Strain identifier

BacDive ID: 133104

Type strain: Yes

Species: Nocardioides phosphati

Strain Designation: WYH11-7

Strain history: <- F. Xie, Henan Engineering Research Center of Industrial Enzymes, Biology Institute of Henan Academy of Sciences, Zhengzhou, China; WYH11-7

NCBI tax ID(s): 1867775 (species)

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General

@ref: 64132

BacDive-ID: 133104

DSM-Number: 104026

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

description: Nocardioides phosphati WYH11-7 is a Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from phosphate rock powder samples collected at a phosphate mining field in Kunming.

NCBI tax id

  • NCBI tax id: 1867775
  • Matching level: species

strain history

  • @ref: 64132
  • history: <- F. Xie, Henan Engineering Research Center of Industrial Enzymes, Biology Institute of Henan Academy of Sciences, Zhengzhou, China; WYH11-7

doi: 10.13145/bacdive133104.20230509.8.1

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 phosphati
  • full scientific name: Nocardioides phosphati Xie et al. 2017

@ref: 64132

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides phosphati

full scientific name: Nocardioides phosphati Xie et al. 2017

strain designation: WYH11-7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25299positive0.7-2.0 µm0.4-0.6 µmrod-shapedno
25299coccus-shaped
69480no92.028
69480positive100

colony morphology

  • @ref: 25299
  • colony color: creamy white
  • colony shape: circular
  • incubation period: 2 days
  • medium used: R2A agar

multicellular morphology

  • @ref: 25299
  • forms multicellular complex: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25299Reasoner's 2A agar (R2A)yes
25299PDA (potato-dextrose agar)yes
25299LB mediayes
25299Trypticase Soy Agar (TSA)no
64132R2A 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
25299positivegrowth4-38
25299positiveoptimum30mesophilic
64132positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
25299positivegrowth5.0-10.0alkaliphile
25299positiveoptimum7

Physiology and metabolism

spore formation

@refspore formationconfidence
25299no
69481no98
69480no99.841

halophily

  • @ref: 25299
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
252993557154-nitrophenyl beta-D-galactopyranoside-hydrolysis
2529927613amygdalin-builds acid from
2529917968butyrate-assimilation
2529915824D-fructose-assimilation
2529912936D-galactose-assimilation
2529916899D-mannitol-assimilation
2529916024D-mannose-assimilation
2529963150D-rhamnose-assimilation
2529917924D-sorbitol-builds acid from
252994853esculin-hydrolysis
2529916236ethanol-assimilation
2529917754glycerol-assimilation
2529917268myo-inositol-builds acid from
2529930849L-arabinose-assimilation
2529929991L-aspartate-assimilation
2529917561L-cysteine-assimilation
2529929985L-glutamate-assimilation
2529915603L-leucine-assimilation
2529916643L-methionine-assimilation
2529917295L-phenylalanine-assimilation
2529917203L-proline-assimilation
2529962345L-rhamnose-builds acid from
2529917115L-serine-assimilation
2529917266L-sorbose-assimilation
2529917716lactose-assimilation
2529917790methanol-assimilation
25299506227N-acetylglucosamine-assimilation
2529917632nitrate-reduction
2529916634raffinose-assimilation
2529917992sucrose-builds acid from
2529917992sucrose-assimilation
2529927082trehalose-assimilation
2529917128adipate+assimilation
2529916947citrate+assimilation
2529917634D-glucose+builds acid from
2529917634D-glucose+assimilation
2529916899D-mannitol+builds acid from
2529924265gluconate+assimilation
2529915428glycine+assimilation
2529930849L-arabinose+builds acid from
2529916467L-arginine+assimilation
2529915971L-histidine+assimilation
2529925115malate+assimilation
2529917306maltose+assimilation
2529928053melibiose+builds acid from

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
252992637amikacinyesyes30 µg
252992676amoxicillinyesyes10 µg
2529928971ampicillinyesyes10 µg
252992955azithromycinyesyes15 µg
25299204928cefotaximeyesyes30 µg
252993508ceftazidimeyesyes30 µg
2529917698chloramphenicolyesyes30 µg
25299100241ciprofloxacinyesyes5 µg
2529948923erythromycinyesyes15 µg
2529917833gentamicinyesyes10 µg
252997507neomycinyesyes30 µg
25299100246norfloxacinyesyes10 µg
2529918208penicillin gyesyes10
252998232piperacillinyesyes100 µg
2529928077rifampicinyesyes5 µg
2529927902tetracyclineyesyes30 µg
2529928001vancomycinyesyes30 µg
2529928669bacitracinyesyes0.04 Unit
252993745clindamycinyesyes2 µg
2529928368novobiocinyesyes5 µg
252999332sulfamethoxazoleyesyes300 µg

metabolite production

@refChebi-IDmetaboliteproduction
2529915688acetoinno
2529916136hydrogen sulfideno
2529935581indoleno

metabolite tests

  • @ref: 25299
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
25299acid phosphatase+3.1.3.2
25299alkaline phosphatase+3.1.3.1
25299alpha-chymotrypsin-3.4.21.1
25299alpha-fucosidase-3.2.1.51
25299alpha-galactosidase-3.2.1.22
25299alpha-glucosidase+3.2.1.20
25299alpha-mannosidase-3.2.1.24
25299amylase+
25299arginine dihydrolase+3.5.3.6
25299beta-galactosidase-3.2.1.23
25299beta-glucosidase-3.2.1.21
25299beta-glucuronidase-3.2.1.31
25299catalase+1.11.1.6
25299cystine arylamidase+/-3.4.11.3
25299cytochrome oxidase-1.9.3.1
25299esterase (C 4)+
25299esterase Lipase (C 8)+
25299gelatinase+
25299leucine arylamidase+3.4.11.1
25299lipase (C 14)-
25299lysine decarboxylase-4.1.1.18
25299N-acetyl-beta-glucosaminidase-3.2.1.52
25299naphthol-AS-BI-phosphohydrolase+
25299ornithine decarboxylase-4.1.1.17
25299trypsin-3.4.21.4
25299tryptophan deaminase-4.1.99.1
25299urease-3.5.1.5
25299valine arylamidase+/-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    2529910-Methyl C17:01
    2529910-Methyl C18:06.8
    25299C10:0 3OH3.4
    25299C12:00.1
    25299C14:01.3
    25299C14:1ω5c0.3
    25299C15:0 2OH0.3
    25299C15:1ω6c1.2
    25299C15:1ω8c0.2
    25299C16:022
    25299C16:0 2OH3.5
    25299C16:1ω6c / C16:1ω7c5.9
    25299C16:1ω9c1.1
    25299C17:010.1
    25299C17:0 2OH1.9
    25299C17:1ω8c7.3
    25299C18:02.1
    25299C18:1ω9c31.3
    25299C19:00.3
    25299C19:1ω9c / C19:1ω11c2.3
    25299C16:0 iso1
    25299C18:0 iso0.2
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation time: 2
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA 6
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
25299phosphate rock powder samples collected at a phosphate mining field in KunmingKunming, Yunnan Province, PR ChinaChinaCHNAsia
64132phosphate rock powder from a phosphate mining fieldYunnan Province, suburb of KunmingChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Terrestrial#Geologic

taxonmaps

  • @ref: 69479
  • File name: preview.99_13235.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_1270;97_6619;98_8221;99_13235&stattab=map
  • Last taxonomy: Nocardioides phosphati
  • 16S sequence: KX426598
  • Sequence Identity:
  • Total samples: 2003
  • soil counts: 1465
  • aquatic counts: 158
  • animal counts: 231
  • plant counts: 149

Safety information

risk assessment

  • @ref: 64132
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64132
  • description: Nocardioides phosphati strain WYH11-7 16S ribosomal RNA gene, partial sequence
  • accession: KX426598
  • length: 1478
  • database: ena
  • NCBI tax ID: 1867775

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides phosphati CGMCC 4.7371GCA_014646375scaffoldncbi1867775
66792Nocardioides phosphati strain CGMCC 4.73711867775.3wgspatric1867775

GC content

  • @ref: 64132
  • GC-content: 71.2
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
flagellatedno98.134yes
gram-positiveyes86.891yes
anaerobicno98.181no
aerobicyes93.372no
halophileno92.757no
spore-formingno90.634no
thermophileno98.555yes
glucose-utilyes86.174yes
motileno98.128yes
glucose-fermentno90.274no

External links

@ref: 64132

culture collection no.: DSM 104026, CGMCC 4.7371

straininfo link

  • @ref: 91366
  • straininfo: 406119

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28005518Nocardioides phosphati sp. nov., an actinomycete isolated from a phosphate mine.Xie F, Yang Y, Ma H, Quan S, Yue D, Sun Y, Feng F, Zhen J, Liu DInt J Syst Evol Microbiol10.1099/ijsem.0.0017542017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Mining, Peptidoglycan/chemistry, *Phosphates, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31637662Nocardioides jejuensis sp. nov., isolated from soil.Jang JH, Maeng S, Jung HY, Kim MK, Subramani GAntonie Van Leeuwenhoek10.1007/s10482-019-01343-y2019DNA, Bacterial, Genome, Bacterial, Genomics/methods, Phylogeny, Propionibacterium/*classification/genetics/*isolation & purification, RNA, Ribosomal, 16S, *Soil Microbiology, Whole Genome SequencingGenetics

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
25299F. Y. Xie, Y.,Ma, H.,Quan, S.,Yue, D.,Sun, Y.,Feng, F.,Zhen, J.,Liu, D.Nocardioides phosphati sp. nov., an actinomycete isolated from a phosphate mine10.1099/ijsem.0.001754IJSEM 67: 1522-1528 201728005518
64132Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104026Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104026)
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
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
91366Reimer, 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-ID406119.1