Strain identifier

BacDive ID: 141143

Type strain: Yes

Species: Nocardioides albidus

Strain Designation: THG-S11.7, THG-S11-7

Strain history: <- Tae-Hoo Yi, Kyung Hee univ.

NCBI tax ID(s): 1517589 (species)

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General

@ref: 44062

BacDive-ID: 141143

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

description: Nocardioides albidus THG-S11.7 is an aerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from garden soil sample.

NCBI tax id

  • NCBI tax id: 1517589
  • Matching level: species

strain history

@refhistory
67770CCTCC AB 2015297 <-- T.-H. Yi; Kyung Hee Univ., South Korea; THG-S11.7.
67771<- Tae-Hoo Yi, Kyung Hee univ.

doi: 10.13145/bacdive141143.20230509.8.1

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 albidus
  • full scientific name: Nocardioides albidus Singh et al. 2016

@ref: 44062

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Propionibacteriales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides albidus

strain designation: THG-S11.7, THG-S11-7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
44062positive1.0-1.2 µm1.0-1.2 µmcoccus-shapedno
69480positive99.999

colony morphology

  • @ref: 44062
  • colony size: 1.0-3.0 mm
  • colony color: white
  • colony shape: circular
  • incubation period: 3 days
  • medium used: Nutrient agar

pigmentation

  • @ref: 44062
  • production: no
  • name: Flexirubin-type

Culture and growth conditions

culture medium

@refnamegrowth
44062LAno
44062Marine agar (MA)yes
44062MacConkeyno
44062Nutrient agar (NA)yes
44062Reasoner's 2A agar (R2A)yes
44062Trypticase Soy Agar (TSA)no

culture temp

@refgrowthtypetemperaturerange
44062positivegrowth20-35
44062positiveoptimum28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepH
44062positivegrowth6.0-7.5
44062positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44062aerobe
67771aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.917

halophily

@refsaltgrowthtested relationconcentration
44062NaClpositivegrowth0.5-3.0 %(w/v)
44062NaClpositiveoptimum2 %(w/v)

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4406217128adipate-assimilation
4406227689decanoate-assimilation
4406216947citrate-assimilation
4406216899D-mannitol-assimilation
4406216024D-mannose-assimilation
4406230849L-arabinose-assimilation
4406225115malate-assimilation
4406217306maltose-assimilation
4406218401phenylacetate-assimilation
4406217234glucose-builds acid from
4406285146carboxymethylcellulose-hydrolysis
44062casein-hydrolysis
4406217029chitin-hydrolysis
4406216991dna-hydrolysis
440625291gelatin-hydrolysis
4406217895L-tyrosine-hydrolysis
4406228017starch-hydrolysis
4406216199urea-hydrolysis
4406217632nitrate-reduction
4406217634D-glucose+assimilation
4406224265gluconate+assimilation
44062506227N-acetylglucosamine+assimilation
440624853esculin+fermentation
440624853esculin+hydrolysis
4406253426tween 80+hydrolysis

metabolite production

  • @ref: 44062
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
44062catalase+1.11.1.6
44062cytochrome oxidase+1.9.3.1
44062arginine dihydrolase-3.5.3.6
44062urease-3.5.1.5
44062gelatinase-
44062alkaline phosphatase+3.1.3.1
44062esterase (C 4)+
44062esterase Lipase (C 8)+
44062leucine arylamidase+3.4.11.1
44062valine arylamidase+
44062cystine arylamidase+3.4.11.3
44062acid phosphatase+3.1.3.2
44062trypsin+3.4.21.4
44062alpha-glucosidase+3.2.1.20
44062beta-galactosidase+3.2.1.23
44062beta-glucosidase+3.2.1.21
44062lipase (C 14)-
44062alpha-chymotrypsin-3.4.21.1
44062alpha-galactosidase-3.2.1.22
44062beta-glucuronidase-3.2.1.31
44062naphthol-AS-BI-phosphohydrolase-
44062N-acetyl-beta-glucosaminidase-3.2.1.52
44062alpha-mannosidase-3.2.1.24
44062alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    44062C17:0 anteiso6.7
    44062C10:01
    44062C16:010
    4406210-methyl C17:01.2
    44062C17:1ω6c4.1
    44062C17:1ω8c1.1
    44062C18:1ω9c3
    44062C14:0 iso4.8
    44062C15:0 iso16.6
    44062C16:0 iso44.4
    44062C17:0 iso2.4
    44062C18:0 iso2.9
  • type of FA analysis: whole cell analysis
  • incubation medium: NA
  • incubation temperature: 28
  • incubation time: 2
  • library/peak naming table: TSBA6.1
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperature
44062garden soil sampleMichuhol library garden, IncheonRepublic of KoreaKORAsiaNA agar7 days28
67770Garden soilIncheonRepublic of KoreaKORAsia
67771From garden soil in IncheonRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Garden
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_15441.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_452;97_518;98_2479;99_15441&stattab=map
  • Last taxonomy: Nocardioides albidus
  • 16S sequence: KM073954
  • Sequence Identity:
  • Total samples: 36
  • soil counts: 17
  • aquatic counts: 5
  • animal counts: 4
  • plant counts: 10

Sequence information

16S sequences

  • @ref: 44062
  • description: 16S rRNA gene sequence
  • accession: KM073954
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides albidus strain CCTCC AB 20152971517589.3wgspatric1517589
66792Nocardioides albidus CCTCC AB 20152972902201542draftimg1517589
67770Nocardioides albidus CCTCC AB 2015297GCA_006335005scaffoldncbi1517589

GC content

  • @ref: 44062
  • GC-content: 72.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno74no
motileno75.913yes
gram-positiveyes90.125yes
anaerobicno97.716no
aerobicyes91.923yes
halophileno95.91no
spore-formingno77.994no
glucose-utilyes88.32no
flagellatedno92.958no
thermophileno95.617yes
glucose-fermentno89.846no

External links

@ref: 44062

culture collection no.: KCTC 39607, CCTCC AB 2015297, JCM 31749

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26530636Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil.Singh H, Du J, Trinh H, Won K, Yang JE, Yin C, Kook M, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0007302015Actinomycetales/*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/chemistryGenetics
Phylogeny31535960Nocardioides vastitatis sp. nov., isolated from Taklamakan desert soil.Liu SW, Xue CM, Li FN, Sun CHInt J Syst Evol Microbiol10.1099/ijsem.0.0037182020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, *Desert Climate, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
44062Hina Singh, Juan Du, Huan Trinh, KyungHwa Won, Jung-Eun Yang, ChangShik Yin, MooChang Kook and Tae-Hoo YiNocardioides albidus sp. nov., an actinobacterium isolated from garden soil10.1099/ijsem.0.000730IJSEM 66: 371-378 201626530636
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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