Strain identifier

BacDive ID: 132514

Type strain: Yes

Species: Nocardioides marmoriginsengisoli

Strain history: KACC 14267 <-- W.-T. Im; Hankyoung Natl. Univ., South Korea; Gsoil 097.

NCBI tax ID(s): 661483 (species)

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General

@ref: 24303

BacDive-ID: 132514

DSM-Number: 22772

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, rod-shaped, colony-forming

description: Nocardioides marmoriginsengisoli DSM 22772 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: 661483
  • Matching level: species

strain history

@refhistory
24303<- S. T. Lee, KAIST; Gsoil 097 <- W.-T. Im
67770KACC 14267 <-- W.-T. Im; Hankyoung Natl. Univ., South Korea; Gsoil 097.

doi: 10.13145/bacdive132514.20230509.8.1

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 marmoriginsengisoli
  • full scientific name: Nocardioides marmoriginsengisoli Wang et al. 2023

  • synonyms

    • @ref: 20215
    • synonym: Marmoricola ginsengisoli

@ref: 24303

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Marmoricola

species: Marmoricola ginsengisoli

full scientific name: Marmoricola ginsengisoli Lee et al. 2016

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43654positive0.8-1.4 µm0.3-0.4 µmrod-shapedno
69480positive100

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

@refnamegrowthlinkcomposition
43654Reasoner's 2A agar (R2A)yes
24303R2A 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

culture temp

@refgrowthtypetemperaturerange
43654positivegrowth10-37
43654positiveoptimum30mesophilic
24303positivegrowth28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
43654positivegrowth6-8
43654positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43654
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
43654no
69481no100
69480no99.602

halophily

@refsaltgrowthtested relationconcentrationhalophily level
43654NaClpositivegrowth0-1 %(w/v)
43654NaClpositiveoptimum0 %(w/v)non-halophilic

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
436542-oxogluconate-assimilation
436543-hydroxybenzoate-assimilation16193
436544-hydroxybenzoate-assimilation17879
436545-dehydro-D-gluconate-assimilation58143
43654adipate-assimilation17128
43654decanoate-assimilation27689
43654citrate-assimilation16947
43654D-mannitol-assimilation16899
43654D-mannose-assimilation16024
43654D-ribose-assimilation16988
43654D-sorbitol-assimilation17924
43654lactate-assimilation24996
43654gluconate-assimilation24265
43654myo-inositol-assimilation17268
43654itaconate-assimilation17240
43654L-alanine-assimilation16977
43654L-arabinose-assimilation30849
43654L-fucose-assimilation18287
43654L-histidine-assimilation15971
43654L-proline-assimilation17203
43654L-rhamnose-assimilation62345
43654L-serine-assimilation17115
43654malonate-assimilation15792
43654maltose-assimilation17306
43654melibiose-assimilation28053
43654N-acetylglucosamine-assimilation506227
43654phenylacetate-assimilation18401
43654salicin-assimilation17814
43654suberic acid-assimilation9300
43654sucrose-assimilation17992
43654glucose-fermentation17234
43654cellulose-hydrolysis62968
43654esculin-hydrolysis4853
43654gelatin-hydrolysis5291
43654starch-hydrolysis28017
43654nitrate-reduction17632
436543-hydroxybutyrate+assimilation37054
43654acetate+assimilation30089
43654D-glucose+assimilation17634
43654malate+assimilation25115
43654glycogen+assimilation28087
43654propionate+assimilation17272
43654valerate+assimilation31011
43654dna+hydrolysis16991
43654skimmed milk+hydrolysis

metabolite production

  • @ref: 43654
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43654catalase+1.11.1.6
43654cytochrome oxidase-1.9.3.1
43654esterase Lipase (C 8)+
43654alkaline phosphatase-3.1.3.1
43654lipase (C 14)-
43654leucine arylamidase-3.4.11.1
43654valine arylamidase-
43654cystine arylamidase-3.4.11.3
43654trypsin-3.4.21.4
43654beta-galactosidase-3.2.1.23
43654alpha-glucosidase-3.2.1.20
43654beta-glucosidase-3.2.1.21
43654esterase (C 4)+
43654acid phosphatase+3.1.3.2
43654naphthol-AS-BI-phosphohydrolase+
43654arginine dihydrolase-3.5.3.6
43654urease-3.5.1.5
43654alpha-chymotrypsin-3.4.21.1
43654alpha-galactosidase-3.2.1.22
43654beta-glucuronidase-3.2.1.31
43654N-acetyl-beta-glucosaminidase-3.2.1.52
43654alpha-mannosidase-3.2.1.24
43654alpha-fucosidase-3.2.1.51

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
24303soil from a ginseng fieldPocheon ProvinceRepublic of KoreaKORAsia
43654Soil of a ginseng fieldPocheon ProvinceRepublic of KoreaKORAsia
67770Ginseng field in Pocheon ProvinceRepublic of KoreaKORAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 24303
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24303
  • description: Marmoricola ginsengisoli strain Gsoil 097 16S ribosomal RNA gene, partial sequence
  • accession: GQ339892
  • length: 1454
  • database: ena
  • NCBI tax ID: 661483

Genome sequences

  • @ref: 67770
  • description: Marmoricola ginsengisoli Gsoil 097
  • accession: GCA_003725695
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 661483

GC content

  • @ref: 24303
  • GC-content: 68.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno74.02no
flagellatedno94.756yes
gram-positiveyes86.491yes
anaerobicno98.853no
aerobicyes90.225no
halophileno97.221yes
spore-formingno89.13yes
glucose-utilyes82.081yes
thermophileno97.403yes
glucose-fermentno88.538no

External links

@ref: 24303

culture collection no.: DSM 22772, KACC 14267, Gsoil 097, JCM 32748

straininfo link

  • @ref: 90840
  • straininfo: 401602

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26883120Marmoricola 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 WTInt J Syst Evol Microbiol10.1099/ijsem.0.0009772016Actinomycetales/*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/chemistryTranscriptome
Phylogeny29498616Marmoricola silvestris sp. nov., a novel actinobacterium isolated from alpine forest soil.Schumann P, Zhang DC, Franca L, Margesin RInt J Syst Evol Microbiol10.1099/ijsem.0.0026742018Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Forests, Italy, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny30821673Marmoricola mangrovicus sp. nov., an endophytic actinobacterium isolated from Kandelia candel.Li FN, Jiang ZK, Liu SW, Tuo L, Lee SM, Sun CHInt J Syst Evol Microbiol10.1099/ijsem.0.0033262019Actinobacteria/*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/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
24303Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-22772Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22772)
43654Hye-Yeon Lee, Qingmei Liu, Myung-Suk Kang, Soo-Ki Kim, Soon-Youl Lee, Wan-Taek ImMarmoricola ginsengisoli sp. nov. and Marmoricola pocheonensis sp. nov. isolated from a ginseng-cultivating field10.1099/ijsem.0.000977IJSEM 66: 1996-2001 201626883120
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
90840Reimer, 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 identifiers10.60712/SI-ID401602.1