Strain identifier

BacDive ID: 4255

Type strain: No

Species: Dietzia maris

Strain history: IFM 10668 <-- DSM 44904 <-- A. F. Yassin IMMIB RIV-399.

NCBI tax ID(s): 321318 (species)

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General

@ref: 12188

BacDive-ID: 4255

DSM-Number: 44904

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

description: Dietzia maris DSM 44904 is an aerobe, spore-forming, mesophilic human pathogen that was isolated from perianal swab of a patient with bonmarrow transplantation.

NCBI tax id

  • NCBI tax id: 321318
  • Matching level: species

strain history

@refhistory
12188<- A. F. Yassin
67770IFM 10668 <-- DSM 44904 <-- A. F. Yassin IMMIB RIV-399.

doi: 10.13145/bacdive4255.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Dietziaceae
  • genus: Dietzia
  • species: Dietzia maris
  • full scientific name: Dietzia maris (Nesterenko et al. 1982 ex Harrison 1929) Rainey et al. 1995

  • synonyms

    @refsynonym
    20215Dietzia cinnamea
    20215Rhodococcus maris

@ref: 12188

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dietziaceae

genus: Dietzia

species: Dietzia maris

full scientific name: Dietzia maris (Nesterenko et al. 1982) Rainey et al. 1995 emend. Nouioui et al. 2018

type strain: no

Morphology

cell morphology

  • @ref: 31593
  • gram stain: positive
  • cell shape: rod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19885Deep orange10-14 daysISP 2
19885Deep orange10-14 daysISP 3
19885Yellow orange10-14 daysISP 4
19885Yellow orange10-14 daysISP 5
19885Yellow orange10-14 daysISP 6
19885Yellow orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19885noISP 2
19885noISP 3
19885noISP 4
19885noISP 5
19885noISP 6
19885noISP 7

pigmentation

  • @ref: 31593
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12188GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
12188BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
19885ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19885ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19885ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19885ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19885ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19885ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
19885positiveoptimum28mesophilic
12188positivegrowth28mesophilic
31593positivegrowth22-45
31593positiveoptimum35-45
59035positivegrowth37mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
31593positivegrowth7
31593positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31593aerobe
59035aerobe

spore formation

  • @ref: 31593
  • spore formation: yes

observation

@refobservation
31593aggregates in chains
67770quinones: MK-8(H2), MK-7(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3159330089acetate+carbon source
3159317234glucose+carbon source
3159317306maltose+carbon source
683794853esculin-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
31593catalase+1.11.1.6
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
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382lipase (C 14)-
68379gelatinase-
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControl
19885--++--+--+-------+-
12188+-+/-+--+-------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19885+++-+++++++---+----
12188+/-+/-+/------------+/------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling date
12188perianal swab of a patient with bonmarrow transplantationGermanyDEUEurope
59035Human perianal,bone-marrow transplantationGermanyDEUEurope1995
67770Perianal swab of a human with a bone marrow transplant

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Infection#Patient#Swab
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_1060.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_611;97_714;98_833;99_1060&stattab=map
  • Last taxonomy: Dietzia
  • 16S sequence: FJ468339
  • Sequence Identity:
  • Total samples: 47853
  • soil counts: 4780
  • aquatic counts: 9470
  • animal counts: 31750
  • plant counts: 1853

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
12188yes, in single cases1Risk group (German classification)
198852Risk group

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Dietzia cinnamea strain DSM 44904 16S ribosomal RNA gene, partial sequenceFJ4683391442ena321318
12188Dietzia cinnamea partial 16S rRNA gene, type strain IMMIB RIV-399TAJ9202891486ena321318

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dietzia cinnamea NBRC 1021471223524.3wgspatric1223524
66792Dietzia cinnamea NBRC 1021472675903565draftimg1223524
67770Dietzia cinnamea NBRC 102147GCA_001571065contigncbi1223524

GC content

@refGC-contentmethod
1218872.3
6777070.8genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno95.332no
gram-positiveyes90.661no
anaerobicno99.112yes
aerobicyes91.889yes
halophileyes61.941no
spore-formingno86.242yes
thermophileno97.907yes
glucose-utilyes87.743yes
flagellatedno98.385no
glucose-fermentno87.172no

External links

@ref: 12188

culture collection no.: DSM 44904, CCUG 50875, CIP 50875, IMMIB RIV-399, JCM 13663, IFM 10668, NBRC 102147

straininfo link

  • @ref: 73751
  • straininfo: 215521

literature

  • topic: Phylogeny
  • Pubmed-ID: 16514042
  • title: Dietzia cinnamea sp. nov., a novel species isolated from a perianal swab of a patient with a bone marrow transplant.
  • authors: Yassin AF, Hupfer H, Schaal KP
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63863-0
  • year: 2006
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Anal Canal/*microbiology, Bone Marrow Transplantation, DNA, Ribosomal/chemistry, Genotype, Humans, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12188Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44904)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44904
19885Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44904.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
31593Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127882
59035Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50875)https://www.ccug.se/strain?id=50875
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/
68379Automatically annotated from API Coryne
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
73751Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID215521.1StrainInfo: A central database for resolving microbial strain identifiers