Strain identifier
BacDive ID: 132515
Type strain:
Species: Nocardioides pocheonensis
Strain history: KACC 14275 <-- W.-T. Im; Hankyoung Natl. Univ., South Korea; Gsoil 818.
NCBI tax ID(s): 661485 (species)
General
@ref: 24304
BacDive-ID: 132515
DSM-Number: 22773
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, rod-shaped, colony-forming
description: Nocardioides pocheonensis DSM 22773 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from soil from a ginseng field.
NCBI tax id
- NCBI tax id: 661485
- Matching level: species
strain history
@ref | history |
---|---|
24304 | <- S.-T. Lee, KAIST <- W.-T. Im; Gsoil 818 |
67770 | KACC 14275 <-- W.-T. Im; Hankyoung Natl. Univ., South Korea; Gsoil 818. |
doi: 10.13145/bacdive132515.20230509.8.1
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 pocheonensis
- full scientific name: Nocardioides pocheonensis (Lee et al. 2016) Wang et al. 2023
synonyms
- @ref: 20215
- synonym: Marmoricola pocheonensis
@ref: 24304
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardioidaceae
genus: Marmoricola
species: Marmoricola pocheonensis
full scientific name: Marmoricola pocheonensis Lee et al. 2016
type strain: yes
Morphology
cell morphology
- @ref: 43654
- gram stain: positive
- cell length: 1-2 µm
- cell width: 0.3-0.4 µm
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 43654
- colony size: 0.5-1 mm
- colony color: Ivory
- colony shape: circular
- incubation period: 3 days
- medium used: R2A agar plates
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
43654 | Reasoner's 2A agar (R2A) | yes | ||
24304 | 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 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43654 | positive | growth | 10-40 | |
43654 | positive | optimum | 30 | mesophilic |
24304 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
43654 | positive | growth | 6-8 |
43654 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 43654
- oxygen tolerance: aerobe
spore formation
- @ref: 43654
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration | halophily level |
---|---|---|---|---|---|
43654 | NaCl | positive | growth | 0-2 %(w/v) | |
43654 | NaCl | positive | optimum | 0 %(w/v) | non-halophilic |
observation
- @ref: 67770
- observation: quinones: MK-8(H4)
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
43654 | 2-oxogluconate | - | assimilation | |
43654 | 3-hydroxybenzoate | - | assimilation | 16193 |
43654 | 5-dehydro-D-gluconate | - | assimilation | 58143 |
43654 | acetate | - | assimilation | 30089 |
43654 | decanoate | - | assimilation | 27689 |
43654 | citrate | - | assimilation | 16947 |
43654 | D-mannitol | - | assimilation | 16899 |
43654 | D-mannose | - | assimilation | 16024 |
43654 | D-ribose | - | assimilation | 16988 |
43654 | D-sorbitol | - | assimilation | 17924 |
43654 | lactate | - | assimilation | 24996 |
43654 | malate | - | assimilation | 25115 |
43654 | itaconate | - | assimilation | 17240 |
43654 | L-alanine 4-nitroanilide | - | assimilation | |
43654 | L-fucose | - | assimilation | 18287 |
43654 | L-rhamnose | - | assimilation | 62345 |
43654 | L-serine | - | assimilation | 17115 |
43654 | malonate | - | assimilation | 15792 |
43654 | maltose | - | assimilation | 17306 |
43654 | melibiose | - | assimilation | 28053 |
43654 | phenylacetate | - | assimilation | 18401 |
43654 | propionate | - | assimilation | 17272 |
43654 | salicin | - | assimilation | 17814 |
43654 | suberic acid | - | assimilation | 9300 |
43654 | sucrose | - | assimilation | 17992 |
43654 | glucose | - | fermentation | 17234 |
43654 | cellulose | - | hydrolysis | 62968 |
43654 | dna | - | hydrolysis | 16991 |
43654 | gelatin | - | hydrolysis | 5291 |
43654 | starch | - | hydrolysis | 28017 |
43654 | 3-hydroxybutyrate | + | assimilation | 37054 |
43654 | 4-hydroxybenzoate | + | assimilation | 17879 |
43654 | adipate | + | assimilation | 17128 |
43654 | D-glucose | + | assimilation | 17634 |
43654 | gluconate | + | assimilation | 24265 |
43654 | glycogen | + | assimilation | 28087 |
43654 | myo-inositol | + | assimilation | 17268 |
43654 | L-arabinose | + | assimilation | 30849 |
43654 | L-histidine | + | assimilation | 15971 |
43654 | L-proline | + | assimilation | 17203 |
43654 | N-acetylglucosamine | + | assimilation | 506227 |
43654 | valerate | + | assimilation | 31011 |
43654 | esculin | + | hydrolysis | 4853 |
43654 | skimmed milk | + | hydrolysis | |
43654 | nitrate | + | reduction | 17632 |
metabolite production
- @ref: 43654
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
43654 | catalase | + | 1.11.1.6 |
43654 | cytochrome oxidase | - | 1.9.3.1 |
43654 | esterase Lipase (C 8) | + | |
43654 | beta-galactosidase | + | 3.2.1.23 |
43654 | alpha-glucosidase | + | 3.2.1.20 |
43654 | beta-glucosidase | + | 3.2.1.21 |
43654 | alkaline phosphatase | - | 3.1.3.1 |
43654 | lipase (C 14) | - | |
43654 | leucine arylamidase | - | 3.4.11.1 |
43654 | valine arylamidase | - | |
43654 | cystine arylamidase | - | 3.4.11.3 |
43654 | trypsin | - | 3.4.21.4 |
43654 | esterase (C 4) | + | |
43654 | acid phosphatase | + | 3.1.3.2 |
43654 | naphthol-AS-BI-phosphohydrolase | + | |
43654 | arginine dihydrolase | - | 3.5.3.6 |
43654 | urease | - | 3.5.1.5 |
43654 | alpha-chymotrypsin | - | 3.4.21.1 |
43654 | alpha-galactosidase | - | 3.2.1.22 |
43654 | beta-glucuronidase | - | 3.2.1.31 |
43654 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
43654 | alpha-mannosidase | - | 3.2.1.24 |
43654 | alpha-fucosidase | - | 3.2.1.51 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
24304 | soil from a ginseng field | Pocheon Province | Republic of Korea | KOR | Asia |
43654 | Soil of a ginseng field | Pocheon Province | Republic of Korea | KOR | Asia |
67770 | Ginseng field in Pocheon Province | 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_56180.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_723;97_7475;98_40112;99_56180&stattab=map
- Last taxonomy: Marmoricola pocheonensis
- 16S sequence: GQ339906
- Sequence Identity:
- Total samples: 276
- soil counts: 226
- aquatic counts: 8
- animal counts: 22
- plant counts: 20
Safety information
risk assessment
- @ref: 24304
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24304
- description: Marmoricola pocheonensis strain Gsoil 818 16S ribosomal RNA gene, partial sequence
- accession: GQ339906
- length: 1457
- database: ena
- NCBI tax ID: 661485
Genome sequences
- @ref: 67770
- description: Marmoricola pocheonensis Gsoil 818
- accession: GCA_003725535
- assembly level: scaffold
- database: ncbi
- NCBI tax ID: 661485
GC content
@ref | GC-content | method |
---|---|---|
43654 | 70 | high performance liquid chromatography (HPLC) |
24304 | 70.0 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 76.265 | yes |
flagellated | no | 93.844 | yes |
gram-positive | yes | 88.278 | no |
anaerobic | no | 98.751 | yes |
aerobic | yes | 92.147 | yes |
halophile | no | 96.693 | yes |
spore-forming | no | 83.259 | yes |
glucose-util | yes | 88 | no |
thermophile | no | 95.181 | yes |
glucose-ferment | no | 88.528 | yes |
External links
@ref: 24304
culture collection no.: DSM 22773, KACC 14275, Gsoil 818, JCM 32749
straininfo link
- @ref: 90841
- straininfo: 406886
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 26883120 | Marmoricola ginsengisoli sp. nov. and Marmoricola pocheonensis sp. nov. isolated from a ginseng-cultivating field. | Lee HY, Liu Q, Kang MS, Kim SK, Lee SY, Im WT | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000977 | 2016 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Panax/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 30821673 | Marmoricola mangrovicus sp. nov., an endophytic actinobacterium isolated from Kandelia candel. | Li FN, Jiang ZK, Liu SW, Tuo L, Lee SM, Sun CH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003326 | 2019 | Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Bark/*microbiology, RNA, Ribosomal, 16S/genetics, Rhizophoraceae/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 31995462 | Marmoricola caldifontis sp. nov., a novel actinobacterium isolated from a hot spring. | Habib N, Khan IU, Xiao M, Li S, Saqib M, Xian WD, Butt S, Li WJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004016 | 2020 | Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Hot Springs/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
24304 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22773 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22773) | |||
43654 | Hye-Yeon Lee, Qingmei Liu, Myung-Suk Kang, Soo-Ki Kim, Soon-Youl Lee, Wan-Taek Im | Marmoricola ginsengisoli sp. nov. and Marmoricola pocheonensis sp. nov. isolated from a ginseng-cultivating field | 10.1099/ijsem.0.000977 | IJSEM 66: 1996-2001 2016 | 26883120 | |
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
90841 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID406886.1 |