Strain identifier

BacDive ID: 11146

Type strain: Yes

Species: Nocardioides humi

Strain history: <- DC Yang, Kyunghee Univ.

NCBI tax ID(s): 449461 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 16723

BacDive-ID: 11146

DSM-Number: 23133

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

description: Nocardioides humi DSM 23133 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from surface soil of a ginseng field.

NCBI tax id

  • NCBI tax id: 449461
  • Matching level: species

strain history

@refhistory
16723<- KCTC <- D.-C. Yang, Kyung Hee University, South Korea
67770D.-C. Yang DCY24.
67771<- DC Yang, Kyunghee Univ.

doi: 10.13145/bacdive11146.20230509.8.1

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 humi
  • full scientific name: Nocardioides humi Kim et al. 2009

@ref: 16723

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides humi

full scientific name: Nocardioides humi Kim et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
29218positive0.9 µm0.4 µmrod-shapedyes
67771positive

colony morphology

@refcolony colorincubation periodmedium used
18349Light grey (7035)10-14 daysISP 2
18349Light grey (7035)10-14 daysISP 3
18349Light grey (7035)10-14 daysISP 4
18349Light grey (7035)10-14 daysISP 5
18349Green beige (1000)10-14 daysISP 6
18349Cream (9001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18349noISP 2
18349noISP 3
18349noISP 4
18349noISP 5
18349noISP 6
18349noISP 7

pigmentation

  • @ref: 29218
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16723R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
18349ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18349ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18349ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18349ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18349ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18349ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
16723TRYPTICASE 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
16723GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16723positivegrowth28mesophilic
18349positiveoptimum28mesophilic
29218positivegrowth25-42
29218positiveoptimum33.5mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29218positivegrowth05-11alkaliphile
29218positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29218aerobe
67771aerobe

observation

@refobservation
67770quinones: MK-8(H4)
67771quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1834917234glucose+
1834922599arabinose-
1834917992sucrose+
1834918222xylose-
1834917268myo-inositol+
1834929864mannitol+
1834928757fructose+
1834926546rhamnose+
1834916634raffinose-
1834962968cellulose+
29218168082-dehydro-D-gluconate+carbon source
29218370543-hydroxybutyrate+carbon source
2921830089acetate+carbon source
2921816449alanine+carbon source
2921824265gluconate+carbon source
2921817234glucose+carbon source
2921828087glycogen+carbon source
2921817240itaconate+carbon source
2921825115malate+carbon source
2921829864mannitol+carbon source
2921828053melibiose+carbon source
2921826271proline+carbon source
2921817272propionate+carbon source
2921826546rhamnose+carbon source
2921833942ribose+carbon source
2921817822serine+carbon source
2921817992sucrose+carbon source
2921831011valerate+carbon source
292184853esculin+hydrolysis
2921817632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 29218
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 29218
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
29218acid phosphatase+3.1.3.2
29218alkaline phosphatase+3.1.3.1
29218alpha-galactosidase+3.2.1.22
29218catalase+1.11.1.6
29218gelatinase+
29218cytochrome oxidase+1.9.3.1
29218urease+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 (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
18349+/--+++-+-+-++/-+/-+/-+/-+/-+/---

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18349+++++++--++-+-++---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
16723surface soil of a ginseng fieldRepublic of KoreaKORAsia
67770Soil of a ginseng fieldRepublic of KoreaKORAsia
67771From soilRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_72779.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_30988;97_39197;98_50989;99_72779&stattab=map
  • Last taxonomy: Nocardioides humi subclade
  • 16S sequence: EF623863
  • Sequence Identity:
  • Total samples: 203
  • soil counts: 130
  • aquatic counts: 17
  • animal counts: 20
  • plant counts: 36

Safety information

risk assessment

  • @ref: 16723
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16723
  • description: Nocardioides humi strain DCY24 16S ribosomal RNA gene, partial sequence
  • accession: EF623863
  • length: 1478
  • database: ena
  • NCBI tax ID: 449461

Genome sequences

  • @ref: 67770
  • description: Nocardioides humi DCY24
  • accession: GCA_006494775
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 449461

GC content

@refGC-contentmethod
1672371.0high performance liquid chromatography (HPLC)
2921871
6777071high performance liquid chromatography (HPLC)
6777171.0

External links

@ref: 16723

culture collection no.: DSM 23133, KCTC 19265, LMG 24128, DCY 24, JCM 14942, JCM 17026

straininfo link

  • @ref: 80395
  • straininfo: 307678

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19625430Nocardioides humi sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field.Kim MK, Srinivasan S, Park MJ, Sathiyaraj G, Kim YJ, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.008821-02009Actinomycetales/classification/enzymology/genetics/*isolation & purification, Bacterial Proteins/*metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, *Panax, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, beta-Glucosidase/*metabolismMetabolism
Phylogeny20833879Nocardioides ultimimeridianus sp. nov. and Nocardioides maradonensis sp. nov., isolated from rhizosphere soil.Lee DW, Lee SY, Yoon JH, Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.022715-02010Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Apiaceae/*microbiology, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, *Soil MicrobiologyMetabolism
Phylogeny29683418Nocardioides pelophilus sp. nov., isolated from freshwater mud.Yan ZF, Lin P, Li CT, Kook M, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0027762018Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Fresh Water, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31513005Nocardioides sambongensis sp. nov., isolated from Dokdo Islands soil.Hwang YJ, Son JS, Lee SY, He Y, Jo Y, Shin JH, Ghim SYInt J Syst Evol Microbiol10.1099/ijsem.0.0036892020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Islands, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16723Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23133)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23133
18349Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM23133.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
29218Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2563928776041
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
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
80395Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID307678.1StrainInfo: A central database for resolving microbial strain identifiers