Strain identifier

BacDive ID: 11152

Type strain: Yes

Species: Nocardioides iriomotensis

Strain Designation: IR27-S3

Strain history: KACC 14926 <-- NBRC 105384 <-- M. Hayakawa IR27-S3.

NCBI tax ID(s): 715784 (species)

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General

@ref: 18127

BacDive-ID: 11152

DSM-Number: 25935

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

description: Nocardioides iriomotensis IR27-S3 is a mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 715784
  • Matching level: species

strain history

@refhistory
18127<- NBRC <- M. Hayakawa, Univ. Yamanashi; IR27-S3
67770KACC 14926 <-- NBRC 105384 <-- M. Hayakawa IR27-S3.

doi: 10.13145/bacdive11152.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides iriomotensis
  • full scientific name: Nocardioides iriomotensis Yamamura et al. 2011

@ref: 18127

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides iriomotensis

full scientific name: Nocardioides iriomotensis Yamamura et al. 2011

strain designation: IR27-S3

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colormedium used
69327ColorlessISP 3
69327ColorlessISP 4
69327Beige (1001)ISP 2
69327Beige (1001)ISP 6
69327Beige (1001)ISP 7
69327Ivory (1014)suter with tyrosine
69327Light ivory (1015)ISP 5
69327Light ivory (1015)suter without tyrosine

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69327noAerial myceliumISP 2
69327noAerial myceliumISP 3
69327noAerial myceliumISP 4
69327noAerial myceliumISP 5
69327noAerial myceliumISP 6
69327noAerial myceliumISP 7
69327noAerial myceliumsuter with tyrosine
69327noAerial myceliumsuter without tyrosine

pigmentation

@refproductionnamecolor
69327noMelanin
69327yessoluble pigmentOchre brown (8001)

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18127RICH MEDIUM (DSMZ Medium 736)yeshttps://mediadive.dsmz.de/medium/736Name: RICH MEDIUM (DSMZ Medium 736) Composition: Agar 20.0 g/l Bacto peptone 10.0 g/l Yeast extract 5.0 g/l Malt extract 5.0 g/l Casamino acids 5.0 g/l Glycerol 2.0 g/l Meat extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Tween 80 0.05 g/l Distilled water
18127TRYPTICASE 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

culture temp

@refgrowthtypetemperaturerange
18127positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 98.805

halophily

  • @ref: 69327
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6932722599arabinose-growth
6932762968cellulose-growth
6932728757fructose+growth
6932717234glucose-growth
6932717268inositol-growth
6932737684mannose+growth
6932716634raffinose-growth
6932726546rhamnose+growth
6932717992sucrose-growth
6932718222xylose-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
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 (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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69327-------------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69327-------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
18127soilOkinawa, Iriomote IslandJapanJPNAsia
67770Forest soil from Iriomote IslandOkinawaJapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

  • @ref: 18127
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18127
  • description: Nocardioides iriomotensis gene for 16S ribosomal RNA, partial sequence
  • accession: AB544079
  • length: 1463
  • database: ena
  • NCBI tax ID: 715784

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides iriomotensis strain NBRC 105384715784.3wgspatric715784
66792Nocardioides iriomotensis NBRC 1053842866601643draftimg715784
67770Nocardioides iriomotensis NBRC 105384GCA_004168035contigncbi715784

GC content

@refGC-contentmethod
1812773.7
6777073.7high performance liquid chromatography (HPLC)
6777072.2genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno75no
motileno60.114no
flagellatedno95.503no
gram-positiveyes89.707no
anaerobicno98.938no
aerobicyes91.349no
halophileno92.798no
spore-formingno79.018no
thermophileno98.48yes
glucose-utilyes86.636no
glucose-fermentno91.014yes

External links

@ref: 18127

culture collection no.: DSM 25935, JCM 17985, KACC 14926, NBRC 105384

straininfo link

  • @ref: 80401
  • straininfo: 402526

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20935090Nocardioides iriomotensis sp. nov., an actinobacterium isolated from forest soil.Yamamura H, Ohkubo SY, Nakagawa Y, Ishida Y, Hamada M, Otoguro M, Tamura T, Hayakawa MInt J Syst Evol Microbiol10.1099/ijs.0.025080-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Hydrogen-Ion Concentration, Japan, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature, TreesGenetics
Phylogeny27170166Nocardioides pakistanensis sp. nov., isolated from a hot water spring of Tatta Pani in Pakistan.Amin A, Ahmed I, Habib N, Abbas S, Xiao M, Hozzein WN, Li WJAntonie Van Leeuwenhoek10.1007/s10482-016-0711-82016Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Aerobiosis, Bacterial Typing Techniques, Diaminopimelic Acid/analysis, Fatty Acids/metabolism, Hot Springs/*microbiology, Nucleic Acid Hybridization, Pakistan, Phenotype, Phospholipids/metabolism, Phylogeny, Sequence Analysis, DNA, Sodium Chloride/metabolism, Water MicrobiologyMetabolism
Phylogeny31535964Nocardioides guangzhouensis sp. nov., an actinobacterium isolated from soil.Chen P, Fu Y, Cai Y, Lin ZInt J Syst Evol Microbiol10.1099/ijsem.0.0037262020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryTranscriptome
Phylogeny35647794Nocardioides panacis sp. nov., isolated from soil of a ginseng field.Park Y, Liu Q, Maeng S, Choi WJ, Chang Y, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0054002022*Actinomycetales, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nocardioides, *Panax, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
18127Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25935)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25935
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
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/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69327Wink, J.https://cdn.dsmz.de/wink/DSM%2025935.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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)
80401Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402526.1StrainInfo: A central database for resolving microbial strain identifiers