Strain identifier
BacDive ID: 11145
Type strain:
Species: Nocardioides caeni
Strain Designation: MN8
Strain history: <- JH Yoon, KRIBB
NCBI tax ID(s): 574700 (species)
General
@ref: 16724
BacDive-ID: 11145
DSM-Number: 23134
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped
description: Nocardioides caeni MN8 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sludge of domestic wastewater.
NCBI tax id
- NCBI tax id: 574700
- Matching level: species
strain history
@ref | history |
---|---|
16724 | <- KCTC <- J. H. Yoon, KRIBB |
67770 | CCUG 57506 <-- J.-H. Yoon MN8. |
67771 | <- JH Yoon, KRIBB |
doi: 10.13145/bacdive11145.20230509.8.1
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 caeni
- full scientific name: Nocardioides caeni Yoon et al. 2009
@ref: 16724
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardioidaceae
genus: Nocardioides
species: Nocardioides caeni
full scientific name: Nocardioides caeni Yoon et al. 2009
strain designation: MN8
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29281 | positive | 1.6 µm | 0.5 µm | rod-shaped | no | |
67771 | positive | |||||
69480 | positive | 100 |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
19803 | Sand yellow | 10-14 days | ISP 2 |
61352 | 7 days |
multicellular morphology
- @ref: 19803
- forms multicellular complex: no
- medium name: ISP 2
pigmentation
- @ref: 29281
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
16724 | 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 |
19803 | 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 | |
16724 | 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 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16724 | positive | growth | 28 | mesophilic |
19803 | positive | optimum | 28 | mesophilic |
29281 | positive | growth | 10-35 | |
29281 | positive | optimum | 30 | mesophilic |
61352 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29281 | positive | growth | 6-9.5 | alkaliphile |
29281 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29281 | aerobe |
61352 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
29281 | no | |
69481 | no | 99 |
69480 | no | 99.974 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29281 | NaCl | positive | growth | 0-1 % |
29281 | NaCl | positive | optimum | 0.5 % |
observation
- @ref: 67770
- observation: quinones: MK-8(H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29281 | 22599 | arabinose | + | carbon source |
29281 | 17057 | cellobiose | + | carbon source |
29281 | 26546 | rhamnose | + | carbon source |
29281 | 53424 | tween 20 | + | carbon source |
29281 | 53423 | tween 40 | + | carbon source |
29281 | 53425 | tween 60 | + | carbon source |
29281 | 53426 | tween 80 | + | carbon source |
29281 | 4853 | esculin | + | hydrolysis |
68379 | 17632 | nitrate | - | reduction |
68379 | 4853 | esculin | - | hydrolysis |
68379 | 16199 | urea | - | hydrolysis |
68379 | 5291 | gelatin | - | hydrolysis |
68379 | 17634 | D-glucose | - | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | - | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17992 | sucrose | - | fermentation |
68379 | 28087 | glycogen | - | fermentation |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
29281 | 16136 | hydrogen sulfide | yes |
29281 | 35581 | indole | yes |
metabolite tests
- @ref: 29281
- Chebi-ID: 35581
- metabolite: indole
- indole test: +
enzymes
@ref | value | activity | ec |
---|---|---|---|
29281 | cytochrome oxidase | + | 1.9.3.1 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19803 | - | - | + | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19803 | + | + | + | + | + | + | + | - | - | + | + | - | - | - | + | + | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date |
---|---|---|---|---|---|---|
16724 | sludge of domestic wastewater | Daejeon | Republic of Korea | KOR | Asia | |
61352 | Sludge of a domestic wastewater | Taejon | Republic of Korea | KOR | Asia | 2006-01-01 |
67770 | Sludge of domestic wastewater | Republic of Korea | KOR | Asia | ||
67771 | From wastewater | Daejeon | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Waste | #Wastewater |
#Environmental | #Terrestrial | #Mud (Sludge) |
taxonmaps
- @ref: 69479
- File name: preview.99_88256.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_452;97_518;98_2479;99_88256&stattab=map
- Last taxonomy: Nocardioides caeni
- 16S sequence: FJ423551
- Sequence Identity:
- Total samples: 24
- soil counts: 14
- aquatic counts: 3
- animal counts: 7
Safety information
risk assessment
- @ref: 16724
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16724
- description: Nocardioides sp. MN8 16S ribosomal RNA gene, partial sequence
- accession: FJ423551
- length: 1474
- database: ena
- NCBI tax ID: 574700
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Nocardioides caeni strain DSM 23134 | 574700.3 | wgs | patric | 574700 |
67770 | Nocardioides caeni DSM 23134 | GCA_004912195 | scaffold | ncbi | 574700 |
GC content
@ref | GC-content | method |
---|---|---|
16724 | 71.5 | high performance liquid chromatography (HPLC) |
29281 | 71.5 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
gram-positive | yes | 91.04 | yes |
anaerobic | no | 98.047 | yes |
halophile | no | 96.667 | yes |
spore-forming | no | 86.873 | no |
glucose-util | yes | 89.442 | no |
thermophile | no | 98.644 | no |
motile | no | 78.819 | no |
flagellated | no | 92.458 | no |
aerobic | yes | 89.903 | yes |
glucose-ferment | no | 88.848 | no |
External links
@ref: 16724
culture collection no.: DSM 23134, CCUG 57506, KCTC 19600, JCM 19119
straininfo link
- @ref: 80394
- straininfo: 397370
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19628618 | Nocardioides caeni sp. nov., isolated from wastewater. | Yoon JH, Kang SJ, Park S, Kim W, Oh TK | Int J Syst Evol Microbiol | 10.1099/ijs.0.010124-0 | 2009 | Actinomycetales/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/*microbiology, *Water Microbiology | Metabolism |
Phylogeny | 26530636 | Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil. | Singh H, Du J, Trinh H, Won K, Yang JE, Yin C, Kook M, Yi TH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000730 | 2015 | Actinomycetales/*classification/genetics/isolation & purification, Agriculture, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 26802009 | Nocardioides flava sp. nov., isolated from rhizosphere of poppy plant, Republic of Korea. | Singh H, Yin CS | Arch Microbiol | 10.1007/s00203-015-1178-0 | 2016 | Actinomycetales/*classification/genetics/isolation & purification, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/metabolism, Fatty Acids/chemistry, Papaver/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species Specificity | Enzymology |
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 |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
16724 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23134) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23134 | ||||
19803 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM23134.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 | ||||
29281 | 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 | 25697 | 28776041 | ||
61352 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 57506) | https://www.ccug.se/strain?id=57506 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
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 | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
80394 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397370.1 | StrainInfo: A central database for resolving microbial strain identifiers |