Strain identifier

BacDive ID: 140673

Type strain: Yes

Species: Nocardioides thalensis

Strain history: <- Ahmed Iftikhar, National Agricultural Research Centre, Pakistan; NCCP-696 <- I. U. Khan, YIM; YIM 73001

NCBI tax ID(s): 1914755 (species)

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General

@ref: 64867

BacDive-ID: 140673

DSM-Number: 103833

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

description: Nocardioides thalensis CCTCC AB 2016296 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from Thal Desert.

NCBI tax id

  • NCBI tax id: 1914755
  • Matching level: species

strain history

  • @ref: 64867
  • history: <- Ahmed Iftikhar, National Agricultural Research Centre, Pakistan; NCCP-696 <- I. U. Khan, YIM; YIM 73001

doi: 10.13145/bacdive140673.20230509.8.1

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 thalensis
  • full scientific name: Nocardioides thalensis Khan et al. 2017

@ref: 64867

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides thalensis

full scientific name: Nocardioides thalensis Khan et al. 2017

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43437positive1.5-2.4 µm0.3-0.4 µmrod-shapedno
69480positive100

colony morphology

  • @ref: 43437
  • colony color: cream-coloured
  • incubation period: 3 days
  • medium used: R2A agar medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43437Reasoner's 2A agar (R2A)yes
64867R2A 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
43437positivegrowth20-42
43437positiveoptimum30-37mesophilic
64867positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
43437positivegrowth5.5-9alkaliphile
43437positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43437
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.923

halophily

@refsaltgrowthtested relationconcentration
43437NaClpositivegrowth0-4 %(w/v)
43437NaClpositiveoptimum0-2 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43437161933-hydroxybenzoate-carbon source
43437370543-hydroxybutyrate-carbon source
4343716947citrate-carbon source
4343716988D-ribose-carbon source
4343717268myo-inositol-carbon source
4343716977L-alanine-carbon source
4343730849L-arabinose-carbon source
4343717203L-proline-carbon source
4343728053melibiose-carbon source
434379300suberic acid-carbon source
4343762968cellulose-degradation
4343728017starch-degradation
4343753424tween 20-degradation
4343753423tween 40-degradation
4343753425tween 60-degradation
4343753426tween 80-degradation
43437309162-oxoglutarate+carbon source
43437739183-O-methyl-D-glucose+carbon source
4343730089acetate+carbon source
4343717925alpha-D-glucose+carbon source
4343717665alpha-D-glucose 6-phosphate+carbon source
4343717057cellobiose+carbon source
4343718333D-arabitol+carbon source
4343729990D-aspartate+carbon source
4343715824D-fructose+carbon source
4343778697D-fructose 6-phosphate+carbon source
4343728847D-fucose+carbon source
4343712936D-galactose+carbon source
434378391D-gluconate+carbon source
4343715748D-glucuronate+carbon source
4343716899D-mannitol+carbon source
4343716634raffinose+carbon source
4343717924D-sorbitol+carbon source
4343716551D-trehalose+carbon source
4343732528turanose+carbon source
4343723652dextrin+carbon source
4343715740formate+carbon source
434375291gelatin+carbon source
4343717754glycerol+carbon source
4343717596inosine+carbon source
4343729991L-aspartate+carbon source
4343718287L-fucose+carbon source
4343729985L-glutamate+carbon source
4343715971L-histidine+carbon source
4343718183L-pyroglutamic acid+carbon source
4343762345L-rhamnose+carbon source
4343724996lactate+carbon source
4343725115malate+carbon source
4343717306maltose+carbon source
4343737657methyl D-glucoside+carbon source
4343763154N-acetyl-beta-D-mannosamine+carbon source
4343728037N-acetylgalactosamine+carbon source
43437506227N-acetylglucosamine+carbon source
4343717309pectin+carbon source
4343764103sodium butyrate+carbon source
4343775228sodium lactate+carbon source
4343717992sucrose+carbon source
434374853esculin+hydrolysis
434375291gelatin+hydrolysis
4343717632nitrate+reduction

metabolite production

  • @ref: 43437
  • Chebi-ID: 89634
  • metabolite: melanin
  • production: yes

enzymes

@refvalueactivityec
43437cytochrome oxidase+1.9.3.1
43437catalase+1.11.1.6
43437alkaline phosphatase+3.1.3.1
43437esterase (C 4)+
43437esterase Lipase (C 8)+
43437leucine arylamidase+3.4.11.1
43437acid phosphatase+3.1.3.2
43437naphthol-AS-BI-phosphohydrolase+
43437alpha-glucosidase+3.2.1.20
43437beta-glucosidase+3.2.1.21

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
43437Thal DesertThal Desert, PunjabPakistanPAKAsia31.38371.434
64867desert soilThal desert, Punjab (31° 23' N, 71° 26' E)PakistanPAKAsia31.383371.4333

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Desert
#Environmental#Terrestrial#Soil
#Condition#Xerophilic

taxonmaps

  • @ref: 69479
  • File name: preview.99_73059.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_7914;97_39340;98_51172;99_73059&stattab=map
  • Last taxonomy: Nocardioides thalensis subclade
  • 16S sequence: LC193943
  • Sequence Identity:
  • Total samples: 219
  • soil counts: 177
  • aquatic counts: 4
  • animal counts: 20
  • plant counts: 18

Safety information

risk assessment

  • @ref: 64867
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64867
  • description: Nocardioides sp. NCCP-696 gene for 16S ribosomal RNA, partial sequence
  • accession: LC193943
  • length: 1469
  • database: ena
  • NCBI tax ID: 1914755

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides thalensis DSM 103833GCA_013410655contigncbi1914755
66792Nocardioides thalensis strain DSM 1038331914755.3wgspatric1914755
66792Nocardioides thalensis DSM 1038332856476943draftimg1914755

GC content

  • @ref: 64867
  • GC-content: 71.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno85no
motileno77.373yes
gram-positiveyes89.247yes
anaerobicno98.133no
aerobicyes89.879no
halophileno96.175no
spore-formingno74.628no
glucose-utilyes88.318no
flagellatedno93.795no
thermophileno94.959yes
glucose-fermentno86.95no

External links

@ref: 64867

culture collection no.: CCTCC AB 2016296, DSM 103833, YIM 73001, NCCP 696

straininfo link

  • @ref: 96775
  • straininfo: 399181

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28853683Nocardioides thalensis sp. nov., isolated from a desert.Khan IU, Hussain F, Habib N, Xiao M, Ahmed I, Amin A, Zhi XY, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0020322017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pakistan, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny30403584Nocardioides silvaticus sp. nov., isolated from forest soil.Li C, Shi K, Zhang Y, Wang GInt J Syst Evol Microbiol10.1099/ijsem.0.0030792018Actinomycetales/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
43437Inam Ullah Khan, Firasat Hussain, Neeli Habib, Min Xiao, Iftikhar Ahmed, Arshia Amin, Xiao-Yang Zhi, Wen-Jun LiNocardioides thalensis sp. nov., isolated from a desert10.1099/ijsem.0.002032IJSEM 67: 2848-2852 201728853683
64867Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103833Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103833)
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
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
96775Reimer, 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-ID399181.1