Strain identifier

BacDive ID: 7615

Type strain: Yes

Species: Pseudarthrobacter scleromae

Strain Designation: YH-2001

Strain history: CIP <- 2005, Y. Huang, Chinese Academy of Sciences, Beijing, China <- CGMCC <- N. Zhao, Weifang Med. Coll., Weifang, China: strain YH-2001

NCBI tax ID(s): 158897 (species)

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General

@ref: 7170

BacDive-ID: 7615

DSM-Number: 17756

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, human pathogen

description: Pseudarthrobacter scleromae YH-2001 is an obligate aerobe, mesophilic human pathogen that was isolated from human, swollen scleromata of a dermatosis patient.

NCBI tax id

  • NCBI tax id: 158897
  • Matching level: species

strain history

@refhistory
7170<- Y. Huang <- N. Zhao; YH-2001
67770Y. Huang YH-2001.
122524CIP <- 2005, Y. Huang, Chinese Academy of Sciences, Beijing, China <- CGMCC <- N. Zhao, Weifang Med. Coll., Weifang, China: strain YH-2001

doi: 10.13145/bacdive7615.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Pseudarthrobacter
  • species: Pseudarthrobacter scleromae
  • full scientific name: Pseudarthrobacter scleromae (Huang et al. 2005) Busse 2016

  • synonyms

    • @ref: 20215
    • synonym: Arthrobacter scleromae

@ref: 7170

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Pseudarthrobacter

species: Pseudarthrobacter scleromae

full scientific name: Pseudarthrobacter scleromae (Huang et al. 2005) Busse 2016

strain designation: YH-2001

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no91.586
69480100positive
122524nopositiveoval-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7170TRYPTICASE 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
41907MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122524CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7170positivegrowth34mesophilic
41907positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122524
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.871

observation

  • @ref: 67770
  • observation: quinones: MK-8(H2), MK-9(H2), MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12252417632nitrate-reduction
12252416301nitrite-reduction

metabolite production

  • @ref: 122524
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
122524oxidase-
122524alcohol dehydrogenase-1.1.1.1
122524catalase+1.11.1.6
122524lysine decarboxylase-4.1.1.18
122524ornithine decarboxylase-4.1.1.17
122524urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122524-+++-+-++-++++-++-+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
7170human, swollen scleromata of a dermatosis patientShang dongChinaCHNAsia
67770Swollen scleromata of a dermatosis patient
122524Human, Clinical specimenChinaCHNAsia2001

isolation source categories

Cat1Cat2
#Infection#Inflammation
#Host#Human

taxonmaps

  • @ref: 69479
  • File name: preview.99_130.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_99;97_106;98_115;99_130&stattab=map
  • Last taxonomy: Pseudarthrobacter
  • 16S sequence: AF330692
  • Sequence Identity:
  • Total samples: 1526
  • soil counts: 822
  • aquatic counts: 109
  • animal counts: 156
  • plant counts: 439

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
7170yes, in single cases1Risk group (German classification)
1225241Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7170
  • description: Arthrobacter scleromae strain YH-2001 16S ribosomal RNA gene, partial sequence
  • accession: AF330692
  • length: 1415
  • database: ena
  • NCBI tax ID: 158897

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudarthrobacter scleromae CGMCC 1.3601GCA_014644515scaffoldncbi158897
66792Pseudarthrobacter scleromae strain CGMCC 1.3601158897.4wgspatric158897

GC content

@refGC-contentmethod
717064.7
6777064.7thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno87no
flagellatedno96.793no
gram-positiveyes92.855no
anaerobicno99.659no
aerobicyes95.394no
halophileno83.847no
spore-formingno87.252no
thermophileno99.138yes
glucose-utilyes86.501no
motileno87.403no
glucose-fermentno81.799no

External links

@ref: 7170

culture collection no.: DSM 17756, CGMCC 1.3601, JCM 12642, CIP 108992, AS 1.3601

straininfo link

  • @ref: 77059
  • straininfo: 231915

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18676480Arthrobacter defluvii sp. nov., 4-chlorophenol-degrading bacteria isolated from sewage.Kim KK, Lee KC, Oh HM, Kim MJ, Eom MK, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.65550-02008Arthrobacter/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Chlorophenols/*metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Species SpecificityGenetics
Phylogeny25150449Arthrobacter ginsengisoli sp. nov., isolated from soil of a ginseng field.Siddiqi MZ, Kim YJ, Hoang VA, Siddiqi MH, Huq MA, Yang DCArch Microbiol10.1007/s00203-014-1025-82014Arthrobacter/classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, rRNA, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Panax, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny31424381Reclassification of Arthrobacter enclensis as Pseudarthrobacter enclensis comb. nov., and emended descriptions of the genus Pseudarthrobacter, and the species Pseudarthrobacter phenanthrenivorans and Pseudarthrobacter scleromae.Busse HJ, Schumann PInt J Syst Evol Microbiol10.1099/ijsem.0.0036522019Arthrobacter/*classification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Micrococcaceae/*classification, Peptidoglycan/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
7170Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17756)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17756
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
41907Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6685
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
77059Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID231915.1StrainInfo: A central database for resolving microbial strain identifiers
122524Curators of the CIPCollection of Institut Pasteur (CIP 108992)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108992