Strain identifier

BacDive ID: 133079

Type strain: Yes

Species: Nocardioides cavernae

Strain history: W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM A1136.

NCBI tax ID(s): 1921566 (species)

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General

@ref: 24867

BacDive-ID: 133079

DSM-Number: 29950

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

description: Nocardioides cavernae DSM 29950 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from soil, karst cave.

NCBI tax id

  • NCBI tax id: 1921566
  • Matching level: species

strain history

@refhistory
24867<- W.-J. Li, Yunnan Institute of Microbiology, Kunming; YIM A1136 <- W. Zhang
67770W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM A1136.

doi: 10.13145/bacdive133079.20230509.8.1

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 cavernae
  • full scientific name: Nocardioides cavernae Han et al. 2017

@ref: 24867

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides cavernae

full scientific name: Nocardioides cavernae Han et al. 2017

type strain: yes

Morphology

cell morphology

  • @ref: 25227
  • gram stain: positive
  • cell length: 2.0-6.0 µm
  • cell width: 0.2-0.5 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 25227
  • colony color: opaque yellowish- white
  • colony shape: circular
  • incubation period: 4 days
  • medium used: Reasoner’s 2A agar (R2A, Difco)

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24867TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
25227Reasoner’s 2A agar (R2A, Difco)yes
24867R2A 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
25227positivegrowth4-35
25227positiveoptimum28mesophilic
24867positivegrowth28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
25227positivegrowth6.0-8.0
25227positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 25227
  • oxygen tolerance: aerobe

spore formation

  • @ref: 25227
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
25227NaClpositivegrowth0.0-5.0 %(w/v)
25227NaCloptimum0 %(w/v)

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2522717128adipate-assimilation
2522762968cellulose-hydrolysis
2522716899D-mannitol-assimilation
2522716024D-mannose-assimilation
252275291gelatin-hydrolysis
2522717234glucose-fermentation
2522730849L-arabinose-assimilation
2522717306maltose-assimilation
25227506227N-acetylglucosamine-assimilation
2522717632nitrate-reduction
2522718401phenylacetate-assimilation
25227skimmed milk-fermentation
2522728017starch-hydrolysis
2522753424tween 20-hydrolysis
2522753426tween 80-hydrolysis
25227309162-oxoglutarate+oxidation
2522730089acetate+oxidation
2522717925alpha-D-glucose+oxidation
2522716947citrate+oxidation
252278391D-gluconate+oxidation
2522717634D-glucose+assimilation
2522727689decanoate+assimilation
252274853esculin+hydrolysis
2522771321fusidate+oxidation
2522716537galactarate+oxidation
2522717754glycerol+oxidation
2522729985L-glutamate+oxidation
2522715589L-malate+oxidation
2522717115L-serine+oxidation
2522724996lactate+oxidation
252276472lincomycin+oxidation
2522725115malate+assimilation
25227100147nalidixic acid+hydrolysis
2522775273niaproof+oxidation
2522732032potassium gluconate+assimilation
2522775248potassium tellurite+oxidation
2522717272propionate+oxidation
2522726490quinate+oxidation
2522729673rifamycin sv+oxidation
2522775229sodium bromate+oxidation
2522753258sodium citrate+assimilation
2522775198tetrazolium blue+oxidation
2522775193tetrazolium violet+oxidation
2522745735troleandomycin+oxidation
2522753423tween 40+hydrolysis
2522753425tween 60+hydrolysis
2522728001vancomycin+oxidation

metabolite production

@refChebi-IDmetaboliteproduction
2522716136hydrogen sulfideno
2522735581indoleno

enzymes

@refvalueactivityec
25227acid phosphatase-3.1.3.2
25227alkaline phosphatase-3.1.3.1
25227alpha-chymotrypsin-3.4.21.1
25227alpha-galactosidase-3.2.1.22
25227alpha-glucosidase-3.2.1.20
25227alpha-mannosidase-3.2.1.24
25227arginine dihydrolase-3.5.3.6
25227beta-D-fucosidase-3.2.1.38
25227beta-galactosidase-3.2.1.23
25227beta-glucosidase-3.2.1.21
25227beta-glucuronidase-3.2.1.31
25227catalase+1.11.1.6
25227cystine arylamidase-3.4.11.3
25227cytochrome oxidase-1.9.3.1
25227esterase (C 4)+
25227esterase Lipase (C 8)+
25227leucine arylamidase+3.4.11.1
25227lipase (C 14)-
25227N-acetyl-beta-glucosaminidase-3.2.1.52
25227naphthol-AS-BI-phosphohydrolase+
25227trypsin-3.4.21.4
25227urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25227C10:0 3OH6.2
    25227C12:0 2OH8.8
    25227C12:0 3OH8.5
    25227C16:026.7
    25227C16:1ω7c / C16:1ω6c15.7
    25227C17:0 cyclo9.2
    25227C18:1ω7c / C18:1ω6c17.5
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 1
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA 6
  • system: MIS MIDI
  • method/protocol: Collins 1980
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
24867soil, karst caveGuizhou province, Xingyi county (25° 09' N 104° 46' E)ChinaCHNAsia25.15104.767
25227Reasonerâ??s 2A agar (R2A, Difco)supplemented with cycloheximide (50 mg/l) and nalidixic acid (20 mg/l)2 weeks28standard dilution plate method
67770Soil from a karst cave in Xingyi CountyGuizhou Province, south-western ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Geologic
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_20569.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_2445;97_2980;98_3734;99_20569&stattab=map
  • Last taxonomy: Nocardioides
  • 16S sequence: KX815990
  • Sequence Identity:
  • Total samples: 190
  • soil counts: 110
  • aquatic counts: 13
  • animal counts: 53
  • plant counts: 14

Safety information

risk assessment

  • @ref: 24867
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24867
  • description: Nocardioides cavernae strain YIM A1136 16S ribosomal RNA gene, partial sequence
  • accession: KX815990
  • length: 1507
  • database: ena
  • NCBI tax ID: 1921566

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides cavernae DSM 29950GCA_016907475contigncbi1921566
66792Nocardioides cavernae KCTC 39551GCA_014779675contigncbi1921566
66792Nocardioides cavernae strain DSM 299501921566.5wgspatric1921566
66792Nocardioides cavernae strain KCTC 395511921566.4wgspatric1921566
66792Nocardioides cavernae DSM 299502893570996draftimg1921566

GC content

  • @ref: 24867
  • GC-content: 71.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno95.321yes
gram-positiveyes92.328yes
anaerobicno99.123yes
aerobicyes93.832yes
halophileno94.371no
spore-formingno87.268no
glucose-utilyes86.053yes
flagellatedno98.551no
thermophileno98.951yes
glucose-fermentno91.223no

External links

@ref: 24867

culture collection no.: DSM 29950, KCTC 39551, YIM A1136, JCM 30631

straininfo link

  • @ref: 91344
  • straininfo: 404125

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27902315Nocardioides cavernae sp. nov., an actinobacterium isolated from a karst cave.Han MX, Fang BZ, Tian Y, Zhang WQ, Jiao JY, Liu L, Zhang ZT, Xiao M, Wei DQ, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0016762017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny34542392Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula.Chhetri G, Kim I, Kang M, Kim J, So Y, Seo TInt J Syst Evol Microbiol10.1099/ijsem.0.0050122021*Actinobacteria/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nocardioides, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *TagetesTranscriptome

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
24867Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29950Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29950)
25227M. X. F. Han, B. Z.,Tian, Y.,Zhang, W. Q.,Jiao, J. Y.,Liu, L.,Zhang, Z. T.,Xiao, M.,Wei, D. Q.,Li, W. J.Nocardioides cavernae sp. nov., an actinobacterium isolated from a karst cave10.1099/ijsem.0.001676IJSEM 67: 633-639 201727902315
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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/
91344Reimer, 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-ID404125.1