Strain identifier

BacDive ID: 132563

Type strain: Yes

Species: Dermabacter jinjuensis

Strain Designation: 32

Strain history: <- Y. K. Park, Korea Natl. Inst. Health (KNIH), South Korea; 32 <- Gyseongsang Nat. Univ. Hospital

NCBI tax ID(s): 1667168 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 24352

BacDive-ID: 132563

DSM-Number: 101003

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

description: Dermabacter jinjuensis 32 is an anaerobe, Gram-positive, rod-shaped human pathogen that forms circular colonies and was isolated from closed pus of a patient having finger necrosis.

NCBI tax id

  • NCBI tax id: 1667168
  • Matching level: species

strain history

  • @ref: 24352
  • history: <- Y. K. Park, Korea Natl. Inst. Health (KNIH), South Korea; 32 <- Gyseongsang Nat. Univ. Hospital

doi: 10.13145/bacdive132563.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Dermabacteraceae
  • genus: Dermabacter
  • species: Dermabacter jinjuensis
  • full scientific name: Dermabacter jinjuensis Park et al. 2016

@ref: 24352

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermabacteraceae

genus: Dermabacter

species: Dermabacter jinjuensis

full scientific name: Dermabacter jinjuensis Park et al. 2016

strain designation: 32

type strain: yes

Morphology

cell morphology

  • @ref: 43946
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43946
  • colony size: 0.5-1.0 mm
  • colony color: greyish-white
  • colony shape: circular
  • medium used: 5 % sheep blood agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
439465 % sheep blood agaryes
24352TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43946positivegrowth20-45
43946positiveoptimum30-40
24352positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
43946positivegrowth5.0-12.0alkaliphile
43946positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43946
  • oxygen tolerance: anaerobe

halophily

  • @ref: 43946
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-6 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4394618305arbutin-builds acid from
4394617057cellobiose-builds acid from
4394615963ribitol-builds acid from
4394617108D-arabinose-builds acid from
4394618333D-arabitol-builds acid from
4394615824D-fructose-builds acid from
4394628847D-fucose-builds acid from
4394612936D-galactose-builds acid from
4394616899D-mannitol-builds acid from
4394616024D-mannose-builds acid from
4394616988D-ribose-builds acid from
4394617924D-sorbitol-builds acid from
4394616443D-tagatose-builds acid from
4394665327D-xylose-builds acid from
4394616813galactitol-builds acid from
4394617113erythritol-builds acid from
4394617754glycerol-builds acid from
4394628087glycogen-builds acid from
4394617268myo-inositol-builds acid from
4394615443inulin-builds acid from
4394630849L-arabinose-builds acid from
4394618403L-arabitol-builds acid from
4394618287L-fucose-builds acid from
4394662345L-rhamnose-builds acid from
4394617266L-sorbose-builds acid from
4394665328L-xylose-builds acid from
4394625097lyxose-builds acid from
439466731melezitose-builds acid from
43946320061methyl alpha-D-glucopyranoside-builds acid from
4394643943methyl alpha-D-mannoside-builds acid from
4394674863methyl beta-D-xylopyranoside-builds acid from
43946potassium 2-dehydro-D-gluconate-builds acid from
43946potassium 5-dehydro-D-gluconate-builds acid from
4394632032potassium gluconate-builds acid from
4394617814salicin-builds acid from
4394628017starch-builds acid from
4394617151xylitol-builds acid from
439465291gelatin-hydrolysis
4394616199urea-hydrolysis
4394627613amygdalin+builds acid from
4394617634D-glucose+builds acid from
4394617716lactose+builds acid from
43946esculin ferric citrate+builds acid from
4394628066gentiobiose+builds acid from
43946maltose hydrate+builds acid from
4394628053melibiose+builds acid from
43946506227N-acetylglucosamine+builds acid from
4394616634raffinose+builds acid from
4394617992sucrose+builds acid from
4394627082trehalose+builds acid from
4394632528turanose+builds acid from

enzymes

@refvalueactivityec
43946catalase+1.11.1.6
43946pyrrolidonyl arylamidase+3.4.19.3
43946alkaline phosphatase+3.1.3.1
43946alpha-galactosidase+3.2.1.22
43946beta-galactosidase+3.2.1.23
43946alpha-glucosidase+3.2.1.20
43946N-acetyl-beta-glucosaminidase+3.2.1.52
43946beta-glucosidase+3.2.1.21
43946alpha-mannosidase+3.2.1.24
43946beta-galactopyranosidase+
43946arginine dihydrolase+3.5.3.6
43946leucine arylamidase+3.4.11.1
43946phenylalanine arylamidase+
43946tyrosine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43946C13:0 anteiso0.51
    43946C15:0 anteiso28.46
    43946C17:0 anteiso29.66
    43946C10:00.44
    43946C12:00.74
    43946C14:02.89
    43946C16:05.5
    43946C20:1ω7c5.5
    43946C14:0 iso1.25
    43946C15:0 iso10.78
    43946C16:0 iso14.26
  • type of FA analysis: whole cell analysis
  • incubation medium: tryptic soy agar
  • agar/liquid: agar
  • incubation temperature: 37
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
24352closed pus of a patient having finger necrosisGyeongsangnam-do Province, Jinju (35° 10' 35'' N 128° 5' 44'' E)Republic of KoreaKORAsia35.1764128.096
43946closed pus sample from a patient having finger necrosis in tertiary hospital located in Jinju, Gyeongsangnam-do, KoreaJinju, Gyeongsangnam-doRepublic of KoreaKORAsia35.1764128.0965 % sheep blood agar1 days37

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Infection#Patient
#Host Body Product#Fluids
#Host Body-Site#Limb#Hand

taxonmaps

  • @ref: 69479
  • File name: preview.99_2911.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_737;97_860;98_1003;99_2911&stattab=map
  • Last taxonomy: Dermabacter
  • 16S sequence: KT036432
  • Sequence Identity:
  • Total samples: 37762
  • soil counts: 2427
  • aquatic counts: 1910
  • animal counts: 32727
  • plant counts: 698

Safety information

risk assessment

  • @ref: 24352
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24352
  • description: Dermabacter jinjuensis strain 32 16S ribosomal RNA gene, partial sequence
  • accession: KT036432
  • length: 1390
  • database: ena
  • NCBI tax ID: 1667168

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dermabacter jinjuensis 322846849301completeimg1667168
66792Dermabacter jinjuensis strain FDAARGOS_15551667168.5completepatric1667168
66792Dermabacter jinjuensis strain FDAARGOS_15551667168.4completepatric1667168

GC content

  • @ref: 24352
  • GC-content: 62.58
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 24352

culture collection no.: DSM 101003, NCCP 16133

straininfo link

  • @ref: 90880
  • straininfo: 406208

literature

  • topic: Phylogeny
  • Pubmed-ID: 27088668
  • title: Dermabacter jinjuensis sp. nov., a novel species of the genus Dermabacter isolated from a clinical specimen.
  • authors: Park YK, Lee KM, Lee WK, Cho MJ, Lee HS, Cho YG, Lee YC, Lee WK, Seong WK, Hwang KJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001092
  • year: 2016
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fingers/*microbiology/pathology, Humans, Necrosis, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Suppuration/*microbiology, Vitamin K 2/chemistry
  • topic2: Pathogenicity

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
24352Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101003Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101003)
43946Young Kyoung Park, Kyeong Min Lee, Woo-Kon Lee, Myung-Je Cho, Hye-Soo Lee, Yong-Gon Cho, Yoo Chul Lee, Won Kil Lee, Won Keun Seong, Kyu Jam HwangDermabacter jinjuensis sp. nov., a novel species of the genus Dermabacter isolated from a clinical specimen10.1099/ijsem.0.001092IJSEM 66: 2573-2577 201627088668
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/
90880Reimer, 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-ID406208.1