburb of BeijingChinaCHNAsiaLonicera maackii

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Fruit (Seed)
#Host Body-Site#Plant#Sterilized plant part

taxonmaps

  • @ref: 69479
  • File name: preview.99_143101.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_54906;97_70812;98_95025;99_143101&stattab=map
  • Last taxonomy: Allonocardiopsis opalescens subclade
  • 16S sequence: JQ309825
  • Sequence Identity:
  • Total samples: 362
  • soil counts: 199
  • aquatic counts: 24
  • animal counts: 115
  • plant counts: 24

Safety information

risk assessment

  • @ref: 17742
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17742
  • description: Allonocardiopsis opalescens strain I10A-01259 16S ribosomal RNA gene, partial sequence
  • accession: JQ309825
  • length: 1476
  • database: ena
  • NCBI tax ID: 1144618

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Allonocardiopsis opalescens strain DSM 456011144618.3wgspatric1144618
66792Allonocardiopsis opalescens DSM 456012728369266draftimg1144618
67770Allonocardiopsis opalescens DSM 45601GCA_003002095scaffoldncbi1144618

GC content

@refGC-contentmethod
1774270.6thermal denaturation, midpoint method (Tm)
3066670.6
6777073.9genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno91.582no
flagellatedno98.226no
gram-positiveyes88.908no
anaerobicno99.19no
aerobicyes95.09no
halophileno65.833no
spore-formingyes90.51no
glucose-utilyes86.189yes
thermophileno96.946no
glucose-fermentno91.29yes

External links

@ref: 17742

culture collection no.: DSM 45601, CPCC 203428, KCTC 19844, JCM 31480, JCM 31481

straininfo link

  • @ref: 80441
  • straininfo: 406097

literature

  • topic: Phylogeny
  • Pubmed-ID: 22634703
  • title: Allonocardiopsis opalescens gen. nov., sp. nov., a new member of the suborder Streptosporangineae, from the surface-sterilized fruit of a medicinal plant.
  • authors: Du HJ, Zhang YQ, Liu HY, Su J, Wei YZ, Ma BP, Guo BL, Yu LY
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.041491-0
  • year: 2012
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Fruit/*microbiology, Lonicera/*microbiology, Molecular Sequence Data, *Phylogeny, Plants, Medicinal/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17742Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45601)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45601
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
30666Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2699728776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69411Wink, J.https://cdn.dsmz.de/wink/DSM%2045601.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
80441Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406097.1StrainInfo: A central database for resolving microbial strain identifiers