Strain identifier

BacDive ID: 164547

Type strain: Yes

Species: Nocardioides yefusunii

Strain Designation: HY056

Strain history: J. Yang; Natl. Inst. for Commun. Dis. Control & Prev., China CDC, China; HY056.

NCBI tax ID(s): 2500546 (species)

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General

@ref: 67770

BacDive-ID: 164547

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

description: Nocardioides yefusunii HY056 is an aerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from Faeces of Equus kiang in Qinghai-Tibetan Plateau.

NCBI tax id

  • NCBI tax id: 2500546
  • Matching level: species

strain history

  • @ref: 67770
  • history: J. Yang; Natl. Inst. for Commun. Dis. Control & Prev., China CDC, China; HY056.

doi: 10.13145/bacdive164547.20230509.8.1

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 yefusunii
  • full scientific name: Nocardioides yefusunii Huang et al. 2019

@ref: 67770

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Propionibacteriales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides yefusunii

full scientific name: Nocardioides yefusunii Huang et al. 2019

strain designation: HY056

type strain: yes

Morphology

cell morphology

  • @ref: 68229
  • gram stain: positive
  • cell length: 1.3-2.5 µm
  • cell width: 0.2-0.5 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 68229
  • colony size: 1-2 mm
  • colony color: pale-yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: BHI 5.0 % sheep blood agar

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
67770positivegrowth28mesophilic
68229positivegrowth16-37
68229positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
68229positivegrowth5-11alkaliphile
68229positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 68229
  • oxygen tolerance: aerobe

spore formation

  • @ref: 68229
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
68229NaClpositivegrowth0-2 %(w/v)
68229NaClpositiveoptimum0-0.5 %(w/v)

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
682294853esculin+hydrolysis
6822917632nitrate+reduction
682295291gelatin-hydrolysis
6822929016arginine-assimilation
6822915824D-fructose+builds acid from
6822916443D-tagatose+builds acid from
68229esculin ferric citrate+builds acid from
68229581435-dehydro-D-gluconate+builds acid from
6822917057cellobiose+/-builds acid from
6822916988D-ribose+/-builds acid from
6822916551D-trehalose+/-builds acid from
6822927613amygdalin-builds acid from
6822918305arbutin-builds acid from
6822917108D-arabinose-builds acid from
6822918333D-arabitol-builds acid from
6822928847D-fucose-builds acid from
6822912936D-galactose-builds acid from
6822917634D-glucose-builds acid from
6822916024D-mannose-builds acid from
6822916899D-mannitol-builds acid from
6822917924D-sorbitol-builds acid from
6822965327D-xylose-builds acid from
6822916813galactitol-builds acid from
6822917113erythritol-builds acid from
6822917754glycerol-builds acid from
6822928087glycogen-builds acid from
6822917268myo-inositol-builds acid from
6822915443inulin-builds acid from
6822917716lactose-builds acid from
6822930849L-arabinose-builds acid from
6822918403L-arabitol-builds acid from
6822918287L-fucose-builds acid from
6822962345L-rhamnose-builds acid from
6822917266L-sorbose-builds acid from
6822917306maltose-builds acid from
682296731melezitose-builds acid from
6822928053melibiose-builds acid from
6822959640N-acetylglucosamine-builds acid from
6822916634raffinose-builds acid from
6822917814salicin-builds acid from
6822917992sucrose-builds acid from
68229168082-dehydro-D-gluconate-builds acid from

metabolite production

  • @ref: 68229
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68229catalase+1.11.1.6
68229cytochrome oxidase-1.9.3.1
68229alkaline phosphatase+/-3.1.3.1
68229beta-glucosidase+3.2.1.21
68229esterase (C 4)+
68229esterase Lipase (C 8)+
68229leucine arylamidase+3.4.11.1
68229lipase+/-
68229valine arylamidase+/-
68229naphthol-AS-BI-phosphohydrolase+
68229acid phosphatase-3.1.3.2
68229alpha-chymotrypsin-3.4.21.1
68229alpha-fucosidase-3.2.1.51
68229alpha-galactosidase-3.2.1.22
68229alpha-glucosidase-3.2.1.20
68229alpha-mannosidase-3.2.1.24
68229beta-galactosidase-3.2.1.23
68229beta-glucuronidase-3.2.1.31
68229N-acetyl-beta-glucosaminidase-3.2.1.52
68229trypsin-3.4.21.4
68229urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68229C18:09.7
    68229C18:1 w9c28.7
    68229C18:0 10-methyl15.3
    68229C16:0 iso11.1
    68229C18:0 iso1
    68229C16:1 w7c/C16:1 w6c5.3
    68229C19:1 w11c / C19:1 w9c1.3
    68229C16:0 10-methyl/C17:1 iso w9c2
  • type of FA analysis: whole cell analysis
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentsampling dategeographic locationenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
67770Faeces of Equus kiang (Tibetan wild ass) in Qinghai-Tibetan PlateauEquus kiangChinaCHNAsia
68229Faecal samples of Tibetan wild ass (Equus kiang)ChinaCHNAsia2017-09-01Qinghai-Tibet PlateauBHIsupplemented with 5.0 % sheep blood7 days28

Sequence information

16S sequences

  • @ref: 68229
  • description: Nocardioides sp. strain HY056 16S ribosomal RNA gene, partial sequence
  • accession: MH607119
  • length: 1481
  • database: ena
  • NCBI tax ID: 35761

Genome sequences

  • @ref: 67770
  • description: Nocardioides yefusunii HY056
  • accession: GCA_004014875
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 2500546

GC content

  • @ref: 67770
  • GC-content: 68.9
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno79.119yes
flagellatedno92.364yes
gram-positiveyes87.532no
anaerobicno98.96yes
aerobicyes91.755yes
halophileno93.793yes
spore-formingno87.106no
thermophileno99.535no
glucose-utilyes82.905no
glucose-fermentno85.957no

External links

@ref: 67770

culture collection no.: JCM 33399, CGMCC 4.7563

literature

  • topic: Phylogeny
  • Pubmed-ID: 31511125
  • title: Nocardioides yefusunii sp. nov., isolated from Equus kiang (Tibetan wild ass) faeces.
  • authors: Huang Y, Wang X, Yang J, Lu S, Lai XH, Jin D, Pu J, Huang Y, Ren Z, Zhu W, Meng J, Dong K, Ge Y, Zhou J, Zhang G, Zhang S, Lei W, Liang H, Xu J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003674
  • year: 2019
  • mesh: Actinobacteria/*classification/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Equidae/*microbiology, Fatty Acids/chemistry, Feces/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournal
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68229Yuyuan Huang, Xiaoxia Wang, Jing Yang, Shan Lu, Xin-He Lai, Dong Jin, Ji Pu, Ying Huang, Zhihong Ren, Wentao Zhu, Jiajia Meng, Kui Dong, Yajun Ge, Juan Zhou, Gui Zhang, Sihui Zhang, Wenjing Lei, Hao Liang and Jianguo XuNocardioides yefusunii sp. nov., isolated from Equus kiang (Tibetan wild ass) faeces10.1099/ijsem.0.003674IJSEM 69: 3629-3635 2019