Strain identifier

BacDive ID: 158627

Type strain: Yes

Species: Tsukamurella ocularis

Strain Designation: HKU63

Strain history: CIP <- 2018, JLL. Teng, Hong Kong Univ., Hong Kong, China: strain HKU63

NCBI tax ID(s): 1970234 (species)

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General

@ref: 65352

BacDive-ID: 158627

DSM-Number: 105034

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

description: Tsukamurella ocularis HKU63 is an aerobe, mesophilic, Gram-positive bacterium that forms irregular colonies and was isolated from eye swab of a patient with conjunctivitis.

NCBI tax id

  • NCBI tax id: 1970234
  • Matching level: species

strain history

@refhistory
67770J. L. L. Teng; Dept. of Microbiol., Univ. of Hong Kong, China; HKU63.
121387CIP <- 2018, JLL. Teng, Hong Kong Univ., Hong Kong, China: strain HKU63

doi: 10.13145/bacdive158627.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Tsukamurellaceae
  • genus: Tsukamurella
  • species: Tsukamurella ocularis
  • full scientific name: Tsukamurella ocularis Teng et al. 2018

@ref: 65352

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Mycobacteriales

family: Tsukamurellaceae

genus: Tsukamurella

species: Tsukamurella ocularis

strain designation: HKU63

type strain: yes

Morphology

cell morphology

@refgram stainmotilitycell shape
65352positiveno
121387positivenorod-shaped

colony morphology

  • @ref: 65352
  • colony size: 2 mm
  • colony color: white and creamy or yellow and creamy
  • colony shape: irregular
  • incubation period: 2 days
  • medium used: Columbia agar

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
65352Columbia agaryeswith 5% defibrinated sheep blood agar
65352brain-heart infusion agaryes
65352Nutrient agar (NA)yes
65352tryptic soy agaryes
65352chocolate agaryes
65352MacConkey agaryes
121387CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
65352positivegrowth37mesophilic
65352nogrowth10psychrophilic
65352nogrowth42thermophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 65352
  • oxygen tolerance: aerobe

spore formation

@refspore formation
65352no
121387no

halophily

  • @ref: 65352
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-7 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6535227613amygdalin-builds acid from
6535218305arbutin+builds acid from
6535217057cellobiose-builds acid from
6535215963ribitol-builds acid from
6535217108D-arabinose+builds acid from
6535218333D-arabitol+builds acid from
6535215824D-fructose+builds acid from
6535228847D-fucose-builds acid from
6535212936D-galactose+builds acid from
6535217634D-glucose+builds acid from
6535262318D-lyxose-builds acid from
6535216899D-mannitol+builds acid from
6535216024D-mannose-builds acid from
6535216988D-ribose+builds acid from
6535217924D-sorbitol+builds acid from
6535216443D-tagatose-builds acid from
6535265327D-xylose-builds acid from
6535216813galactitol-builds acid from
6535217113erythritol-builds acid from
65352esculin ferric citrate+builds acid from
6535228066gentiobiose-builds acid from
6535217754glycerol+builds acid from
6535228087glycogen-builds acid from
6535217268myo-inositol+builds acid from
6535215443inulin-builds acid from
6535230849L-arabinose-builds acid from
6535218403L-arabitol-builds acid from
6535218287L-fucose+builds acid from
6535262345L-rhamnose-builds acid from
6535217266L-sorbose-builds acid from
6535265328L-xylose-builds acid from
6535217716lactose-builds acid from
6535217306maltose+builds acid from
653526731melezitose-builds acid from
6535228053melibiose-builds acid from
65352320061methyl alpha-D-glucopyranoside-builds acid from
6535243943methyl alpha-D-mannoside-builds acid from
6535274863methyl beta-D-xylopyranoside-builds acid from
65352506227N-acetylglucosamine+builds acid from
65352potassium 2-dehydro-D-gluconate+builds acid from
65352potassium 5-dehydro-D-gluconate-builds acid from
6535232032potassium gluconate+builds acid from
6535216634raffinose-builds acid from
6535217814salicin-builds acid from
6535228017starch-builds acid from
6535217992sucrose+builds acid from
6535227082trehalose+builds acid from
6535232528turanose+builds acid from
6535218186tyrosine+hydrolysis
6535215318xanthine-hydrolysis
6535217151xylitol+builds acid from

enzymes

@refvalueactivityec
65352catalase+1.11.1.6
65352cytochrome oxidase-1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture temperaturegeographic locationisolation date
65352eye swab of a patient with conjunctivitisHong KongHKGAsiaColumbia agarwith 5 % defibrinated sheep blood37
67770Eye swab of a patient with conjunctivitis in Hong KongChinaCHNAsia
121387Human, ConjunctivitisChinaCHNAsiaHong Kong2008-06-11

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Organ#Eye
#Infection#Patient#Swab
#Infection#Inflammation

taxonmaps

  • @ref: 69479
  • File name: preview.99_3845.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1974;97_2373;98_2929;99_3845&stattab=map
  • Last taxonomy: Tsukamurella
  • 16S sequence: KY787187
  • Sequence Identity:
  • Total samples: 12359
  • soil counts: 3431
  • aquatic counts: 2978
  • animal counts: 5160
  • plant counts: 790

Safety information

risk assessment

  • @ref: 121387
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 65352
  • description: 16S rRNA gene sequence
  • accession: KY787187
  • database: nuccore

GC content

  • @ref: 67770
  • GC-content: 69.4-73.2
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 65352

culture collection no.: JCM 31969, DSM 105034, CIP 111612

literature

  • topic: Phylogeny
  • Pubmed-ID: 29458478
  • title: Tsukamurella ocularis sp. nov. and Tsukamurella hominis sp. nov., isolated from patients with conjunctivitis in Hong Kong.
  • authors: Teng JLL, Tang Y, Wong SSY, Chiu TH, Zhao Z, Chan E, Ngan AHY, Lau SKP, Woo PCY
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002589
  • year: 2018
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Conjunctiva/*microbiology, Conjunctivitis/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Hong Kong, Humans, Mycolic Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Pathogenicity

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
65352Jade L. L. Teng, Ying Tang, Samson S. Y. Wong, Tsz Ho Chiu, Zhe Zhao, Elaine Chan, Antonio H. Y. Ngan, Susanna K. P. Lau, Patrick C. Y. WooTsukamurella ocularis sp. nov. and Tsukamurella hominis sp. nov., isolated from patients with conjunctivitis in Hong Kong10.1099/ijsem.0.002589IJSEM 68: 810-818 201829458478
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/
121387Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111612Collection of Institut Pasteur (CIP 111612)