Strain identifier
BacDive ID: 11146
Type strain:
Species: Nocardioides humi
Strain history: <- DC Yang, Kyunghee Univ.
NCBI tax ID(s): 449461 (species)
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
@ref | history |
---|---|
16723 | <- KCTC <- D.-C. Yang, Kyung Hee University, South Korea |
67770 | D.-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
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
29218 | positive | 0.9 µm | 0.4 µm | rod-shaped | yes |
67771 | positive |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
18349 | Light grey (7035) | 10-14 days | ISP 2 |
18349 | Light grey (7035) | 10-14 days | ISP 3 |
18349 | Light grey (7035) | 10-14 days | ISP 4 |
18349 | Light grey (7035) | 10-14 days | ISP 5 |
18349 | Green beige (1000) | 10-14 days | ISP 6 |
18349 | Cream (9001) | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
18349 | no | ISP 2 |
18349 | no | ISP 3 |
18349 | no | ISP 4 |
18349 | no | ISP 5 |
18349 | no | ISP 6 |
18349 | no | ISP 7 |
pigmentation
- @ref: 29218
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
16723 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: 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 |
18349 | ISP 2 | yes | Name: 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 | |
18349 | ISP 3 | yes | Name: 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: | |
18349 | ISP 4 | yes | Name: 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 | |
18349 | ISP 5 | yes | Name: 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 | |
18349 | ISP 6 | yes | Name: 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 | |
18349 | ISP 7 | yes | Name: 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 | |
16723 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
16723 | GPHF-MEDIUM (DSMZ Medium 553) | yes | https://mediadive.dsmz.de/medium/553 | Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
16723 | positive | growth | 28 | mesophilic |
18349 | positive | optimum | 28 | mesophilic |
29218 | positive | growth | 25-42 | |
29218 | positive | optimum | 33.5 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29218 | positive | growth | 05-11 | alkaliphile |
29218 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29218 | aerobe |
67771 | aerobe |
observation
@ref | observation |
---|---|
67770 | quinones: MK-8(H4) |
67771 | quinones: MK-8(H4) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
18349 | 17234 | glucose | + | |
18349 | 22599 | arabinose | - | |
18349 | 17992 | sucrose | + | |
18349 | 18222 | xylose | - | |
18349 | 17268 | myo-inositol | + | |
18349 | 29864 | mannitol | + | |
18349 | 28757 | fructose | + | |
18349 | 26546 | rhamnose | + | |
18349 | 16634 | raffinose | - | |
18349 | 62968 | cellulose | + | |
29218 | 16808 | 2-dehydro-D-gluconate | + | carbon source |
29218 | 37054 | 3-hydroxybutyrate | + | carbon source |
29218 | 30089 | acetate | + | carbon source |
29218 | 16449 | alanine | + | carbon source |
29218 | 24265 | gluconate | + | carbon source |
29218 | 17234 | glucose | + | carbon source |
29218 | 28087 | glycogen | + | carbon source |
29218 | 17240 | itaconate | + | carbon source |
29218 | 25115 | malate | + | carbon source |
29218 | 29864 | mannitol | + | carbon source |
29218 | 28053 | melibiose | + | carbon source |
29218 | 26271 | proline | + | carbon source |
29218 | 17272 | propionate | + | carbon source |
29218 | 26546 | rhamnose | + | carbon source |
29218 | 33942 | ribose | + | carbon source |
29218 | 17822 | serine | + | carbon source |
29218 | 17992 | sucrose | + | carbon source |
29218 | 31011 | valerate | + | carbon source |
29218 | 4853 | esculin | + | hydrolysis |
29218 | 17632 | nitrate | + | reduction |
68379 | 4853 | esculin | + | hydrolysis |
68379 | 16199 | urea | - | hydrolysis |
68379 | 5291 | gelatin | + | hydrolysis |
68379 | 17992 | sucrose | - | fermentation |
68379 | 28087 | glycogen | - | fermentation |
metabolite production
- @ref: 29218
- Chebi-ID: 35581
- metabolite: indole
- production: yes
metabolite tests
- @ref: 29218
- Chebi-ID: 35581
- metabolite: indole
- indole test: +
enzymes
@ref | value | activity | ec |
---|---|---|---|
29218 | acid phosphatase | + | 3.1.3.2 |
29218 | alkaline phosphatase | + | 3.1.3.1 |
29218 | alpha-galactosidase | + | 3.2.1.22 |
29218 | catalase | + | 1.11.1.6 |
29218 | gelatinase | + | |
29218 | cytochrome oxidase | + | 1.9.3.1 |
29218 | urease | + | 3.5.1.5 |
68379 | gelatinase | + | |
68379 | urease | - | 3.5.1.5 |
68379 | beta-glucosidase | + | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68379 | alpha-glucosidase | + | 3.2.1.20 |
68379 | beta-galactosidase | - | 3.2.1.23 |
68379 | beta-glucuronidase | + | 3.2.1.31 |
68379 | alkaline phosphatase | + | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | + | 3.4.19.3 |
68379 | pyrazinamidase | - | 3.5.1.B15 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18349 | +/- | - | + | + | + | - | + | - | + | - | + | +/- | +/- | +/- | +/- | +/- | +/- | - | - |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18349 | + | + | + | + | + | + | + | - | - | + | + | - | + | - | + | + | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
16723 | surface soil of a ginseng field | Republic of Korea | KOR | Asia |
67770 | Soil of a ginseng field | Republic of Korea | KOR | Asia |
67771 | From soil | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | GC-content | method |
---|---|---|
16723 | 71.0 | high performance liquid chromatography (HPLC) |
29218 | 71 | |
67770 | 71 | high performance liquid chromatography (HPLC) |
67771 | 71.0 |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19625430 | Nocardioides 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 DC | Int J Syst Evol Microbiol | 10.1099/ijs.0.008821-0 | 2009 | Actinomycetales/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/*metabolism | Metabolism |
Phylogeny | 20833879 | Nocardioides ultimimeridianus sp. nov. and Nocardioides maradonensis sp. nov., isolated from rhizosphere soil. | Lee DW, Lee SY, Yoon JH, Lee SD | Int J Syst Evol Microbiol | 10.1099/ijs.0.022715-0 | 2010 | Actinomycetales/*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 Microbiology | Metabolism |
Phylogeny | 29683418 | Nocardioides pelophilus sp. nov., isolated from freshwater mud. | Yan ZF, Lin P, Li CT, Kook M, Yi TH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002776 | 2018 | Actinomycetales/*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/chemistry | Transcriptome |
Phylogeny | 31513005 | Nocardioides sambongensis sp. nov., isolated from Dokdo Islands soil. | Hwang YJ, Son JS, Lee SY, He Y, Jo Y, Shin JH, Ghim SY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003689 | 2020 | Actinobacteria/*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 Microbiology | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
16723 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23133) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23133 | |||
18349 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM23133.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
29218 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25639 | 28776041 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
68379 | Automatically annotated from API Coryne | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
80395 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID307678.1 | StrainInfo: A central database for resolving microbial strain identifiers |