Strain identifier

BacDive ID: 14650

Type strain: Yes

Species: Staphylococcus succinus

Strain Designation: AMG-D1

Strain history: <- ATCC <- R.J. Cano; AMG-D1

NCBI tax ID(s): 61015 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 5411

BacDive-ID: 14650

DSM-Number: 14617

keywords: Bacteria, 16S sequence, genome sequence, mesophilic

description: Staphylococcus succinus AMG-D1 is a mesophilic bacterium that was isolated from plant and soil inclusions within 25-35 million-year-old Dominican amber.

NCBI tax id

  • NCBI tax id: 61015
  • Matching level: species

strain history: <- ATCC <- R.J. Cano; AMG-D1

doi: 10.13145/bacdive14650.20220920.7

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Staphylococcaceae
  • genus: Staphylococcus
  • species: Staphylococcus succinus
  • full scientific name: Staphylococcus succinus Lambert et al. 1998

@ref: 5411

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus succinus

full scientific name: Staphylococcus succinus Lambert et al. 1998

strain designation: AMG-D1

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5411COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://bacmedia.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
5411TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://bacmedia.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
35496MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)

culture temp

@refgrowthtypetemperaturerange
5411positivegrowth30mesophilic
5411positivegrowth25mesophilic
35496positivegrowth37mesophilic

Physiology and metabolism

murein

  • @ref: 5411
  • murein short key: A11.02
  • type: A3alpha L-Lys-Gly5-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837532528turanose-fermentation
6837559640N-acetylglucosamine+fermentation
6837517992sucrose+fermentation
6837516988D-ribose-fermentation
6837516899D-mannitol+fermentation
6837527082trehalose+fermentation
6837517716lactose+fermentation
6837517306maltose+fermentation
6837516024D-mannose+fermentation
6837515824D-fructose+fermentation
6837517634D-glucose+fermentation
683754853esculin+hydrolysis
6837518257ornithine-degradation
6837529016arginine-hydrolysis
6837516199urea+hydrolysis

antibiotic resistance

  • @ref: 68375
  • ChEBI: 28368
  • metabolite: novobiocin
  • is antibiotic: yes
  • is resistant: yes
  • resistance conc.: 1.8 µg

metabolite production

  • @ref: 68375
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: no

metabolite tests

  • @ref: 68375
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68375beta-glucuronidase+3.2.1.31
68375pyrrolidonyl arylamidase-3.4.19.3
68375alkaline phosphatase+3.1.3.1
68375L-arginine arylamidase-
68375beta-galactosidase+3.2.1.23
68375beta-glucosidase+3.2.1.21
68375ornithine decarboxylase-4.1.1.17
68375arginine dihydrolase-3.5.3.6
68375urease+3.5.1.5

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
5411+--+++++++++-++-+-+-+++--+
5411+--++++++++-----+-+-+++-++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5411plant and soil inclusions within 25-35 million-year-old Dominican amberDominican RepublicDOMMiddle and South America
55943Plant and soil inclusions within amber

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants

Safety information

risk assessment

  • @ref: 5411
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Staphylococcus succinus subsp. succinus strain DSM 14617 16S ribosomal RNA gene, partial sequenceAY688103464ena224030
5411Staphylococcus succinus 16S ribosomal RNA gene, complete sequenceAF0042201548ena224030

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Staphylococcus succinus subsp. succinus DSM 14617GCA_001006765contigncbi224030
66792Staphylococcus succinus subsp. succinus DSM 14617GCA_002902045scaffoldncbi224030
66792Staphylococcus succinus subsp. succinus strain DSM 14617224030.5wgspatric224030
66792Staphylococcus succinus subsp. succinus strain DSM 14617224030.8wgspatric224030
66792Staphylococcus succinus succinus DSM 146172917463979draftimg224030
66792Staphylococcus succinus succinus DSM 146172639763042draftimg224030

GC content

  • @ref: 5411
  • GC-content: 35
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 5411

culture collection no.: DSM 14617, ATCC 700337, CIP 107307, CCUG 43571, CCM 7157

straininfo link

@refpassport
20218http://www.straininfo.net/strains/163965
20218http://www.straininfo.net/strains/117843
20218http://www.straininfo.net/strains/340502

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9731292Staphylococcus succinus sp. nov., isolated from Dominican amber.Lambert LH, Cox T, Mitchell K, Rossello-Mora RA, Del Cueto C, Dodge DE, Orkand P, Cano RJInt J Syst Bacteriol10.1099/00207713-48-2-5111998*Amber, Anti-Bacterial Agents/pharmacology, Base Composition, Base Sequence, Cell Wall, DNA, Bacterial/analysis, Dominica, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, Staphylococcus/*classification/drug effects/isolation & purification/ultrastructureGenetics
Phylogeny12421073Staphylococcus succinus subsp. casei subsp. nov., a dominant isolate from a surface ripened cheese.Place RB, Hiestand D, Burri S, Teuber MSyst Appl Microbiol10.1078/0723-2020-001302002Bacterial Typing Techniques, Cell Wall/chemistry, Chaperonin 60/*genetics, Cheese/*microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Food Microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, DNA, Staphylococcus/*classification/*genetics/isolation & purification/metabolismBiotechnology
Phylogeny14657137Staphylococcus nepalensis sp. nov., isolated from goats of the Himalayan region.Spergser J, Wieser M, Taubel M, Rossello-Mora RA, Rosengarten R, Busse HJInt J Syst Evol Microbiol10.1099/ijs.0.02646-02003Altitude, Animals, DNA Fingerprinting, Geography, Goats/*microbiology, India, Microbial Sensitivity Tests, Molecular Sequence Data, *Phylogeny, Polymerase Chain Reaction, Staphylococcus/*classification/genetics/isolation & purification/physiologyGenetics
Genetics28126945Draft Genome Sequence of Staphylococcus succinus subsp. succinus Type Strain DSM 14617, Isolated from Plant and Soil Inclusions within 25- to 35-Million-Year-Old Dominican Amber.Zhou H, Yao Z, Shi H, Wang B, Li D, Hou J, Ma SGenome Announc10.1128/genomeA.01521-162017Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5411Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14617)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14617
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
35496Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4729
55943Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 43571)https://www.ccug.se/strain?id=43571
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)
68375Automatically annotated from API ID32STA